Karr Lab :: KarrLab / karr_lab_build_utils / project.tests.test_core.TestKarrLabBuildUtils / test_upgrade_karr_lab

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-2rum66mz/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-2rum66mz/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=0723fc5d87ebc79349dfd7bf9dfff010e3be3204a9165691bdce6fd651266cc2 Stored in directory: /tmp/pip-ephem-wheel-cache-mak_rwbq/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.24-py2.py3-none-any.whl size=69337 sha256=026a52f337a278e87d0efce0bd8e2e8a71d7c2e93842a999fabba0fa7b3baed5 Stored in directory: /tmp/pip-ephem-wheel-cache-mak_rwbq/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.24 Uninstalling wc-utils-0.0.24: Successfully uninstalled wc-utils-0.0.24 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.24 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-5xtj_c2d/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-5xtj_c2d/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=fe72e3edbfbf506d4fd9e64507402b5e2915ca2bf055ec47620e80c79132ac8a Stored in directory: /tmp/pip-ephem-wheel-cache-wbpfw6wc/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.24-py2.py3-none-any.whl size=69337 sha256=12f8508bc2e4cc0fb583a6ea31bd973b5df06f1dd6019c2fc09de5289204fa34 Stored in directory: /tmp/pip-ephem-wheel-cache-wbpfw6wc/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.24 Uninstalling wc-utils-0.0.24: Successfully uninstalled wc-utils-0.0.24 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.24
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-2rum66mz/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-2rum66mz/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.3.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-5xtj_c2d/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-5xtj_c2d/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.3.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

893

3.7.6

master

f922...

project/tests/test_core.py

532

2020-12-15 20:30:21

Pass

18.488

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-5yqb7zut/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-5yqb7zut/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already 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sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already 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mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in 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satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=7dbe6ba5bbcffdceefb9ecc590daf9d3b29cfa0df60227c675c4254bfddeea2f Stored in directory: /tmp/pip-ephem-wheel-cache-hq_v58qf/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.24-py2.py3-none-any.whl size=69337 sha256=ec2a6aa9bbaac2ae1ccdbbffa8e5129c1c0b1fedc65c4b89a75779ba24e01647 Stored in directory: /tmp/pip-ephem-wheel-cache-hq_v58qf/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.24 Uninstalling wc-utils-0.0.24: Successfully uninstalled wc-utils-0.0.24 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.24 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-bfmno5tv/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-bfmno5tv/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in 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Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=30dba09f7684401bb957b742b799424b9d3836a484e3b4cda066e06c47b20865 Stored in directory: /tmp/pip-ephem-wheel-cache-0qj534ki/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.24-py2.py3-none-any.whl size=69337 sha256=440b7a45c723f0ac16e73b89562ce9888b2dfa698662f9c0cc034af7c7a31bf5 Stored in directory: /tmp/pip-ephem-wheel-cache-0qj534ki/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.24 Uninstalling wc-utils-0.0.24: Successfully uninstalled wc-utils-0.0.24 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.24
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-5yqb7zut/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-5yqb7zut/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.3.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-bfmno5tv/pkg-utils Warning: Permanently added the RSA host key for IP address '140.82.113.4' to the list of known hosts. Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-bfmno5tv/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.3.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-09-28 18:53:21

Pass

17.071

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-vaxw5gvt/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-vaxw5gvt/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=5112eb8b6bb7a740e2af092b98f3fb2a6b19116da51b922c360753d7b9f611aa Stored in directory: /tmp/pip-ephem-wheel-cache-s1xs098u/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.24-py2.py3-none-any.whl size=69337 sha256=abf34135e592962afc17d09d75b055a0e77487befe30c7aa9fdb85bf369ecca5 Stored in directory: /tmp/pip-ephem-wheel-cache-s1xs098u/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.24 Uninstalling wc-utils-0.0.24: Successfully uninstalled wc-utils-0.0.24 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.24 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-igu44q67/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-igu44q67/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=e9784d83d6a21ce30d3ac4822c3f9e6c2b04b92d54d993c6591ee36351e09616 Stored in directory: /tmp/pip-ephem-wheel-cache-t3pipl1p/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.24-py2.py3-none-any.whl size=69337 sha256=75559bd75d2b422960e3ca93dd8b6d7072da3aa86ead812122b4b82d95b098e7 Stored in directory: /tmp/pip-ephem-wheel-cache-t3pipl1p/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.24 Uninstalling wc-utils-0.0.24: Successfully uninstalled wc-utils-0.0.24 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.24
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-vaxw5gvt/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-vaxw5gvt/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-igu44q67/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-igu44q67/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-09-26 12:52:12

Pass

30.393

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-u9rfqr54/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-u9rfqr54/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=5436252b88eeafef4ac9573386779d08ab22a1d89adfa751e9a2c4bcbb881bff Stored in directory: /tmp/pip-ephem-wheel-cache-q4n__dn_/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.22-py2.py3-none-any.whl size=69349 sha256=de1c702abf471777e22782e0e317904eeceac340c1c482e0383249b72f0978f6 Stored in directory: /tmp/pip-ephem-wheel-cache-q4n__dn_/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.22 Uninstalling wc-utils-0.0.22: Successfully uninstalled wc-utils-0.0.22 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.22 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-hw8n4ypa/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-hw8n4ypa/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=1e37248ae6c5433ab8c17b3ac96f5bd9df54816aa25c63df200abfc2939dd2d0 Stored in directory: /tmp/pip-ephem-wheel-cache-ed57namw/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.22-py2.py3-none-any.whl size=69349 sha256=bf37b87c75d3cb17cef83c2020553c2ebcb055aeef7bfafc433f0caf4d66ace4 Stored in directory: /tmp/pip-ephem-wheel-cache-ed57namw/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.22 Uninstalling wc-utils-0.0.22: Successfully uninstalled wc-utils-0.0.22 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.22
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-u9rfqr54/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-u9rfqr54/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-hw8n4ypa/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-hw8n4ypa/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-09-08 10:29:12

Pass

22.531

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-ib5357a4/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-ib5357a4/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=b6ad3d6c6207940663ff45fa1177870ed6c742e2d016f55da01bc01155672c00 Stored in directory: /tmp/pip-ephem-wheel-cache-exgyu0a7/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.22-py2.py3-none-any.whl size=69210 sha256=a4933a2c328c113c808f6ff868776a246bb282a8056bee58848417825439fc2c Stored in directory: /tmp/pip-ephem-wheel-cache-exgyu0a7/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.22 Uninstalling wc-utils-0.0.22: Successfully uninstalled wc-utils-0.0.22 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.22 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-uygu64hk/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-uygu64hk/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=57114fb6cec1548e8d68135b78c515d20ddadd48fb376244d5711054024b02ca Stored in directory: /tmp/pip-ephem-wheel-cache-u4duclhr/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.22-py2.py3-none-any.whl size=69210 sha256=c339965ae4caba67935dc17ac81a96be2da78f390582189f504d9625f5579862 Stored in directory: /tmp/pip-ephem-wheel-cache-u4duclhr/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.22 Uninstalling wc-utils-0.0.22: Successfully uninstalled wc-utils-0.0.22 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.22
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-ib5357a4/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-ib5357a4/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-uygu64hk/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-uygu64hk/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-09-03 20:25:37

Pass

21.349

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-yiozuwfx/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-yiozuwfx/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping 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sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping 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/usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=6bcded7fcf37c50f51a88c1cbb6fc3281d823ec627a443a340b30fb8f7cdee8c Stored in directory: /tmp/pip-ephem-wheel-cache-f0yccr61/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.21-py2.py3-none-any.whl size=69212 sha256=3884ae073233dc923233ab7dd4fe5f5cf803f8e344c382ccd9f032331888c3a5 Stored in directory: /tmp/pip-ephem-wheel-cache-f0yccr61/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.21 Uninstalling wc-utils-0.0.21: Successfully uninstalled wc-utils-0.0.21 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.21 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-z0m9xb2e/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-z0m9xb2e/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in 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Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=fbed974764da05788bec3fad3dcf83ea4de45a3d13f92b19458538257f9bfd7c Stored in directory: /tmp/pip-ephem-wheel-cache-008ulb6r/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.21-py2.py3-none-any.whl size=69212 sha256=cca9e7021c62d072515a4960c6fa0840e139273fe8566e2b5806f951c923b72f Stored in directory: /tmp/pip-ephem-wheel-cache-008ulb6r/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.21 Uninstalling wc-utils-0.0.21: Successfully uninstalled wc-utils-0.0.21 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.21
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-yiozuwfx/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-yiozuwfx/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-z0m9xb2e/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-z0m9xb2e/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-09-03 17:23:27

Pass

22.146

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-qusa7zu_/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-qusa7zu_/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=a61eebca93edf706670ce4ea27a64758edeca25a8285fe98a121e2ca5991bba1 Stored in directory: /tmp/pip-ephem-wheel-cache-g5nvfqux/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.21-py2.py3-none-any.whl size=69212 sha256=d9eeadd705b79265c65d4c5f72b0dc642e674c84458e3a290043a15052c2c00f Stored in directory: /tmp/pip-ephem-wheel-cache-g5nvfqux/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.21 Uninstalling wc-utils-0.0.21: Successfully uninstalled wc-utils-0.0.21 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.21 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-2fv_tdhj/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-2fv_tdhj/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=3184e3de03b3955c7d11faee58c87bcac2fb691fb6cc758c8a2ff8aa2b01e921 Stored in directory: /tmp/pip-ephem-wheel-cache-2ubbm8yq/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.21-py2.py3-none-any.whl size=69212 sha256=91524b63a3ea5898303e9765255cde85f4168a288461274e5d5f42d966a2e0c7 Stored in directory: /tmp/pip-ephem-wheel-cache-2ubbm8yq/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.21 Uninstalling wc-utils-0.0.21: Successfully uninstalled wc-utils-0.0.21 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.21
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-qusa7zu_/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-qusa7zu_/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-2fv_tdhj/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-2fv_tdhj/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-08-26 13:42:46

Pass

18.617

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-ux7c2r9c/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-ux7c2r9c/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=b2c1e60a7bc7cc9b5432cae2323adfb0e3f78f48cfac27f46e88a00b30e07974 Stored in directory: /tmp/pip-ephem-wheel-cache-1rnww15k/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.21-py2.py3-none-any.whl size=69242 sha256=ecfbc5bc8358fa84e3eea0dce2553fd5457feed3197ede5b14331f8f0cf27d31 Stored in directory: /tmp/pip-ephem-wheel-cache-1rnww15k/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.21 Uninstalling wc-utils-0.0.21: Successfully uninstalled wc-utils-0.0.21 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.21 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-vtjv6be8/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-vtjv6be8/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=b45fe840438fee4f4ab55bd99e42fc512f976c2a17b5dcd8e8acb676989c8640 Stored in directory: /tmp/pip-ephem-wheel-cache-vsedq649/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.21-py2.py3-none-any.whl size=69242 sha256=9e9accf96356c9b1bbcc105a3b93d9148f9c90599cf2ffe1a3a5c9072465f1d8 Stored in directory: /tmp/pip-ephem-wheel-cache-vsedq649/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.21 Uninstalling wc-utils-0.0.21: Successfully uninstalled wc-utils-0.0.21 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.21
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-ux7c2r9c/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-ux7c2r9c/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-vtjv6be8/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-vtjv6be8/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-08-26 11:00:11

Pass

20.374

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-aqg30sfw/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-aqg30sfw/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=4c89d2f7996c1eaf654506c5e2aa05e581fac1cdecc53af2e9db4f795229d008 Stored in directory: /tmp/pip-ephem-wheel-cache-gyryjkw2/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.21-py2.py3-none-any.whl size=69188 sha256=ab1a51a2cca676cde063b125e389ebec1087ad6a3cc2a63f4c8ebc47ca6641af Stored in directory: /tmp/pip-ephem-wheel-cache-gyryjkw2/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.21 Uninstalling wc-utils-0.0.21: Successfully uninstalled wc-utils-0.0.21 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.21 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-mg8b5tho/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-mg8b5tho/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=9d812c6d912a77b2b0cc05861057caf9b3a9ef1c51f0d6b2271a454551ee1949 Stored in directory: /tmp/pip-ephem-wheel-cache-zesfvu6h/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.21-py2.py3-none-any.whl size=69188 sha256=3d928815af7eb1be3927999587e23db37cf00aec945793f7bd5d4fcdec394a68 Stored in directory: /tmp/pip-ephem-wheel-cache-zesfvu6h/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.21 Uninstalling wc-utils-0.0.21: Successfully uninstalled wc-utils-0.0.21 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.21
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-aqg30sfw/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-aqg30sfw/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-mg8b5tho/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-mg8b5tho/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-08-05 22:08:29

Pass

17.399

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-nt_lnamb/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-nt_lnamb/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping 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sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already 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mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already 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/usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=0859e218d95567bf9268e1bb559d0f346de843ba14178f118edcf81b5891edb7 Stored in directory: /tmp/pip-ephem-wheel-cache-goajs9uw/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.20-py2.py3-none-any.whl size=68777 sha256=9ada715ddbcc7a42e77fda5047abcae46993e853ad459f8eb78b801edfdbfb19 Stored in directory: /tmp/pip-ephem-wheel-cache-goajs9uw/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.20 Uninstalling wc-utils-0.0.20: Successfully uninstalled wc-utils-0.0.20 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.20 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-l8ievduf/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-l8ievduf/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=e5942fc04f337b8d4658da2504ac6afc9d4557059f9f7e6056b3d05ea438ba46 Stored in directory: /tmp/pip-ephem-wheel-cache-joewif05/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.20-py2.py3-none-any.whl size=68777 sha256=8fe59dc0b4e49995bf9d7834492eb1a177e1f69d0af8d002206866714ddea7a6 Stored in directory: /tmp/pip-ephem-wheel-cache-joewif05/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.20 Uninstalling wc-utils-0.0.20: Successfully uninstalled wc-utils-0.0.20 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.20
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-nt_lnamb/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-nt_lnamb/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-l8ievduf/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-l8ievduf/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-08-05 17:36:13

Pass

19.245

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-i2s64hwd/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-i2s64hwd/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: natsort in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (6.2.0) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask-json in 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Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=a3e13bc92bac5a09aef02f14c410a5af363c2244516cf69eddb13d3d7d5f035f Stored in directory: /tmp/pip-ephem-wheel-cache-atw57m07/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.19-py2.py3-none-any.whl size=68776 sha256=86355e239f2f90474e1904155e40a2de8feea7fb9c4f6276a51145ab2a92bd3c Stored in directory: /tmp/pip-ephem-wheel-cache-atw57m07/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.19 Uninstalling wc-utils-0.0.19: Successfully uninstalled wc-utils-0.0.19 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.19 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-3fjw9jwf/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-3fjw9jwf/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already 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capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already 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already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=6206843a11601df84e78a783eb91e1c9e8c8cf854e53b11c6cd11cff9b9e5946 Stored in directory: /tmp/pip-ephem-wheel-cache-e0dhpjy4/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.19-py2.py3-none-any.whl size=68776 sha256=976b871bbea340d079ccfa97db4ee93c0b73d0326e4ebc01c52c9969546832fa Stored in directory: /tmp/pip-ephem-wheel-cache-e0dhpjy4/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.19 Uninstalling wc-utils-0.0.19: Successfully uninstalled wc-utils-0.0.19 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.19
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-i2s64hwd/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-i2s64hwd/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-3fjw9jwf/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-3fjw9jwf/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.2.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-07-24 23:24:32

Pass

16.581

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-1r3c2716/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-1r3c2716/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=30d577fc466e7e23ca08b0075d77bc8099ee980ba6c261b63ccc271da3842d47 Stored in directory: /tmp/pip-ephem-wheel-cache-b7h6clf0/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.19-py2.py3-none-any.whl size=68732 sha256=d26b9f6e15ed23e72169e7555cce756febf8b0a3a1cf91306ee83a198a205ece Stored in directory: /tmp/pip-ephem-wheel-cache-b7h6clf0/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.19 Uninstalling wc-utils-0.0.19: Successfully uninstalled wc-utils-0.0.19 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.19 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-eq8beuy4/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-eq8beuy4/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=924ec36ff29a858dafa5ace8e418d0341c685efc8e9ad181271519f6c4c473cf Stored in directory: /tmp/pip-ephem-wheel-cache-963oz3in/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.19-py2.py3-none-any.whl size=68732 sha256=744dcc846c34c2d60e7ba5825173b69cc11c0b6608f9e937e5d83e9bad3f3b01 Stored in directory: /tmp/pip-ephem-wheel-cache-963oz3in/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.19 Uninstalling wc-utils-0.0.19: Successfully uninstalled wc-utils-0.0.19 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.19
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-1r3c2716/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-1r3c2716/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-eq8beuy4/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-eq8beuy4/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-07-24 22:50:22

Pass

17.110

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-7fbw7984/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-7fbw7984/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=f61935abff678419a1296ec22b1337de84143a2354b7965f260ccaa505236fef Stored in directory: /tmp/pip-ephem-wheel-cache-v9rbbew_/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.19-py2.py3-none-any.whl size=68732 sha256=17792dec29676049db07b1f3a3130b0903d5ea2605603e0217f4ca8d1178a472 Stored in directory: /tmp/pip-ephem-wheel-cache-v9rbbew_/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.19 Uninstalling wc-utils-0.0.19: Successfully uninstalled wc-utils-0.0.19 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.19 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-0ss93bdn/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-0ss93bdn/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=05a4e4447c6477ae677b51d9844409d3bedb26c81454dbc5bbb0cff556f02183 Stored in directory: /tmp/pip-ephem-wheel-cache-m366y3u_/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.19-py2.py3-none-any.whl size=68732 sha256=f92ab8f52e3e855284b77329d743cf66a6b57dfe663d387723f08cd69c3455e3 Stored in directory: /tmp/pip-ephem-wheel-cache-m366y3u_/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.19 Uninstalling wc-utils-0.0.19: Successfully uninstalled wc-utils-0.0.19 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.19
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-7fbw7984/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-7fbw7984/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-0ss93bdn/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-0ss93bdn/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-07-23 15:56:08

Pass

18.784

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-m_u4i4dm/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-m_u4i4dm/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) 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sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=7bac87146126acbe8ecd375b891f20535115500b23edac9fdad49aa12a7235c4 Stored in directory: /tmp/pip-ephem-wheel-cache-xr1vtq3e/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.19-py2.py3-none-any.whl size=68732 sha256=e47348cdf64121ca4f6a249bfce5855755e7724b2da8753ccb9154887fc5e175 Stored in directory: /tmp/pip-ephem-wheel-cache-xr1vtq3e/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.19 Uninstalling wc-utils-0.0.19: Successfully uninstalled wc-utils-0.0.19 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.19 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-v_jb9ng2/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-v_jb9ng2/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=924bbf1b912b06a094fe0978daa9edf3dc1bcb066f235016ff2a4169ece5bd71 Stored in directory: /tmp/pip-ephem-wheel-cache-gc9vuyba/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.19-py2.py3-none-any.whl size=68732 sha256=9f501ca6b91bfabafac1c362db51e5aec421c0b2e3d9a0153523309c16b9d6c1 Stored in directory: /tmp/pip-ephem-wheel-cache-gc9vuyba/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.19 Uninstalling wc-utils-0.0.19: Successfully uninstalled wc-utils-0.0.19 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.19
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-m_u4i4dm/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-m_u4i4dm/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-v_jb9ng2/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-v_jb9ng2/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-07-19 15:17:27

Pass

19.989

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-s5jjy5l7/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-s5jjy5l7/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=72ae9cf00eccb1c8f46c52db35be82715ae81dfb77247dd291f678d59a61776a Stored in directory: /tmp/pip-ephem-wheel-cache-aq5pmku8/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.19-py2.py3-none-any.whl size=68732 sha256=375fca04ff6deaae5343e09310367403609fc27bf9364d736157a829b481ab43 Stored in directory: /tmp/pip-ephem-wheel-cache-aq5pmku8/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.19 Uninstalling wc-utils-0.0.19: Successfully uninstalled wc-utils-0.0.19 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.19 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-ocfkln_x/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-ocfkln_x/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in 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satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: networkx~=2.3 in 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(1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=86831b0d98cca0020051c206c588bdb70d6f107b5bdc9f1fd14e8c874fa9a13f Stored in directory: /tmp/pip-ephem-wheel-cache-iixspdnf/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.19-py2.py3-none-any.whl size=68732 sha256=7a231e370e24818ba38c3f7270e7f134c06a83e1013b10988993817f2fa291c8 Stored in directory: /tmp/pip-ephem-wheel-cache-iixspdnf/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.19 Uninstalling wc-utils-0.0.19: Successfully uninstalled wc-utils-0.0.19 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.19
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-s5jjy5l7/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-s5jjy5l7/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-ocfkln_x/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-ocfkln_x/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-07-09 10:36:16

Pass

32.880

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-2lxks4xw/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-2lxks4xw/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=8784c61390a9948492492bdf7c7d1b5443cba9c841085280367c7ae38be6c9f4 Stored in directory: /tmp/pip-ephem-wheel-cache-r_ex_fep/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.18-py2.py3-none-any.whl size=68731 sha256=13e742bdd9bff1bd64468448ce19bdc8d4878d04f9de96082d1e5f33aa245237 Stored in directory: /tmp/pip-ephem-wheel-cache-r_ex_fep/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.18 Uninstalling wc-utils-0.0.18: Successfully uninstalled wc-utils-0.0.18 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.18 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-2zqxrtxg/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-2zqxrtxg/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel<3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=0e3ae697827e6bcee15b7109b26c796b95ace805359cbc0a52fdbd613c0033df Stored in directory: /tmp/pip-ephem-wheel-cache-16ceh4k5/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.18-py2.py3-none-any.whl size=68731 sha256=5e1c8d9afbc98667b0619d834e0caa83b998c9e33c305dda98c557df132f8a0f Stored in directory: /tmp/pip-ephem-wheel-cache-16ceh4k5/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.18 Uninstalling wc-utils-0.0.18: Successfully uninstalled wc-utils-0.0.18 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.18
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-2lxks4xw/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-2lxks4xw/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-2zqxrtxg/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-2zqxrtxg/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-07-07 17:34:25

Pass

18.066

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-gby1215w/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-gby1215w/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=95fd609225336768e31fc8b070a8cef9a4ce1f2c1a45ca3639bfdf82b32d3fd1 Stored in directory: /tmp/pip-ephem-wheel-cache-7ikryf_2/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.17-py2.py3-none-any.whl size=68727 sha256=f5945e9d03a452b51199387e34ec985990f5fa34bb9aa170186dacf8e3a153b4 Stored in directory: /tmp/pip-ephem-wheel-cache-7ikryf_2/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.17 Uninstalling wc-utils-0.0.17: Successfully uninstalled wc-utils-0.0.17 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.17 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-mjf4raqu/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-mjf4raqu/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=9a81777d0c2e14bf021689378adc385dcec445af9e072883a4a5314fb3f78e0c Stored in directory: /tmp/pip-ephem-wheel-cache-t8z6huja/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.17-py2.py3-none-any.whl size=68727 sha256=8363cfa1e00dd7a5d465531a422ddb98bc345f2ea8398a23839b81b46dc89c16 Stored in directory: /tmp/pip-ephem-wheel-cache-t8z6huja/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.17 Uninstalling wc-utils-0.0.17: Successfully uninstalled wc-utils-0.0.17 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.17
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-gby1215w/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-gby1215w/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-mjf4raqu/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-mjf4raqu/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-06-29 16:01:58

Pass

22.141

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-30p2d83_/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-30p2d83_/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=dfd2e175f187dcf9b0bbcc035750134c187fde896b6e6ecf357d1311e7d56cd0 Stored in directory: /tmp/pip-ephem-wheel-cache-fajgwgo2/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.16-py2.py3-none-any.whl size=68423 sha256=9e1f8a516563ca1ade9db4dbfbea81a60e5f8a21589e0a6341b61f2151b3f122 Stored in directory: /tmp/pip-ephem-wheel-cache-fajgwgo2/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.16 Uninstalling wc-utils-0.0.16: Successfully uninstalled wc-utils-0.0.16 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.16 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-a1hnqf91/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-a1hnqf91/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=d764657fc0d7946db607552813363b1897673242c0bfd4522cff32d383876332 Stored in directory: /tmp/pip-ephem-wheel-cache-0h_tkrrr/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.16-py2.py3-none-any.whl size=68423 sha256=7b34a62de347a4642f46c961dc7f092754b30624d871e9c5fcb815e1857db720 Stored in directory: /tmp/pip-ephem-wheel-cache-0h_tkrrr/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.16 Uninstalling wc-utils-0.0.16: Successfully uninstalled wc-utils-0.0.16 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.16
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-30p2d83_/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-30p2d83_/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-a1hnqf91/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-a1hnqf91/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-06-26 22:42:36

Pass

24.161

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-4b4u8xu7/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-4b4u8xu7/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=7137ca17eba41fae165226b3491c0ca11c3a21296606d8007d3238bfd424f3e4 Stored in directory: /tmp/pip-ephem-wheel-cache-4zi25_8s/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.16-py2.py3-none-any.whl size=68254 sha256=a014e614e23af9b6f2dc4ba39b92e2ed9f11f02ab981e03480b8d4a23b083d04 Stored in directory: /tmp/pip-ephem-wheel-cache-4zi25_8s/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.16 Uninstalling wc-utils-0.0.16: Successfully uninstalled wc-utils-0.0.16 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.16 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-7n5un8a1/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-7n5un8a1/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages 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wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping 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Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in 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satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping 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(from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=27480273a12805c6b7fcef887859d7066f5dd1924968a399595ae9c1e1eaad9d Stored in directory: /tmp/pip-ephem-wheel-cache-a6ynyii7/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.16-py2.py3-none-any.whl size=68254 sha256=bda42be064bc9de9b4af35ff3851b63a7887dd6622d6ce6d253aceee0cdd0698 Stored in directory: /tmp/pip-ephem-wheel-cache-a6ynyii7/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.16 Uninstalling wc-utils-0.0.16: Successfully uninstalled wc-utils-0.0.16 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.16
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-4b4u8xu7/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-4b4u8xu7/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-7n5un8a1/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-7n5un8a1/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-06-26 22:21:08

Pass

25.910

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-_mo12tw4/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-_mo12tw4/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=93de470b0b3712611b8f3e9d0d78c79309fba801d045a1ef9cfe48a7b2a99712 Stored in directory: /tmp/pip-ephem-wheel-cache-v_xwy3ry/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.16-py2.py3-none-any.whl size=68254 sha256=77db154f41a01a72d85c40474b668c9774c8e6ed6f0a8e71d2dbfaf181602880 Stored in directory: /tmp/pip-ephem-wheel-cache-v_xwy3ry/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.15 Uninstalling wc-utils-0.0.15: Successfully uninstalled wc-utils-0.0.15 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.16 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-v1badciu/pkg-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: requests>=2.5.0 in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from sphinx>=1.8->pkg-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from requests>=2.5.0->sphinx>=1.8->pkg-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests>=2.5.0->sphinx>=1.8->pkg-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests>=2.5.0->sphinx>=1.8->pkg-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests>=2.5.0->sphinx>=1.8->pkg-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /usr/local/lib/python3.7/site-packages (from packaging->sphinx>=1.8->pkg-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: PyYAML>=3.01 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (5.3) Building wheels for collected packages: pkg-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=47701fd73fe05ccd8c0bd44349a06fe15a7d1c99cb16da5c6b8500fa113cceda Stored in directory: /tmp/pip-ephem-wheel-cache-z4mesoly/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Successfully built pkg-utils Installing collected packages: pkg-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Successfully installed pkg-utils-0.0.5
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-_mo12tw4/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-_mo12tw4/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-v1badciu/pkg-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-06-26 18:17:49

Pass

17.746

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-q9g0zg__/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-q9g0zg__/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=87a59903b74b0eb1ac6f5f373df6b1ab7bfb2fc713b063808b84f5299df36e46 Stored in directory: /tmp/pip-ephem-wheel-cache-6wmmet79/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.15-py2.py3-none-any.whl size=68255 sha256=c15183d1d8c0343388c6ea15bb74f7a99c66d97fe21518e5043b8ea928f967fe Stored in directory: /tmp/pip-ephem-wheel-cache-6wmmet79/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.15 Uninstalling wc-utils-0.0.15: Successfully uninstalled wc-utils-0.0.15 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.15 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-om_8tp9e/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-om_8tp9e/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping 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Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=97dc265754be96216f1a4c447b16eac86691fd9967d0bcad5a9436559f063209 Stored in directory: /tmp/pip-ephem-wheel-cache-os40zscp/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.15-py2.py3-none-any.whl size=68255 sha256=2fd64d5ad6a3237d474c7987be8fe06edd65cae50398a3a750061998bd535561 Stored in directory: /tmp/pip-ephem-wheel-cache-os40zscp/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.15 Uninstalling wc-utils-0.0.15: Successfully uninstalled wc-utils-0.0.15 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.15
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-q9g0zg__/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-q9g0zg__/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-om_8tp9e/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-om_8tp9e/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-06-26 17:04:21

Pass

18.906

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-xw__cl6q/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-xw__cl6q/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=cd798b8c8d90ae01ad015211e5e1b1a0a15eb8cb139c651517c5e8bed3610be3 Stored in directory: /tmp/pip-ephem-wheel-cache-rg80dpei/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.15-py2.py3-none-any.whl size=68255 sha256=2aa196024fcd01d2b0062e007488099de9d36972b12da3db36a6acf8c21a462a Stored in directory: /tmp/pip-ephem-wheel-cache-rg80dpei/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.15 Uninstalling wc-utils-0.0.15: Successfully uninstalled wc-utils-0.0.15 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.15 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-21ee5ovq/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-21ee5ovq/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=498cbd239e8399e05df15f1a9a9992e5f4234e5731948fc0ef6295f1fa7cd411 Stored in directory: /tmp/pip-ephem-wheel-cache-xvgevtti/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.15-py2.py3-none-any.whl size=68255 sha256=18648c2908f20391e25f72dc6258556c0479229112091c87590bf6224da565b3 Stored in directory: /tmp/pip-ephem-wheel-cache-xvgevtti/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.15 Uninstalling wc-utils-0.0.15: Successfully uninstalled wc-utils-0.0.15 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.15
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-xw__cl6q/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-xw__cl6q/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-21ee5ovq/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-21ee5ovq/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-06-26 16:16:56

Pass

26.286

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-rmcli6fg/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-rmcli6fg/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=5e65c48154b785a53ba2a4a6402ab29c1ee76a074e2171485dff6bd8f43e7ed3 Stored in directory: /tmp/pip-ephem-wheel-cache-ve62a2j0/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.15-py2.py3-none-any.whl size=68255 sha256=a87dd32788c5d1bec807b0e980858bfc1858396a611cf2cc02c103a67043f272 Stored in directory: /tmp/pip-ephem-wheel-cache-ve62a2j0/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.15 Uninstalling wc-utils-0.0.15: Successfully uninstalled wc-utils-0.0.15 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.15 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-yngsqszz/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-yngsqszz/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7558 sha256=728732ece35a61162a90595b5b52c69864712491b0a71fca4670d2221bd22d08 Stored in directory: /tmp/pip-ephem-wheel-cache-pi6tv8i0/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.15-py2.py3-none-any.whl size=68255 sha256=671a1e85c3ea6a21a3af9fe3e8116c3bae7b39991e718e7a75e69f22162eca42 Stored in directory: /tmp/pip-ephem-wheel-cache-pi6tv8i0/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.15 Uninstalling wc-utils-0.0.15: Successfully uninstalled wc-utils-0.0.15 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.15
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-rmcli6fg/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-rmcli6fg/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-yngsqszz/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-yngsqszz/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-06-26 14:52:03

Pass

16.901

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-ld37pu9a/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-ld37pu9a/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already 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sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7560 sha256=ad0e7c3172c91a88a194a69950cc985fe3b5be27fc778fcbc4ab98fd7c7ab979 Stored in directory: /tmp/pip-ephem-wheel-cache-26rx40w1/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.15-py2.py3-none-any.whl size=68255 sha256=29a9cb5d0b25f365f3a3d4b181f884bafcb0ab5d943cf99574847e49b90d5167 Stored in directory: /tmp/pip-ephem-wheel-cache-26rx40w1/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.15 Uninstalling wc-utils-0.0.15: Successfully uninstalled wc-utils-0.0.15 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.15 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-zlma7l5q/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-zlma7l5q/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7560 sha256=85b92a13a977f16893121bd52953c978715b075519dc461f1d16cbdbc136b883 Stored in directory: /tmp/pip-ephem-wheel-cache-3nakl90d/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.15-py2.py3-none-any.whl size=68255 sha256=dfc69cb377d63659cb2ad89e0b23d8b1af95d1b97a85e3ca9bb11ff4c82c31bd Stored in directory: /tmp/pip-ephem-wheel-cache-3nakl90d/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.15 Uninstalling wc-utils-0.0.15: Successfully uninstalled wc-utils-0.0.15 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.15
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-ld37pu9a/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-ld37pu9a/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-zlma7l5q/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-zlma7l5q/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-06-26 13:28:04

Pass

21.219

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-ppeavd8j/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-ppeavd8j/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7560 sha256=5fa7335eca2d4b157dafdc6546d29f7ea0b21540ef27d1dee50affeb017f8ae0 Stored in directory: /tmp/pip-ephem-wheel-cache-pvtlrzbt/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.15-py2.py3-none-any.whl size=68255 sha256=4207618991cb02a642d6fa134da997262cb5108291aa372186ee7a81b10610ce Stored in directory: /tmp/pip-ephem-wheel-cache-pvtlrzbt/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.15 Uninstalling wc-utils-0.0.15: Successfully uninstalled wc-utils-0.0.15 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.15 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-2szz0t70/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-2szz0t70/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7560 sha256=b28a5b1ac3741da84e1d37b74099ebfa8f3b7e27eef0cce45fb47d1fb89e275c Stored in directory: /tmp/pip-ephem-wheel-cache-8l9fn7ev/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.15-py2.py3-none-any.whl size=68255 sha256=26dff50fcca51e8c51b0385bb3c5d3c4706d7919c9ef3ba39b43181bdb174f59 Stored in directory: /tmp/pip-ephem-wheel-cache-8l9fn7ev/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.15 Uninstalling wc-utils-0.0.15: Successfully uninstalled wc-utils-0.0.15 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.15
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-ppeavd8j/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-ppeavd8j/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-2szz0t70/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-2szz0t70/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-06-14 15:54:10

Pass

31.532

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-62k6oib9/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-62k6oib9/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7560 sha256=8de2d3b47c7df27b15c9b6dccbbb8394643d5f97bb2dd978d3b0f3c858cf3d5e Stored in directory: /tmp/pip-ephem-wheel-cache-6ygsm9rj/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.15-py2.py3-none-any.whl size=68255 sha256=b291ebba847c576c2609adb8c7ed8040a0f59837d73012a630e88ab35b675499 Stored in directory: /tmp/pip-ephem-wheel-cache-6ygsm9rj/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.15 Uninstalling wc-utils-0.0.15: Successfully uninstalled wc-utils-0.0.15 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.15 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-xcbqpw0l/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-xcbqpw0l/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7560 sha256=70b1ff1dc9b3ce0078e1b8baa7f0d03e32388d28fde956c13969ec4b6c38bf4f Stored in directory: /tmp/pip-ephem-wheel-cache-v6lbyx78/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.15-py2.py3-none-any.whl size=68255 sha256=d4561fbde1baacff8433c408385f8aa89bf4439c268ad35af4bb144fe06acfcc Stored in directory: /tmp/pip-ephem-wheel-cache-v6lbyx78/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.15 Uninstalling wc-utils-0.0.15: Successfully uninstalled wc-utils-0.0.15 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.15
Standard error	Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-62k6oib9/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-62k6oib9/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Running command git clone -q https://github.com/KarrLab/pkg_utils.git /tmp/pip-install-xcbqpw0l/pkg-utils Running command git clone -q https://github.com/KarrLab/wc_utils.git /tmp/pip-install-xcbqpw0l/wc-utils WARNING: You are using pip version 19.3.1; however, version 20.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

project/tests/test_core.py

532

2020-06-14 15:12:07

Pass

31.931

Result type
Message
Details
Standard output	Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-2fi2is_a/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-2fi2is_a/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.3.0) Requirement already satisfied, skipping upgrade: sphinxprettysearchresults in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.3.5) Requirement already satisfied, skipping upgrade: abduct in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: attrdict in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.0.1) Requirement already satisfied, skipping upgrade: configobj in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.0.6) Requirement already satisfied, skipping upgrade: dataclasses in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.6) Requirement already satisfied, skipping upgrade: diskcache in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.1.0) Requirement already satisfied, skipping upgrade: humanfriendly in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (4.18) Requirement already satisfied, skipping upgrade: mendeleev in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.1) Requirement already satisfied, skipping upgrade: numpy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.18.1) Requirement already satisfied, skipping upgrade: objsize in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.3.2) Requirement already satisfied, skipping upgrade: openpyxl<=3.0.1,>=2.6.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.1) Requirement already satisfied, skipping upgrade: pint>=0.10 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.10) Requirement already satisfied, skipping upgrade: pronto>=1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: pyexcel>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.15) Requirement already satisfied, skipping upgrade: pyexcel_io>=0.5.9.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.5.20) Requirement already satisfied, skipping upgrade: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (5.3) Requirement already satisfied, skipping upgrade: qualname in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.0) Requirement already satisfied, skipping upgrade: requests in /usr/local/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg (from wc-utils[all]) (2.22.0) Requirement already satisfied, skipping upgrade: xlsxwriter in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: boto3 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.10.47) Requirement already satisfied, skipping upgrade: capturer in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: gitpython in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: logging2 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (0.1.2) Requirement already satisfied, skipping upgrade: matplotlib in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.2) Requirement already satisfied, skipping upgrade: mock in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.0.5) Requirement already satisfied, skipping upgrade: openbabel in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (2.4.1) Requirement already satisfied, skipping upgrade: pygithub in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.45) Requirement already satisfied, skipping upgrade: pyjnius in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.2.1) Requirement already satisfied, skipping upgrade: quilt3>=3.1.5 in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (3.1.8) Requirement already satisfied, skipping upgrade: scipy in /usr/local/lib/python3.7/site-packages (from wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: wheel>=0.25.0 in /usr/local/lib/python3.7/site-packages (from pypandoc->pkg-utils[all]) (0.33.6) Requirement already satisfied, skipping upgrade: docutils>=0.12 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.15.2) Requirement already satisfied, skipping upgrade: imagesize in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.1.3) Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.2) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.10.3) Requirement already satisfied, skipping upgrade: packaging in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (20.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (0.7.12) Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: Pygments>=2.0 in /usr/local/lib/python3.7/site-packages (from sphinx>=1.8->pkg-utils[all]) (2.5.2) Requirement already satisfied, skipping upgrade: pybtex-docutils>=0.2.0 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.2.2) Requirement already satisfied, skipping upgrade: oset>=0.1.3 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: pybtex>=0.20 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_bibtex->pkg-utils[all]) (0.22.2) Requirement already satisfied, skipping upgrade: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->pkg-utils[all]) (2.0.0) Requirement already satisfied, skipping upgrade: six in /usr/local/lib/python3.7/site-packages/six-1.12.0-py3.7.egg (from sphinxcontrib_spelling->pkg-utils[all]) (1.12.0) Requirement already satisfied, skipping upgrade: contextlib2 in /usr/local/lib/python3.7/site-packages (from abduct->wc-utils[all]) (0.6.0.post1) Requirement already satisfied, skipping upgrade: pyfiglet in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.8.post1) Requirement already satisfied, skipping upgrade: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (0.25.3) Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12) Requirement already satisfied, skipping upgrade: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.0.1) Requirement already satisfied, skipping upgrade: jdcal in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc-utils[all]) (1.4.1) Requirement already satisfied, skipping upgrade: networkx~=2.3 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.4) Requirement already satisfied, skipping upgrade: contexter~=0.1.4 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.4) Requirement already satisfied, skipping upgrade: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.6.1) Requirement already satisfied, skipping upgrade: frozendict~=1.2 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (1.2) Requirement already satisfied, skipping upgrade: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (0.1.3) Requirement already satisfied, skipping upgrade: chardet~=3.0 in /usr/local/lib/python3.7/site-packages/chardet-3.0.4-py3.7.egg (from pronto>=1->wc-utils[all]) (3.0.4) Requirement already satisfied, skipping upgrade: python-dateutil~=2.8 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc-utils[all]) (2.8.0) Requirement already satisfied, skipping upgrade: lml>=0.0.4 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (0.0.9) Requirement already satisfied, skipping upgrade: texttable>=0.8.2 in /usr/local/lib/python3.7/site-packages (from pyexcel>=0.5.9.1->wc-utils[all]) (1.6.2) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /usr/local/lib/python3.7/site-packages/idna-2.8-py3.7.egg (from requests->wc-utils[all]) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/site-packages (from requests->wc-utils[all]) (1.24.2) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/lib/python3.7/site-packages/certifi-2019.9.11-py3.7.egg (from requests->wc-utils[all]) (2019.9.11) Requirement already satisfied, skipping upgrade: s3transfer<0.3.0,>=0.2.0 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.2.1) Requirement already satisfied, skipping upgrade: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (1.13.47) Requirement already satisfied, skipping upgrade: jmespath<1.0.0,>=0.7.1 in /usr/local/lib/python3.7/site-packages (from boto3->wc-utils[all]) (0.9.4) Requirement already satisfied, skipping upgrade: gitdb2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitpython->wc-utils[all]) (2.0.6) Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (0.10.0) Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->wc-utils[all]) (2.4.6) Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7) Requirement already satisfied, skipping upgrade: pyjwt in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.7.1) Requirement already satisfied, skipping upgrade: cython in /usr/local/lib/python3.7/site-packages (from pyjnius->wc-utils[all]) (0.29.14) Requirement already satisfied, skipping upgrade: appdirs>=1.4.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.4.3) Requirement already satisfied, skipping upgrade: flask in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: requests-futures==1.0.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: flask-json in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.3.4) Requirement already satisfied, skipping upgrade: jsonlines==1.2.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (1.2.0) Requirement already satisfied, skipping upgrade: ruamel.yaml>=0.15.78 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.16.5) Requirement already satisfied, skipping upgrade: tqdm>=4.26.0 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (4.41.1) Requirement already satisfied, skipping upgrade: flask-cors in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (3.0.8) Requirement already satisfied, skipping upgrade: aws-requests-auth>=0.4.2 in /usr/local/lib/python3.7/site-packages (from quilt3>=3.1.5->wc-utils[all]) (0.4.2) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /usr/local/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->pkg-utils[all]) (1.1.1) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->pkg-utils[all]) (2019.3) Requirement already satisfied, skipping upgrade: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->pkg-utils[all]) (1.0.7) Requirement already satisfied, skipping upgrade: decorator>=4.3.0 in /usr/local/lib/python3.7/site-packages (from networkx~=2.3->pronto>=1->wc-utils[all]) (4.4.1) Requirement already satisfied, skipping upgrade: smmap2>=2.0.0 in /usr/local/lib/python3.7/site-packages (from gitdb2>=2.0.0->gitpython->wc-utils[all]) (2.0.5) Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in /usr/local/lib/python3.7/site-packages (from deprecated->pygithub->wc-utils[all]) (1.11.2) Requirement already satisfied, skipping upgrade: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (0.16.0) Requirement already satisfied, skipping upgrade: click>=5.1 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (7.0) Requirement already satisfied, skipping upgrade: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask->quilt3>=3.1.5->wc-utils[all]) (1.1.0) Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.8" in /usr/local/lib/python3.7/site-packages (from ruamel.yaml>=0.15.78->quilt3>=3.1.5->wc-utils[all]) (0.2.0) Building wheels for collected packages: pkg-utils, wc-utils Building wheel for pkg-utils (setup.py): started Building wheel for pkg-utils (setup.py): finished with status 'done' Created wheel for pkg-utils: filename=pkg_utils-0.0.5-py2.py3-none-any.whl size=7560 sha256=9253010952eee5b14bc1fb4937770c702f79ffd592dcd9373bcab3bcbe07c0f7 Stored in directory: /tmp/pip-ephem-wheel-cache-ky4zt9ad/wheels/57/3a/20/6f82ae6d2e86c270594fde48c8eb5bd0f1c901e3afc411cd4f Building wheel for wc-utils (setup.py): started Building wheel for wc-utils (setup.py): finished with status 'done' Created wheel for wc-utils: filename=wc_utils-0.0.15-py2.py3-none-any.whl size=68255 sha256=d7ea6020c0640a3a3529a106a85905fd37ebbd2248619f4b60651c34f7a390f3 Stored in directory: /tmp/pip-ephem-wheel-cache-ky4zt9ad/wheels/33/7d/4c/660999fd6582d65839f94335bf2e65501591e27798b0871c35 Successfully built pkg-utils wc-utils Installing collected packages: pkg-utils, wc-utils Found existing installation: pkg-utils 0.0.5 Uninstalling pkg-utils-0.0.5: Successfully uninstalled pkg-utils-0.0.5 Found existing installation: wc-utils 0.0.15 Uninstalling wc-utils-0.0.15: Successfully uninstalled wc-utils-0.0.15 Successfully installed pkg-utils-0.0.5 wc-utils-0.0.15 Collecting pkg-utils[all] Cloning https://github.com/KarrLab/pkg_utils.git to /tmp/pip-install-6t8h6hvs/pkg-utils Collecting wc-utils[all] Cloning https://github.com/KarrLab/wc_utils.git to /tmp/pip-install-6t8h6hvs/wc-utils Requirement already satisfied, skipping upgrade: configparser in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (4.0.2) Requirement already satisfied, skipping upgrade: glob2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.7) Requirement already satisfied, skipping upgrade: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (19.3.1) Requirement already satisfied, skipping upgrade: requirements_parser>=0.2.0 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.2.0) Requirement already satisfied, skipping upgrade: setuptools in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (44.0.0) Requirement already satisfied, skipping upgrade: pypandoc in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.4) Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1) Requirement already satisfied, skipping upgrade: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.0.6) Requirement already satisfied, skipping upgrade: sphinx_rtd_theme>=0.4.2 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.4.3) Requirement already satisfied, skipping upgrade: sphinxcontrib_addmetahtml>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Requirement already satisfied, skipping upgrade: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (1.0.0) Requirement already satisfied, skipping upgrade: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (0.1.1) Req