============================= test session starts ==============================
platform linux -- Python 3.7.6, pytest-5.3.2, py-1.8.1, pluggy-0.13.1
rootdir: /root, inifile: pytest.ini
collected 1 item

tests/test_core.py .                                                     [100%]

=============================== warnings summary ===============================
/usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436
  /usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436: PytestDeprecationWarning: The 'junit_family' default value will change to 'xunit2' in pytest 6.0.
  Add 'junit_family=legacy' to your pytest.ini file to silence this warning and make your suite compatible.
    _issue_warning_captured(deprecated.JUNIT_XML_DEFAULT_FAMILY, config.hook, 2)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
----- generated xml file: /root/project/tests/reports/latest.0-1.3.7.6.xml -----
========================= 1 passed, 1 warning in 0.02s =========================

Coverage.py warning: No data was collected. (no-data-collected)

============================= test session starts ==============================
platform linux -- Python 3.7.6, pytest-5.3.2, py-1.8.1, pluggy-0.13.1
rootdir: /root, inifile: pytest.ini
collected 1 item

tests/test_core.py .                                                     [100%]

=============================== warnings summary ===============================
/usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436
  /usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436: PytestDeprecationWarning: The 'junit_family' default value will change to 'xunit2' in pytest 6.0.
  Add 'junit_family=legacy' to your pytest.ini file to silence this warning and make your suite compatible.
    _issue_warning_captured(deprecated.JUNIT_XML_DEFAULT_FAMILY, config.hook, 2)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
----- generated xml file: /root/project/tests/reports/latest.0-1.3.7.6.xml -----
========================= 1 passed, 1 warning in 0.02s =========================

Coverage.py warning: No data was collected. (no-data-collected)

============================= test session starts ==============================
platform linux -- Python 3.7.6, pytest-5.3.2, py-1.8.1, pluggy-0.13.1
rootdir: /root, inifile: pytest.ini
collected 1 item

tests/test_core.py .                                                     [100%]

=============================== warnings summary ===============================
/usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436
  /usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436: PytestDeprecationWarning: The 'junit_family' default value will change to 'xunit2' in pytest 6.0.
  Add 'junit_family=legacy' to your pytest.ini file to silence this warning and make your suite compatible.
    _issue_warning_captured(deprecated.JUNIT_XML_DEFAULT_FAMILY, config.hook, 2)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
----- generated xml file: /root/project/tests/reports/latest.0-1.3.7.6.xml -----
========================= 1 passed, 1 warning in 0.02s =========================

Coverage.py warning: No data was collected. (no-data-collected)

============================= test session starts ==============================
platform linux -- Python 3.7.6, pytest-5.3.2, py-1.8.1, pluggy-0.13.1
rootdir: /root, inifile: pytest.ini
collected 1 item

tests/test_core.py .                                                     [100%]

=============================== warnings summary ===============================
/usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436
  /usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436: PytestDeprecationWarning: The 'junit_family' default value will change to 'xunit2' in pytest 6.0.
  Add 'junit_family=legacy' to your pytest.ini file to silence this warning and make your suite compatible.
    _issue_warning_captured(deprecated.JUNIT_XML_DEFAULT_FAMILY, config.hook, 2)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
----- generated xml file: /root/project/tests/reports/latest.0-1.3.7.6.xml -----
========================= 1 passed, 1 warning in 0.02s =========================

Coverage.py warning: No data was collected. (no-data-collected)

self = <test_core.TestKarrLabBuildUtils testMethod=test_create_package>

    def test_create_package(self):
        bh = self.construct_build_helper()
    
        tempdirname = tempfile.mkdtemp()
    
        g = github.Github(bh.github_api_token)
        org = g.get_organization('KarrLab')
        for name in ['test_a', 'test_a2', 'test_a_2', 'test_b', 'test_c']:
            try:
                repo = org.get_repo(name)
                repo.delete()
            except github.UnknownObjectException:
                pass
    
        """ test API """
        # test_a
        name = 'test_a'
        description = 'description_a'
        keywords = ['word_a', 'word_b']
        dependencies = ['__undefined__']
        private = True
        dirname = os.path.join(tempdirname, 'test_a')
    
        confirm_side_effects = 29 * [True]
        prompt_side_effects = [
            name, description, ', '.join(keywords), ', '.join(dependencies), dirname, '0.0.1',
            'code_climate_repo_token', 'code_climate_repo_id', 'code_climate_repo_badge_token',
            'coveralls_repo_token', 'coveralls_repo_badge_token', 'circleci_repo_token',
        ]
        with mock.patch('click.confirm', side_effect=confirm_side_effects):
            with mock.patch('click.prompt', side_effect=prompt_side_effects):
                with mock.patch.object(core.BuildHelper, 'upload_package_to_pypi', return_value=None):
                    with pytest.warns(UserWarning, match='Unable to append package to downstream dependency'):
>                       bh.create_package(pypi_repository='testpypi')

tests/test_core.py:156: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
karr_lab_build_utils/core.py:317: in create_package
    self.create_repository(name, description=description, private=private, dirname=dirname)
karr_lab_build_utils/core.py:582: in create_repository
    git.Repo.clone_from('https://github.com/KarrLab/{}.git'.format(name), dirname)
/usr/local/lib/python3.7/site-packages/git/repo/base.py:1023: in clone_from
    return cls._clone(git, url, to_path, GitCmdObjectDB, progress, multi_options, **kwargs)
/usr/local/lib/python3.7/site-packages/git/repo/base.py:964: in _clone
    finalize_process(proc, stderr=stderr)
/usr/local/lib/python3.7/site-packages/git/util.py:332: in finalize_process
    proc.wait(**kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <git.cmd.Git.AutoInterrupt object at 0x7f5a02105e50>
stderr = b"Cloning into '/tmp/tmpy5t4u0n9/test_a'...\nWarning: Permanently added the RSA host key for IP address '140.82.112.4'... not read from remote repository.\n\nPlease make sure you have the correct access rights\nand the repository exists.\n"

    def wait(self, stderr=b''):  # TODO: Bad choice to mimic `proc.wait()` but with different args.
        """Wait for the process and return its status code.
    
        :param stderr: Previously read value of stderr, in case stderr is already closed.
        :warn: may deadlock if output or error pipes are used and not handled separately.
        :raise GitCommandError: if the return status is not 0"""
        if stderr is None:
            stderr = b''
        stderr = force_bytes(data=stderr, encoding='utf-8')
    
        status = self.proc.wait()
    
        def read_all_from_possibly_closed_stream(stream):
            try:
                return stderr + force_bytes(stream.read())
            except ValueError:
                return stderr or b''
    
        if status != 0:
            errstr = read_all_from_possibly_closed_stream(self.proc.stderr)
            log.debug('AutoInterrupt wait stderr: %r' % (errstr,))
>           raise GitCommandError(self.args, status, errstr)
E           git.exc.GitCommandError: Cmd('git') failed due to: exit code(128)
E             cmdline: git clone -v https://github.com/KarrLab/test_a.git /tmp/tmpy5t4u0n9/test_a
E             stderr: 'Cloning into '/tmp/tmpy5t4u0n9/test_a'...
E           Warning: Permanently added the RSA host key for IP address '140.82.112.4' to the list of known hosts.
E           ERROR: Repository not found.
E           fatal: Could not read from remote repository.
E           
E           Please make sure you have the correct access rights
E           and the repository exists.
E           '

/usr/local/lib/python3.7/site-packages/git/cmd.py:417: GitCommandError

This program will guide you through creating a new package.
Creating private remote Git repository "KarrLab/test_a" on GitHub and cloning this repository to "/tmp/tmpy5t4u0n9/test_a"

self = <test_core.TestKarrLabBuildUtils testMethod=test_create_repository>

    def test_create_repository(self):
        build_helper = self.construct_build_helper()
    
        tempdirname = tempfile.mkdtemp()
    
        g = github.Github(build_helper.github_api_token)
        org = g.get_organization('KarrLab')
        for name in ['test_a', 'test_a2', 'test_a_2', 'test_b']:
            try:
                repo = org.get_repo(name)
                repo.delete()
            except github.UnknownObjectException:
                pass
    
        """ test API """
        # test valid repo names
        build_helper.create_repository('test_a', dirname=os.path.join(tempdirname, 'test_a'))
>       build_helper.create_repository('test_a2', dirname=os.path.join(tempdirname, 'test_a2'))

tests/test_core.py:285: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
karr_lab_build_utils/core.py:582: in create_repository
    git.Repo.clone_from('https://github.com/KarrLab/{}.git'.format(name), dirname)
/usr/local/lib/python3.7/site-packages/git/repo/base.py:1023: in clone_from
    return cls._clone(git, url, to_path, GitCmdObjectDB, progress, multi_options, **kwargs)
/usr/local/lib/python3.7/site-packages/git/repo/base.py:964: in _clone
    finalize_process(proc, stderr=stderr)
/usr/local/lib/python3.7/site-packages/git/util.py:332: in finalize_process
    proc.wait(**kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <git.cmd.Git.AutoInterrupt object at 0x7f5a0255c3d0>
stderr = b"Cloning into '/tmp/tmpdgr1poup/test_a2'...\nERROR: Repository not found.\nfatal: Could not read from remote repository.\n\nPlease make sure you have the correct access rights\nand the repository exists.\n"

    def wait(self, stderr=b''):  # TODO: Bad choice to mimic `proc.wait()` but with different args.
        """Wait for the process and return its status code.
    
        :param stderr: Previously read value of stderr, in case stderr is already closed.
        :warn: may deadlock if output or error pipes are used and not handled separately.
        :raise GitCommandError: if the return status is not 0"""
        if stderr is None:
            stderr = b''
        stderr = force_bytes(data=stderr, encoding='utf-8')
    
        status = self.proc.wait()
    
        def read_all_from_possibly_closed_stream(stream):
            try:
                return stderr + force_bytes(stream.read())
            except ValueError:
                return stderr or b''
    
        if status != 0:
            errstr = read_all_from_possibly_closed_stream(self.proc.stderr)
            log.debug('AutoInterrupt wait stderr: %r' % (errstr,))
>           raise GitCommandError(self.args, status, errstr)
E           git.exc.GitCommandError: Cmd('git') failed due to: exit code(128)
E             cmdline: git clone -v https://github.com/KarrLab/test_a2.git /tmp/tmpdgr1poup/test_a2
E             stderr: 'Cloning into '/tmp/tmpdgr1poup/test_a2'...
E           ERROR: Repository not found.
E           fatal: Could not read from remote repository.
E           
E           Please make sure you have the correct access rights
E           and the repository exists.
E           '

/usr/local/lib/python3.7/site-packages/git/cmd.py:417: GitCommandError

usage: karr_lab_build_utils docker [-h]
                                   {remove-container,run-tests-in-container,install-package-to-container,create-container}
                                   ...

Docker utilities

optional arguments:
  -h, --help            show this help message and exit

sub-commands:
  {remove-container,run-tests-in-container,install-package-to-container,create-container}
    remove-container    Remove a Docker container
    run-tests-in-container
                        Run tests in a Docker container
    install-package-to-container
                        Copy and install a package to a Docker container
    create-container    Create a Docker container for running tests

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Requirement already satisfied: logging2; extra == "all" in /usr/local/lib/python3.7/site-packages (from wc_utils[all]->-r /tmp/tmpeojrmwv2.txt (line 37)) (0.1.2)
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Requirement already satisfied: zipp>=0.5 in /usr/local/lib/python3.7/site-packages (from importlib-metadata>=0.12; python_version < "3.8"->pytest->-r /tmp/tmpeojrmwv2.txt (line 22)) (0.6.0)
Requirement already satisfied: 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>=3.1.3->-r /tmp/tmpeojrmwv2.txt (line 25)) (0.2.0)
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Requirement already satisfied: botocore<1.14.0,>=1.13.47 in /usr/local/lib/python3.7/site-packages (from boto3>=1.8.0->quilt3>=3.1.3->-r /tmp/tmpeojrmwv2.txt (line 25)) (1.13.47)
Requirement already satisfied: pytz>=2015.7 in /usr/local/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->-r /tmp/tmpeojrmwv2.txt (line 28)) (2019.3)
Requirement already satisfied: latexcodec>=1.0.4 in /usr/local/lib/python3.7/site-packages (from pybtex>=0.20->sphinxcontrib_bibtex->-r /tmp/tmpeojrmwv2.txt (line 32)) (1.0.7)
Requirement already satisfied: bleach>=2.1.0 in /usr/local/lib/python3.7/site-packages (from readme-renderer>=21.0->twine->-r /tmp/tmpeojrmwv2.txt (line 36)) (3.1.0)
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Requirement already satisfied: colorama in /usr/local/lib/python3.7/site-packages (from mendeleev->wc_utils[all]->-r /tmp/tmpeojrmwv2.txt (line 37)) (0.4.3)
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Requirement already satisfied: fastobo~=0.6.0 in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc_utils[all]->-r /tmp/tmpeojrmwv2.txt (line 37)) (0.6.1)
Requirement already satisfied: nanoset~=0.1.2; platform_python_implementation == "CPython" in /usr/local/lib/python3.7/site-packages (from pronto>=1->wc_utils[all]->-r /tmp/tmpeojrmwv2.txt (line 37)) (0.1.3)
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Requirement already satisfied: cython in /usr/local/lib/python3.7/site-packages (from pyjnius; extra == "all"->wc_utils[all]->-r /tmp/tmpeojrmwv2.txt (line 37)) (0.29.14)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib; extra == "all"->wc_utils[all]->-r /tmp/tmpeojrmwv2.txt (line 37)) (1.1.0)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib; extra == "all"->wc_utils[all]->-r /tmp/tmpeojrmwv2.txt (line 37)) (0.10.0)
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Requirement already satisfied: cryptography in /usr/local/lib/python3.7/site-packages (from secretstorage; sys_platform == "linux"->keyring>=15.1->twine->-r /tmp/tmpeojrmwv2.txt (line 36)) (2.8)
Requirement already satisfied: jeepney in /usr/local/lib/python3.7/site-packages (from secretstorage; sys_platform == "linux"->keyring>=15.1->twine->-r /tmp/tmpeojrmwv2.txt (line 36)) (0.4.2)
Requirement already satisfied: cffi!=1.11.3,>=1.8 in /usr/local/lib/python3.7/site-packages (from cryptography->secretstorage; sys_platform == "linux"->keyring>=15.1->twine->-r /tmp/tmpeojrmwv2.txt (line 36)) (1.13.2)
Requirement already satisfied: pycparser in /usr/local/lib/python3.7/site-packages (from cffi!=1.11.3,>=1.8->cryptography->secretstorage; sys_platform == "linux"->keyring>=15.1->twine->-r /tmp/tmpeojrmwv2.txt (line 36)) (2.19)
Requirement already satisfied: setuptools in /usr/local/lib/python3.7/site-packages (44.0.0)
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Requirement already satisfied: nose in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 15)) (1.3.7)
Requirement already satisfied: pip>=19.3 in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 16)) (19.3.1)
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Requirement already satisfied: pkg_utils[all] in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 18)) (0.0.5)
Requirement already satisfied: pygithub in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 19)) (1.45)
Requirement already satisfied: pylint>=2.1.1 in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 20)) (2.4.4)
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Requirement already satisfied: pytest in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 22)) (5.3.2)
Requirement already satisfied: python_dateutil in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 23)) (2.8.0)
Requirement already satisfied: pyyaml>=5.1 in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 24)) (5.3)
Requirement already satisfied: quilt3>=3.1.3 in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 25)) (3.1.8)
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Requirement already satisfied: setuptools>=40.0.0 in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 27)) (44.0.0)
Requirement already satisfied: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 28)) (2.3.1)
Requirement already satisfied: sphinx_fontawesome in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 29)) (0.0.6)
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Requirement already satisfied: sphinxcontrib_bibtex in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 32)) (1.0.0)
Requirement already satisfied: sphinxcontrib_googleanalytics>=0.1.1 in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 33)) (0.1.1)
Requirement already satisfied: sphinxcontrib_spelling in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 34)) (4.3.0)
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Requirement already satisfied: wheel in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 38)) (0.33.6)
Requirement already satisfied: whichcraft in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 39)) (0.6.1)
Requirement already satisfied: capturer in /usr/local/lib/python3.7/site-packages (from -r /tmp/tmpg1ar39om.txt (line 40)) (2.4)
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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.
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.
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.
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.
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.
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.

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Requirement already satisfied: PyEnchant>=1.6.5 in /usr/local/lib/python3.7/site-packages (from sphinxcontrib_spelling->-r /tmp/tmpfrbk51_g.txt (line 34)) (2.0.0)
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Requirement already satisfied: 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>=3.1.3->-r /tmp/tmpfrbk51_g.txt (line 25)) (0.2.0)
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Requirement already satisfied: et-xmlfile in /usr/local/lib/python3.7/site-packages (from openpyxl<=3.0.1,>=2.6.1->wc_utils[all]->-r /tmp/tmpfrbk51_g.txt (line 37)) (1.0.1)
Requirement already satisfied: pandas in /usr/local/lib/python3.7/site-packages (from mendeleev->wc_utils[all]->-r /tmp/tmpfrbk51_g.txt (line 37)) (0.25.3)
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Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib; extra == "all"->wc_utils[all]->-r /tmp/tmpfrbk51_g.txt (line 37)) (1.1.0)
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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.
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.
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:718: Test requires Docker and Docker isnt installed. See installation instructions at `https://docs.karrlab.org/intro_to_wc_modeling/latest/installation.html`

============================= test session starts ==============================
platform linux -- Python 3.7.6, pytest-5.3.2, py-1.8.1, pluggy-0.13.1
rootdir: /root, inifile: pytest.ini
collected 1 item

tests/test_core.py .                                                     [100%]

=============================== warnings summary ===============================
/usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436
  /usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436: PytestDeprecationWarning: The 'junit_family' default value will change to 'xunit2' in pytest 6.0.
  Add 'junit_family=legacy' to your pytest.ini file to silence this warning and make your suite compatible.
    _issue_warning_captured(deprecated.JUNIT_XML_DEFAULT_FAMILY, config.hook, 2)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
----- generated xml file: /root/project/tests/reports/latest.0-1.3.7.6.xml -----
========================= 1 passed, 1 warning in 0.02s =========================
************* Module karr_lab_build_utils.core
 karr_lab_build_utils/core.py:1119: warning (W0613, unused-argument, BuildHelper._get_test_cases) Unused argument 'with_xunit'
 karr_lab_build_utils/core.py:1119: warning (W0613, unused-argument, BuildHelper._get_test_cases) Unused argument 'exit_on_failure'
 karr_lab_build_utils/core.py:1155: warning (W0612, unused-variable, BuildHelper._get_test_cases) Unused variable 'files'
 karr_lab_build_utils/core.py:1292: warning (W0612, unused-variable, BuildHelper.install_package_to_docker_container) Unused variable 'rel_filenames'
 karr_lab_build_utils/core.py:1678: warning (W0612, unused-variable, BuildHelper.get_test_results_status) Unused variable 'upstream_build_num'
 karr_lab_build_utils/core.py:35: warning (W0611, unused-import, ) Unused import json
 karr_lab_build_utils/core.py:54: warning (W0611, unused-import, ) Unused import _pytest
 ************* Module karr_lab_build_utils.__main__
 karr_lab_build_utils/__main__.py:192: warning (W0612, unused-variable, DownloadInstallPackageConfigFilesController._default) Unused variable 'args'
 karr_lab_build_utils/__main__.py:10: warning (W0611, unused-import, ) Unused BuildHelperError imported from karr_lab_build_utils.core
 karr_lab_build_utils/__main__.py:13: warning (W0611, unused-import, ) Unused import sys
 ************* Module karr_lab_build_utils.config.core
 karr_lab_build_utils/config/core.py:9: warning (W0611, unused-import, ) Unused import configobj
 Creating file docs/source/karr_lab_build_utils.rst.
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build succeeded, 7 warnings.

The HTML pages are in docs/_build/html.
Running Sphinx v2.3.1
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build succeeded, 7 warnings.

The text files are in _build_txt.
************* Module karr_lab_build_utils.core
 karr_lab_build_utils/core.py:1119: warning (W0613, unused-argument, BuildHelper._get_test_cases) Unused argument 'with_xunit'
 karr_lab_build_utils/core.py:1119: warning (W0613, unused-argument, BuildHelper._get_test_cases) Unused argument 'exit_on_failure'
 karr_lab_build_utils/core.py:1155: warning (W0612, unused-variable, BuildHelper._get_test_cases) Unused variable 'files'
 karr_lab_build_utils/core.py:1292: warning (W0612, unused-variable, BuildHelper.install_package_to_docker_container) Unused variable 'rel_filenames'
 karr_lab_build_utils/core.py:1678: warning (W0612, unused-variable, BuildHelper.get_test_results_status) Unused variable 'upstream_build_num'
 karr_lab_build_utils/core.py:35: warning (W0611, unused-import, ) Unused import json
 karr_lab_build_utils/core.py:54: warning (W0611, unused-import, ) Unused import _pytest
 ************* Module karr_lab_build_utils.__main__
 karr_lab_build_utils/__main__.py:192: warning (W0612, unused-variable, DownloadInstallPackageConfigFilesController._default) Unused variable 'args'
 karr_lab_build_utils/__main__.py:10: warning (W0611, unused-import, ) Unused BuildHelperError imported from karr_lab_build_utils.core
 karr_lab_build_utils/__main__.py:13: warning (W0611, unused-import, ) Unused import sys
 ************* Module karr_lab_build_utils.config.core
 karr_lab_build_utils/config/core.py:9: warning (W0611, unused-import, ) Unused import configobj
 Creating file docs/source/karr_lab_build_utils.rst.
Creating file docs/source/karr_lab_build_utils.config.rst.
Creating file docs/source/modules.rst.
Running Sphinx v2.3.1
Initializing Spelling Checker
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 0 source files that are out of date
updating environment: 0 added, 0 changed, 0 removed
looking for now-outdated files... none found
no targets are out of date.
build succeeded.

The HTML pages are in docs/_build/html.
Running Sphinx v2.3.1
loading translations [en]... done
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updating environment: [new config] 8 added, 0 changed, 0 removed
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build succeeded, 7 warnings.

The text files are in _build_txt.

Coverage.py warning: No data was collected. (no-data-collected)
/root/project/docs/about.rst:2: WARNING: Duplicate explicit target name: "karr lab".
/root/project/karr_lab_build_utils/core.py:docstring of karr_lab_build_utils.core.BuildHelper.do_post_test_tasks:18: WARNING: Unexpected indentation.
/root/project/karr_lab_build_utils/core.py:docstring of karr_lab_build_utils.core.BuildHelper.do_post_test_tasks:19: WARNING: Block quote ends without a blank line; unexpected unindent.
/root/project/karr_lab_build_utils/core.py:docstring of karr_lab_build_utils.core.BuildHelper.trigger_tests_of_downstream_dependencies:11: WARNING: Unexpected indentation.
/root/project/docs/source/karr_lab_build_utils.config.rst:5: WARNING: duplicate label submodules, other instance in /root/project/docs/source/karr_lab_build_utils.rst
/root/project/docs/source/karr_lab_build_utils.config.rst:17: WARNING: duplicate label module contents, other instance in /root/project/docs/source/karr_lab_build_utils.rst
/root/project/docs/tutorial_admins.rst:45: WARNING: Unknown target name: "pylint https://www.pylint.org/".
/root/project/docs/about.rst:2: WARNING: Duplicate explicit target name: "karr lab".
/root/project/karr_lab_build_utils/core.py:docstring of karr_lab_build_utils.core.BuildHelper.do_post_test_tasks:18: WARNING: Unexpected indentation.
/root/project/karr_lab_build_utils/core.py:docstring of karr_lab_build_utils.core.BuildHelper.do_post_test_tasks:19: WARNING: Block quote ends without a blank line; unexpected unindent.
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/root/project/docs/source/karr_lab_build_utils.config.rst:5: WARNING: duplicate label submodules, other instance in /root/project/docs/source/karr_lab_build_utils.rst
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/root/project/docs/tutorial_admins.rst:45: WARNING: Unknown target name: "pylint https://www.pylint.org/".

============================= test session starts ==============================
platform linux -- Python 3.7.6, pytest-5.3.2, py-1.8.1, pluggy-0.13.1
rootdir: /root, inifile: pytest.ini
collected 1 item

tests/test_core.py .                                                     [100%]

=============================== warnings summary ===============================
/usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436
  /usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436: PytestDeprecationWarning: The 'junit_family' default value will change to 'xunit2' in pytest 6.0.
  Add 'junit_family=legacy' to your pytest.ini file to silence this warning and make your suite compatible.
    _issue_warning_captured(deprecated.JUNIT_XML_DEFAULT_FAMILY, config.hook, 2)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
----- generated xml file: /root/project/tests/reports/latest.0-1.3.7.6.xml -----
========================= 1 passed, 1 warning in 0.02s =========================
************* Module karr_lab_build_utils.core
 karr_lab_build_utils/core.py:1119: warning (W0613, unused-argument, BuildHelper._get_test_cases) Unused argument 'with_xunit'
 karr_lab_build_utils/core.py:1119: warning (W0613, unused-argument, BuildHelper._get_test_cases) Unused argument 'exit_on_failure'
 karr_lab_build_utils/core.py:1155: warning (W0612, unused-variable, BuildHelper._get_test_cases) Unused variable 'files'
 karr_lab_build_utils/core.py:1292: warning (W0612, unused-variable, BuildHelper.install_package_to_docker_container) Unused variable 'rel_filenames'
 karr_lab_build_utils/core.py:1678: warning (W0612, unused-variable, BuildHelper.get_test_results_status) Unused variable 'upstream_build_num'
 karr_lab_build_utils/core.py:35: warning (W0611, unused-import, ) Unused import json
 karr_lab_build_utils/core.py:54: warning (W0611, unused-import, ) Unused import _pytest
 ************* Module karr_lab_build_utils.__main__
 karr_lab_build_utils/__main__.py:192: warning (W0612, unused-variable, DownloadInstallPackageConfigFilesController._default) Unused variable 'args'
 karr_lab_build_utils/__main__.py:10: warning (W0611, unused-import, ) Unused BuildHelperError imported from karr_lab_build_utils.core
 karr_lab_build_utils/__main__.py:13: warning (W0611, unused-import, ) Unused import sys
 ************* Module karr_lab_build_utils.config.core
 karr_lab_build_utils/config/core.py:9: warning (W0611, unused-import, ) Unused import configobj
 Creating file docs/source/karr_lab_build_utils.rst.
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Running Sphinx v2.3.1
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build succeeded.

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Running Sphinx v2.3.1
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build succeeded, 7 warnings.

The text files are in _build_txt.

Coverage.py warning: No data was collected. (no-data-collected)
/root/project/docs/about.rst:2: WARNING: Duplicate explicit target name: "karr lab".
/root/project/karr_lab_build_utils/core.py:docstring of karr_lab_build_utils.core.BuildHelper.do_post_test_tasks:18: WARNING: Unexpected indentation.
/root/project/karr_lab_build_utils/core.py:docstring of karr_lab_build_utils.core.BuildHelper.do_post_test_tasks:19: WARNING: Block quote ends without a blank line; unexpected unindent.
/root/project/karr_lab_build_utils/core.py:docstring of karr_lab_build_utils.core.BuildHelper.trigger_tests_of_downstream_dependencies:11: WARNING: Unexpected indentation.
/root/project/docs/source/karr_lab_build_utils.config.rst:5: WARNING: duplicate label submodules, other instance in /root/project/docs/source/karr_lab_build_utils.rst
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build succeeded, 7 warnings.

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Running Sphinx v2.3.1
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build succeeded, 7 warnings.

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source/karr_lab_build_utils.rst:15:utils:
source/karr_lab_build_utils.rst:1:Karr:
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source/karr_lab_build_utils.rst:5:karrlab:
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source/karr_lab_build_utils.rst:248:pytest:
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source/karr_lab_build_utils.rst:7:init:
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Spelling checker messages written to /root/project/docs/_build/spelling/output.txt
build succeeded, 8 warnings.
Creating file docs/source/karr_lab_build_utils.rst.
Creating file docs/source/karr_lab_build_utils.config.rst.
Creating file docs/source/modules.rst.
Running Sphinx v2.3.1
Initializing Spelling Checker
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 0 source files that are out of date
updating environment: 0 added, 0 changed, 0 removed
looking for now-outdated files... none found
no targets are out of date.
build succeeded.

The HTML pages are in docs/_build/html.
Running Sphinx v2.3.1
loading translations [en]... done
Initializing Spelling Checker
building [mo]: all of 0 po files
building [text]: all source files
updating environment: [new config] 8 added, 0 changed, 0 removed
reading sources... [ 12%] about
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reading sources... [ 37%] installation
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reading sources... [ 62%] source/karr_lab_build_utils.config
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reading sources... [100%] tutorial_developers

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 12%] about
writing output... [ 25%] index
writing output... [ 37%] installation
writing output... [ 50%] source/karr_lab_build_utils
writing output... [ 62%] source/karr_lab_build_utils.config
writing output... [ 75%] source/modules
writing output... [ 87%] tutorial_admins
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build succeeded, 7 warnings.

The text files are in _build_txt.

/root/project/docs/about.rst:2: WARNING: Duplicate explicit target name: "karr lab".
/root/project/karr_lab_build_utils/core.py:docstring of karr_lab_build_utils.core.BuildHelper.do_post_test_tasks:18: WARNING: Unexpected indentation.
/root/project/karr_lab_build_utils/core.py:docstring of karr_lab_build_utils.core.BuildHelper.do_post_test_tasks:19: WARNING: Block quote ends without a blank line; unexpected unindent.
/root/project/karr_lab_build_utils/core.py:docstring of karr_lab_build_utils.core.BuildHelper.trigger_tests_of_downstream_dependencies:11: WARNING: Unexpected indentation.
/root/project/docs/source/karr_lab_build_utils.config.rst:5: WARNING: duplicate label submodules, other instance in /root/project/docs/source/karr_lab_build_utils.rst
/root/project/docs/source/karr_lab_build_utils.config.rst:17: WARNING: duplicate label module contents, other instance in /root/project/docs/source/karr_lab_build_utils.rst
/root/project/docs/tutorial_admins.rst:45: WARNING: Unknown target name: "pylint https://www.pylint.org/".
/root/project/docs/about.rst:2: WARNING: Duplicate explicit target name: "karr lab".
/root/project/karr_lab_build_utils/core.py:docstring of karr_lab_build_utils.core.BuildHelper.do_post_test_tasks:18: WARNING: Unexpected indentation.
/root/project/karr_lab_build_utils/core.py:docstring of karr_lab_build_utils.core.BuildHelper.do_post_test_tasks:19: WARNING: Block quote ends without a blank line; unexpected unindent.
/root/project/karr_lab_build_utils/core.py:docstring of karr_lab_build_utils.core.BuildHelper.trigger_tests_of_downstream_dependencies:11: WARNING: Unexpected indentation.
/root/project/docs/source/karr_lab_build_utils.config.rst:5: WARNING: duplicate label submodules, other instance in /root/project/docs/source/karr_lab_build_utils.rst
/root/project/docs/source/karr_lab_build_utils.config.rst:17: WARNING: duplicate label module contents, other instance in /root/project/docs/source/karr_lab_build_utils.rst
/root/project/docs/tutorial_admins.rst:45: WARNING: Unknown target name: "pylint https://www.pylint.org/".

Creating file docs/source/karr_lab_build_utils.rst.
Creating file docs/source/karr_lab_build_utils.config.rst.
Creating file docs/source/modules.rst.

Exception occurred:
  File "/usr/local/lib/python3.7/site-packages/mock/mock.py", line 1143, in _mock_call
    raise effect
Exception: Test exception
The full traceback has been saved in /tmp/sphinx-err-3aw5_wfx.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!

usage: karr_lab_build_utils [-h] [-d] [-q] [-v]
                            {upload-package-to-pypi,find-unused-requirements,find-missing-requirements,analyze-package,visualize-package-dependencies,are-package-dependencies-acyclic,compile-downstream-dependencies,make-documentation,upload-coverage-report-to-code-climate,upload-coverage-report-to-coveralls,archive-coverage-report,combine-coverage-reports,make-and-archive-reports,do-post-test-tasks,create-code-climate-github-webhook,delete-circleci-environment-variable,set-circleci-environment-variable,get-circleci-environment-variables,follow-circleci-build,docker,run-tests,download-install-package-config-files,create-documentation-template,setup-repository,create-repository,create-package,archive-test-report,install-requirements,upgrade-karr-lab-packages}
                            ...

Karr Lab build utilities

optional arguments:
  -h, --help            show this help message and exit
  -d, --debug           full application debug mode
  -q, --quiet           suppress all console output
  -v, --version         show program's version number and exit

sub-commands:
  {upload-package-to-pypi,find-unused-requirements,find-missing-requirements,analyze-package,visualize-package-dependencies,are-package-dependencies-acyclic,compile-downstream-dependencies,make-documentation,upload-coverage-report-to-code-climate,upload-coverage-report-to-coveralls,archive-coverage-report,combine-coverage-reports,make-and-archive-reports,do-post-test-tasks,create-code-climate-github-webhook,delete-circleci-environment-variable,set-circleci-environment-variable,get-circleci-environment-variables,follow-circleci-build,docker,run-tests,download-install-package-config-files,create-documentation-template,setup-repository,create-repository,create-package,archive-test-report,install-requirements,upgrade-karr-lab-packages}
    upload-package-to-pypi
                        Upload package to PyPI
    find-unused-requirements
                        Finding unused requirements for a package.
    find-missing-requirements
                        Finding missing requirements for a package.
    analyze-package     Perform static analyses of a package using Pylint
    visualize-package-dependencies
                        Visualize downstream package dependencies as a graph
    are-package-dependencies-acyclic
                        Check if the package dependencies are acyclic so they
                        are supported by CircleCI
    compile-downstream-dependencies
                        Compile the downstream dependencies of a package by
                        analyzing the requirements files of other packages
    make-documentation  Make HTML documentation. Optionally, spell check
                        documentation.
    upload-coverage-report-to-code-climate
                        Upload coverage report to Code Climate
    upload-coverage-report-to-coveralls
                        Upload coverage report to Coveralls
    archive-coverage-report
                        Archive coverage report
    combine-coverage-reports
                        Combine coverage reports (.coverage.*) into a single
                        file (.coverage)
    make-and-archive-reports
                        Make and archive reports
    do-post-test-tasks  Do all post-test tasks for CircleCI
    create-code-climate-github-webhook
                        Create Code Climate GitHub webhook for the current
                        repository
    delete-circleci-environment-variable
                        Delete a CircleCI environment variable for a
                        repository
    set-circleci-environment-variable
                        Set a CircleCI environment variable for a repository
    get-circleci-environment-variables
                        Get the CircleCI environment variables for a
                        repository and their partial values
    follow-circleci-build
                        Follow a CircleCI build for a repository
    docker              Docker utilities
    run-tests           Run unit tests located at `test_path`
    download-install-package-config-files
                        Download and install configuration files from GitHub
                        configuration repository
    create-documentation-template
                        Create a Sphinx documentation template for a package
    setup-repository    Setup a local Git repository with the default
                        directory structure
    create-repository   Create a GitHub repository and clone the repository
                        locally
    create-package      - Create local and remote Git repositories; - Setup
                        the directory structure of the repository; - Add the
                        repository to CircleCI, Coveralls, Code Climate, Read
                        the Docs, and code.karrlab.org; - Update the
                        downstream dependencies of the packages dependencies
    archive-test-report
                        Archive test report
    install-requirements
                        Install requirements
    upgrade-karr-lab-packages
                        Upgrade the packages from the Karr Lab's GitHub
                        organization

============================= test session starts ==============================
platform linux -- Python 3.7.6, pytest-5.3.2, py-1.8.1, pluggy-0.13.1
rootdir: /root, inifile: pytest.ini
collected 1 item

tests/test_core.py .                                                     [100%]

=============================== warnings summary ===============================
/usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436
  /usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436: PytestDeprecationWarning: The 'junit_family' default value will change to 'xunit2' in pytest 6.0.
  Add 'junit_family=legacy' to your pytest.ini file to silence this warning and make your suite compatible.
    _issue_warning_captured(deprecated.JUNIT_XML_DEFAULT_FAMILY, config.hook, 2)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
---------- generated xml file: /tmp/tmp5_8oew67/latest.0-1.3.7.6.xml -----------
========================= 1 passed, 1 warning in 0.02s =========================
============================= test session starts ==============================
platform linux -- Python 3.7.6, pytest-5.3.2, py-1.8.1, pluggy-0.13.1
rootdir: /root, inifile: pytest.ini
collected 1 item

tests/test_core.py .                                                     [100%]

=============================== warnings summary ===============================
/usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436
  /usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436: PytestDeprecationWarning: The 'junit_family' default value will change to 'xunit2' in pytest 6.0.
  Add 'junit_family=legacy' to your pytest.ini file to silence this warning and make your suite compatible.
    _issue_warning_captured(deprecated.JUNIT_XML_DEFAULT_FAMILY, config.hook, 2)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
---------- generated xml file: /tmp/tmp5_8oew67/latest.0-1.3.7.6.xml -----------
========================= 1 passed, 1 warning in 0.01s =========================
============================= test session starts ==============================
platform linux -- Python 3.7.6, pytest-5.3.2, py-1.8.1, pluggy-0.13.1
rootdir: /root, inifile: pytest.ini
collected 1 item

tests/test_core.py .                                                     [100%]

=============================== warnings summary ===============================
/usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436
  /usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436: PytestDeprecationWarning: The 'junit_family' default value will change to 'xunit2' in pytest 6.0.
  Add 'junit_family=legacy' to your pytest.ini file to silence this warning and make your suite compatible.
    _issue_warning_captured(deprecated.JUNIT_XML_DEFAULT_FAMILY, config.hook, 2)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
----- generated xml file: /root/project/tests/reports/latest.0-1.3.7.6.xml -----
========================= 1 passed, 1 warning in 0.02s =========================
============================= test session starts ==============================
platform linux -- Python 3.7.6, pytest-5.3.2, py-1.8.1, pluggy-0.13.1
rootdir: /root, inifile: pytest.ini
collected 1 item

tests/test_core.py .                                                     [100%]

=============================== warnings summary ===============================
/usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436
  /usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436: PytestDeprecationWarning: The 'junit_family' default value will change to 'xunit2' in pytest 6.0.
  Add 'junit_family=legacy' to your pytest.ini file to silence this warning and make your suite compatible.
    _issue_warning_captured(deprecated.JUNIT_XML_DEFAULT_FAMILY, config.hook, 2)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
----- generated xml file: /root/project/tests/reports/latest.0-1.3.7.6.xml -----
========================= 1 passed, 1 warning in 0.02s =========================

Coverage.py warning: No data was collected. (no-data-collected)
Coverage.py warning: No data was collected. (no-data-collected)
Coverage.py warning: No data was collected. (no-data-collected)
.
----------------------------------------------------------------------
Ran 1 test in 0.003s

OK
Coverage.py warning: No data was collected. (no-data-collected)
Coverage.py warning: No data was collected. (no-data-collected)

project/tests/test_core.py:2773: Test requires the CircleCI command line utility (local executor) and this isnt installed. See installation instructions at `https://docs.karrlab.org/intro_to_wc_modeling/latest/installation.html`.

project/tests/test_core.py:2785: Test requires the CircleCI command line utility (local executor) and this isnt installed. See installation instructions at `https://docs.karrlab.org/intro_to_wc_modeling/latest/installation.html`.

project/tests/test_core.py:740: Test requires Docker and Docker isnt installed. See installation instructions at `https://docs.karrlab.org/intro_to_wc_modeling/latest/installation.html`

project/tests/test_core.py:629: Todo

============================= test session starts ==============================
platform linux -- Python 3.7.6, pytest-5.3.2, py-1.8.1, pluggy-0.13.1
rootdir: /root, inifile: pytest.ini
collected 1 item

tests/test_core.py .                                                     [100%]

============================== 1 passed in 0.02s ===============================

============================= test session starts ==============================
platform linux -- Python 3.7.6, pytest-5.3.2, py-1.8.1, pluggy-0.13.1
rootdir: /root, inifile: pytest.ini
collected 1 item

tests/test_core.py .

============================== 1 passed in 0.02s ===============================

.
----------------------------------------------------------------------
Ran 1 test in 0.001s

OK

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
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Requirement already satisfied, skipping upgrade: deprecated in /usr/local/lib/python3.7/site-packages (from pygithub->wc-utils[all]) (1.2.7)
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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)
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Requirement already satisfied, skipping upgrade: sphinx>=1.8 in /usr/local/lib/python3.7/site-packages (from pkg-utils[all]) (2.3.1)
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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)
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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)
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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)
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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)
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Requirement already satisfied, skipping upgrade: sqlalchemy in /usr/local/lib/python3.7/site-packages (from mendeleev->wc-utils[all]) (1.3.12)
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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)
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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)
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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)
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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

  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.

============================= test session starts ==============================
platform linux -- Python 3.7.6, pytest-5.3.2, py-1.8.1, pluggy-0.13.1
rootdir: /root, inifile: pytest.ini
collected 1 item

tests/test_core.py .                                                     [100%]

=============================== warnings summary ===============================
/usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436
  /usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436: PytestDeprecationWarning: The 'junit_family' default value will change to 'xunit2' in pytest 6.0.
  Add 'junit_family=legacy' to your pytest.ini file to silence this warning and make your suite compatible.
    _issue_warning_captured(deprecated.JUNIT_XML_DEFAULT_FAMILY, config.hook, 2)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
----- generated xml file: /root/project/tests/reports/latest.0-1.3.7.6.xml -----
========================= 1 passed, 1 warning in 0.02s =========================

Coverage.py warning: No data was collected. (no-data-collected)

============================= test session starts ==============================
platform linux -- Python 3.7.6, pytest-5.3.2, py-1.8.1, pluggy-0.13.1
rootdir: /root, inifile: pytest.ini
collected 1 item

tests/test_core.py .                                                     [100%]

=============================== warnings summary ===============================
/usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436
  /usr/local/lib/python3.7/site-packages/_pytest/junitxml.py:436: PytestDeprecationWarning: The 'junit_family' default value will change to 'xunit2' in pytest 6.0.
  Add 'junit_family=legacy' to your pytest.ini file to silence this warning and make your suite compatible.
    _issue_warning_captured(deprecated.JUNIT_XML_DEFAULT_FAMILY, config.hook, 2)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
----- generated xml file: /root/project/tests/reports/latest.0-1.3.7.6.xml -----
========================= 1 passed, 1 warning in 0.02s =========================

Coverage.py warning: No data was collected. (no-data-collected)

project/tests/test_core.py:766: Test requires Docker and Docker isnt installed. See installation instructions at `https://docs.karrlab.org/intro_to_wc_modeling/latest/installation.html`

project/tests/test_core.py:777: Test requires Docker and Docker isnt installed. See installation instructions at `https://docs.karrlab.org/intro_to_wc_modeling/latest/installation.html`