Read the Docs build information
Build id: 920565
Project: beliveau-lab-tigerfish
Version: latest
Commit: 9181459cc492db3bcf73296798318a4ee61512d3
Date: 2022-04-19T02:23:38.033143Z
State: finished
Success: False


[rtd-command-info] start-time: 2022-04-19T02:23:39.815220Z, end-time: 2022-04-19T02:23:41.978745Z, duration: 2, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:beliveau-lab/TigerFISH.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.113' (ECDSA) to the list of known hosts.

[rtd-command-info] start-time: 2022-04-19T02:23:42.163698Z, end-time: 2022-04-19T02:23:42.520912Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to 'origin/master'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 9181459 removed false yml

[rtd-command-info] start-time: 2022-04-19T02:23:42.692657Z, end-time: 2022-04-19T02:23:42.765349Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-04-19T02:23:43.820499Z, end-time: 2022-04-19T02:23:48.246964Z, duration: 4, exit-code: 0
python3.7 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2022-04-19T02:23:48.438266Z, end-time: 2022-04-19T02:23:50.483519Z, duration: 2, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (22.0.4)
Collecting setuptools<58.3.0
  Downloading setuptools-58.2.0-py3-none-any.whl (946 kB)
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Installing collected packages: setuptools
  Attempting uninstall: setuptools
    Found existing installation: setuptools 62.1.0
    Uninstalling setuptools-62.1.0:
      Successfully uninstalled setuptools-62.1.0
Successfully installed setuptools-58.2.0

[rtd-command-info] start-time: 2022-04-19T02:23:50.682087Z, end-time: 2022-04-19T02:23:59.074918Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx sphinx-rtd-theme readthedocs-sphinx-ext<2.2
Collecting mock==1.0.1
  Downloading mock-1.0.1.zip (861 kB)
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  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting pillow==5.4.1
  Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB)
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Collecting alabaster!=0.7.5,<0.8,>=0.7
  Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB)
Collecting commonmark==0.8.1
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Collecting recommonmark==0.5.0
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Collecting sphinx
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Collecting sphinx-rtd-theme
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Collecting readthedocs-sphinx-ext<2.2
  Downloading readthedocs_sphinx_ext-2.1.5-py2.py3-none-any.whl (11 kB)
Collecting future
  Downloading future-0.18.2.tar.gz (829 kB)
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  Preparing metadata (setup.py): started
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Collecting docutils>=0.11
  Downloading docutils-0.18.1-py2.py3-none-any.whl (570 kB)
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Collecting importlib-metadata>=4.4
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Collecting Jinja2>=2.3
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Collecting sphinxcontrib-qthelp
  Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
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Collecting sphinxcontrib-serializinghtml>=1.1.5
  Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB)
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Collecting imagesize
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Collecting babel>=1.3
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Collecting sphinxcontrib-jsmath
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting docutils>=0.11
  Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB)
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Collecting sphinxcontrib-applehelp
  Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB)
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Collecting packaging
  Downloading packaging-21.3-py3-none-any.whl (40 kB)
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Collecting requests>=2.5.0
  Downloading requests-2.27.1-py2.py3-none-any.whl (63 kB)
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Collecting sphinxcontrib-devhelp
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Collecting Pygments>=2.0
  Downloading Pygments-2.11.2-py3-none-any.whl (1.1 MB)
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Collecting snowballstemmer>=1.1
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Collecting sphinxcontrib-htmlhelp>=2.0.0
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Collecting pytz>=2015.7
  Downloading pytz-2022.1-py2.py3-none-any.whl (503 kB)
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Collecting typing-extensions>=3.6.4
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Collecting zipp>=0.5
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Collecting MarkupSafe>=2.0
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Collecting idna<4,>=2.5
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Collecting certifi>=2017.4.17
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Collecting charset-normalizer~=2.0.0
  Downloading charset_normalizer-2.0.12-py3-none-any.whl (39 kB)
Collecting urllib3<1.27,>=1.21.1
  Downloading urllib3-1.26.9-py2.py3-none-any.whl (138 kB)
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Collecting pyparsing!=3.0.5,>=2.0.2
  Downloading pyparsing-3.0.8-py3-none-any.whl (98 kB)
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Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23773 sha256=a8e3d2e9d7a0c6af45a6165a7b40545c0b21a7cec154e90b216c467422725f0b
  Stored in directory: /tmp/pip-ephem-wheel-cache-d6xu7ve4/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=6914ef1b7bfd5168385a86123f26b7e6e49ab0fd91735b04e1fe69490c900de0
  Stored in directory: /tmp/pip-ephem-wheel-cache-d6xu7ve4/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Successfully built mock future
Installing collected packages: snowballstemmer, pytz, mock, certifi, alabaster, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, babel, requests, packaging, Jinja2, importlib-metadata, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed Jinja2-3.1.1 MarkupSafe-2.1.1 Pygments-2.11.2 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.12 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 importlib-metadata-4.11.3 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.8 pytz-2022.1 readthedocs-sphinx-ext-2.1.5 recommonmark-0.5.0 requests-2.27.1 snowballstemmer-2.2.0 sphinx-4.5.0 sphinx-rtd-theme-1.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 typing-extensions-4.2.0 urllib3-1.26.9 zipp-3.8.0

[rtd-command-info] start-time: 2022-04-19T02:23:59.246944Z, end-time: 2022-04-19T02:24:00.176824Z, duration: 0, exit-code: 1
python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[docs]
Processing /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'error'
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [41 lines of output]
      Traceback (most recent call last):
        File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/pkg_resources/_vendor/packaging/requirements.py", line 98, in __init__
          req = REQUIREMENT.parseString(requirement_string)
        File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/pkg_resources/_vendor/pyparsing.py", line 1654, in parseString
          raise exc
        File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/pkg_resources/_vendor/pyparsing.py", line 1644, in parseString
          loc, tokens = self._parse( instring, 0 )
        File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/pkg_resources/_vendor/pyparsing.py", line 1402, in _parseNoCache
          loc,tokens = self.parseImpl( instring, preloc, doActions )
        File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/pkg_resources/_vendor/pyparsing.py", line 3417, in parseImpl
          loc, exprtokens = e._parse( instring, loc, doActions )
        File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/pkg_resources/_vendor/pyparsing.py", line 1406, in _parseNoCache
          loc,tokens = self.parseImpl( instring, preloc, doActions )
        File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/pkg_resources/_vendor/pyparsing.py", line 3205, in parseImpl
          raise ParseException(instring, loc, self.errmsg, self)
      pkg_resources._vendor.pyparsing.ParseException: Expected stringEnd (at char 8), (line:1, col:9)
      
      During handling of the above exception, another exception occurred:
      
      Traceback (most recent call last):
        File "<string>", line 36, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/setup.py", line 6, in <module>
          setuptools.setup()
        File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/setuptools/__init__.py", line 152, in setup
          _install_setup_requires(attrs)
        File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/setuptools/__init__.py", line 145, in _install_setup_requires
          dist.parse_config_files(ignore_option_errors=True)
        File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/setuptools/dist.py", line 801, in parse_config_files
          self._finalize_requires()
        File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/setuptools/dist.py", line 528, in _finalize_requires
          self._move_install_requirements_markers()
        File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/setuptools/dist.py", line 567, in _move_install_requirements_markers
          inst_reqs = list(pkg_resources.parse_requirements(spec_inst_reqs))
        File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3084, in parse_requirements
          yield Requirement(line)
        File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3094, in __init__
          super(Requirement, self).__init__(requirement_string)
        File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/pkg_resources/_vendor/packaging/requirements.py", line 102, in __init__
          requirement_string[e.loc : e.loc + 8], e.msg
      pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error at "'=2.29.2'": Expected stringEnd
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.