Read the Docs build information
Build id: 920343
Project: beliveau-lab-tigerfish
Version: latest
Commit: ca35b1ca943e29801f9d2e0a1b24819f2617b1b4
Date: 2022-04-18T21:51:33.653177Z
State: finished
Success: False


[rtd-command-info] start-time: 2022-04-18T21:51:35.460174Z, end-time: 2022-04-18T21:51:37.960958Z, 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,192.30.255.112' (ECDSA) to the list of known hosts.

[rtd-command-info] start-time: 2022-04-18T21:51:38.140548Z, end-time: 2022-04-18T21:51:38.502710Z, 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 ca35b1c sphinx quickstart

[rtd-command-info] start-time: 2022-04-18T21:51:38.676124Z, end-time: 2022-04-18T21:51:38.749030Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-04-18T21:51:39.810230Z, end-time: 2022-04-18T21:51:44.361967Z, 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: 2022-04-18T21:51:44.538109Z, end-time: 2022-04-18T21:51:46.475409Z, duration: 1, 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 KB 33.0 MB/s eta 0:00:00
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: 2022-04-18T21:51:46.683091Z, end-time: 2022-04-18T21:51:55.200194Z, 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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 KB 25.3 MB/s eta 0:00:00
  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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 144.9 MB/s eta 0:00:00
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
  Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.4/47.4 KB 174.2 MB/s eta 0:00:00
Collecting recommonmark==0.5.0
  Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB)
Collecting sphinx
  Downloading Sphinx-4.5.0-py3-none-any.whl (3.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 166.6 MB/s eta 0:00:00
Collecting sphinx-rtd-theme
  Downloading sphinx_rtd_theme-1.0.0-py2.py3-none-any.whl (2.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 196.9 MB/s eta 0:00:00
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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 829.2/829.2 KB 145.2 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting docutils>=0.11
  Downloading docutils-0.18.1-py2.py3-none-any.whl (570 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.0/570.0 KB 241.6 MB/s eta 0:00:00
Collecting snowballstemmer>=1.1
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 KB 197.2 MB/s eta 0:00:00
Collecting Jinja2>=2.3
  Downloading Jinja2-3.1.1-py3-none-any.whl (132 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 132.6/132.6 KB 215.2 MB/s eta 0:00:00
Collecting sphinxcontrib-serializinghtml>=1.1.5
  Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.0/94.0 KB 206.8 MB/s eta 0:00:00
Collecting requests>=2.5.0
  Downloading requests-2.27.1-py2.py3-none-any.whl (63 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.1/63.1 KB 175.9 MB/s eta 0:00:00
Collecting sphinxcontrib-applehelp
  Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.2/121.2 KB 210.1 MB/s eta 0:00:00
Collecting sphinxcontrib-devhelp
  Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.7/84.7 KB 203.8 MB/s eta 0:00:00
Collecting imagesize
  Downloading imagesize-1.3.0-py2.py3-none-any.whl (5.2 kB)
Collecting sphinxcontrib-jsmath
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting importlib-metadata>=4.4
  Downloading importlib_metadata-4.11.3-py3-none-any.whl (18 kB)
Collecting babel>=1.3
  Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.8/8.8 MB 196.3 MB/s eta 0:00:00
Collecting Pygments>=2.0
  Downloading Pygments-2.11.2-py3-none-any.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 212.6 MB/s eta 0:00:00
Collecting docutils>=0.11
  Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 KB 9.3 MB/s eta 0:00:00
Collecting sphinxcontrib-qthelp
  Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 90.6/90.6 KB 206.9 MB/s eta 0:00:00
Collecting sphinxcontrib-htmlhelp>=2.0.0
  Downloading sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl (100 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.5/100.5 KB 215.0 MB/s eta 0:00:00
Collecting packaging
  Downloading packaging-21.3-py3-none-any.whl (40 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 KB 169.0 MB/s eta 0:00:00
Collecting pytz>=2015.7
  Downloading pytz-2022.1-py2.py3-none-any.whl (503 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 503.5/503.5 KB 232.4 MB/s eta 0:00:00
Collecting typing-extensions>=3.6.4
  Downloading typing_extensions-4.2.0-py3-none-any.whl (24 kB)
Collecting zipp>=0.5
  Downloading zipp-3.8.0-py3-none-any.whl (5.4 kB)
Collecting MarkupSafe>=2.0
  Downloading MarkupSafe-2.1.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Collecting charset-normalizer~=2.0.0
  Downloading charset_normalizer-2.0.12-py3-none-any.whl (39 kB)
Collecting idna<4,>=2.5
  Downloading idna-3.3-py3-none-any.whl (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.2/61.2 KB 198.0 MB/s eta 0:00:00
Collecting urllib3<1.27,>=1.21.1
  Downloading urllib3-1.26.9-py2.py3-none-any.whl (138 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 139.0/139.0 KB 224.9 MB/s eta 0:00:00
Collecting certifi>=2017.4.17
  Downloading certifi-2021.10.8-py2.py3-none-any.whl (149 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 149.2/149.2 KB 220.7 MB/s eta 0:00:00
Collecting pyparsing!=3.0.5,>=2.0.2
  Downloading pyparsing-3.0.8-py3-none-any.whl (98 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.5/98.5 KB 188.1 MB/s eta 0:00:00
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=c4b4c99f1b4d72db831d01a8381d164a19a8870f3a2e59d7e6f76867a847e900
  Stored in directory: /tmp/pip-ephem-wheel-cache-zhbrh_tc/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=ca184fdba2a780684d9fd16c0d54940d4a84739bd24afd9d509755fee8e0ab16
  Stored in directory: /tmp/pip-ephem-wheel-cache-zhbrh_tc/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: 2022-04-18T21:51:55.363941Z, end-time: 2022-04-18T21:51:56.901573Z, duration: 1, exit-code: 1
python -m pip install --exists-action=w --no-cache-dir -r requirements/docs.txt
Collecting git+https://github.com/readthedocs/sphinx-hoverxref@master (from -r requirements/docs.txt (line 13))
  Cloning https://github.com/readthedocs/sphinx-hoverxref (to revision master) to /tmp/pip-req-build-1i8s06u8
  Running command git clone --filter=blob:none --quiet https://github.com/readthedocs/sphinx-hoverxref /tmp/pip-req-build-1i8s06u8
  WARNING: Did not find branch or tag 'master', assuming revision or ref.
  Running command git checkout -q master
  error: pathspec 'master' did not match any file(s) known to git.
  error: subprocess-exited-with-error
  
  × git checkout -q master did not run successfully.
  │ exit code: 1
  ╰─> See above for output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× git checkout -q master did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.