Read the Docs build information
Build id: 956458
Project: beliveau-lab-tigerfish
Version: latest
Commit: 6953f9bf397c178e967ba56508724409c913655b
Date: 2022-05-23T18:24:27.482618Z
State: finished
Success: True


[rtd-command-info] start-time: 2022-05-23T18:24:29.423278Z, end-time: 2022-05-23T18:24:31.802336Z, 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: 2022-05-23T18:24:32.015045Z, end-time: 2022-05-23T18:24:32.389998Z, 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 6953f9b updated cli and tutorials

[rtd-command-info] start-time: 2022-05-23T18:24:32.579272Z, end-time: 2022-05-23T18:24:32.657184Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-05-23T18:24:33.715337Z, end-time: 2022-05-23T18:24:38.409028Z, 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: 2022-05-23T18:24:38.651839Z, end-time: 2022-05-23T18:24:40.742321Z, 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 (22.1.1)
Collecting setuptools<58.3.0
  Downloading setuptools-58.2.0-py3-none-any.whl (946 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 kB 35.1 MB/s eta 0:00:00
Installing collected packages: setuptools
  Attempting uninstall: setuptools
    Found existing installation: setuptools 62.3.2
    Uninstalling setuptools-62.3.2:
      Successfully uninstalled setuptools-62.3.2
Successfully installed setuptools-58.2.0

[rtd-command-info] start-time: 2022-05-23T18:24:40.959309Z, end-time: 2022-05-23T18:24:49.382124Z, 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 22.0 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 158.2 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 193.9 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 186.6 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 177.0 MB/s eta 0:00:00
Collecting readthedocs-sphinx-ext<2.2
  Downloading readthedocs_sphinx_ext-2.1.6-py2.py3-none-any.whl (11 kB)
Collecting future
  Downloading future-0.18.2.tar.gz (829 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 829.2/829.2 kB 253.3 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 241.3 MB/s eta 0:00:00
Collecting babel>=1.3
  Downloading Babel-2.10.1-py3-none-any.whl (9.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 176.7 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 218.2 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 223.0 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 211.9 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 187.5 MB/s eta 0:00:00
Collecting Pygments>=2.0
  Downloading Pygments-2.12.0-py3-none-any.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 246.6 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 packaging
  Downloading packaging-21.3-py3-none-any.whl (40 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 196.9 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 220.0 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 226.2 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 213.7 MB/s eta 0:00:00
Collecting importlib-metadata>=4.4
  Downloading importlib_metadata-4.11.4-py3-none-any.whl (18 kB)
Collecting docutils>=0.11
  Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 258.7 MB/s eta 0:00:00
Collecting Jinja2>=2.3
  Downloading Jinja2-3.1.2-py3-none-any.whl (133 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.1/133.1 kB 223.9 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 252.5 MB/s eta 0:00:00
Collecting zipp>=0.5
  Downloading zipp-3.8.0-py3-none-any.whl (5.4 kB)
Collecting typing-extensions>=3.6.4
  Downloading typing_extensions-4.2.0-py3-none-any.whl (24 kB)
Collecting MarkupSafe>=2.0
  Downloading MarkupSafe-2.1.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Collecting certifi>=2017.4.17
  Downloading certifi-2022.5.18.1-py3-none-any.whl (155 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.2/155.2 kB 233.2 MB/s eta 0:00:00
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 207.4 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 226.3 MB/s eta 0:00:00
Collecting pyparsing!=3.0.5,>=2.0.2
  Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 kB 224.3 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=eef9dd8bce25f31d4f91ea2cfeea1890e3a34f7787839196943be7ff629fba5c
  Stored in directory: /tmp/pip-ephem-wheel-cache-88tg6la_/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=c272a6414c6f1d25f864f9b6f93f2c9accc3e0eb2b10815231e3f13b188e49c1
  Stored in directory: /tmp/pip-ephem-wheel-cache-88tg6la_/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Successfully built mock future
Installing collected packages: snowballstemmer, pytz, mock, 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, certifi, babel, requests, packaging, Jinja2, importlib-metadata, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.1 Pygments-2.12.0 alabaster-0.7.12 babel-2.10.1 certifi-2022.5.18.1 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-4.11.4 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.9 pytz-2022.1 readthedocs-sphinx-ext-2.1.6 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: 2022-05-23T18:24:49.653045Z, end-time: 2022-05-23T18:24:56.917354Z, duration: 7, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Collecting Sphinx==4.4.0
  Downloading Sphinx-4.4.0-py3-none-any.whl (3.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 51.6 MB/s eta 0:00:00
Collecting Pygments==2.11.2
  Downloading Pygments-2.11.2-py3-none-any.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 262.6 MB/s eta 0:00:00
Requirement already satisfied: sphinx_rtd_theme==1.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from -r docs/requirements.txt (line 6)) (1.0.0)
Collecting sphinx-tabs==3.2.0
  Downloading sphinx_tabs-3.2.0-py3-none-any.whl (9.8 kB)
Collecting sphinx-intl==2.0.1
  Downloading sphinx-intl-2.0.1.tar.gz (17 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting readthedocs-sphinx-search==0.1.1
  Downloading readthedocs_sphinx_search-0.1.1-py3-none-any.whl (18 kB)
Collecting sphinxemoji==0.2.0
  Downloading sphinxemoji-0.2.0.tar.gz (44 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 44.4/44.4 kB 181.9 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting sphinxcontrib-httpdomain==1.8.0
  Downloading sphinxcontrib_httpdomain-1.8.0-py2.py3-none-any.whl (19 kB)
Collecting sphinx-prompt==1.4.0
  Downloading sphinx_prompt-1.4.0-py3-none-any.whl (4.1 kB)
Collecting sphinx-notfound-page==0.8
  Downloading sphinx_notfound_page-0.8-py3-none-any.whl (15 kB)
Collecting sphinx-autobuild==2021.3.14
  Downloading sphinx_autobuild-2021.3.14-py3-none-any.whl (9.9 kB)
Collecting rstcheck==3.3.1
  Downloading rstcheck-3.3.1.tar.gz (13 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting myst_parser==0.16.1
  Downloading myst_parser-0.16.1-py3-none-any.whl (48 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.8/48.8 kB 184.4 MB/s eta 0:00:00
Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.1.5)
Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.27.1)
Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.0.3)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (0.7.12)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.3.0)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.2.0)
Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.0.2)
Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.0.2)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (21.3)
Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.10.1)
Requirement already satisfied: importlib-metadata>=4.4 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (4.11.4)
Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.0.0)
Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.0.1)
Requirement already satisfied: docutils<0.18,>=0.14 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (0.17.1)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (3.1.2)
Collecting docutils<0.18,>=0.14
  Downloading docutils-0.16-py2.py3-none-any.whl (548 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 548.2/548.2 kB 250.7 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx-intl==2.0.1->-r docs/requirements.txt (line 8)) (58.2.0)
Collecting click
  Downloading click-8.1.3-py3-none-any.whl (96 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 96.6/96.6 kB 216.5 MB/s eta 0:00:00
Collecting six
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting livereload
  Downloading livereload-2.6.3.tar.gz (25 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting colorama
  Downloading colorama-0.4.4-py2.py3-none-any.whl (16 kB)
Collecting pyyaml
  Downloading PyYAML-6.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (596 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 596.3/596.3 kB 253.1 MB/s eta 0:00:00
Collecting markdown-it-py<3.0.0,>=1.0.0
  Downloading markdown_it_py-2.1.0-py3-none-any.whl (84 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.5/84.5 kB 212.2 MB/s eta 0:00:00
Collecting mdit-py-plugins~=0.3.0
  Downloading mdit_py_plugins-0.3.0-py3-none-any.whl (43 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.7/43.7 kB 155.4 MB/s eta 0:00:00
Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from babel>=1.3->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2022.1)
Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from importlib-metadata>=4.4->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (3.8.0)
Requirement already satisfied: typing-extensions>=3.6.4 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from importlib-metadata>=4.4->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (4.2.0)
Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.1.1)
Collecting mdurl~=0.1
  Downloading mdurl-0.1.1-py3-none-any.whl (10 kB)
Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (3.3)
Requirement already satisfied: charset-normalizer~=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.0.12)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.26.9)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2022.5.18.1)
Collecting tornado
  Downloading tornado-6.1-cp37-cp37m-manylinux2010_x86_64.whl (428 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 428.5/428.5 kB 251.4 MB/s eta 0:00:00
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from packaging->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (3.0.9)
Building wheels for collected packages: sphinx-intl, sphinxemoji, rstcheck, livereload
  Building wheel for sphinx-intl (setup.py): started
  Building wheel for sphinx-intl (setup.py): finished with status 'done'
  Created wheel for sphinx-intl: filename=sphinx_intl-2.0.1-py3-none-any.whl size=11640 sha256=87c49a845c6fe3e19e40097506e6ab65930c66c723a437b91f58c60b3be06137
  Stored in directory: /tmp/pip-ephem-wheel-cache-9ed3j12l/wheels/a9/7d/2d/5518c1be71b597869a2411fc0c585551bf9162a846710f76af
  Building wheel for sphinxemoji (setup.py): started
  Building wheel for sphinxemoji (setup.py): finished with status 'done'
  Created wheel for sphinxemoji: filename=sphinxemoji-0.2.0-py3-none-any.whl size=44427 sha256=75357949ed4b0d426992afcee07c5d60a854f943da43a688e25e2cf3f1164b88
  Stored in directory: /tmp/pip-ephem-wheel-cache-9ed3j12l/wheels/09/10/81/0438103576aeaea47d55fe341a8e89d7561afc4e414741bf87
  Building wheel for rstcheck (setup.py): started
  Building wheel for rstcheck (setup.py): finished with status 'done'
  Created wheel for rstcheck: filename=rstcheck-3.3.1-py3-none-any.whl size=13737 sha256=bb1182bd0cda3fbeaa4f10f82f34e79dc3175bf1a4df7c123d8f5908dd1e85eb
  Stored in directory: /tmp/pip-ephem-wheel-cache-9ed3j12l/wheels/54/66/a1/0e58261ec13ca13b14d11834d840917318f6f96457a47b3145
  Building wheel for livereload (setup.py): started
  Building wheel for livereload (setup.py): finished with status 'done'
  Created wheel for livereload: filename=livereload-2.6.3-py2.py3-none-any.whl size=24724 sha256=00291b6fe93e1a2d852363350d6934bd6de884dbf9cac070ac87fd6a2f5602ed
  Stored in directory: /tmp/pip-ephem-wheel-cache-9ed3j12l/wheels/d4/f2/03/55f37093eb8cb0c89d7efb206f792dba55cd5bd67b1c5b1ce1
Successfully built sphinx-intl sphinxemoji rstcheck livereload
Installing collected packages: sphinx-notfound-page, tornado, six, readthedocs-sphinx-search, pyyaml, Pygments, mdurl, docutils, colorama, Sphinx, rstcheck, markdown-it-py, livereload, click, sphinxemoji, sphinxcontrib-httpdomain, sphinx-tabs, sphinx-prompt, sphinx-intl, sphinx-autobuild, mdit-py-plugins, myst_parser
  Attempting uninstall: Pygments
    Found existing installation: Pygments 2.12.0
    Uninstalling Pygments-2.12.0:
      Successfully uninstalled Pygments-2.12.0
  Attempting uninstall: docutils
    Found existing installation: docutils 0.17.1
    Uninstalling docutils-0.17.1:
      Successfully uninstalled docutils-0.17.1
  Attempting uninstall: Sphinx
    Found existing installation: Sphinx 4.5.0
    Uninstalling Sphinx-4.5.0:
      Successfully uninstalled Sphinx-4.5.0
Successfully installed Pygments-2.11.2 Sphinx-4.4.0 click-8.1.3 colorama-0.4.4 docutils-0.16 livereload-2.6.3 markdown-it-py-2.1.0 mdit-py-plugins-0.3.0 mdurl-0.1.1 myst_parser-0.16.1 pyyaml-6.0 readthedocs-sphinx-search-0.1.1 rstcheck-3.3.1 six-1.16.0 sphinx-autobuild-2021.3.14 sphinx-intl-2.0.1 sphinx-notfound-page-0.8 sphinx-prompt-1.4.0 sphinx-tabs-3.2.0 sphinxcontrib-httpdomain-1.8.0 sphinxemoji-0.2.0 tornado-6.1

[rtd-command-info] start-time: 2022-05-23T18:24:58.373211Z, end-time: 2022-05-23T18:24:58.454934Z, duration: 0, exit-code: 0
cat docs/source/conf.py
# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html

# -- Path setup --------------------------------------------------------------

# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import os
import sys
import subprocess
from configparser import RawConfigParser
import sphinx_rtd_theme

sys.path.insert(0, os.path.abspath(os.path.join("..", "..")))

#sys.path.insert(0, os.path.abspath('..'))
#sys.path.append(os.path.dirname(__file__))

#try:
#    import numpydoc
#except ModuleNotFoundError:
#    subprocess.run(["pip", "install", "numpydoc"], check=True)


# -- Project information -----------------------------------------------------

project = 'Tigerfish'
copyright = '2022, Robin Aguilar'
author = 'Robin Aguilar'

# The full version, including alpha/beta/rc tags
release = '2022'


# -- General configuration ---------------------------------------------------

#def get_version():
#    """Return package version from setup.cfg."""
#    config = RawConfigParser()
#    config.read(os.path.join('.', 'setup.cfg'))
#    return config.get('metadata', 'version')

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    'sphinx.ext.duration',
    'sphinx.ext.doctest',
    'sphinx.ext.autodoc',
    'sphinx_tabs.tabs',
    'sphinx-prompt',
    'sphinx_search.extension',
    'sphinx.ext.autosummary',
    'sphinx.ext.intersphinx',
    'sphinxemoji.sphinxemoji'
]


nbsphinx_execute = "never"

#autosummary_generate = True
#autodoc_default_options = {
#    "members": True,
#    "inherited-members": True,
#    "member-order": "bysource",
#}

#numpydoc_show_class_members = True
#numpydoc_show_inherited_class_members = True
#numpydoc_attributes_as_param_list = True
#intersphinx_mapping = {
#    "pandas": ("https://pandas.pydata.org/docs", None),
#    "sklearn": ("https://scikit-learn.org/stable", None),
#    "numpy": ("https://numpy.org/doc/stable", None),
#    "matplotlib": ("https://matplotlib.org", None),
#}

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']


# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = ["build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]


# -- Options for HTML output -------------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
#
html_theme = 'sphinx_rtd_theme'

html_static_path = ["_static"]

master_doc = "index"
source_suffix = [".rst", ".md"]

html_theme_options = {
    "style_nav_header_background": "#343131",
    "logo_only": True,
}

html_css_files = [
    "custom.css",
]

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_logo = "_static/tigerfish.png"




###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')

# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
    (
        'html_theme' in globals() and
        html_theme in ['default'] and
        # Allow people to bail with a hack of having an html_style
        'html_style' not in globals()
    ) or 'html_theme' not in globals()
)
if using_rtd_theme:
    theme = importlib.import_module('sphinx_rtd_theme')
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    websupport2_static_url = 'https://assets.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'proxied_static_path': "/_/static/",
    'versions': [
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'beliveau-lab-tigerfish',
    'name': u'TigerFISH',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://beliveau-lab-tigerfish.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/source/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'beliveau-lab',
    'proxied_api_host': '/_',
    'github_repo': 'TigerFISH',
    'github_version': 'master',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'master',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'master',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '6953f9bf',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





if 'html_context' in globals():
    
    html_context.update(context)
    
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/beliveau-lab-tigerfish/builds/956458/'

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2022-05-23T18:24:58.689151Z, end-time: 2022-05-23T18:24:59.976304Z, duration: 1, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v4.4.0
loading translations [en]... done
making output directory... done
[autosummary] generating autosummary for: CODE_OF_CONDUCT.md, cli.rst, faq.rst, index.rst, tutorials.rst
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 5 source files that are out of date
updating environment: [new config] 5 added, 0 changed, 0 removed
reading sources... [ 20%] CODE_OF_CONDUCT
reading sources... [ 40%] cli
reading sources... [ 60%] faq
reading sources... [ 80%] index
reading sources... [100%] tutorials

/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:243: WARNING: Title underline too short.

generate_bt2_indices
------------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:243: WARNING: Title underline too short.

generate_bt2_indices
------------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:499: WARNING: Title underline too short.

gather_repeat_regions (checkpoint)
---------------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:499: WARNING: Title underline too short.

gather_repeat_regions (checkpoint)
---------------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:731: ERROR: Error in "code-block" directive:
maximum 1 argument(s) allowed, 22 supplied.

.. code-block:: bash
   "bedtools intersect -wa -wb -a {input.derived_bed} -b {input.genome_bin} > {output.alignments_out} |"
   "bedtools intersect -wa -wb -a {input.repeat_bed} -b {input.genome_bin} > {output.repeat_out}"
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:: WARNING: image file not readable: imgs/tigerfish_main_overview.png:width:500
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:: WARNING: image file not readable: imgs/tigerfish_postprocess_overview.png:width:500
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/faq.rst:40: WARNING: Title underline too short.

How do I do <insert task> with Tigerfish?
---------------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/faq.rst:40: WARNING: Title underline too short.

How do I do <insert task> with Tigerfish?
---------------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:98: WARNING: toctree contains reference to nonexisting document 'vignettes/index'
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:75: ERROR: Unknown target name: "here <>".
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:75: ERROR: Unknown target name: "here <>".
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "config.yml".
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here".
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 20%] CODE_OF_CONDUCT
writing output... [ 40%] cli
writing output... [ 60%] faq
writing output... [ 80%] index
writing output... [100%] tutorials

/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:98: WARNING: toctree contains reference to document 'CODE_OF_CONDUCT' that doesn't have a title: no link will be generated
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:98: WARNING: toctree contains reference to document 'CODE_OF_CONDUCT' that doesn't have a title: no link will be generated
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:98: WARNING: toctree contains reference to document 'CODE_OF_CONDUCT' that doesn't have a title: no link will be generated
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:98: WARNING: toctree contains reference to document 'CODE_OF_CONDUCT' that doesn't have a title: no link will be generated
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:98: WARNING: toctree contains reference to document 'CODE_OF_CONDUCT' that doesn't have a title: no link will be generated
generating indices... genindex /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:98: WARNING: toctree contains reference to document 'CODE_OF_CONDUCT' that doesn't have a title: no link will be generated
done
writing additional pages... search /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:98: WARNING: toctree contains reference to document 'CODE_OF_CONDUCT' that doesn't have a title: no link will be generated
done
copying images... [ 25%] imgs/snakemake.svg
copying images... [ 50%] imgs/tigerfish_fish.jpg
copying images... [ 75%] imgs/tiger.jpg
copying images... [100%] imgs/tutorials_summary.png

copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 21 warnings.

The HTML pages are in _build/html.
Updating searchtools for Read the Docs search... 
====================== slowest reading durations =======================
0.165 cli
0.029 index
0.028 CODE_OF_CONDUCT
0.021 tutorials
0.015 faq