Read the Docs build information
Build id: 1336536
Project: beliveau-lab-tigerfish
Version: stable
Commit: 404c699832f587519ab407551655e9ea93d111bd
Date: 2023-03-07T22:36:00.536774Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-03-07T22:36:02.176941Z, end-time: 2023-03-07T22:36:10.676037Z, duration: 8, 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: 2023-03-07T22:36:10.958340Z, end-time: 2023-03-07T22:36:11.606072Z, duration: 0, exit-code: 0
git checkout --force 404c699832f587519ab407551655e9ea93d111bd
Note: switching to '404c699832f587519ab407551655e9ea93d111bd'.

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 404c699 Update README.md

[rtd-command-info] start-time: 2023-03-07T22:36:11.798863Z, end-time: 2023-03-07T22:36:11.893267Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-03-07T22:36:13.649959Z, end-time: 2023-03-07T22:36:18.270739Z, duration: 4, exit-code: 0
python3.7 -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
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/stable/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2023-03-07T22:36:18.453382Z, end-time: 2023-03-07T22:36:20.244091Z, 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/stable/lib/python3.7/site-packages (23.0.1)
Collecting setuptools<58.3.0
  Downloading setuptools-58.2.0-py3-none-any.whl (946 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 kB 23.5 MB/s eta 0:00:00
Installing collected packages: setuptools
  Attempting uninstall: setuptools
    Found existing installation: setuptools 67.5.1
    Uninstalling setuptools-67.5.1:
      Successfully uninstalled setuptools-67.5.1
Successfully installed setuptools-58.2.0

[rtd-command-info] start-time: 2023-03-07T22:36:20.431667Z, end-time: 2023-03-07T22:36:27.939412Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx sphinx-rtd-theme readthedocs-sphinx-ext<2.3
Collecting pillow
  Downloading Pillow-9.4.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 66.7 MB/s eta 0:00:00
Collecting mock==1.0.1
  Downloading mock-1.0.1.zip (861 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 240.0 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting alabaster!=0.7.5,<0.8,>=0.7
  Downloading alabaster-0.7.13-py3-none-any.whl (13 kB)
Collecting commonmark==0.9.1
  Downloading commonmark-0.9.1-py2.py3-none-any.whl (51 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.1/51.1 kB 175.2 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-5.3.0-py3-none-any.whl (3.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 215.0 MB/s eta 0:00:00
Collecting sphinx-rtd-theme
  Downloading sphinx_rtd_theme-1.2.0-py2.py3-none-any.whl (2.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 219.4 MB/s eta 0:00:00
Collecting readthedocs-sphinx-ext<2.3
  Downloading readthedocs_sphinx_ext-2.2.0-py2.py3-none-any.whl (11 kB)
Collecting docutils>=0.11
  Downloading docutils-0.19-py3-none-any.whl (570 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.5/570.5 kB 241.9 MB/s eta 0:00:00
Collecting babel>=2.9
  Downloading Babel-2.12.1-py3-none-any.whl (10.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.1/10.1 MB 183.7 MB/s eta 0:00:00
Collecting requests>=2.5.0
  Downloading requests-2.28.2-py3-none-any.whl (62 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 189.6 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 213.6 MB/s eta 0:00:00
Collecting Jinja2>=3.0
  Downloading Jinja2-3.1.2-py3-none-any.whl (133 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.1/133.1 kB 227.5 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 217.3 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 227.1 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 131.2 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 215.6 MB/s eta 0:00:00
Collecting packaging>=21.0
  Downloading packaging-23.0-py3-none-any.whl (42 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.7/42.7 kB 170.0 MB/s eta 0:00:00
Collecting importlib-metadata>=4.8
  Downloading importlib_metadata-6.0.0-py3-none-any.whl (21 kB)
Collecting sphinxcontrib-jsmath
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting snowballstemmer>=2.0
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 196.1 MB/s eta 0:00:00
Collecting Pygments>=2.12
  Downloading Pygments-2.14.0-py3-none-any.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 249.6 MB/s eta 0:00:00
Collecting imagesize>=1.3
  Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Collecting sphinxcontrib-jquery!=3.0.0,>=2.0.0
  Downloading sphinxcontrib_jquery-2.0.0-py3-none-any.whl (3.2 kB)
Collecting docutils>=0.11
  Downloading docutils-0.18.1-py2.py3-none-any.whl (570 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.0/570.0 kB 255.3 MB/s eta 0:00:00
Collecting pytz>=2015.7
  Downloading pytz-2022.7.1-py2.py3-none-any.whl (499 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 499.4/499.4 kB 243.5 MB/s eta 0:00:00
Collecting zipp>=0.5
  Downloading zipp-3.15.0-py3-none-any.whl (6.8 kB)
Collecting typing-extensions>=3.6.4
  Downloading typing_extensions-4.5.0-py3-none-any.whl (27 kB)
Collecting MarkupSafe>=2.0
  Downloading MarkupSafe-2.1.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Collecting certifi>=2017.4.17
  Downloading certifi-2022.12.7-py3-none-any.whl (155 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.3/155.3 kB 232.7 MB/s eta 0:00:00
Collecting charset-normalizer<4,>=2
  Downloading charset_normalizer-3.1.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (171 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 171.0/171.0 kB 222.6 MB/s eta 0:00:00
Collecting idna<4,>=2.5
  Downloading idna-3.4-py3-none-any.whl (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.5/61.5 kB 161.1 MB/s eta 0:00:00
Collecting urllib3<1.27,>=1.21.1
  Downloading urllib3-1.26.14-py2.py3-none-any.whl (140 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 140.6/140.6 kB 229.4 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from sphinxcontrib-jquery!=3.0.0,>=2.0.0->sphinx-rtd-theme) (58.2.0)
Building wheels for collected packages: mock
  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=23772 sha256=69be3ce1f06f7be5b9e6f57f836a3a92db15e86f117885e7f038a4088f0db4ad
  Stored in directory: /tmp/pip-ephem-wheel-cache-drow_2_o/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1
Successfully built mock
Installing collected packages: snowballstemmer, pytz, mock, commonmark, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-jquery, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.2 Pygments-2.14.0 alabaster-0.7.13 babel-2.12.1 certifi-2022.12.7 charset-normalizer-3.1.0 commonmark-0.9.1 docutils-0.18.1 idna-3.4 imagesize-1.4.1 importlib-metadata-6.0.0 mock-1.0.1 packaging-23.0 pillow-9.4.0 pytz-2022.7.1 readthedocs-sphinx-ext-2.2.0 recommonmark-0.5.0 requests-2.28.2 snowballstemmer-2.2.0 sphinx-5.3.0 sphinx-rtd-theme-1.2.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jquery-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 typing-extensions-4.5.0 urllib3-1.26.14 zipp-3.15.0

[rtd-command-info] start-time: 2023-03-07T22:36:28.155227Z, end-time: 2023-03-07T22:36:35.278318Z, 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 53.7 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 247.5 MB/s eta 0:00:00
Collecting sphinx_rtd_theme==1.0.0
  Downloading sphinx_rtd_theme-1.0.0-py2.py3-none-any.whl (2.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 197.2 MB/s eta 0:00:00
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 172.2 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 174.8 MB/s eta 0:00:00
Collecting docutils<0.18,>=0.14
  Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 253.6 MB/s eta 0:00:00
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (0.7.13)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (23.0)
Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.0.3)
Requirement already satisfied: importlib-metadata>=4.4 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (6.0.0)
Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.0.1)
Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.28.2)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.4.1)
Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.0.0)
Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.0.2)
Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.1.5)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (3.1.2)
Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.0.2)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.2.0)
Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.12.1)
  Downloading docutils-0.16-py2.py3-none-any.whl (548 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 548.2/548.2 kB 242.6 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/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 217.3 MB/s eta 0:00:00
Collecting six
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting colorama
  Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Collecting livereload
  Downloading livereload-2.6.3-py2.py3-none-any.whl (24 kB)
Collecting mdit-py-plugins~=0.3.0
  Downloading mdit_py_plugins-0.3.5-py3-none-any.whl (52 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 52.1/52.1 kB 177.2 MB/s eta 0:00:00
Collecting markdown-it-py<3.0.0,>=1.0.0
  Downloading markdown_it_py-2.2.0-py3-none-any.whl (84 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.5/84.5 kB 204.1 MB/s eta 0:00:00
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 243.4 MB/s eta 0:00:00
Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from babel>=1.3->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2022.7.1)
Requirement already satisfied: typing-extensions>=3.6.4 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from importlib-metadata>=4.4->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (4.5.0)
Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from importlib-metadata>=4.4->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (3.15.0)
Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from Jinja2>=2.3->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.1.2)
Collecting mdurl~=0.1
  Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from requests>=2.5.0->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (3.1.0)
Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from requests>=2.5.0->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (3.4)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from requests>=2.5.0->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2022.12.7)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/stable/lib/python3.7/site-packages (from requests>=2.5.0->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.26.14)
Collecting tornado
  Downloading tornado-6.2-cp37-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (423 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 424.0/424.0 kB 245.3 MB/s eta 0:00:00
Building wheels for collected packages: sphinx-intl, sphinxemoji, rstcheck
  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=11639 sha256=21ad0aff5e90570fe73089c5ef36e09b826057792f33276da3fd7cadf8664847
  Stored in directory: /tmp/pip-ephem-wheel-cache-2o07kbv5/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=dbca357dd8596f72797661dc618af2c349e4bdbbf31b18fa4b3e06aedd888870
  Stored in directory: /tmp/pip-ephem-wheel-cache-2o07kbv5/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=13738 sha256=382d545eec9b8200c055363a469c442a58c605837dcd0ef48f9836eb4c0c8273
  Stored in directory: /tmp/pip-ephem-wheel-cache-2o07kbv5/wheels/54/66/a1/0e58261ec13ca13b14d11834d840917318f6f96457a47b3145
Successfully built sphinx-intl sphinxemoji rstcheck
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_rtd_theme, sphinx-prompt, sphinx-intl, sphinx-autobuild, mdit-py-plugins, myst_parser
  Attempting uninstall: Pygments
    Found existing installation: Pygments 2.14.0
    Uninstalling Pygments-2.14.0:
      Successfully uninstalled Pygments-2.14.0
  Attempting uninstall: docutils
    Found existing installation: docutils 0.18.1
    Uninstalling docutils-0.18.1:
      Successfully uninstalled docutils-0.18.1
  Attempting uninstall: Sphinx
    Found existing installation: Sphinx 5.3.0
    Uninstalling Sphinx-5.3.0:
      Successfully uninstalled Sphinx-5.3.0
  Attempting uninstall: sphinx_rtd_theme
    Found existing installation: sphinx-rtd-theme 1.2.0
    Uninstalling sphinx-rtd-theme-1.2.0:
      Successfully uninstalled sphinx-rtd-theme-1.2.0
Successfully installed Pygments-2.11.2 Sphinx-4.4.0 click-8.1.3 colorama-0.4.6 docutils-0.16 livereload-2.6.3 markdown-it-py-2.2.0 mdit-py-plugins-0.3.5 mdurl-0.1.2 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 sphinx_rtd_theme-1.0.0 sphinxcontrib-httpdomain-1.8.0 sphinxemoji-0.2.0 tornado-6.2

[rtd-command-info] start-time: 2023-03-07T22:36:36.720391Z, end-time: 2023-03-07T22:36:36.790180Z, 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:
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}


# This following legacy behavior will gradually be sliced out until its deprecated and removed.
# Skipped for Sphinx 6+
# Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH
# Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023)
if (
        using_rtd_theme
        and version_info < (6,0)
        and not False
    ):
    theme = importlib.import_module('sphinx_rtd_theme')
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

# Define websupport2_base_url and websupport2_static_url
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': "stable",
    'version_slug': "stable",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ],
    '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': '404c699832f587519ab407551655e9ea93d111bd',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '404c699832f587519ab407551655e9ea93d111bd',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '404c699832f587519ab407551655e9ea93d111bd',
    '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': '404c6998',
}

# 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 'tag' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/beliveau-lab-tigerfish/builds/1336536/'

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: 2023-03-07T22:36:37.003847Z, end-time: 2023-03-07T22:36:38.609190Z, duration: 1, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v4.4.0
loading translations [en]... done
making output directory... done
[autosummary] generating autosummary for: cli.rst, faq.rst, index.rst, parameters.rst, snakemake_view.rst, tutorials.rst
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 6 source files that are out of date
updating environment: [new config] 6 added, 0 changed, 0 removed
reading sources... [ 16%] cli
reading sources... [ 33%] faq
reading sources... [ 50%] index
reading sources... [ 66%] parameters
reading sources... [ 83%] snakemake_view
reading sources... [100%] tutorials

/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/cli.rst:17: WARNING: Title underline too short.

Named Arguments in `config.yml <https://github.com/beliveau-lab/TigerFISH/blob/master/example_run/main/main_pipeline/config.yml>`_ for main workflow
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/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/stable/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/stable/docs/source/index.rst:68: WARNING: toctree contains reference to nonexisting document 'vignettes/index'
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:5: WARNING: Title underline too short.

`Main workflow <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main_pipeline/Snakefile>`_
^^^^^^^^^^^^^
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:35: WARNING: Title underline too short.

generate_bt2_indices
------------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:35: WARNING: Title underline too short.

generate_bt2_indices
------------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:58: WARNING: Title underline too short.

`generate_jf_idx <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/generate_jf_idx.py>`_
-----------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:58: WARNING: Title underline too short.

`generate_jf_idx <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/generate_jf_idx.py>`_
-----------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:88: WARNING: Title underline too short.

`split_bed <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/split_bed.py>`_
---------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:88: WARNING: Title underline too short.

`split_bed <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/split_bed.py>`_
---------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:112: WARNING: Title underline too short.

`repeat_ID <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/repeat_ID.py>`_
---------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:112: WARNING: Title underline too short.

`repeat_ID <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/repeat_ID.py>`_
---------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:143: WARNING: Title underline too short.

`design_probes <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/design_probes.py>`_
-------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:143: WARNING: Title underline too short.

`design_probes <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/design_probes.py>`_
-------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:175: WARNING: Title underline too short.

`kmer_filter <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/kmer_filter.py>`_
-----------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:175: WARNING: Title underline too short.

`kmer_filter <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/kmer_filter.py>`_
-----------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:203: WARNING: Title underline too short.

`probe_mer_filter <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/probe_mer_filter.py>`_
----------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:203: WARNING: Title underline too short.

`probe_mer_filter <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/probe_mer_filter.py>`_
----------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:259: WARNING: Title underline too short.

`make_chrom_dir (checkpoint) <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/split_filter.py>`_
---------------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:259: WARNING: Title underline too short.

`make_chrom_dir (checkpoint) <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/main/scripts/main/split_filter.py>`_
---------------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:283: WARNING: Title underline too short.

`alignment_filter <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/alignment_filter.py>`_
----------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:283: WARNING: Title underline too short.

`alignment_filter <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/alignment_filter.py>`_
----------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:344: WARNING: Title underline too short.

`split_rm_alignments <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/split_rm_alignments.py>`_
-------------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:344: WARNING: Title underline too short.

`split_rm_alignments <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/split_rm_alignments.py>`_
-------------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:367: WARNING: Title underline too short.

`align_probes <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/generate_alignments.py>`_
------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:367: WARNING: Title underline too short.

`align_probes <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/generate_alignments.py>`_
------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:395: WARNING: Title underline too short.

`derived_beds <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/make_derived_beds.py>`_
------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:395: WARNING: Title underline too short.

`derived_beds <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/make_derived_beds.py>`_
------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:419: WARNING: Title underline too short.

`get_region_bed <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/get_region_bed.py>`_
--------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:419: WARNING: Title underline too short.

`get_region_bed <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/get_region_bed.py>`_
--------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:451: 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/stable/docs/source/snakemake_view.rst:470: WARNING: Title underline too short.

`get_alignments <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/get_alignments.py>`_
--------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:470: WARNING: Title underline too short.

`get_alignments <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/get_alignments.py>`_
--------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:501: WARNING: Title underline too short.

`generate_chromomap <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/make_chromomap.R>`_
------------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:501: WARNING: Title underline too short.

`generate_chromomap <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/make_chromomap.R>`_
------------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:518: WARNING: Title underline too short.

`map_region_coords <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/collapse_repeat.py>`_
--------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:518: WARNING: Title underline too short.

`map_region_coords <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/collapse_repeat.py>`_
--------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:569: WARNING: Title underline too short.

`summary <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/finish_summary.py>`_
-------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/snakemake_view.rst:569: WARNING: Title underline too short.

`summary <https://github.com/beliveau-lab/TigerFISH/blob/master/workflow/scripts/finish_summary.py>`_
-------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "this directory".
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "this directory".
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/tutorials.rst:502: WARNING: Title underline too short.

Probe Analysis Mode on a Test Genome
----------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/docs/source/tutorials.rst:502: WARNING: Title underline too short.

Probe Analysis Mode on a Test Genome
----------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/stable/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... [ 16%] cli
writing output... [ 33%] faq
writing output... [ 50%] index
writing output... [ 66%] parameters
writing output... [ 83%] snakemake_view
writing output... [100%] tutorials

generating indices... genindex done
writing additional pages... search done
copying images... [  5%] imgs/tigerfish_fish.jpg
copying images... [ 11%] imgs/tiger.jpg
copying images... [ 16%] imgs/DAG.pdf
copying images... [ 22%] imgs/repeat_disc_fasta.png
copying images... [ 27%] imgs/chrom_sizes_repeat_disc.png
copying images... [ 33%] imgs/bt2_repeat_disc.png
copying images... [ 38%] imgs/run_pipeline_repeat_disc.png
copying images... [ 44%] imgs/check_repeat_disc.png
copying images... [ 50%] imgs/step_2_repeat_disc.png
copying images... [ 55%] imgs/step_4_repeat_disc.png
copying images... [ 61%] imgs/step_5_repeat_disc.png
copying images... [ 66%] imgs/step_6_repeat_disc.png
copying images... [ 72%] imgs/step_7_repeat_disc.png
copying images... [ 77%] imgs/step_1_probe_design.png
copying images... [ 83%] imgs/step_2_probe_design.png
copying images... [ 88%] imgs/step_3_probe_design.png
copying images... [ 94%] imgs/step_4_probe_design.png
copying images... [100%] imgs/chm13_probe_design_dir.png

copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 52 warnings.

The HTML pages are in ../../_readthedocs/html.
Updating searchtools for Read the Docs search... 
====================== slowest reading durations =======================
0.143 tutorials
0.112 snakemake_view
0.084 cli
0.039 parameters
0.027 index