Read the Docs build information Build id: 955384 Project: beliveau-lab-tigerfish Version: latest Commit: e94a6d7c4b3acaf0577113947b34848bc9e937c1 Date: 2022-05-22T03:59:40.430093Z State: finished Success: True [rtd-command-info] start-time: 2022-05-22T03:59:42.367296Z, end-time: 2022-05-22T03:59:44.200034Z, duration: 1, 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: 2022-05-22T03:59:44.404456Z, end-time: 2022-05-22T03:59:44.775680Z, 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 Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at e94a6d7 main worflow cli [rtd-command-info] start-time: 2022-05-22T03:59:44.984306Z, end-time: 2022-05-22T03:59:45.048992Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-05-22T03:59:46.113949Z, end-time: 2022-05-22T03:59:50.671171Z, 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: 2022-05-22T03:59:50.866868Z, end-time: 2022-05-22T03:59:53.024573Z, 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 24.0 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: 2022-05-22T03:59:53.217956Z, end-time: 2022-05-22T04:00:01.584047Z, 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 24.9 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 141.0 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 183.2 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 205.6 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 163.2 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 235.4 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 242.0 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 193.5 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 248.0 MB/s eta 0:00:00 Collecting packaging Downloading packaging-21.3-py3-none-any.whl (40 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 174.1 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 207.5 MB/s eta 0:00:00 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-4.11.4-py3-none-any.whl (18 kB) Collecting sphinxcontrib-serializinghtml>=1.1.5 Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.0/94.0 kB 198.9 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 250.2 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 221.8 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 200.5 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 211.5 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 198.7 MB/s eta 0:00:00 Collecting imagesize Downloading imagesize-1.3.0-py2.py3-none-any.whl (5.2 kB) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.7/84.7 kB 188.9 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 210.9 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 245.2 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 urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.9-py2.py3-none-any.whl (138 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 139.0/139.0 kB 222.2 MB/s eta 0:00:00 Collecting certifi>=2017.4.17 Downloading certifi-2022.5.18.1-py3-none-any.whl (155 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.2/155.2 kB 208.6 MB/s eta 0:00:00 Collecting idna<4,>=2.5 Downloading idna-3.3-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.2/61.2 kB 197.2 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 pyparsing!=3.0.5,>=2.0.2 Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 kB 197.3 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=5e0431e2fbbab9d4737c8e8a9f9d8d212365958f2e0986eee0daec1cbd8626a0 Stored in directory: /tmp/pip-ephem-wheel-cache-95n40_6n/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=1b3057ee4e719a9ad602e7e22b99cdd141d42a039e8264c539646c2999dc67f7 Stored in directory: /tmp/pip-ephem-wheel-cache-95n40_6n/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: 2022-05-22T04:00:01.768952Z, end-time: 2022-05-22T04:00:10.154948Z, duration: 8, 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 62.6 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 242.8 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 153.0 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 158.8 MB/s eta 0:00:00 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-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: 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: 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-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: 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: 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 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/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 233.6 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=c6734d2b908ff0ea39a4d69473621eb0139dd873a1a1a0b9c654bd81231b1b84 Stored in directory: /tmp/pip-ephem-wheel-cache-_3p0l255/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=591b850b18f944c797b8e9a7cc9d142b1af87a12f0ad0166aa445345ca799e00 Stored in directory: /tmp/pip-ephem-wheel-cache-_3p0l255/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=66ba990c031c300bae5a073cc59352ae01db5491f91fddb276f0aac653efb29f Stored in directory: /tmp/pip-ephem-wheel-cache-_3p0l255/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=becb1a2e0d8fe6b2603491f82deaff32152c4d9e6a3ffcc2810895a469f5c26a Stored in directory: /tmp/pip-ephem-wheel-cache-_3p0l255/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: 2022-05-22T04:00:11.624045Z, end-time: 2022-05-22T04:00:11.715480Z, 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': 'e94a6d7c', } # 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/955384/' 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: 2022-05-22T04:00:11.900406Z, end-time: 2022-05-22T04:00:13.200843Z, 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, vignettes/index.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%] CODE_OF_CONDUCT reading sources... [ 33%] cli reading sources... [ 50%] faq reading sources... [ 66%] index reading sources... [ 83%] tutorials reading sources... [100%] vignettes/index /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:239: WARNING: Title underline too short. generate_bt2_indices ------------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:239: WARNING: Title underline too short. generate_bt2_indices ------------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:495: 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:495: 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:633: 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/faq.rst:40: WARNING: Title underline too short. How do I do 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 with Tigerfish? --------------------------------------- /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 <>". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 16%] CODE_OF_CONDUCT writing output... [ 33%] cli writing output... [ 50%] faq writing output... [ 66%] index writing output... [ 83%] tutorials writing output... [100%] vignettes/index /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:98: WARNING: toctree contains reference to document 'vignettes/index' 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 'vignettes/index' 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 'vignettes/index' 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 'vignettes/index' 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 'vignettes/index' 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 'vignettes/index' 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 'vignettes/index' 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 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 'vignettes/index' 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 done copying images... [ 33%] imgs/snakemake.svg copying images... [ 66%] imgs/tigerfish_fish.jpg copying images... [100%] imgs/tiger.jpg copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 25 warnings. The HTML pages are in _build/html. Updating searchtools for Read the Docs search... ====================== slowest reading durations ======================= 0.140 cli 0.029 index 0.029 CODE_OF_CONDUCT 0.024 tutorials 0.016 faq