Read the Docs build information Build id: 1239614 Project: beliveau-lab-tigerfish Version: latest Commit: c81ef520654bead02d790a13c3a882d2ef82fcae Date: 2023-01-03T21:15:19.160122Z State: cancelled Success: False [rtd-command-info] start-time: 2023-01-03T21:15:21.130201Z, end-time: 2023-01-03T21:15:25.067699Z, duration: 3, 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: 2023-01-03T21:15:25.298682Z, end-time: 2023-01-03T21:15:25.539525Z, 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 c81ef52 Update snakemake_view.rst [rtd-command-info] start-time: 2023-01-03T21:15:25.767261Z, end-time: 2023-01-03T21:15:25.839616Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-01-03T21:15:27.668032Z, end-time: 2023-01-03T21:15:46.145717Z, duration: 18, 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: 2023-01-03T21:15:46.364825Z, end-time: 2023-01-03T21:15:48.345502Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0 Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (22.3.1) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 kB 23.1 MB/s eta 0:00:00 Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 65.6.3 Uninstalling setuptools-65.6.3: Successfully uninstalled setuptools-65.6.3 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2023-01-03T21:15:48.607364Z, end-time: 2023-01-03T21:15:56.156292Z, 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 53.7 MB/s eta 0:00:00 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 244.2 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-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.9.1 Downloading commonmark-0.9.1-py2.py3-none-any.whl (51 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.1/51.1 kB 175.4 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 193.3 MB/s eta 0:00:00 Collecting sphinx-rtd-theme Downloading sphinx_rtd_theme-1.1.1-py2.py3-none-any.whl (2.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 214.9 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 238.1 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 212.6 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 185.1 MB/s eta 0:00:00 Collecting snowballstemmer>=2.0 Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 205.2 MB/s eta 0:00:00 Collecting babel>=2.9 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importlib-metadata>=4.8 Downloading importlib_metadata-6.0.0-py3-none-any.whl (21 kB) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.2/121.2 kB 223.6 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 222.6 MB/s eta 0:00:00 Collecting requests>=2.5.0 Downloading requests-2.28.1-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 174.6 MB/s eta 0:00:00 Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 245.7 MB/s eta 0:00:00 Collecting pytz>=2015.7 Downloading pytz-2022.7-py2.py3-none-any.whl (499 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 499.4/499.4 kB 247.1 MB/s eta 0:00:00 Collecting typing-extensions>=3.6.4 Downloading typing_extensions-4.4.0-py3-none-any.whl (26 kB) Collecting zipp>=0.5 Downloading zipp-3.11.0-py3-none-any.whl (6.6 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.1.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Collecting idna<4,>=2.5 Downloading idna-3.4-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.5/61.5 kB 188.5 MB/s eta 0:00:00 Collecting certifi>=2017.4.17 Downloading certifi-2022.12.7-py3-none-any.whl (155 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.3/155.3 kB 231.1 MB/s eta 0:00:00 Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.13-py2.py3-none-any.whl (140 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 140.6/140.6 kB 222.8 MB/s eta 0:00:00 Collecting charset-normalizer<3,>=2 Downloading charset_normalizer-2.1.1-py3-none-any.whl (39 kB) 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=636d934a327b924e99fda4f6389129d2893bb012a3b2608b9236d47bad9e7ce3 Stored in directory: /tmp/pip-ephem-wheel-cache-7mf5ajvq/wheels/d1/33/8e/f9d24f00cc130866aacfe7c3bc15571217e2b22cc4c4e1b443 Successfully built mock Installing collected packages: snowballstemmer, pytz, mock, commonmark, alabaster, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, requests, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.1 Pygments-2.14.0 alabaster-0.7.12 babel-2.11.0 certifi-2022.12.7 charset-normalizer-2.1.1 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 importlib-metadata-6.0.0 mock-1.0.1 packaging-22.0 pillow-9.4.0 pytz-2022.7 readthedocs-sphinx-ext-2.2.0 recommonmark-0.5.0 requests-2.28.1 snowballstemmer-2.2.0 sphinx-5.3.0 sphinx-rtd-theme-1.1.1 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-4.4.0 urllib3-1.26.13 zipp-3.11.0 [rtd-command-info] start-time: 2023-01-03T21:15:56.391280Z, end-time: 2023-01-03T21:16:03.399651Z, 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 64.8 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 248.1 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 211.0 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 145.7 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 149.4 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: 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: 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)) (22.0) 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: 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) 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: 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)) (1.4.1) 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)) (2.28.1) 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: alabaster<0.8,>=0.7 in 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/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) Collecting docutils<0.18,>=0.14 Downloading docutils-0.16-py2.py3-none-any.whl (548 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 548.2/548.2 kB 232.9 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 193.0 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 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(line 3)) (4.4.0) 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)) (3.11.0) 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-0.1.2-py3-none-any.whl (10.0 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)) (3.4) Requirement already satisfied: charset-normalizer<3,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from 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Created wheel for sphinx-intl: filename=sphinx_intl-2.0.1-py3-none-any.whl size=11639 sha256=de1ea020887bc8e91883d288358769a1d07d3c2e3f85ab50b8cb8b3f3045c427 Stored in directory: /tmp/pip-ephem-wheel-cache-julfg857/wheels/34/8b/64/f66ece8e7e9ce3b9d4ccdf27db4ae70a6b52be427d9a97abdf 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=7e8833e7fdd1938fd0a04a8160ba97f5421943e8dc0ecca87ace16e56a48b463 Stored in directory: /tmp/pip-ephem-wheel-cache-julfg857/wheels/f3/e4/e7/2cb9215232a72987a89f82e8811ff518e18c2fb967c64c7d64 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=734085d557db79fbf9082a66b1779525c03fe4c32047ed188fbc0ec844e0e4dd Stored in directory: /tmp/pip-ephem-wheel-cache-julfg857/wheels/eb/54/de/a2bb06a8fc7b91ec80ff45e58e82e51cd54a39109ab5f9f2e4 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 0.17.1 Uninstalling docutils-0.17.1: Successfully uninstalled docutils-0.17.1 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 1.1.1 Uninstalling sphinx-rtd-theme-1.1.1: Successfully uninstalled sphinx-rtd-theme-1.1.1 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-2.1.0 mdit-py-plugins-0.3.3 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