Read the Docs build information Build id: 1147193 Project: beliveau-lab-tigerfish Version: latest Commit: 73c1128371b171855c5bf0c407b2a4005da7534b Date: 2022-10-20T17:57:08.402089Z State: finished Success: False [rtd-command-info] start-time: 2022-10-20T17:57:10.519677Z, end-time: 2022-10-20T17:57:14.928004Z, duration: 4, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:beliveau-lab/TigerFISH.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.113' (ECDSA) to the list of known hosts. [rtd-command-info] start-time: 2022-10-20T17:57:15.158731Z, end-time: 2022-10-20T17:57:15.856040Z, 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 73c1128 Add files via upload [rtd-command-info] start-time: 2022-10-20T17:57:16.058680Z, end-time: 2022-10-20T17:57:16.138602Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-10-20T17:57:17.271310Z, end-time: 2022-10-20T17:57:21.914234Z, 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: 2022-10-20T17:57:22.216712Z, end-time: 2022-10-20T17:57:24.040044Z, 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) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 kB 19.4 MB/s eta 0:00:00 Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 65.5.0 Uninstalling setuptools-65.5.0: Successfully uninstalled setuptools-65.5.0 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2022-10-20T17:57:24.313724Z, end-time: 2022-10-20T17:57:31.844336Z, 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<2.2 Collecting pillow Downloading Pillow-9.2.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 63.8 MB/s eta 0:00:00 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 237.0 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-0.7.12-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 165.7 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 215.7 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 214.2 MB/s eta 0:00:00 Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.9-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 236.6 MB/s eta 0:00:00 Collecting babel>=2.9 Downloading Babel-2.10.3-py3-none-any.whl (9.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 190.3 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 177.0 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 208.1 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 195.9 MB/s eta 0:00:00 Collecting importlib-metadata>=4.8 Downloading importlib_metadata-5.0.0-py3-none-any.whl (21 kB) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 90.6/90.6 kB 202.5 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 200.3 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-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.7/84.7 kB 198.4 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 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typing-extensions>=3.6.4 Downloading typing_extensions-4.4.0-py3-none-any.whl (26 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.1.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 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 198.9 MB/s eta 0:00:00 Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.12-py2.py3-none-any.whl (140 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 140.4/140.4 kB 212.3 MB/s eta 0:00:00 Collecting charset-normalizer<3,>=2 Downloading charset_normalizer-2.1.1-py3-none-any.whl (39 kB) Collecting idna<4,>=2.5 Downloading idna-3.4-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.5/61.5 kB 180.7 MB/s eta 0:00:00 Collecting certifi>=2017.4.17 Downloading certifi-2022.9.24-py3-none-any.whl (161 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 161.1/161.1 kB 220.6 MB/s eta 0:00:00 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=23773 sha256=5c36522ce7a26e3c2d6940a95367f4bfa78f718384cfd4e72b6c1c1198bb1d2d Stored in directory: /tmp/pip-ephem-wheel-cache-7lhdypey/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, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, requests, packaging, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.1 Pygments-2.13.0 alabaster-0.7.12 babel-2.10.3 certifi-2022.9.24 charset-normalizer-2.1.1 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 importlib-metadata-5.0.0 mock-1.0.1 packaging-21.3 pillow-9.2.0 pyparsing-3.0.9 pytz-2022.5 readthedocs-sphinx-ext-2.1.9 recommonmark-0.5.0 requests-2.28.1 snowballstemmer-2.2.0 sphinx-5.3.0 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-4.4.0 urllib3-1.26.12 zipp-3.9.0 [rtd-command-info] start-time: 2022-10-20T17:57:32.045537Z, end-time: 2022-10-20T17:57:39.394378Z, 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 58.0 MB/s eta 0:00:00 Collecting Pygments==2.11.2 Downloading Pygments-2.11.2-py3-none-any.whl (1.1 MB) 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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 171.6 MB/s eta 0:00:00 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: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (0.7.12) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.4.1) Requirement already satisfied: docutils<0.18,>=0.14 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (0.17.1) Requirement already satisfied: packaging in 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Collecting livereload Downloading livereload-2.6.3.tar.gz (25 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting colorama Downloading colorama-0.4.5-py2.py3-none-any.whl (16 kB) Collecting pyyaml Downloading PyYAML-6.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (596 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 596.3/596.3 kB 229.5 MB/s eta 0:00:00 Collecting mdit-py-plugins~=0.3.0 Downloading mdit_py_plugins-0.3.1-py3-none-any.whl (46 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 46.5/46.5 kB 161.5 MB/s eta 0:00:00 Collecting markdown-it-py<3.0.0,>=1.0.0 Downloading markdown_it_py-2.1.0-py3-none-any.whl (84 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.5/84.5 kB 187.5 MB/s eta 0:00:00 Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from babel>=1.3->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2022.5) Requirement already satisfied: typing-extensions>=3.6.4 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from importlib-metadata>=4.4->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (4.4.0) 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)) (3.9.0) 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: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.26.12) 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)) (2022.9.24) 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 requests>=2.5.0->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.1.1) 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 229.7 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=a123cf7e6fa8f9941d690971a2e90f26c429c1a6d5e896dda2169b03b7bcd346 Stored in directory: /tmp/pip-ephem-wheel-cache-n0mfyfe4/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=0716475f423f49dd9f03c4bd55ab498ef968d695cf6b4cbab8648798ab1ee626 Stored in directory: /tmp/pip-ephem-wheel-cache-n0mfyfe4/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=13737 sha256=ec8d2d9dcf39b80e74ee347cc306a1ef817ca72c69ecc068df1e5e81ca957245 Stored in directory: /tmp/pip-ephem-wheel-cache-n0mfyfe4/wheels/eb/54/de/a2bb06a8fc7b91ec80ff45e58e82e51cd54a39109ab5f9f2e4 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=41affbe657165df1a732333eb19fefcf33307e9bf7d8acac0f837fefcbef3657 Stored in directory: /tmp/pip-ephem-wheel-cache-n0mfyfe4/wheels/0a/da/85/bbc4365bb71f2214c599aeeb901517e5f883c5f1988b92515f 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 2.13.0 Uninstalling Pygments-2.13.0: Successfully uninstalled Pygments-2.13.0 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 Successfully installed Pygments-2.11.2 Sphinx-4.4.0 click-8.1.3 colorama-0.4.5 docutils-0.16 livereload-2.6.3 markdown-it-py-2.1.0 mdit-py-plugins-0.3.1 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 sphinxcontrib-httpdomain-1.8.0 sphinxemoji-0.2.0 tornado-6.2 [rtd-command-info] start-time: 2022-10-20T17:57:40.870315Z, end-time: 2022-10-20T17:57:40.960639Z, 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', 'sphinxcontrib.video' ] 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': '73c11283', } # 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/1147193/' 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: 2022-10-20T17:57:41.183886Z, end-time: 2022-10-20T17:57:41.780736Z, duration: 0, exit-code: 2 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v4.4.0 loading translations [en]... done Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/sphinx/registry.py", line 433, in load_extension mod = import_module(extname) File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/importlib/__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1006, in _gcd_import File "", line 983, in _find_and_load File "", line 965, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinxcontrib.video' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/sphinx/cmd/build.py", line 283, in build_main args.tags, args.verbosity, args.jobs, args.keep_going) File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 230, in __init__ self.setup_extension(extension) File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 387, in setup_extension self.registry.load_extension(self, extname) File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/sphinx/registry.py", line 437, in load_extension err) from err sphinx.errors.ExtensionError: Could not import extension sphinxcontrib.video (exception: No module named 'sphinxcontrib.video') Extension error: Could not import extension sphinxcontrib.video (exception: No module named 'sphinxcontrib.video')