Read the Docs build information Build id: 1669816 Project: beliveau-lab-tigerfish Version: latest Commit: e32af7e6a2a87f359b257f59b9e24aaf239c1748 Date: 2023-08-18T19:46:10.951201Z State: finished Success: True [rtd-command-info] start-time: 2023-08-18T19:46:19.224663Z, end-time: 2023-08-18T19:46:22.347671Z, duration: 3, exit-code: 0 git clone --depth 1 git@github.com:beliveau-lab/TigerFISH.git . Cloning into '.'... Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. [rtd-command-info] start-time: 2023-08-18T19:46:22.925907Z, end-time: 2023-08-18T19:46:28.519417Z, duration: 5, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/master:refs/remotes/origin/master Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. From github.com:beliveau-lab/TigerFISH * [new tag] v1.1.0 -> v1.1.0 [rtd-command-info] start-time: 2023-08-18T19:46:29.065213Z, end-time: 2023-08-18T19:46:29.730640Z, 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 e32af7e Update .readthedocs.yml [rtd-command-info] start-time: 2023-08-18T19:46:30.524865Z, end-time: 2023-08-18T19:46:30.607681Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-08-18T19:46:31.423725Z, end-time: 2023-08-18T19:46:31.490034Z, duration: 0, exit-code: 0 cat .readthedocs.yml version: 2 build: os: "ubuntu-22.04" tools: python: "3.11" sphinx: configuration: docs/source/conf.py python: install: - requirements: docs/requirements.txt [rtd-command-info] start-time: 2023-08-18T19:46:40.456114Z, end-time: 2023-08-18T19:46:40.574929Z, duration: 0, exit-code: 0 asdf global python 3.11.4 [rtd-command-info] start-time: 2023-08-18T19:46:41.566310Z, end-time: 2023-08-18T19:46:42.468993Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.11.4.final.0-64 in 584ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==21.2.3, setuptools==57.4.0, wheel==0.37.0 activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2023-08-18T19:46:43.026063Z, end-time: 2023-08-18T19:46:56.531167Z, duration: 13, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (21.2.3) Collecting pip Downloading pip-23.2.1-py3-none-any.whl (2.1 MB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (57.4.0) Collecting setuptools Downloading setuptools-68.1.2-py3-none-any.whl (805 kB) Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 57.4.0 Uninstalling setuptools-57.4.0: Successfully uninstalled setuptools-57.4.0 Attempting uninstall: pip Found existing installation: pip 21.2.3 Uninstalling pip-21.2.3: Successfully uninstalled pip-21.2.3 Successfully installed pip-23.2.1 setuptools-68.1.2 [rtd-command-info] start-time: 2023-08-18T19:46:57.005384Z, end-time: 2023-08-18T19:47:06.841757Z, duration: 9, 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 Obtaining dependency information for pillow from 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Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23753 sha256=d9176dd9ec52953dba6ddec81b7f95a01843d89f59fd25305dcb060be305d7f4 Stored in directory: /tmp/pip-ephem-wheel-cache-me2ltb7c/wheels/80/c2/c8/630c9eb889f0be0202cb11bf30b47aa54bf7588e8d50b70005 Successfully built mock Installing collected packages: snowballstemmer, mock, commonmark, urllib3, sphinxcontrib-jsmath, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, readthedocs-sphinx-ext, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, sphinx, sphinxcontrib-jquery, sphinx-rtd-theme, recommonmark Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.3 Pygments-2.16.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.7.22 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.18.1 idna-3.4 imagesize-1.4.1 mock-1.0.1 packaging-23.1 pillow-10.0.0 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 snowballstemmer-2.2.0 sphinx-6.2.1 sphinx-rtd-theme-1.2.2 sphinxcontrib-applehelp-1.0.7 sphinxcontrib-devhelp-1.0.5 sphinxcontrib-htmlhelp-2.0.4 sphinxcontrib-jquery-4.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.6 sphinxcontrib-serializinghtml-1.1.8 urllib3-2.0.4 [rtd-command-info] start-time: 2023-08-18T19:47:07.346946Z, end-time: 2023-08-18T19:47:15.466405Z, duration: 8, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting Sphinx==4.4.0 (from -r docs/requirements.txt (line 3)) Downloading Sphinx-4.4.0-py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 47.8 MB/s eta 0:00:00 Collecting Pygments==2.11.2 (from -r docs/requirements.txt (line 4)) Downloading Pygments-2.11.2-py3-none-any.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 273.1 MB/s eta 0:00:00 Collecting sphinx_rtd_theme==1.0.0 (from -r docs/requirements.txt (line 6)) Downloading sphinx_rtd_theme-1.0.0-py2.py3-none-any.whl (2.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 216.0 MB/s eta 0:00:00 Collecting sphinx-tabs==3.2.0 (from -r docs/requirements.txt (line 7)) Downloading sphinx_tabs-3.2.0-py3-none-any.whl (9.8 kB) Collecting sphinx-intl==2.0.1 (from -r docs/requirements.txt (line 8)) 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 (from -r docs/requirements.txt (line 10)) Downloading readthedocs_sphinx_search-0.1.1-py3-none-any.whl (18 kB) Collecting sphinxemoji==0.2.0 (from -r docs/requirements.txt (line 13)) Downloading sphinxemoji-0.2.0.tar.gz (44 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 44.4/44.4 kB 228.1 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 (from -r docs/requirements.txt (line 14)) Downloading sphinxcontrib_httpdomain-1.8.0-py2.py3-none-any.whl (19 kB) Collecting sphinx-prompt==1.4.0 (from -r docs/requirements.txt (line 15)) Downloading sphinx_prompt-1.4.0-py3-none-any.whl (4.1 kB) Collecting sphinx-notfound-page==0.8 (from -r docs/requirements.txt (line 16)) Downloading sphinx_notfound_page-0.8-py3-none-any.whl (15 kB) Collecting sphinx-autobuild==2021.3.14 (from -r docs/requirements.txt (line 17)) Downloading sphinx_autobuild-2021.3.14-py3-none-any.whl (9.9 kB) Collecting rstcheck==3.3.1 (from -r docs/requirements.txt (line 20)) 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 (from -r docs/requirements.txt (line 23)) Downloading myst_parser-0.16.1-py3-none-any.whl (48 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.8/48.8 kB 227.5 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/python3.11/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.0.7) Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.0.5) Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.0.1) Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.0.4) Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.1.8) Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.0.6) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (3.1.2) Collecting docutils<0.18,>=0.14 (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 286.1 MB/s eta 0:00:00 Requirement already satisfied: snowballstemmer>=1.1 in 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/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.31.0) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (23.1) Downloading docutils-0.16-py2.py3-none-any.whl (548 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 548.2/548.2 kB 286.3 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (from sphinx-intl==2.0.1->-r docs/requirements.txt (line 8)) (68.1.2) Collecting click (from sphinx-intl==2.0.1->-r docs/requirements.txt (line 8)) Obtaining dependency information for click from https://files.pythonhosted.org/packages/00/2e/d53fa4befbf2cfa713304affc7ca780ce4fc1fd8710527771b58311a3229/click-8.1.7-py3-none-any.whl.metadata Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB) Collecting six (from sphinxcontrib-httpdomain==1.8.0->-r docs/requirements.txt (line 14)) Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting livereload (from sphinx-autobuild==2021.3.14->-r docs/requirements.txt (line 17)) Downloading livereload-2.6.3-py2.py3-none-any.whl (24 kB) Collecting colorama (from sphinx-autobuild==2021.3.14->-r docs/requirements.txt (line 17)) Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB) Collecting markdown-it-py<3.0.0,>=1.0.0 (from myst_parser==0.16.1->-r docs/requirements.txt (line 23)) Downloading markdown_it_py-2.2.0-py3-none-any.whl (84 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.5/84.5 kB 259.4 MB/s eta 0:00:00 Collecting mdit-py-plugins~=0.3.0 (from myst_parser==0.16.1->-r docs/requirements.txt (line 23)) Downloading mdit_py_plugins-0.3.5-py3-none-any.whl (52 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 52.1/52.1 kB 238.7 MB/s eta 0:00:00 Collecting pyyaml (from myst_parser==0.16.1->-r docs/requirements.txt (line 23)) Obtaining dependency information for pyyaml from https://files.pythonhosted.org/packages/7b/5e/efd033ab7199a0b2044dab3b9f7a4f6670e6a52c089de572e928d2873b06/PyYAML-6.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata Downloading PyYAML-6.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (from Jinja2>=2.3->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.1.3) Collecting mdurl~=0.1 (from markdown-it-py<3.0.0,>=1.0.0->myst_parser==0.16.1->-r docs/requirements.txt (line 23)) 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/latest/lib/python3.11/site-packages (from requests>=2.5.0->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (3.2.0) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (from requests>=2.5.0->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (3.4) Requirement already satisfied: urllib3<3,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (from requests>=2.5.0->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.0.4) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (from requests>=2.5.0->Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2023.7.22) INFO: pip is looking at multiple versions 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PyYAML-6.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (757 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 757.7/757.7 kB 289.4 MB/s eta 0:00:00 Downloading tornado-6.3.3-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (427 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 427.7/427.7 kB 281.5 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=11615 sha256=a5bce63739eae37cdcfe46716e7e1a7fb972791509240131318dfddca6d97d99 Stored in directory: /tmp/pip-ephem-wheel-cache-81wgpuxg/wheels/17/4c/42/ed7529920684c8534a0c2541942f1c70fd1baa7fdd02918321 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=44409 sha256=6aeab2a69ca4c65839c0ff5c532d16cb9207a6de0d2843a1432fd8173754557e Stored in directory: /tmp/pip-ephem-wheel-cache-81wgpuxg/wheels/d4/b0/a5/92b0e0b5611fc4d37f90711172a680959318c4474df5d2718d 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=13716 sha256=dcdd640b1efcbc23c32b3645ea3024ebdc963307ced3025e9a2cfa16523311d0 Stored in directory: /tmp/pip-ephem-wheel-cache-81wgpuxg/wheels/e0/57/d7/2af930ae6114f46c59f8f9807d39657196c217e4af0c4a9435 Successfully built sphinx-intl sphinxemoji rstcheck Installing collected packages: sphinx-notfound-page, tornado, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, six, readthedocs-sphinx-search, pyyaml, Pygments, mdurl, docutils, colorama, click, Sphinx, rstcheck, markdown-it-py, livereload, sphinxemoji, sphinxcontrib-httpdomain, sphinx-tabs, sphinx_rtd_theme, sphinx-prompt, sphinx-intl, sphinx-autobuild, mdit-py-plugins, myst_parser Attempting uninstall: sphinxcontrib-serializinghtml Found existing installation: sphinxcontrib-serializinghtml 1.1.8 Uninstalling sphinxcontrib-serializinghtml-1.1.8: Successfully uninstalled sphinxcontrib-serializinghtml-1.1.8 Attempting uninstall: sphinxcontrib-qthelp Found existing installation: sphinxcontrib-qthelp 1.0.6 Uninstalling sphinxcontrib-qthelp-1.0.6: Successfully uninstalled sphinxcontrib-qthelp-1.0.6 Attempting uninstall: sphinxcontrib-htmlhelp Found existing installation: sphinxcontrib-htmlhelp 2.0.4 Uninstalling sphinxcontrib-htmlhelp-2.0.4: Successfully uninstalled sphinxcontrib-htmlhelp-2.0.4 Attempting uninstall: sphinxcontrib-devhelp Found existing installation: sphinxcontrib-devhelp 1.0.5 Uninstalling sphinxcontrib-devhelp-1.0.5: Successfully uninstalled sphinxcontrib-devhelp-1.0.5 Attempting uninstall: sphinxcontrib-applehelp Found existing installation: sphinxcontrib-applehelp 1.0.7 Uninstalling sphinxcontrib-applehelp-1.0.7: Successfully uninstalled sphinxcontrib-applehelp-1.0.7 Attempting uninstall: Pygments Found existing installation: Pygments 2.16.1 Uninstalling Pygments-2.16.1: Successfully uninstalled Pygments-2.16.1 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 6.2.1 Uninstalling Sphinx-6.2.1: Successfully uninstalled Sphinx-6.2.1 Attempting uninstall: sphinx_rtd_theme Found existing installation: sphinx-rtd-theme 1.2.2 Uninstalling sphinx-rtd-theme-1.2.2: Successfully uninstalled sphinx-rtd-theme-1.2.2 Successfully installed Pygments-2.11.2 Sphinx-4.4.0 click-8.1.7 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-6.0.1 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-applehelp-1.0.4 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-httpdomain-1.8.0 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 sphinxemoji-0.2.0 tornado-6.3.3 [rtd-command-info] start-time: 2023-08-18T19:47:22.201376Z, end-time: 2023-08-18T19:47:22.260012Z, 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': "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': [ ("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': '', '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': 'e32af7e6', } # 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(): for key in context: if key not in html_context: html_context[key] = context[key] 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/1669816/' 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: 2023-08-18T19:47:22.743644Z, end-time: 2023-08-18T19:47:24.090339Z, 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/latest/docs/source/cli.rst:17: WARNING: Title underline too short. Named Arguments in `config.yml `_ for main workflow ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /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:68: WARNING: toctree contains reference to nonexisting document 'vignettes/index' /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:5: WARNING: Title underline too short. `Main workflow `_ ^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/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/latest/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/latest/docs/source/snakemake_view.rst:58: WARNING: Title underline too short. `generate_jf_idx `_ ----------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:58: WARNING: Title underline too short. `generate_jf_idx `_ ----------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:88: WARNING: Title underline too short. `split_bed `_ --------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:88: WARNING: Title underline too short. `split_bed `_ --------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:112: WARNING: Title underline too short. `repeat_ID `_ --------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:112: WARNING: Title underline too short. `repeat_ID `_ --------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:143: WARNING: Title underline too short. `design_probes `_ ------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:143: WARNING: Title underline too short. `design_probes `_ ------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:175: WARNING: Title underline too short. `kmer_filter `_ ----------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:175: WARNING: Title underline too short. `kmer_filter `_ ----------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:203: WARNING: Title underline too short. `probe_mer_filter `_ ---------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:203: WARNING: Title underline too short. `probe_mer_filter `_ ---------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:259: WARNING: Title underline too short. `make_chrom_dir (checkpoint) `_ --------------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:259: WARNING: Title underline too short. `make_chrom_dir (checkpoint) `_ --------------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:283: WARNING: Title underline too short. `alignment_filter `_ ---------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:283: WARNING: Title underline too short. `alignment_filter `_ ---------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:344: WARNING: Title underline too short. `split_rm_alignments `_ ------------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:344: WARNING: Title underline too short. `split_rm_alignments `_ ------------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:367: WARNING: Title underline too short. `align_probes `_ ------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:367: WARNING: Title underline too short. `align_probes `_ ------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:395: WARNING: Title underline too short. `derived_beds `_ ------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:395: WARNING: Title underline too short. `derived_beds `_ ------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:419: WARNING: Title underline too short. `get_region_bed `_ -------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:419: WARNING: Title underline too short. `get_region_bed `_ -------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/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/latest/docs/source/snakemake_view.rst:470: WARNING: Title underline too short. `get_alignments `_ -------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:470: WARNING: Title underline too short. `get_alignments `_ -------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:501: WARNING: Title underline too short. `generate_chromomap `_ ------------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:501: WARNING: Title underline too short. `generate_chromomap `_ ------------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:518: WARNING: Title underline too short. `map_region_coords `_ -------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:518: WARNING: Title underline too short. `map_region_coords `_ -------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:569: WARNING: Title underline too short. `summary `_ ------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:569: WARNING: Title underline too short. `summary `_ ------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "this directory". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "this directory". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/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/latest/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/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 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 ======================= 0.120 tutorials 0.088 snakemake_view 0.064 cli 0.031 parameters 0.023 index