Read the Docs build information Build id: 2006852 Project: institute-for-disease-modeling-fpsim Version: latest Commit: 99c5a086dc2cadcf7c350893a8f7587f7af62b6b Date: 2024-02-09T15:58:11.982341Z State: finished Success: False [rtd-command-info] start-time: 2024-02-09T15:58:13.180155Z, end-time: 2024-02-09T15:58:13.931910Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/fpsim/fpsim.git . Cloning into '.'... [rtd-command-info] start-time: 2024-02-09T15:58:13.998202Z, end-time: 2024-02-09T15:58:14.569648Z, duration: 0, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main [rtd-command-info] start-time: 2024-02-09T15:58:14.709788Z, end-time: 2024-02-09T15:58:14.810892Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: switching to 'origin/main'. 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 99c5a08 Merge pull request #259 from fpsim/tidy-analyzers [rtd-command-info] start-time: 2024-02-09T15:58:14.882538Z, end-time: 2024-02-09T15:58:14.940030Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2024-02-09T15:58:15.013617Z, end-time: 2024-02-09T15:58:15.075172Z, duration: 0, exit-code: 0 cat .readthedocs.yaml # .readthedocs.yaml # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details # Required version: 2 # Set the version of Python and other tools you might need build: os: ubuntu-20.04 tools: python: "3.9" # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py # If using Sphinx, optionally build your docs in additional formats such as PDF # formats: # Optionally declare the Python requirements required to build your docs python: install: - requirements: docs/requirements.txt - method: pip path: . [rtd-command-info] start-time: 2024-02-09T15:58:20.123913Z, end-time: 2024-02-09T15:58:20.207441Z, duration: 0, exit-code: 0 asdf global python 3.9.18 [rtd-command-info] start-time: 2024-02-09T15:58:20.619039Z, end-time: 2024-02-09T15:58:21.864686Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.18.final.0-64 in 908ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/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==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2024-02-09T15:58:21.930152Z, end-time: 2024-02-09T15:58:32.493773Z, duration: 10, 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/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (23.1) Collecting pip Downloading pip-24.0-py3-none-any.whl (2.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 38.7 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (67.6.1) Collecting setuptools Downloading setuptools-69.0.3-py3-none-any.whl (819 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 819.5/819.5 kB 59.0 MB/s eta 0:00:00 Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 67.6.1 Uninstalling setuptools-67.6.1: Successfully uninstalled setuptools-67.6.1 Attempting uninstall: pip Found existing installation: pip 23.1 Uninstalling pip-23.1: Successfully uninstalled pip-23.1 Successfully installed pip-24.0 setuptools-69.0.3 [rtd-command-info] start-time: 2024-02-09T15:58:32.564918Z, end-time: 2024-02-09T15:58:38.711856Z, duration: 6, exit-code: 0 python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext Collecting sphinx Downloading sphinx-7.2.6-py3-none-any.whl.metadata (5.9 kB) Collecting readthedocs-sphinx-ext Downloading readthedocs_sphinx_ext-2.2.5-py2.py3-none-any.whl.metadata (1.5 kB) Collecting sphinxcontrib-applehelp (from sphinx) Downloading sphinxcontrib_applehelp-1.0.8-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-devhelp (from sphinx) Downloading sphinxcontrib_devhelp-1.0.6-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-jsmath (from sphinx) Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting sphinxcontrib-htmlhelp>=2.0.0 (from sphinx) Downloading sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-serializinghtml>=1.1.9 (from sphinx) Downloading sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl.metadata (2.4 kB) Collecting sphinxcontrib-qthelp (from sphinx) Downloading sphinxcontrib_qthelp-1.0.7-py3-none-any.whl.metadata (2.2 kB) Collecting Jinja2>=3.0 (from sphinx) Downloading Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB) Collecting Pygments>=2.14 (from sphinx) Downloading pygments-2.17.2-py3-none-any.whl.metadata (2.6 kB) Collecting docutils<0.21,>=0.18.1 (from sphinx) Downloading docutils-0.20.1-py3-none-any.whl.metadata (2.8 kB) Collecting snowballstemmer>=2.0 (from sphinx) Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 7.9 MB/s eta 0:00:00 Collecting babel>=2.9 (from sphinx) Downloading Babel-2.14.0-py3-none-any.whl.metadata (1.6 kB) Collecting alabaster<0.8,>=0.7 (from sphinx) Downloading alabaster-0.7.16-py3-none-any.whl.metadata (2.9 kB) Collecting imagesize>=1.3 (from sphinx) Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Collecting requests>=2.25.0 (from sphinx) Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB) Collecting packaging>=21.0 (from sphinx) Downloading packaging-23.2-py3-none-any.whl.metadata (3.2 kB) Collecting importlib-metadata>=4.8 (from sphinx) Downloading importlib_metadata-7.0.1-py3-none-any.whl.metadata (4.9 kB) Collecting zipp>=0.5 (from importlib-metadata>=4.8->sphinx) Downloading zipp-3.17.0-py3-none-any.whl.metadata (3.7 kB) Collecting MarkupSafe>=2.0 (from Jinja2>=3.0->sphinx) Downloading MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB) Collecting charset-normalizer<4,>=2 (from requests>=2.25.0->sphinx) Downloading charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB) Collecting idna<4,>=2.5 (from requests>=2.25.0->sphinx) Downloading idna-3.6-py3-none-any.whl.metadata (9.9 kB) Collecting urllib3<3,>=1.21.1 (from requests>=2.25.0->sphinx) Downloading urllib3-2.2.0-py3-none-any.whl.metadata (6.4 kB) Collecting certifi>=2017.4.17 (from requests>=2.25.0->sphinx) Downloading certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB) Downloading sphinx-7.2.6-py3-none-any.whl (3.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 84.1 MB/s eta 0:00:00 Downloading readthedocs_sphinx_ext-2.2.5-py2.py3-none-any.whl (11 kB) Downloading alabaster-0.7.16-py3-none-any.whl (13 kB) Downloading Babel-2.14.0-py3-none-any.whl (11.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.0/11.0 MB 196.6 MB/s eta 0:00:00 Downloading docutils-0.20.1-py3-none-any.whl (572 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 572.7/572.7 kB 260.2 MB/s eta 0:00:00 Downloading importlib_metadata-7.0.1-py3-none-any.whl (23 kB) Downloading Jinja2-3.1.3-py3-none-any.whl (133 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.2/133.2 kB 237.9 MB/s eta 0:00:00 Downloading packaging-23.2-py3-none-any.whl (53 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.0/53.0 kB 199.3 MB/s eta 0:00:00 Downloading pygments-2.17.2-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 257.0 MB/s eta 0:00:00 Downloading requests-2.31.0-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.6/62.6 kB 207.3 MB/s eta 0:00:00 Downloading sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl (99 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 99.2/99.2 kB 230.6 MB/s eta 0:00:00 Downloading sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl (92 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 92.7/92.7 kB 207.4 MB/s eta 0:00:00 Downloading sphinxcontrib_applehelp-1.0.8-py3-none-any.whl (120 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 120.0/120.0 kB 219.1 MB/s eta 0:00:00 Downloading sphinxcontrib_devhelp-1.0.6-py3-none-any.whl (83 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 83.5/83.5 kB 219.0 MB/s eta 0:00:00 Downloading sphinxcontrib_qthelp-1.0.7-py3-none-any.whl (89 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 89.4/89.4 kB 227.2 MB/s eta 0:00:00 Downloading certifi-2024.2.2-py3-none-any.whl (163 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 163.8/163.8 kB 248.8 MB/s eta 0:00:00 Downloading charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 142.3/142.3 kB 235.8 MB/s eta 0:00:00 Downloading idna-3.6-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.6/61.6 kB 210.0 MB/s eta 0:00:00 Downloading MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Downloading urllib3-2.2.0-py3-none-any.whl (120 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 120.9/120.9 kB 242.6 MB/s eta 0:00:00 Downloading zipp-3.17.0-py3-none-any.whl (7.4 kB) Installing collected packages: snowballstemmer, zipp, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext Successfully installed Jinja2-3.1.3 MarkupSafe-2.1.5 Pygments-2.17.2 alabaster-0.7.16 babel-2.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.6 imagesize-1.4.1 importlib-metadata-7.0.1 packaging-23.2 readthedocs-sphinx-ext-2.2.5 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.8 sphinxcontrib-devhelp-1.0.6 sphinxcontrib-htmlhelp-2.0.5 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.7 sphinxcontrib-serializinghtml-1.1.10 urllib3-2.2.0 zipp-3.17.0 [rtd-command-info] start-time: 2024-02-09T15:58:38.773923Z, end-time: 2024-02-09T15:58:57.446602Z, duration: 18, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting pandoc (from -r docs/requirements.txt (line 1)) Downloading pandoc-2.3.tar.gz (33 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pypandoc (from -r docs/requirements.txt (line 2)) Downloading pypandoc-1.12-py3-none-any.whl.metadata (16 kB) Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from -r docs/requirements.txt (line 3)) (7.2.6) Collecting sphinx-autodoc-typehints (from -r docs/requirements.txt (line 4)) Downloading sphinx_autodoc_typehints-2.0.0-py3-none-any.whl.metadata (7.7 kB) Collecting pydata-sphinx-theme (from -r docs/requirements.txt (line 5)) Downloading pydata_sphinx_theme-0.15.2-py3-none-any.whl.metadata (7.3 kB) Collecting sphinx-design (from -r docs/requirements.txt (line 6)) Downloading sphinx_design-0.5.0-py3-none-any.whl.metadata (5.1 kB) Collecting readthedocs-sphinx-search (from -r docs/requirements.txt (line 7)) Downloading readthedocs_sphinx_search-0.3.2-py3-none-any.whl.metadata (2.4 kB) Collecting ipykernel (from -r docs/requirements.txt (line 8)) Downloading ipykernel-6.29.2-py3-none-any.whl.metadata (6.0 kB) Collecting nbsphinx (from -r docs/requirements.txt (line 9)) Downloading nbsphinx-0.9.3-py3-none-any.whl.metadata (2.1 kB) Collecting plantweb (from -r docs/requirements.txt (line 10)) Downloading plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting optuna (from -r docs/requirements.txt (line 13)) Downloading optuna-3.5.0-py3-none-any.whl.metadata (17 kB) Collecting plumbum (from pandoc->-r docs/requirements.txt (line 1)) Downloading plumbum-1.8.2-py3-none-any.whl.metadata (10 kB) Collecting ply (from pandoc->-r docs/requirements.txt (line 1)) Downloading ply-3.11-py2.py3-none-any.whl (49 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 49.6/49.6 kB 157.3 MB/s eta 0:00:00 Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 3)) (1.0.8) Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 3)) (1.0.6) Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sphinx->-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/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 3)) (2.0.5) Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.9 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 3)) (1.1.10) Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 3)) (1.0.7) Requirement already satisfied: Jinja2>=3.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 3)) (3.1.3) Requirement already satisfied: Pygments>=2.14 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 3)) (2.17.2) Requirement already satisfied: docutils<0.21,>=0.18.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 3)) (0.20.1) Requirement already satisfied: snowballstemmer>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 3)) (2.2.0) Requirement already satisfied: babel>=2.9 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 3)) (2.14.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 3)) (0.7.16) Requirement already satisfied: imagesize>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 3)) (1.4.1) Requirement already satisfied: requests>=2.25.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 3)) (2.31.0) Requirement already satisfied: packaging>=21.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 3)) (23.2) Requirement already satisfied: importlib-metadata>=4.8 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sphinx->-r docs/requirements.txt (line 3)) (7.0.1) Collecting beautifulsoup4 (from pydata-sphinx-theme->-r docs/requirements.txt (line 5)) Downloading beautifulsoup4-4.12.3-py3-none-any.whl.metadata (3.8 kB) Collecting accessible-pygments (from pydata-sphinx-theme->-r docs/requirements.txt (line 5)) Downloading accessible_pygments-0.0.4-py2.py3-none-any.whl (29 kB) Collecting typing-extensions (from pydata-sphinx-theme->-r docs/requirements.txt (line 5)) Downloading typing_extensions-4.9.0-py3-none-any.whl.metadata (3.0 kB) Collecting comm>=0.1.1 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading comm-0.2.1-py3-none-any.whl.metadata (3.7 kB) Collecting debugpy>=1.6.5 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading debugpy-1.8.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.1 kB) Collecting ipython>=7.23.1 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading ipython-8.18.1-py3-none-any.whl.metadata (6.0 kB) Collecting jupyter-client>=6.1.12 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading jupyter_client-8.6.0-py3-none-any.whl.metadata (8.3 kB) Collecting jupyter-core!=5.0.*,>=4.12 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading jupyter_core-5.7.1-py3-none-any.whl.metadata (3.4 kB) Collecting matplotlib-inline>=0.1 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading matplotlib_inline-0.1.6-py3-none-any.whl (9.4 kB) Collecting nest-asyncio (from ipykernel->-r docs/requirements.txt (line 8)) Downloading nest_asyncio-1.6.0-py3-none-any.whl.metadata (2.8 kB) Collecting psutil (from ipykernel->-r docs/requirements.txt (line 8)) Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB) Collecting pyzmq>=24 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading pyzmq-25.1.2-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (4.9 kB) Collecting tornado>=6.1 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading tornado-6.4-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB) Collecting traitlets>=5.4.0 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading traitlets-5.14.1-py3-none-any.whl.metadata (10 kB) Collecting nbconvert!=5.4 (from nbsphinx->-r docs/requirements.txt (line 9)) Downloading nbconvert-7.16.0-py3-none-any.whl.metadata (7.7 kB) Collecting nbformat (from nbsphinx->-r docs/requirements.txt (line 9)) Downloading nbformat-5.9.2-py3-none-any.whl.metadata (3.4 kB) Collecting six (from plantweb->-r docs/requirements.txt (line 10)) Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting alembic>=1.5.0 (from optuna->-r docs/requirements.txt (line 13)) Downloading alembic-1.13.1-py3-none-any.whl.metadata (7.4 kB) Collecting colorlog (from optuna->-r docs/requirements.txt (line 13)) Downloading colorlog-6.8.2-py3-none-any.whl.metadata (10 kB) Collecting numpy (from optuna->-r docs/requirements.txt (line 13)) Downloading numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.0/61.0 kB 203.7 MB/s eta 0:00:00 Collecting sqlalchemy>=1.3.0 (from optuna->-r docs/requirements.txt (line 13)) Downloading SQLAlchemy-2.0.25-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.6 kB) Collecting tqdm (from optuna->-r docs/requirements.txt (line 13)) Downloading tqdm-4.66.1-py3-none-any.whl.metadata (57 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.6/57.6 kB 168.8 MB/s eta 0:00:00 Collecting PyYAML (from optuna->-r docs/requirements.txt (line 13)) Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB) Collecting Mako (from alembic>=1.5.0->optuna->-r docs/requirements.txt (line 13)) Downloading Mako-1.3.2-py3-none-any.whl.metadata (2.9 kB) Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from importlib-metadata>=4.8->sphinx->-r docs/requirements.txt (line 3)) (3.17.0) Collecting decorator (from ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading decorator-5.1.1-py3-none-any.whl (9.1 kB) Collecting jedi>=0.16 (from ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading jedi-0.19.1-py2.py3-none-any.whl.metadata (22 kB) Collecting prompt-toolkit<3.1.0,>=3.0.41 (from ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading prompt_toolkit-3.0.43-py3-none-any.whl.metadata (6.5 kB) Collecting stack-data (from ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading stack_data-0.6.3-py3-none-any.whl.metadata (18 kB) Collecting exceptiongroup (from ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading exceptiongroup-1.2.0-py3-none-any.whl.metadata (6.6 kB) Collecting pexpect>4.3 (from ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading pexpect-4.9.0-py2.py3-none-any.whl.metadata (2.5 kB) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from Jinja2>=3.0->sphinx->-r docs/requirements.txt (line 3)) (2.1.5) Collecting python-dateutil>=2.8.2 (from jupyter-client>=6.1.12->ipykernel->-r docs/requirements.txt (line 8)) Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 31.4 MB/s eta 0:00:00 Collecting platformdirs>=2.5 (from jupyter-core!=5.0.*,>=4.12->ipykernel->-r docs/requirements.txt (line 8)) Downloading platformdirs-4.2.0-py3-none-any.whl.metadata (11 kB) Collecting bleach!=5.0.0 (from nbconvert!=5.4->nbsphinx->-r docs/requirements.txt (line 9)) Downloading bleach-6.1.0-py3-none-any.whl.metadata (30 kB) Collecting defusedxml (from nbconvert!=5.4->nbsphinx->-r docs/requirements.txt (line 9)) Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) Collecting jupyterlab-pygments (from nbconvert!=5.4->nbsphinx->-r docs/requirements.txt (line 9)) Downloading jupyterlab_pygments-0.3.0-py3-none-any.whl.metadata (4.4 kB) Collecting mistune<4,>=2.0.3 (from nbconvert!=5.4->nbsphinx->-r docs/requirements.txt (line 9)) Downloading mistune-3.0.2-py3-none-any.whl.metadata (1.7 kB) Collecting nbclient>=0.5.0 (from nbconvert!=5.4->nbsphinx->-r docs/requirements.txt (line 9)) Downloading nbclient-0.9.0-py3-none-any.whl.metadata (7.8 kB) Collecting pandocfilters>=1.4.1 (from nbconvert!=5.4->nbsphinx->-r docs/requirements.txt (line 9)) Downloading pandocfilters-1.5.1-py2.py3-none-any.whl.metadata (9.0 kB) Collecting tinycss2 (from nbconvert!=5.4->nbsphinx->-r docs/requirements.txt (line 9)) Downloading tinycss2-1.2.1-py3-none-any.whl (21 kB) Collecting fastjsonschema (from nbformat->nbsphinx->-r docs/requirements.txt (line 9)) Downloading fastjsonschema-2.19.1-py3-none-any.whl.metadata (2.1 kB) Collecting jsonschema>=2.6 (from nbformat->nbsphinx->-r docs/requirements.txt (line 9)) Downloading jsonschema-4.21.1-py3-none-any.whl.metadata (7.8 kB) Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from requests>=2.25.0->sphinx->-r docs/requirements.txt (line 3)) (3.3.2) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from requests>=2.25.0->sphinx->-r docs/requirements.txt (line 3)) (3.6) Requirement already satisfied: urllib3<3,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from requests>=2.25.0->sphinx->-r docs/requirements.txt (line 3)) (2.2.0) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from requests>=2.25.0->sphinx->-r docs/requirements.txt (line 3)) (2024.2.2) Collecting greenlet!=0.4.17 (from sqlalchemy>=1.3.0->optuna->-r docs/requirements.txt (line 13)) Downloading greenlet-3.0.3-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.8 kB) Collecting soupsieve>1.2 (from beautifulsoup4->pydata-sphinx-theme->-r docs/requirements.txt (line 5)) Downloading soupsieve-2.5-py3-none-any.whl.metadata (4.7 kB) Collecting webencodings (from bleach!=5.0.0->nbconvert!=5.4->nbsphinx->-r docs/requirements.txt (line 9)) Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Collecting parso<0.9.0,>=0.8.3 (from jedi>=0.16->ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading parso-0.8.3-py2.py3-none-any.whl (100 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.8/100.8 kB 223.7 MB/s eta 0:00:00 Collecting attrs>=22.2.0 (from jsonschema>=2.6->nbformat->nbsphinx->-r docs/requirements.txt (line 9)) Downloading attrs-23.2.0-py3-none-any.whl.metadata (9.5 kB) Collecting jsonschema-specifications>=2023.03.6 (from jsonschema>=2.6->nbformat->nbsphinx->-r docs/requirements.txt (line 9)) Downloading jsonschema_specifications-2023.12.1-py3-none-any.whl.metadata (3.0 kB) Collecting referencing>=0.28.4 (from jsonschema>=2.6->nbformat->nbsphinx->-r docs/requirements.txt (line 9)) Downloading referencing-0.33.0-py3-none-any.whl.metadata (2.7 kB) Collecting rpds-py>=0.7.1 (from jsonschema>=2.6->nbformat->nbsphinx->-r docs/requirements.txt (line 9)) Downloading rpds_py-0.17.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.1 kB) Collecting ptyprocess>=0.5 (from pexpect>4.3->ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB) Collecting wcwidth (from prompt-toolkit<3.1.0,>=3.0.41->ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading wcwidth-0.2.13-py2.py3-none-any.whl.metadata (14 kB) Collecting executing>=1.2.0 (from stack-data->ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading executing-2.0.1-py2.py3-none-any.whl.metadata (9.0 kB) Collecting asttokens>=2.1.0 (from stack-data->ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading asttokens-2.4.1-py2.py3-none-any.whl.metadata (5.2 kB) Collecting pure-eval (from stack-data->ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading pure_eval-0.2.2-py3-none-any.whl (11 kB) Downloading pypandoc-1.12-py3-none-any.whl (20 kB) Downloading sphinx_autodoc_typehints-2.0.0-py3-none-any.whl (19 kB) Downloading pydata_sphinx_theme-0.15.2-py3-none-any.whl (4.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 152.5 MB/s eta 0:00:00 Downloading sphinx_design-0.5.0-py3-none-any.whl (2.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 233.9 MB/s eta 0:00:00 Downloading readthedocs_sphinx_search-0.3.2-py3-none-any.whl (21 kB) Downloading ipykernel-6.29.2-py3-none-any.whl (116 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 116.1/116.1 kB 207.7 MB/s eta 0:00:00 Downloading nbsphinx-0.9.3-py3-none-any.whl (31 kB) Downloading optuna-3.5.0-py3-none-any.whl (413 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 413.4/413.4 kB 255.7 MB/s eta 0:00:00 Downloading alembic-1.13.1-py3-none-any.whl (233 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 233.4/233.4 kB 251.0 MB/s eta 0:00:00 Downloading comm-0.2.1-py3-none-any.whl (7.2 kB) Downloading debugpy-1.8.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 202.1 MB/s eta 0:00:00 Downloading ipython-8.18.1-py3-none-any.whl (808 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 808.2/808.2 kB 242.8 MB/s eta 0:00:00 Downloading jupyter_client-8.6.0-py3-none-any.whl (105 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 105.9/105.9 kB 235.1 MB/s eta 0:00:00 Downloading jupyter_core-5.7.1-py3-none-any.whl (28 kB) Downloading nbconvert-7.16.0-py3-none-any.whl (257 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 257.2/257.2 kB 252.5 MB/s eta 0:00:00 Downloading nbformat-5.9.2-py3-none-any.whl (77 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.6/77.6 kB 218.6 MB/s eta 0:00:00 Downloading pyzmq-25.1.2-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 252.2 MB/s eta 0:00:00 Downloading SQLAlchemy-2.0.25-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 230.4 MB/s eta 0:00:00 Downloading tornado-6.4-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (435 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 435.4/435.4 kB 254.3 MB/s eta 0:00:00 Downloading traitlets-5.14.1-py3-none-any.whl (85 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 85.4/85.4 kB 229.3 MB/s eta 0:00:00 Downloading typing_extensions-4.9.0-py3-none-any.whl (32 kB) Downloading beautifulsoup4-4.12.3-py3-none-any.whl (147 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 147.9/147.9 kB 227.0 MB/s eta 0:00:00 Downloading colorlog-6.8.2-py3-none-any.whl (11 kB) Downloading nest_asyncio-1.6.0-py3-none-any.whl (5.2 kB) Downloading numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 18.2/18.2 MB 213.7 MB/s eta 0:00:00 Downloading plumbum-1.8.2-py3-none-any.whl (127 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 127.0/127.0 kB 210.2 MB/s eta 0:00:00 Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (288 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 288.2/288.2 kB 252.6 MB/s eta 0:00:00 Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (738 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 738.9/738.9 kB 257.5 MB/s eta 0:00:00 Downloading tqdm-4.66.1-py3-none-any.whl (78 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.3/78.3 kB 225.2 MB/s eta 0:00:00 Downloading bleach-6.1.0-py3-none-any.whl (162 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 162.8/162.8 kB 244.8 MB/s eta 0:00:00 Downloading greenlet-3.0.3-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (614 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 614.3/614.3 kB 261.0 MB/s eta 0:00:00 Downloading jedi-0.19.1-py2.py3-none-any.whl (1.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 264.8 MB/s eta 0:00:00 Downloading jsonschema-4.21.1-py3-none-any.whl (85 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 85.5/85.5 kB 226.2 MB/s eta 0:00:00 Downloading mistune-3.0.2-py3-none-any.whl (47 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.0/48.0 kB 202.9 MB/s eta 0:00:00 Downloading nbclient-0.9.0-py3-none-any.whl (24 kB) Downloading pandocfilters-1.5.1-py2.py3-none-any.whl (8.7 kB) Downloading pexpect-4.9.0-py2.py3-none-any.whl (63 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.8/63.8 kB 220.4 MB/s eta 0:00:00 Downloading platformdirs-4.2.0-py3-none-any.whl (17 kB) Downloading prompt_toolkit-3.0.43-py3-none-any.whl (386 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 386.1/386.1 kB 257.4 MB/s eta 0:00:00 Downloading soupsieve-2.5-py3-none-any.whl (36 kB) Downloading exceptiongroup-1.2.0-py3-none-any.whl (16 kB) Downloading fastjsonschema-2.19.1-py3-none-any.whl (23 kB) Downloading jupyterlab_pygments-0.3.0-py3-none-any.whl (15 kB) Downloading Mako-1.3.2-py3-none-any.whl (78 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.7/78.7 kB 225.3 MB/s eta 0:00:00 Downloading stack_data-0.6.3-py3-none-any.whl (24 kB) Downloading asttokens-2.4.1-py2.py3-none-any.whl (27 kB) Downloading attrs-23.2.0-py3-none-any.whl (60 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.8/60.8 kB 212.9 MB/s eta 0:00:00 Downloading executing-2.0.1-py2.py3-none-any.whl (24 kB) Downloading jsonschema_specifications-2023.12.1-py3-none-any.whl (18 kB) Downloading referencing-0.33.0-py3-none-any.whl (26 kB) Downloading rpds_py-0.17.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 253.2 MB/s eta 0:00:00 Downloading wcwidth-0.2.13-py2.py3-none-any.whl (34 kB) Building wheels for collected packages: pandoc Building wheel for pandoc (setup.py): started Building wheel for pandoc (setup.py): finished with status 'done' Created wheel for pandoc: filename=pandoc-2.3-py3-none-any.whl size=33262 sha256=acab47426d31be91561704b59b493c15db49662fcd146d287c6800fa3dab66b5 Stored in directory: /tmp/pip-ephem-wheel-cache-nf80dbb4/wheels/69/e6/a1/1daa96d919c9e09a71473649b717b8da286f3f8d7719d1cfc5 Successfully built pandoc Installing collected packages: webencodings, wcwidth, pure-eval, ptyprocess, ply, fastjsonschema, typing-extensions, traitlets, tqdm, tornado, tinycss2, soupsieve, six, rpds-py, readthedocs-sphinx-search, pyzmq, PyYAML, pypandoc, psutil, prompt-toolkit, plumbum, platformdirs, pexpect, parso, pandocfilters, numpy, nest-asyncio, mistune, Mako, jupyterlab-pygments, greenlet, executing, exceptiongroup, defusedxml, decorator, debugpy, colorlog, attrs, accessible-pygments, sqlalchemy, referencing, python-dateutil, plantweb, pandoc, matplotlib-inline, jupyter-core, jedi, comm, bleach, beautifulsoup4, asttokens, stack-data, sphinx-design, sphinx-autodoc-typehints, pydata-sphinx-theme, jupyter-client, jsonschema-specifications, alembic, optuna, jsonschema, ipython, nbformat, ipykernel, nbclient, nbconvert, nbsphinx Successfully installed Mako-1.3.2 PyYAML-6.0.1 accessible-pygments-0.0.4 alembic-1.13.1 asttokens-2.4.1 attrs-23.2.0 beautifulsoup4-4.12.3 bleach-6.1.0 colorlog-6.8.2 comm-0.2.1 debugpy-1.8.1 decorator-5.1.1 defusedxml-0.7.1 exceptiongroup-1.2.0 executing-2.0.1 fastjsonschema-2.19.1 greenlet-3.0.3 ipykernel-6.29.2 ipython-8.18.1 jedi-0.19.1 jsonschema-4.21.1 jsonschema-specifications-2023.12.1 jupyter-client-8.6.0 jupyter-core-5.7.1 jupyterlab-pygments-0.3.0 matplotlib-inline-0.1.6 mistune-3.0.2 nbclient-0.9.0 nbconvert-7.16.0 nbformat-5.9.2 nbsphinx-0.9.3 nest-asyncio-1.6.0 numpy-1.26.4 optuna-3.5.0 pandoc-2.3 pandocfilters-1.5.1 parso-0.8.3 pexpect-4.9.0 plantweb-1.2.1 platformdirs-4.2.0 plumbum-1.8.2 ply-3.11 prompt-toolkit-3.0.43 psutil-5.9.8 ptyprocess-0.7.0 pure-eval-0.2.2 pydata-sphinx-theme-0.15.2 pypandoc-1.12 python-dateutil-2.8.2 pyzmq-25.1.2 readthedocs-sphinx-search-0.3.2 referencing-0.33.0 rpds-py-0.17.1 six-1.16.0 soupsieve-2.5 sphinx-autodoc-typehints-2.0.0 sphinx-design-0.5.0 sqlalchemy-2.0.25 stack-data-0.6.3 tinycss2-1.2.1 tornado-6.4 tqdm-4.66.1 traitlets-5.14.1 typing-extensions-4.9.0 wcwidth-0.2.13 webencodings-0.5.1 [rtd-command-info] start-time: 2024-02-09T15:58:57.530588Z, end-time: 2024-02-09T15:59:29.627709Z, duration: 32, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir . Processing /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/latest Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Requirement already satisfied: numpy in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from fpsim==0.26.8) (1.26.4) Collecting numba (from fpsim==0.26.8) Downloading numba-0.59.0-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.7 kB) Collecting scipy (from fpsim==0.26.8) Downloading scipy-1.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.4/60.4 kB 5.9 MB/s eta 0:00:00 Collecting pandas>=1.3 (from fpsim==0.26.8) Downloading pandas-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB) Collecting sciris>=2.0.3 (from fpsim==0.26.8) Downloading sciris-3.1.3-py3-none-any.whl.metadata (3.6 kB) Collecting matplotlib>=3.5.0 (from fpsim==0.26.8) Downloading matplotlib-3.8.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB) Collecting seaborn>=0.9 (from fpsim==0.26.8) Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB) Requirement already satisfied: optuna in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from fpsim==0.26.8) (3.5.0) Collecting plotnine (from fpsim==0.26.8) Downloading plotnine-0.12.4-py3-none-any.whl.metadata (8.9 kB) Collecting pyarrow (from fpsim==0.26.8) Downloading pyarrow-15.0.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (3.0 kB) Requirement already satisfied: pyyaml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from fpsim==0.26.8) (6.0.1) Collecting contourpy>=1.0.1 (from matplotlib>=3.5.0->fpsim==0.26.8) Downloading contourpy-1.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB) Collecting cycler>=0.10 (from matplotlib>=3.5.0->fpsim==0.26.8) Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB) Collecting fonttools>=4.22.0 (from matplotlib>=3.5.0->fpsim==0.26.8) Downloading fonttools-4.48.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (158 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 158.9/158.9 kB 24.6 MB/s eta 0:00:00 Collecting kiwisolver>=1.3.1 (from matplotlib>=3.5.0->fpsim==0.26.8) Downloading kiwisolver-1.4.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (6.4 kB) Requirement already satisfied: packaging>=20.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from matplotlib>=3.5.0->fpsim==0.26.8) (23.2) Collecting pillow>=8 (from matplotlib>=3.5.0->fpsim==0.26.8) Downloading pillow-10.2.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (9.7 kB) Collecting pyparsing>=2.3.1 (from matplotlib>=3.5.0->fpsim==0.26.8) Downloading pyparsing-3.1.1-py3-none-any.whl.metadata (5.1 kB) Requirement already satisfied: python-dateutil>=2.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from matplotlib>=3.5.0->fpsim==0.26.8) (2.8.2) Collecting importlib-resources>=3.2.0 (from matplotlib>=3.5.0->fpsim==0.26.8) Downloading importlib_resources-6.1.1-py3-none-any.whl.metadata (4.1 kB) Collecting pytz>=2020.1 (from pandas>=1.3->fpsim==0.26.8) Downloading pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB) Collecting tzdata>=2022.7 (from pandas>=1.3->fpsim==0.26.8) Downloading tzdata-2023.4-py2.py3-none-any.whl.metadata (1.4 kB) Collecting openpyxl (from sciris>=2.0.3->fpsim==0.26.8) Downloading openpyxl-3.1.2-py2.py3-none-any.whl (249 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 250.0/250.0 kB 235.2 MB/s eta 0:00:00 Collecting xlsxwriter (from sciris>=2.0.3->fpsim==0.26.8) Downloading XlsxWriter-3.1.9-py3-none-any.whl.metadata (2.6 kB) Requirement already satisfied: psutil in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sciris>=2.0.3->fpsim==0.26.8) (5.9.8) Collecting dill (from sciris>=2.0.3->fpsim==0.26.8) Downloading dill-0.3.8-py3-none-any.whl.metadata (10 kB) Collecting zstandard (from sciris>=2.0.3->fpsim==0.26.8) Downloading zstandard-0.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.9 kB) Collecting multiprocess (from sciris>=2.0.3->fpsim==0.26.8) Downloading multiprocess-0.70.16-py39-none-any.whl.metadata (7.2 kB) Collecting jsonpickle (from sciris>=2.0.3->fpsim==0.26.8) Downloading jsonpickle-3.0.2-py3-none-any.whl.metadata (7.5 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sciris>=2.0.3->fpsim==0.26.8) (69.0.3) Collecting gitpython (from sciris>=2.0.3->fpsim==0.26.8) Downloading GitPython-3.1.41-py3-none-any.whl.metadata (14 kB) Collecting jellyfish (from sciris>=2.0.3->fpsim==0.26.8) Downloading jellyfish-1.0.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB) Requirement already satisfied: tqdm in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sciris>=2.0.3->fpsim==0.26.8) (4.66.1) Collecting memory-profiler (from sciris>=2.0.3->fpsim==0.26.8) Downloading memory_profiler-0.61.0-py3-none-any.whl (31 kB) Collecting line-profiler (from sciris>=2.0.3->fpsim==0.26.8) Downloading line_profiler-4.1.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (31 kB) Collecting llvmlite<0.43,>=0.42.0dev0 (from numba->fpsim==0.26.8) Downloading llvmlite-0.42.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.8 kB) Requirement already satisfied: alembic>=1.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from optuna->fpsim==0.26.8) (1.13.1) Requirement already satisfied: colorlog in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from optuna->fpsim==0.26.8) (6.8.2) Requirement already satisfied: sqlalchemy>=1.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from optuna->fpsim==0.26.8) (2.0.25) Collecting mizani<0.10.0,>0.9.0 (from plotnine->fpsim==0.26.8) Downloading mizani-0.9.3-py3-none-any.whl.metadata (4.6 kB) Collecting patsy>=0.5.1 (from plotnine->fpsim==0.26.8) Downloading patsy-0.5.6-py2.py3-none-any.whl.metadata (3.5 kB) Collecting statsmodels>=0.14.0 (from plotnine->fpsim==0.26.8) Downloading statsmodels-0.14.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.5 kB) Requirement already satisfied: Mako in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from alembic>=1.5.0->optuna->fpsim==0.26.8) (1.3.2) Requirement already satisfied: typing-extensions>=4 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from alembic>=1.5.0->optuna->fpsim==0.26.8) (4.9.0) Requirement already satisfied: zipp>=3.1.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from importlib-resources>=3.2.0->matplotlib>=3.5.0->fpsim==0.26.8) (3.17.0) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from patsy>=0.5.1->plotnine->fpsim==0.26.8) (1.16.0) Requirement already satisfied: greenlet!=0.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from sqlalchemy>=1.3.0->optuna->fpsim==0.26.8) (3.0.3) Collecting gitdb<5,>=4.0.1 (from gitpython->sciris>=2.0.3->fpsim==0.26.8) Downloading gitdb-4.0.11-py3-none-any.whl.metadata (1.2 kB) Collecting et-xmlfile (from openpyxl->sciris>=2.0.3->fpsim==0.26.8) Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB) Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->gitpython->sciris>=2.0.3->fpsim==0.26.8) Downloading smmap-5.0.1-py3-none-any.whl.metadata (4.3 kB) Requirement already satisfied: MarkupSafe>=0.9.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/latest/lib/python3.9/site-packages (from Mako->alembic>=1.5.0->optuna->fpsim==0.26.8) (2.1.5) Downloading matplotlib-3.8.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 204.1 MB/s eta 0:00:00 Downloading pandas-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.0/13.0 MB 197.2 MB/s eta 0:00:00 Downloading sciris-3.1.3-py3-none-any.whl (231 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 231.7/231.7 kB 250.8 MB/s eta 0:00:00 Downloading seaborn-0.13.2-py3-none-any.whl (294 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 294.9/294.9 kB 256.7 MB/s eta 0:00:00 Downloading numba-0.59.0-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.7/3.7 MB 234.1 MB/s eta 0:00:00 Downloading plotnine-0.12.4-py3-none-any.whl (1.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 275.2 MB/s eta 0:00:00 Downloading scipy-1.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (38.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.5/38.5 MB 196.2 MB/s eta 0:00:00 Downloading pyarrow-15.0.0-cp39-cp39-manylinux_2_28_x86_64.whl (38.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.3/38.3 MB 199.7 MB/s eta 0:00:00 Downloading contourpy-1.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (310 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 311.0/311.0 kB 208.2 MB/s eta 0:00:00 Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB) Downloading fonttools-4.48.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 211.1 MB/s eta 0:00:00 Downloading importlib_resources-6.1.1-py3-none-any.whl (33 kB) Downloading kiwisolver-1.4.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 264.6 MB/s eta 0:00:00 Downloading llvmlite-0.42.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (43.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.8/43.8 MB 218.2 MB/s eta 0:00:00 Downloading mizani-0.9.3-py3-none-any.whl (73 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 73.7/73.7 kB 222.1 MB/s eta 0:00:00 Downloading patsy-0.5.6-py2.py3-none-any.whl (233 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 233.9/233.9 kB 259.6 MB/s eta 0:00:00 Downloading pillow-10.2.0-cp39-cp39-manylinux_2_28_x86_64.whl (4.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 221.7 MB/s eta 0:00:00 Downloading pyparsing-3.1.1-py3-none-any.whl (103 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.1/103.1 kB 236.7 MB/s eta 0:00:00 Downloading pytz-2024.1-py2.py3-none-any.whl (505 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 505.5/505.5 kB 266.1 MB/s eta 0:00:00 Downloading statsmodels-0.14.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (10.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.8/10.8 MB 218.1 MB/s eta 0:00:00 Downloading tzdata-2023.4-py2.py3-none-any.whl (346 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 346.6/346.6 kB 265.4 MB/s eta 0:00:00 Downloading dill-0.3.8-py3-none-any.whl (116 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 116.3/116.3 kB 247.3 MB/s eta 0:00:00 Downloading GitPython-3.1.41-py3-none-any.whl (196 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 196.4/196.4 kB 252.8 MB/s eta 0:00:00 Downloading jellyfish-1.0.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 260.9 MB/s eta 0:00:00 Downloading jsonpickle-3.0.2-py3-none-any.whl (40 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.7/40.7 kB 173.9 MB/s eta 0:00:00 Downloading line_profiler-4.1.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (715 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 715.2/715.2 kB 264.3 MB/s eta 0:00:00 Downloading multiprocess-0.70.16-py39-none-any.whl (133 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.4/133.4 kB 243.7 MB/s eta 0:00:00 Downloading XlsxWriter-3.1.9-py3-none-any.whl (154 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 154.8/154.8 kB 228.7 MB/s eta 0:00:00 Downloading zstandard-0.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.4/5.4 MB 225.3 MB/s eta 0:00:00 Downloading gitdb-4.0.11-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.7/62.7 kB 203.6 MB/s eta 0:00:00 Downloading smmap-5.0.1-py3-none-any.whl (24 kB) Building wheels for collected packages: fpsim Building wheel for fpsim (setup.py): started Building wheel for fpsim (setup.py): finished with status 'done' Created wheel for fpsim: filename=fpsim-0.26.8-py3-none-any.whl size=525439 sha256=b17880e30fc1f9b8552e7db0fc21fb40c7cab693d2e9755cbe32cee1a2646812 Stored in directory: /tmp/pip-ephem-wheel-cache-zy4rzxa2/wheels/54/be/71/b6a93e28e1af4f52153fe34b99119b980ee057025c8abb6ee6 Successfully built fpsim Installing collected packages: pytz, zstandard, xlsxwriter, tzdata, smmap, scipy, pyparsing, pyarrow, pillow, patsy, memory-profiler, llvmlite, line-profiler, kiwisolver, jsonpickle, jellyfish, importlib-resources, fonttools, et-xmlfile, dill, cycler, contourpy, pandas, openpyxl, numba, multiprocess, matplotlib, gitdb, statsmodels, seaborn, mizani, gitpython, sciris, plotnine, fpsim Successfully installed contourpy-1.2.0 cycler-0.12.1 dill-0.3.8 et-xmlfile-1.1.0 fonttools-4.48.1 fpsim-0.26.8 gitdb-4.0.11 gitpython-3.1.41 importlib-resources-6.1.1 jellyfish-1.0.3 jsonpickle-3.0.2 kiwisolver-1.4.5 line-profiler-4.1.2 llvmlite-0.42.0 matplotlib-3.8.2 memory-profiler-0.61.0 mizani-0.9.3 multiprocess-0.70.16 numba-0.59.0 openpyxl-3.1.2 pandas-2.2.0 patsy-0.5.6 pillow-10.2.0 plotnine-0.12.4 pyarrow-15.0.0 pyparsing-3.1.1 pytz-2024.1 scipy-1.12.0 sciris-3.1.3 seaborn-0.13.2 smmap-5.0.1 statsmodels-0.14.1 tzdata-2023.4 xlsxwriter-3.1.9 zstandard-0.22.0 [rtd-command-info] start-time: 2024-02-09T15:59:30.253281Z, end-time: 2024-02-09T15:59:30.311379Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Configuration file for the Sphinx documentation builder. import os import sys import sciris as sc import fpsim as fp # Set environment os.environ['SPHINX_BUILD'] = 'True' # This is used so fp.options.set('jupyter') doesn't reset the Matplotlib renderer os.environ['FPSIM_WARNINGS'] = 'error' # Don't let warnings pass in the tutorials on_rtd = os.environ.get('READTHEDOCS') == 'True' # -- Project information ----------------------------------------------------- project = 'FPsim' copyright = f'2020 - {sc.now().year}, Bill & Melinda Gates Foundation. All rights reserved.\nThese docs were built for FPsim version {fp.__version__}\n' author = 'Institute for Disease Modeling' # The short X.Y version version = fp.__version__ # The full version, including alpha/beta/rc tags release = fp.__version__ # -- General configuration --------------------------------------------------- # Add any Sphinx extension module names here extensions = [ "sphinx.ext.autodoc", # Core Sphinx library for auto html doc generation from docstrings "sphinx.ext.autosummary", # Create neat summary tables for modules/classes/methods etc -- causes warnings with Napoleon however "sphinx.ext.intersphinx", "sphinx.ext.viewcode", # Add a link to the Python source code for classes, functions etc. "sphinx.ext.napoleon", "sphinx.ext.autosectionlabel", "sphinx_autodoc_typehints", # Automatically document param types (less noise in class signature) "sphinx_design", # Add e.g. grid layout 'sphinx_search.extension', # search across multiple docsets in domain "nbsphinx", ] # Use Google docstrings napoleon_google_docstring = True # Configure autosummary autosummary_generate = True # Turn on sphinx.ext.autosummary autosummary_ignore_module_all = False # Respect __all__ autodoc_member_order = 'bysource' # Keep original ordering add_module_names = False # NB, does not work autodoc_inherit_docstrings = False # Stops sublcasses from including docs from parent classes # Add any paths that contain templates here, relative to this directory. templates_path = ["_templates"] # Syntax highlighting style pygments_style = "sphinx" modindex_common_prefix = ["fpsim."] # List of patterns, relative to source directory, to exclude exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"] # Suppress certain warnings suppress_warnings = ['autosectionlabel.*'] # -- Options for HTML output ------------------------------------------------- html_theme = "pydata_sphinx_theme" html_theme_options = { "collapse_navigation": False, "navigation_depth": 3, "show_prev_next": True, "icon_links": [ {"name": "Web", "url": "https://fpsim.org", "icon": "fas fa-home"}, { "name": "GitHub", "url": "https://github.com/fpsim/fpsim", "icon": "fab fa-github-square", }, ], "navbar_end": ["theme-switcher", "navbar-icon-links"], "secondary_sidebar_items": ["navbar-side"], "header_links_before_dropdown": 5, } html_sidebars = { "**": ["sidebar-nav-bs", "page-toc"], } html_logo = "images/IDM_white.png" html_favicon = "images/favicon.ico" html_static_path = ['_static'] html_baseurl = "https://docs.idmod.org/projects/fpsim/en/latest" html_context = { 'rtd_url': 'https://docs.idmod.org/projects/fpsim/en/latest', "versions_dropdown": { "latest": "devel (latest)", "stable": "current (stable)", }, "default_mode": "light", } # Add any extra paths that contain custom files if not on_rtd: html_extra_path = ['robots.txt'] # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. html_last_updated_fmt = '%Y-%b-%d' html_show_sourcelink = True html_show_sphinx = False html_copy_source = False htmlhelp_basename = 'FPsim' # Add customizations def setup(app): app.add_css_file("theme_overrides.css") # Modify this to not rerun the Jupyter notebook cells -- usually set by build_docs nb_ex_default = ['auto', 'never'][0] nb_ex = os.getenv('NBSPHINX_EXECUTE') if not nb_ex: nb_ex = nb_ex_default print(f'\n\nBuilding Jupyter notebooks with build option: {nb_ex}\n\n') nbsphinx_execute = nb_ex # OpenSearch options html_use_opensearch = 'docs.idmod.org/projects/fpsim/en/latest' # -- RTD Sphinx search for searching across the entire domain, default child ------------- if os.environ.get('READTHEDOCS') == 'True': search_project_parent = "institute-for-disease-modeling-idm" search_project = os.environ["READTHEDOCS_PROJECT"] search_version = os.environ["READTHEDOCS_VERSION"] rtd_sphinx_search_default_filter = f"subprojects:{search_project}/{search_version}" rtd_sphinx_search_filters = { "Search this project": f"project:{search_project}/{search_version}", "Search all IDM docs": f"subprojects:{search_project_parent}/{search_version}", } ########################################################################### # 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') # Define this variable in case it's not defined by the user. # It defaults to `alabaster` which is the default from Sphinx. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme html_theme = globals().get('html_theme', 'alabaster') #Add project information to the template context. context = { '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/"), ("v0.24.0", "/en/v0.24.0/"), ("v0.23.0", "/en/v0.23.0/"), ("v0.22.1", "/en/v0.22.1/"), ("v0.22.0", "/en/v0.22.0/"), ("v0.19.2", "/en/v0.19.2/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-fpsim', 'name': u'fpsim', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': '', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'fpsim', 'proxied_api_host': '/_', 'github_repo': 'fpsim', 'github_version': 'main', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'main', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'main', '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': '99c5a086', } # 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/institute-for-disease-modeling-fpsim/builds/2006852/' 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'])