Read the Docs build information Build id: 3482505 Project: institute-for-disease-modeling-fpsim Version: 653 Commit: 6ed37165dadd6d3265375d72fe944689314a2e4b Date: 2025-10-29T17:03:58.784767Z State: finished Success: False [rtd-command-info] start-time: 2025-10-29T17:03:59.588230Z, end-time: 2025-10-29T17:04:00.142140Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/fpsim/fpsim.git . Cloning into '.'... [rtd-command-info] start-time: 2025-10-29T17:04:00.229498Z, end-time: 2025-10-29T17:04:01.996290Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/653/head:external-653 From https://github.com/fpsim/fpsim * [new ref] refs/pull/653/head -> external-653 * [new tag] v.1.latest -> v.1.latest * [new tag] v0.28.1 -> v0.28.1 * [new tag] v1.0.4 -> v1.0.4 * [new tag] v2.0.0 -> v2.0.0 [rtd-command-info] start-time: 2025-10-29T17:04:02.679423Z, end-time: 2025-10-29T17:04:02.748648Z, duration: 0, exit-code: 0 git checkout --force 6ed37165dadd6d3265375d72fe944689314a2e4b Note: switching to '6ed37165dadd6d3265375d72fe944689314a2e4b'. 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 6ed3716 Update defaults.py [rtd-command-info] start-time: 2025-10-29T17:04:02.856883Z, end-time: 2025-10-29T17:04:02.894559Z, 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-22.04 tools: python: "3.11" # 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: 2025-10-29T17:04:06.981930Z, end-time: 2025-10-29T17:04:07.040072Z, duration: 0, exit-code: 0 asdf global python 3.11.12 [rtd-command-info] start-time: 2025-10-29T17:04:07.362165Z, end-time: 2025-10-29T17:04:08.080639Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.11.12.final.0-64 in 478ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653, 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: 2025-10-29T17:04:08.183015Z, end-time: 2025-10-29T17:04:14.375312Z, duration: 6, 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/653/lib/python3.11/site-packages (23.1) Collecting pip Downloading pip-25.3-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 23.4 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (67.6.1) Collecting setuptools Downloading setuptools-80.9.0-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 209.0 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-25.3 setuptools-80.9.0 [rtd-command-info] start-time: 2025-10-29T17:04:14.529159Z, end-time: 2025-10-29T17:04:18.776651Z, duration: 4, exit-code: 0 python -m pip install --upgrade --no-cache-dir sphinx Collecting sphinx Downloading sphinx-8.2.3-py3-none-any.whl.metadata (7.0 kB) Collecting sphinxcontrib-applehelp>=1.0.7 (from sphinx) Downloading sphinxcontrib_applehelp-2.0.0-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-devhelp>=1.0.6 (from sphinx) Downloading sphinxcontrib_devhelp-2.0.0-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-htmlhelp>=2.0.6 (from sphinx) Downloading sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-jsmath>=1.0.1 (from sphinx) Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl.metadata (1.4 kB) Collecting sphinxcontrib-qthelp>=1.0.6 (from sphinx) Downloading sphinxcontrib_qthelp-2.0.0-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-serializinghtml>=1.1.9 (from sphinx) Downloading sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl.metadata (2.4 kB) Collecting Jinja2>=3.1 (from sphinx) Downloading jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB) Collecting Pygments>=2.17 (from sphinx) Downloading pygments-2.19.2-py3-none-any.whl.metadata (2.5 kB) Collecting docutils<0.22,>=0.20 (from sphinx) Downloading docutils-0.21.2-py3-none-any.whl.metadata (2.8 kB) Collecting snowballstemmer>=2.2 (from sphinx) Downloading snowballstemmer-3.0.1-py3-none-any.whl.metadata (7.9 kB) Collecting babel>=2.13 (from sphinx) Downloading babel-2.17.0-py3-none-any.whl.metadata (2.0 kB) Collecting alabaster>=0.7.14 (from sphinx) Downloading alabaster-1.0.0-py3-none-any.whl.metadata (2.8 kB) Collecting imagesize>=1.3 (from sphinx) Downloading imagesize-1.4.1-py2.py3-none-any.whl.metadata (1.5 kB) Collecting requests>=2.30.0 (from sphinx) Downloading requests-2.32.5-py3-none-any.whl.metadata (4.9 kB) Collecting roman-numerals-py>=1.0.0 (from sphinx) Downloading roman_numerals_py-3.1.0-py3-none-any.whl.metadata (3.6 kB) Collecting packaging>=23.0 (from sphinx) Downloading packaging-25.0-py3-none-any.whl.metadata (3.3 kB) Collecting MarkupSafe>=2.0 (from Jinja2>=3.1->sphinx) Downloading markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.7 kB) Collecting charset_normalizer<4,>=2 (from requests>=2.30.0->sphinx) Downloading charset_normalizer-3.4.4-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (37 kB) Collecting idna<4,>=2.5 (from requests>=2.30.0->sphinx) Downloading idna-3.11-py3-none-any.whl.metadata (8.4 kB) Collecting urllib3<3,>=1.21.1 (from requests>=2.30.0->sphinx) Downloading urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB) Collecting certifi>=2017.4.17 (from requests>=2.30.0->sphinx) Downloading certifi-2025.10.5-py3-none-any.whl.metadata (2.5 kB) Downloading sphinx-8.2.3-py3-none-any.whl (3.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.6/3.6 MB 154.6 MB/s 0:00:00 Downloading docutils-0.21.2-py3-none-any.whl (587 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 587.4/587.4 kB 670.0 MB/s 0:00:00 Downloading alabaster-1.0.0-py3-none-any.whl (13 kB) Downloading babel-2.17.0-py3-none-any.whl (10.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.2/10.2 MB 404.5 MB/s 0:00:00 Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Downloading jinja2-3.1.6-py3-none-any.whl (134 kB) Downloading markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB) Downloading packaging-25.0-py3-none-any.whl (66 kB) Downloading pygments-2.19.2-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 690.5 MB/s 0:00:00 Downloading requests-2.32.5-py3-none-any.whl (64 kB) Downloading charset_normalizer-3.4.4-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (151 kB) Downloading idna-3.11-py3-none-any.whl (71 kB) Downloading urllib3-2.5.0-py3-none-any.whl (129 kB) Downloading certifi-2025.10.5-py3-none-any.whl (163 kB) Downloading roman_numerals_py-3.1.0-py3-none-any.whl (7.7 kB) Downloading snowballstemmer-3.0.1-py3-none-any.whl (103 kB) Downloading sphinxcontrib_applehelp-2.0.0-py3-none-any.whl (119 kB) Downloading sphinxcontrib_devhelp-2.0.0-py3-none-any.whl (82 kB) Downloading sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl (98 kB) Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Downloading sphinxcontrib_qthelp-2.0.0-py3-none-any.whl (88 kB) Downloading sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl (92 kB) Installing collected packages: urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, roman-numerals-py, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset_normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx Successfully installed Jinja2-3.1.6 MarkupSafe-3.0.3 Pygments-2.19.2 alabaster-1.0.0 babel-2.17.0 certifi-2025.10.5 charset_normalizer-3.4.4 docutils-0.21.2 idna-3.11 imagesize-1.4.1 packaging-25.0 requests-2.32.5 roman-numerals-py-3.1.0 snowballstemmer-3.0.1 sphinx-8.2.3 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.5.0 [rtd-command-info] start-time: 2025-10-29T17:04:18.874653Z, end-time: 2025-10-29T17:04:33.023068Z, duration: 14, 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-2.4.tar.gz (34 kB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting pypandoc (from -r docs/requirements.txt (line 2)) Downloading pypandoc-1.15-py3-none-any.whl.metadata (16 kB) Collecting sphinx<=8.1 (from -r docs/requirements.txt (line 3)) Downloading sphinx-8.1.0-py3-none-any.whl.metadata (6.4 kB) Collecting sphinx-autodoc-typehints (from -r docs/requirements.txt (line 4)) Downloading sphinx_autodoc_typehints-3.5.2-py3-none-any.whl.metadata (8.7 kB) Collecting pydata-sphinx-theme (from -r docs/requirements.txt (line 5)) Downloading pydata_sphinx_theme-0.16.1-py3-none-any.whl.metadata (7.5 kB) Collecting sphinx-design (from -r docs/requirements.txt (line 6)) Downloading sphinx_design-0.6.1-py3-none-any.whl.metadata (5.5 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-7.1.0-py3-none-any.whl.metadata (4.5 kB) Collecting nbconvert==7.13.0 (from -r docs/requirements.txt (line 9)) Downloading nbconvert-7.13.0-py3-none-any.whl.metadata (7.7 kB) Collecting nbsphinx (from -r docs/requirements.txt (line 10)) Downloading nbsphinx-0.9.7-py3-none-any.whl.metadata (2.3 kB) Collecting plantweb (from -r docs/requirements.txt (line 11)) Downloading plantweb-1.3.0-py3-none-any.whl.metadata (4.1 kB) Collecting optuna (from -r docs/requirements.txt (line 14)) Downloading optuna-4.5.0-py3-none-any.whl.metadata (17 kB) Collecting beautifulsoup4 (from nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading beautifulsoup4-4.14.2-py3-none-any.whl.metadata (3.8 kB) Collecting bleach!=5.0.0 (from nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading bleach-6.3.0-py3-none-any.whl.metadata (31 kB) Collecting defusedxml (from nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading defusedxml-0.7.1-py2.py3-none-any.whl.metadata (32 kB) Requirement already satisfied: jinja2>=3.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from nbconvert==7.13.0->-r docs/requirements.txt (line 9)) (3.1.6) Collecting jupyter-core>=4.7 (from nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading jupyter_core-5.9.1-py3-none-any.whl.metadata (1.5 kB) Collecting jupyterlab-pygments (from nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading jupyterlab_pygments-0.3.0-py3-none-any.whl.metadata (4.4 kB) Requirement already satisfied: markupsafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from nbconvert==7.13.0->-r docs/requirements.txt (line 9)) (3.0.3) Collecting mistune<4,>=2.0.3 (from nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading mistune-3.1.4-py3-none-any.whl.metadata (1.8 kB) Collecting nbclient>=0.5.0 (from nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading nbclient-0.10.2-py3-none-any.whl.metadata (8.3 kB) Collecting nbformat>=5.7 (from nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading nbformat-5.10.4-py3-none-any.whl.metadata (3.6 kB) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from nbconvert==7.13.0->-r docs/requirements.txt (line 9)) (25.0) Collecting pandocfilters>=1.4.1 (from nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading pandocfilters-1.5.1-py2.py3-none-any.whl.metadata (9.0 kB) Requirement already satisfied: pygments>=2.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from nbconvert==7.13.0->-r docs/requirements.txt (line 9)) (2.19.2) Collecting tinycss2 (from nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading tinycss2-1.4.0-py3-none-any.whl.metadata (3.0 kB) Collecting traitlets>=5.1 (from nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading traitlets-5.14.3-py3-none-any.whl.metadata (10 kB) Requirement already satisfied: sphinxcontrib-applehelp>=1.0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from sphinx<=8.1->-r docs/requirements.txt (line 3)) (2.0.0) Requirement already satisfied: sphinxcontrib-devhelp>=1.0.6 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from sphinx<=8.1->-r docs/requirements.txt (line 3)) (2.0.0) Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.6 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from sphinx<=8.1->-r docs/requirements.txt (line 3)) (2.1.0) Requirement already satisfied: sphinxcontrib-jsmath>=1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from sphinx<=8.1->-r docs/requirements.txt (line 3)) (1.0.1) Requirement already satisfied: sphinxcontrib-qthelp>=1.0.6 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from sphinx<=8.1->-r docs/requirements.txt (line 3)) (2.0.0) Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.9 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from sphinx<=8.1->-r docs/requirements.txt (line 3)) (2.0.0) Requirement already satisfied: docutils<0.22,>=0.20 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from sphinx<=8.1->-r docs/requirements.txt (line 3)) (0.21.2) Requirement already satisfied: snowballstemmer>=2.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from sphinx<=8.1->-r docs/requirements.txt (line 3)) (3.0.1) Requirement already satisfied: babel>=2.13 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from sphinx<=8.1->-r docs/requirements.txt (line 3)) (2.17.0) Requirement already satisfied: alabaster>=0.7.14 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from sphinx<=8.1->-r docs/requirements.txt (line 3)) (1.0.0) Requirement already satisfied: imagesize>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from sphinx<=8.1->-r docs/requirements.txt (line 3)) (1.4.1) Requirement already satisfied: requests>=2.30.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from sphinx<=8.1->-r docs/requirements.txt (line 3)) (2.32.5) Collecting plumbum (from pandoc->-r docs/requirements.txt (line 1)) Downloading plumbum-1.9.0-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.metadata (844 bytes) INFO: pip is looking at multiple versions of sphinx-autodoc-typehints to determine which version is compatible with other requirements. This could take a while. Collecting sphinx-autodoc-typehints (from -r docs/requirements.txt (line 4)) Downloading sphinx_autodoc_typehints-3.5.1-py3-none-any.whl.metadata (8.7 kB) Downloading sphinx_autodoc_typehints-3.5.0-py3-none-any.whl.metadata (8.6 kB) Downloading sphinx_autodoc_typehints-3.4.0-py3-none-any.whl.metadata (8.6 kB) Downloading sphinx_autodoc_typehints-3.3.0-py3-none-any.whl.metadata (8.4 kB) Downloading sphinx_autodoc_typehints-3.2.0-py3-none-any.whl.metadata (8.0 kB) Downloading sphinx_autodoc_typehints-3.1.0-py3-none-any.whl.metadata (7.9 kB) Downloading sphinx_autodoc_typehints-3.0.1-py3-none-any.whl.metadata (7.9 kB) INFO: pip is still looking at multiple versions of sphinx-autodoc-typehints to determine which version is compatible with other requirements. This could take a while. Downloading sphinx_autodoc_typehints-3.0.0-py3-none-any.whl.metadata (7.9 kB) Downloading sphinx_autodoc_typehints-2.5.0-py3-none-any.whl.metadata (8.0 kB) Collecting accessible-pygments (from pydata-sphinx-theme->-r docs/requirements.txt (line 5)) Downloading accessible_pygments-0.0.5-py3-none-any.whl.metadata (10 kB) Collecting typing-extensions (from pydata-sphinx-theme->-r docs/requirements.txt (line 5)) Downloading typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB) Collecting comm>=0.1.1 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading comm-0.2.3-py3-none-any.whl.metadata (3.7 kB) Collecting debugpy>=1.6.5 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading debugpy-1.8.17-cp311-cp311-manylinux_2_34_x86_64.whl.metadata (1.4 kB) Collecting ipython>=7.23.1 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading ipython-9.6.0-py3-none-any.whl.metadata (4.4 kB) Collecting jupyter-client>=8.0.0 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading jupyter_client-8.6.3-py3-none-any.whl.metadata (8.3 kB) Collecting matplotlib-inline>=0.1 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading matplotlib_inline-0.2.1-py3-none-any.whl.metadata (2.3 kB) Collecting nest-asyncio>=1.4 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading nest_asyncio-1.6.0-py3-none-any.whl.metadata (2.8 kB) Collecting psutil>=5.7 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading psutil-7.1.2-cp36-abi3-manylinux2010_x86_64.manylinux_2_12_x86_64.manylinux_2_28_x86_64.whl.metadata (23 kB) Collecting pyzmq>=25 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading pyzmq-27.1.0-cp311-cp311-manylinux_2_26_x86_64.manylinux_2_28_x86_64.whl.metadata (6.0 kB) Collecting tornado>=6.2 (from ipykernel->-r docs/requirements.txt (line 8)) Downloading tornado-6.5.2-cp39-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.8 kB) Collecting six (from plantweb->-r docs/requirements.txt (line 11)) Downloading six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB) Collecting alembic>=1.5.0 (from optuna->-r docs/requirements.txt (line 14)) Downloading alembic-1.17.1-py3-none-any.whl.metadata (7.2 kB) Collecting colorlog (from optuna->-r docs/requirements.txt (line 14)) Downloading colorlog-6.10.1-py3-none-any.whl.metadata (11 kB) Collecting numpy (from optuna->-r docs/requirements.txt (line 14)) Downloading numpy-2.3.4-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB) Collecting sqlalchemy>=1.4.2 (from optuna->-r docs/requirements.txt (line 14)) Downloading sqlalchemy-2.0.44-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.5 kB) Collecting tqdm (from optuna->-r docs/requirements.txt (line 14)) Downloading tqdm-4.67.1-py3-none-any.whl.metadata (57 kB) Collecting PyYAML (from optuna->-r docs/requirements.txt (line 14)) Downloading pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB) Collecting Mako (from alembic>=1.5.0->optuna->-r docs/requirements.txt (line 14)) Downloading mako-1.3.10-py3-none-any.whl.metadata (2.9 kB) Collecting webencodings (from bleach!=5.0.0->nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading webencodings-0.5.1-py2.py3-none-any.whl.metadata (2.1 kB) Collecting decorator (from ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading decorator-5.2.1-py3-none-any.whl.metadata (3.9 kB) Collecting ipython-pygments-lexers (from ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading ipython_pygments_lexers-1.1.1-py3-none-any.whl.metadata (1.1 kB) Collecting jedi>=0.16 (from ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading jedi-0.19.2-py2.py3-none-any.whl.metadata (22 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) Collecting prompt_toolkit<3.1.0,>=3.0.41 (from ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading prompt_toolkit-3.0.52-py3-none-any.whl.metadata (6.4 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 wcwidth (from prompt_toolkit<3.1.0,>=3.0.41->ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading wcwidth-0.2.14-py2.py3-none-any.whl.metadata (15 kB) Collecting parso<0.9.0,>=0.8.4 (from jedi>=0.16->ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading parso-0.8.5-py2.py3-none-any.whl.metadata (8.3 kB) Collecting python-dateutil>=2.8.2 (from jupyter-client>=8.0.0->ipykernel->-r docs/requirements.txt (line 8)) Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) Collecting platformdirs>=2.5 (from jupyter-core>=4.7->nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading platformdirs-4.5.0-py3-none-any.whl.metadata (12 kB) Collecting fastjsonschema>=2.15 (from nbformat>=5.7->nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading fastjsonschema-2.21.2-py3-none-any.whl.metadata (2.3 kB) Collecting jsonschema>=2.6 (from nbformat>=5.7->nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading jsonschema-4.25.1-py3-none-any.whl.metadata (7.6 kB) Collecting attrs>=22.2.0 (from jsonschema>=2.6->nbformat>=5.7->nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading attrs-25.4.0-py3-none-any.whl.metadata (10 kB) Collecting jsonschema-specifications>=2023.03.6 (from jsonschema>=2.6->nbformat>=5.7->nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading jsonschema_specifications-2025.9.1-py3-none-any.whl.metadata (2.9 kB) Collecting referencing>=0.28.4 (from jsonschema>=2.6->nbformat>=5.7->nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading referencing-0.37.0-py3-none-any.whl.metadata (2.8 kB) Collecting rpds-py>=0.7.1 (from jsonschema>=2.6->nbformat>=5.7->nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading rpds_py-0.28.0-cp311-cp311-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.metadata (1.3 kB) Requirement already satisfied: charset_normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from requests>=2.30.0->sphinx<=8.1->-r docs/requirements.txt (line 3)) (3.4.4) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from requests>=2.30.0->sphinx<=8.1->-r docs/requirements.txt (line 3)) (3.11) Requirement already satisfied: urllib3<3,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from requests>=2.30.0->sphinx<=8.1->-r docs/requirements.txt (line 3)) (2.5.0) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from requests>=2.30.0->sphinx<=8.1->-r docs/requirements.txt (line 3)) (2025.10.5) Collecting greenlet>=1 (from sqlalchemy>=1.4.2->optuna->-r docs/requirements.txt (line 14)) Downloading greenlet-3.2.4-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (4.1 kB) Collecting soupsieve>1.2 (from beautifulsoup4->nbconvert==7.13.0->-r docs/requirements.txt (line 9)) Downloading soupsieve-2.8-py3-none-any.whl.metadata (4.6 kB) Collecting executing>=1.2.0 (from stack_data->ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading executing-2.2.1-py2.py3-none-any.whl.metadata (8.9 kB) Collecting asttokens>=2.1.0 (from stack_data->ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading asttokens-3.0.0-py3-none-any.whl.metadata (4.7 kB) Collecting pure-eval (from stack_data->ipython>=7.23.1->ipykernel->-r docs/requirements.txt (line 8)) Downloading pure_eval-0.2.3-py3-none-any.whl.metadata (6.3 kB) Downloading nbconvert-7.13.0-py3-none-any.whl (256 kB) Downloading sphinx-8.1.0-py3-none-any.whl (3.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.5/3.5 MB 17.2 MB/s 0:00:00 Downloading mistune-3.1.4-py3-none-any.whl (53 kB) Downloading pypandoc-1.15-py3-none-any.whl (21 kB) Downloading sphinx_autodoc_typehints-2.5.0-py3-none-any.whl (20 kB) Downloading pydata_sphinx_theme-0.16.1-py3-none-any.whl (6.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.7/6.7 MB 43.8 MB/s 0:00:00 Downloading sphinx_design-0.6.1-py3-none-any.whl (2.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 68.8 MB/s 0:00:00 Downloading readthedocs_sphinx_search-0.3.2-py3-none-any.whl (21 kB) Downloading ipykernel-7.1.0-py3-none-any.whl (117 kB) Downloading nbsphinx-0.9.7-py3-none-any.whl (31 kB) Downloading plantweb-1.3.0-py3-none-any.whl (20 kB) Downloading optuna-4.5.0-py3-none-any.whl (400 kB) Downloading alembic-1.17.1-py3-none-any.whl (247 kB) Downloading bleach-6.3.0-py3-none-any.whl (164 kB) Downloading comm-0.2.3-py3-none-any.whl (7.3 kB) Downloading debugpy-1.8.17-cp311-cp311-manylinux_2_34_x86_64.whl (3.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 83.7 MB/s 0:00:00 Downloading ipython-9.6.0-py3-none-any.whl (616 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 616.2/616.2 kB 130.2 MB/s 0:00:00 Downloading prompt_toolkit-3.0.52-py3-none-any.whl (391 kB) Downloading jedi-0.19.2-py2.py3-none-any.whl (1.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 102.4 MB/s 0:00:00 Downloading parso-0.8.5-py2.py3-none-any.whl (106 kB) Downloading jupyter_client-8.6.3-py3-none-any.whl (106 kB) Downloading jupyter_core-5.9.1-py3-none-any.whl (29 kB) Downloading matplotlib_inline-0.2.1-py3-none-any.whl (9.5 kB) Downloading nbclient-0.10.2-py3-none-any.whl (25 kB) Downloading nbformat-5.10.4-py3-none-any.whl (78 kB) Downloading fastjsonschema-2.21.2-py3-none-any.whl (24 kB) Downloading jsonschema-4.25.1-py3-none-any.whl (90 kB) Downloading attrs-25.4.0-py3-none-any.whl (67 kB) Downloading jsonschema_specifications-2025.9.1-py3-none-any.whl (18 kB) Downloading nest_asyncio-1.6.0-py3-none-any.whl (5.2 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) Downloading platformdirs-4.5.0-py3-none-any.whl (18 kB) Downloading psutil-7.1.2-cp36-abi3-manylinux2010_x86_64.manylinux_2_12_x86_64.manylinux_2_28_x86_64.whl (258 kB) Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB) Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) Downloading pyzmq-27.1.0-cp311-cp311-manylinux_2_26_x86_64.manylinux_2_28_x86_64.whl (857 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 857.0/857.0 kB 133.3 MB/s 0:00:00 Downloading referencing-0.37.0-py3-none-any.whl (26 kB) Downloading rpds_py-0.28.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (382 kB) Downloading six-1.17.0-py2.py3-none-any.whl (11 kB) Downloading sqlalchemy-2.0.44-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 112.5 MB/s 0:00:00 Downloading greenlet-3.2.4-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (587 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 587.7/587.7 kB 166.2 MB/s 0:00:00 Downloading tornado-6.5.2-cp39-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (443 kB) Downloading traitlets-5.14.3-py3-none-any.whl (85 kB) Downloading typing_extensions-4.15.0-py3-none-any.whl (44 kB) Downloading accessible_pygments-0.0.5-py3-none-any.whl (1.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 124.8 MB/s 0:00:00 Downloading beautifulsoup4-4.14.2-py3-none-any.whl (106 kB) Downloading soupsieve-2.8-py3-none-any.whl (36 kB) Downloading colorlog-6.10.1-py3-none-any.whl (11 kB) Downloading decorator-5.2.1-py3-none-any.whl (9.2 kB) Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) Downloading ipython_pygments_lexers-1.1.1-py3-none-any.whl (8.1 kB) Downloading jupyterlab_pygments-0.3.0-py3-none-any.whl (15 kB) Downloading mako-1.3.10-py3-none-any.whl (78 kB) Downloading numpy-2.3.4-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.9/16.9 MB 173.6 MB/s 0:00:00 Downloading plumbum-1.9.0-py3-none-any.whl (127 kB) Downloading ply-3.11-py2.py3-none-any.whl (49 kB) Downloading pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 806.6/806.6 kB 470.1 MB/s 0:00:00 Downloading stack_data-0.6.3-py3-none-any.whl (24 kB) Downloading asttokens-3.0.0-py3-none-any.whl (26 kB) Downloading executing-2.2.1-py2.py3-none-any.whl (28 kB) Downloading pure_eval-0.2.3-py3-none-any.whl (11 kB) Downloading tinycss2-1.4.0-py3-none-any.whl (26 kB) Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Downloading tqdm-4.67.1-py3-none-any.whl (78 kB) Downloading wcwidth-0.2.14-py2.py3-none-any.whl (37 kB) Building wheels for collected packages: pandoc Building wheel for pandoc (pyproject.toml): started Building wheel for pandoc (pyproject.toml): finished with status 'done' Created wheel for pandoc: filename=pandoc-2.4-py3-none-any.whl size=34871 sha256=9ef1545c10ccc1f9b4be2bdfad9f3e97387909f38cbe0d08bee75f4209bfd938 Stored in directory: /tmp/pip-ephem-wheel-cache-cd02b2td/wheels/4f/d7/32/c6c9b7b05e852e920fd72174487be3a0f18e633a7adcc303be Successfully built pandoc Installing collected packages: webencodings, pure-eval, ptyprocess, ply, fastjsonschema, wcwidth, typing-extensions, traitlets, tqdm, tornado, tinycss2, soupsieve, six, rpds-py, readthedocs-sphinx-search, pyzmq, PyYAML, pypandoc, psutil, plumbum, platformdirs, pexpect, parso, pandocfilters, numpy, nest-asyncio, mistune, Mako, jupyterlab-pygments, ipython-pygments-lexers, greenlet, executing, defusedxml, decorator, debugpy, comm, colorlog, bleach, attrs, asttokens, accessible-pygments, stack_data, sqlalchemy, sphinx, referencing, python-dateutil, prompt_toolkit, plantweb, pandoc, matplotlib-inline, jupyter-core, jedi, beautifulsoup4, sphinx-design, sphinx-autodoc-typehints, pydata-sphinx-theme, jupyter-client, jsonschema-specifications, ipython, alembic, optuna, jsonschema, ipykernel, nbformat, nbclient, nbconvert, nbsphinx Attempting uninstall: sphinx Found existing installation: Sphinx 8.2.3 Uninstalling Sphinx-8.2.3: Successfully uninstalled Sphinx-8.2.3 Successfully installed Mako-1.3.10 PyYAML-6.0.3 accessible-pygments-0.0.5 alembic-1.17.1 asttokens-3.0.0 attrs-25.4.0 beautifulsoup4-4.14.2 bleach-6.3.0 colorlog-6.10.1 comm-0.2.3 debugpy-1.8.17 decorator-5.2.1 defusedxml-0.7.1 executing-2.2.1 fastjsonschema-2.21.2 greenlet-3.2.4 ipykernel-7.1.0 ipython-9.6.0 ipython-pygments-lexers-1.1.1 jedi-0.19.2 jsonschema-4.25.1 jsonschema-specifications-2025.9.1 jupyter-client-8.6.3 jupyter-core-5.9.1 jupyterlab-pygments-0.3.0 matplotlib-inline-0.2.1 mistune-3.1.4 nbclient-0.10.2 nbconvert-7.13.0 nbformat-5.10.4 nbsphinx-0.9.7 nest-asyncio-1.6.0 numpy-2.3.4 optuna-4.5.0 pandoc-2.4 pandocfilters-1.5.1 parso-0.8.5 pexpect-4.9.0 plantweb-1.3.0 platformdirs-4.5.0 plumbum-1.9.0 ply-3.11 prompt_toolkit-3.0.52 psutil-7.1.2 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.16.1 pypandoc-1.15 python-dateutil-2.9.0.post0 pyzmq-27.1.0 readthedocs-sphinx-search-0.3.2 referencing-0.37.0 rpds-py-0.28.0 six-1.17.0 soupsieve-2.8 sphinx-8.1.0 sphinx-autodoc-typehints-2.5.0 sphinx-design-0.6.1 sqlalchemy-2.0.44 stack_data-0.6.3 tinycss2-1.4.0 tornado-6.5.2 tqdm-4.67.1 traitlets-5.14.3 typing-extensions-4.15.0 wcwidth-0.2.14 webencodings-0.5.1 [rtd-command-info] start-time: 2025-10-29T17:04:33.123508Z, end-time: 2025-10-29T17:04:57.630980Z, duration: 24, 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/653 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Requirement already satisfied: numpy in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from fpsim==3.3.1) (2.3.4) Collecting numba (from fpsim==3.3.1) Downloading numba-0.62.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.8 kB) Collecting scipy (from fpsim==3.3.1) Downloading scipy-1.16.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (62 kB) Collecting starsim>=3.0.2 (from fpsim==3.3.1) Downloading starsim-3.0.4-py3-none-any.whl.metadata (11 kB) Collecting pandas>=1.3 (from fpsim==3.3.1) Downloading pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB) Collecting sciris>=2.1.0 (from fpsim==3.3.1) Downloading sciris-3.2.4-py3-none-any.whl.metadata (3.8 kB) Collecting matplotlib>=3.5.0 (from fpsim==3.3.1) Downloading matplotlib-3.10.7-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (11 kB) Collecting seaborn>=0.9 (from fpsim==3.3.1) 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/653/lib/python3.11/site-packages (from fpsim==3.3.1) (4.5.0) Collecting plotnine (from fpsim==3.3.1) Downloading plotnine-0.15.0-py3-none-any.whl.metadata (9.5 kB) Collecting pyarrow (from fpsim==3.3.1) Downloading pyarrow-22.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.2 kB) Requirement already satisfied: pyyaml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from fpsim==3.3.1) (6.0.3) Collecting contourpy>=1.0.1 (from matplotlib>=3.5.0->fpsim==3.3.1) Downloading contourpy-1.3.3-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (5.5 kB) Collecting cycler>=0.10 (from matplotlib>=3.5.0->fpsim==3.3.1) Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB) Collecting fonttools>=4.22.0 (from matplotlib>=3.5.0->fpsim==3.3.1) Downloading fonttools-4.60.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (112 kB) Collecting kiwisolver>=1.3.1 (from matplotlib>=3.5.0->fpsim==3.3.1) Downloading kiwisolver-1.4.9-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (6.3 kB) Requirement already satisfied: packaging>=20.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from matplotlib>=3.5.0->fpsim==3.3.1) (25.0) Collecting pillow>=8 (from matplotlib>=3.5.0->fpsim==3.3.1) Downloading pillow-12.0.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (8.8 kB) Collecting pyparsing>=3 (from matplotlib>=3.5.0->fpsim==3.3.1) Downloading pyparsing-3.2.5-py3-none-any.whl.metadata (5.0 kB) Requirement already satisfied: python-dateutil>=2.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from matplotlib>=3.5.0->fpsim==3.3.1) (2.9.0.post0) Collecting pytz>=2020.1 (from pandas>=1.3->fpsim==3.3.1) Downloading pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB) Collecting tzdata>=2022.7 (from pandas>=1.3->fpsim==3.3.1) Downloading tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from python-dateutil>=2.7->matplotlib>=3.5.0->fpsim==3.3.1) (1.17.0) Collecting openpyxl (from sciris>=2.1.0->fpsim==3.3.1) Downloading openpyxl-3.1.5-py2.py3-none-any.whl.metadata (2.5 kB) Collecting xlsxwriter (from sciris>=2.1.0->fpsim==3.3.1) Downloading xlsxwriter-3.2.9-py3-none-any.whl.metadata (2.7 kB) Requirement already satisfied: psutil in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from sciris>=2.1.0->fpsim==3.3.1) (7.1.2) Collecting dill (from sciris>=2.1.0->fpsim==3.3.1) Downloading dill-0.4.0-py3-none-any.whl.metadata (10 kB) Collecting zstandard (from sciris>=2.1.0->fpsim==3.3.1) Downloading zstandard-0.25.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (3.3 kB) Collecting multiprocess (from sciris>=2.1.0->fpsim==3.3.1) Downloading multiprocess-0.70.18-py311-none-any.whl.metadata (7.5 kB) Collecting jsonpickle (from sciris>=2.1.0->fpsim==3.3.1) Downloading jsonpickle-4.1.1-py3-none-any.whl.metadata (8.1 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from sciris>=2.1.0->fpsim==3.3.1) (80.9.0) Collecting gitpython (from sciris>=2.1.0->fpsim==3.3.1) Downloading gitpython-3.1.45-py3-none-any.whl.metadata (13 kB) Collecting jellyfish (from sciris>=2.1.0->fpsim==3.3.1) Downloading jellyfish-1.2.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (642 bytes) Requirement already satisfied: tqdm in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from sciris>=2.1.0->fpsim==3.3.1) (4.67.1) Collecting memory_profiler (from sciris>=2.1.0->fpsim==3.3.1) Downloading memory_profiler-0.61.0-py3-none-any.whl.metadata (20 kB) Collecting line_profiler (from sciris>=2.1.0->fpsim==3.3.1) Downloading line_profiler-5.0.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (30 kB) Collecting networkx (from starsim>=3.0.2->fpsim==3.3.1) Downloading networkx-3.5-py3-none-any.whl.metadata (6.3 kB) Collecting llvmlite<0.46,>=0.45.0dev0 (from numba->fpsim==3.3.1) Downloading llvmlite-0.45.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (4.9 kB) Collecting gitdb<5,>=4.0.1 (from gitpython->sciris>=2.1.0->fpsim==3.3.1) Downloading gitdb-4.0.12-py3-none-any.whl.metadata (1.2 kB) Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->gitpython->sciris>=2.1.0->fpsim==3.3.1) Downloading smmap-5.0.2-py3-none-any.whl.metadata (4.3 kB) Collecting et-xmlfile (from openpyxl->sciris>=2.1.0->fpsim==3.3.1) Downloading et_xmlfile-2.0.0-py3-none-any.whl.metadata (2.7 kB) Requirement already satisfied: alembic>=1.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from optuna->fpsim==3.3.1) (1.17.1) Requirement already satisfied: colorlog in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from optuna->fpsim==3.3.1) (6.10.1) Requirement already satisfied: sqlalchemy>=1.4.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from optuna->fpsim==3.3.1) (2.0.44) Requirement already satisfied: Mako in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from alembic>=1.5.0->optuna->fpsim==3.3.1) (1.3.10) Requirement already satisfied: typing-extensions>=4.12 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from alembic>=1.5.0->optuna->fpsim==3.3.1) (4.15.0) Requirement already satisfied: greenlet>=1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from sqlalchemy>=1.4.2->optuna->fpsim==3.3.1) (3.2.4) Requirement already satisfied: MarkupSafe>=0.9.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (from Mako->alembic>=1.5.0->optuna->fpsim==3.3.1) (3.0.3) Collecting mizani~=0.14.0 (from plotnine->fpsim==3.3.1) Downloading mizani-0.14.2-py3-none-any.whl.metadata (4.8 kB) Collecting statsmodels>=0.14.5 (from plotnine->fpsim==3.3.1) Downloading statsmodels-0.14.5-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (9.5 kB) Collecting patsy>=0.5.6 (from statsmodels>=0.14.5->plotnine->fpsim==3.3.1) Downloading patsy-1.0.2-py2.py3-none-any.whl.metadata (3.6 kB) Downloading matplotlib-3.10.7-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (8.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.7/8.7 MB 32.7 MB/s 0:00:00 Downloading contourpy-1.3.3-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (355 kB) Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB) Downloading fonttools-4.60.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (5.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.0/5.0 MB 87.4 MB/s 0:00:00 Downloading kiwisolver-1.4.9-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (1.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 110.1 MB/s 0:00:00 Downloading pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (12.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.8/12.8 MB 156.9 MB/s 0:00:00 Downloading pillow-12.0.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (7.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.0/7.0 MB 236.6 MB/s 0:00:00 Downloading pyparsing-3.2.5-py3-none-any.whl (113 kB) Downloading pytz-2025.2-py2.py3-none-any.whl (509 kB) Downloading sciris-3.2.4-py3-none-any.whl (256 kB) Downloading seaborn-0.13.2-py3-none-any.whl (294 kB) Downloading starsim-3.0.4-py3-none-any.whl (933 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 933.3/933.3 kB 284.5 MB/s 0:00:00 Downloading numba-0.62.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.7/3.7 MB 295.9 MB/s 0:00:00 Downloading llvmlite-0.45.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (56.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.3/56.3 MB 241.3 MB/s 0:00:00 Downloading tzdata-2025.2-py2.py3-none-any.whl (347 kB) Downloading dill-0.4.0-py3-none-any.whl (119 kB) Downloading gitpython-3.1.45-py3-none-any.whl (208 kB) Downloading gitdb-4.0.12-py3-none-any.whl (62 kB) Downloading smmap-5.0.2-py3-none-any.whl (24 kB) Downloading jellyfish-1.2.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (360 kB) Downloading jsonpickle-4.1.1-py3-none-any.whl (47 kB) Downloading line_profiler-5.0.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.5/1.5 MB 213.6 MB/s 0:00:00 Downloading memory_profiler-0.61.0-py3-none-any.whl (31 kB) Downloading multiprocess-0.70.18-py311-none-any.whl (144 kB) Downloading networkx-3.5-py3-none-any.whl (2.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 540.4 MB/s 0:00:00 Downloading openpyxl-3.1.5-py2.py3-none-any.whl (250 kB) Downloading et_xmlfile-2.0.0-py3-none-any.whl (18 kB) Downloading plotnine-0.15.0-py3-none-any.whl (1.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 904.0 MB/s 0:00:00 Downloading mizani-0.14.2-py3-none-any.whl (133 kB) Downloading scipy-1.16.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (35.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 35.9/35.9 MB 520.0 MB/s 0:00:00 Downloading statsmodels-0.14.5-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (10.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.5/10.5 MB 277.4 MB/s 0:00:00 Downloading patsy-1.0.2-py2.py3-none-any.whl (233 kB) Downloading pyarrow-22.0.0-cp311-cp311-manylinux_2_28_x86_64.whl (47.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.7/47.7 MB 477.1 MB/s 0:00:00 Downloading xlsxwriter-3.2.9-py3-none-any.whl (175 kB) Downloading zstandard-0.25.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (5.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.6/5.6 MB 355.7 MB/s 0:00:00 Building wheels for collected packages: fpsim Building wheel for fpsim (pyproject.toml): started Building wheel for fpsim (pyproject.toml): finished with status 'done' Created wheel for fpsim: filename=fpsim-3.3.1-py3-none-any.whl size=1115263 sha256=67e2e34e9c1caa7564941d03d4d90749d8810456abe4ec0bc0137ace81f101cd Stored in directory: /tmp/pip-ephem-wheel-cache-6uly34w3/wheels/8a/23/3d/61d81664027dc2469f471055c1568c45ccd69d33e9ee36e292 Successfully built fpsim Installing collected packages: pytz, zstandard, xlsxwriter, tzdata, smmap, scipy, pyparsing, pyarrow, pillow, patsy, networkx, memory_profiler, llvmlite, line_profiler, kiwisolver, jsonpickle, jellyfish, fonttools, et-xmlfile, dill, cycler, contourpy, pandas, openpyxl, numba, multiprocess, matplotlib, gitdb, statsmodels, seaborn, mizani, gitpython, sciris, plotnine, starsim, fpsim Successfully installed contourpy-1.3.3 cycler-0.12.1 dill-0.4.0 et-xmlfile-2.0.0 fonttools-4.60.1 fpsim-3.3.1 gitdb-4.0.12 gitpython-3.1.45 jellyfish-1.2.1 jsonpickle-4.1.1 kiwisolver-1.4.9 line_profiler-5.0.0 llvmlite-0.45.1 matplotlib-3.10.7 memory_profiler-0.61.0 mizani-0.14.2 multiprocess-0.70.18 networkx-3.5 numba-0.62.1 openpyxl-3.1.5 pandas-2.3.3 patsy-1.0.2 pillow-12.0.0 plotnine-0.15.0 pyarrow-22.0.0 pyparsing-3.2.5 pytz-2025.2 scipy-1.16.3 sciris-3.2.4 seaborn-0.13.2 smmap-5.0.2 starsim-3.0.4 statsmodels-0.14.5 tzdata-2025.2 xlsxwriter-3.2.9 zstandard-0.25.0 [rtd-command-info] start-time: 2025-10-29T17:04:57.785219Z, end-time: 2025-10-29T17:04:57.822467Z, 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'2019 - {sc.now().year}, 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, "footer_start": ["copyright", "footer_start"], "footer_end": ["theme-version", "footer_end"], "logo": { "text": "FPsim", }, } html_sidebars = { "**": ["sidebar-nav-bs", "page-toc"], } html_logo = "images/idm-logo-transparent.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}", } [rtd-command-info] start-time: 2025-10-29T17:04:57.912602Z, end-time: 2025-10-29T17:05:17.714101Z, duration: 19, exit-code: 2 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v8.1.0 Rebuilding font cache, please be patient... Font cache rebuilt in folder: /home/docs/.cache/matplotlib Note: rebuilding the font cache only happens once on first import, or set the environment variable STARSIM_INSTALL_FONTS=0 to disable. Building Jupyter notebooks with build option: auto loading translations [en]... done making output directory... done [autosummary] generating autosummary for: api/index.rst, index.rst, overview.rst, tutorials.rst, tutorials/README.rst, tutorials/T1_intro.ipynb, tutorials/T2_intro_to_new_features.ipynb, tutorials/T3_interventions_methods.ipynb, tutorials/T4_intervention_eligibility.ipynb, tutorials/T5_new_method.ipynb, tutorials/T6_calibration.ipynb, whatsnew.rst /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/starsim/arrays.py:361: RuntimeWarning: Trying to access non-initialized Arr object; in most cases, Arr objects need to be initialized with a Sim object, but set skip_init=True if this is intentional. ss.warn('Trying to access non-initialized Arr object; in most cases, Arr objects need to be initialized with a Sim object, but set skip_init=True if this is intentional.') [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.analyzers.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.arrays.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.calibration.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.defaults.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.demographics.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.education.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.experiment.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.interventions.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.methods.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.parameters.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.scenarios.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.settings.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.utils.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.analyzers.age_pyramids.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.analyzers.cpr_by_age.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.analyzers.education_recorder.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.analyzers.lifeof_recorder.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.analyzers.method_mix_by_age.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.analyzers.method_mix_over_time.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.analyzers.snapshot.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.analyzers.state_tracker.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.analyzers.track_as.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.arrays.TwoDimensionalArr.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.parameters.FPPars.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.parameters.SimPars.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.parameters.all_pars.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.parameters.make_fp_pars.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.parameters.make_sim_pars.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.scenarios.Scenario.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.scenarios.Scenarios.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.scenarios.make_scen.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.sim.Sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/api/_autosummary/fpsim.utils.DuplicateNameException.rst Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/_readthedocs/html/_static/nbsphinx-code-cells.css building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 12 source files that are out of date updating environment: [new config] 72 added, 0 changed, 0 removed reading sources... [ 1%] api/_autosummary/fpsim.analyzers reading sources... [ 3%] api/_autosummary/fpsim.analyzers.age_pyramids reading sources... [ 4%] api/_autosummary/fpsim.analyzers.cpr_by_age reading sources... [ 6%] api/_autosummary/fpsim.analyzers.education_recorder reading sources... [ 7%] api/_autosummary/fpsim.analyzers.lifeof_recorder reading sources... [ 8%] api/_autosummary/fpsim.analyzers.method_mix_by_age reading sources... [ 10%] api/_autosummary/fpsim.analyzers.method_mix_over_time reading sources... [ 11%] api/_autosummary/fpsim.analyzers.snapshot reading sources... [ 12%] api/_autosummary/fpsim.analyzers.state_tracker reading sources... [ 14%] api/_autosummary/fpsim.analyzers.track_as reading sources... [ 15%] api/_autosummary/fpsim.arrays reading sources... [ 17%] api/_autosummary/fpsim.arrays.TwoDimensionalArr reading sources... [ 18%] api/_autosummary/fpsim.calibration reading sources... [ 19%] api/_autosummary/fpsim.calibration.Calibration reading sources... [ 21%] api/_autosummary/fpsim.defaults reading sources... [ 22%] api/_autosummary/fpsim.defaults.get_location reading sources... [ 24%] api/_autosummary/fpsim.defaults.register_location reading sources... [ 25%] api/_autosummary/fpsim.demographics reading sources... [ 26%] api/_autosummary/fpsim.demographics.get_partnership_init_vals reading sources... [ 28%] api/_autosummary/fpsim.demographics.init_partnership_states reading sources... [ 29%] api/_autosummary/fpsim.education reading sources... [ 31%] api/_autosummary/fpsim.education.EduPars reading sources... [ 32%] api/_autosummary/fpsim.education.Education reading sources... [ 33%] api/_autosummary/fpsim.education.make_edu_pars reading sources... [ 35%] api/_autosummary/fpsim.experiment reading sources... [ 36%] api/_autosummary/fpsim.experiment.Experiment reading sources... [ 38%] api/_autosummary/fpsim.experiment.Fit reading sources... [ 39%] api/_autosummary/fpsim.experiment.compute_gof reading sources... [ 40%] api/_autosummary/fpsim.experiment.diff_summaries reading sources... [ 42%] api/_autosummary/fpsim.interventions reading sources... [ 43%] api/_autosummary/fpsim.interventions.change_initiation reading sources... [ 44%] api/_autosummary/fpsim.interventions.change_initiation_prob reading sources... [ 46%] api/_autosummary/fpsim.interventions.change_par reading sources... [ 47%] api/_autosummary/fpsim.interventions.change_people_state reading sources... [ 49%] api/_autosummary/fpsim.interventions.update_methods reading sources... [ 50%] api/_autosummary/fpsim.methods reading sources... [ 51%] api/_autosummary/fpsim.methods.ContraPars reading sources... [ 53%] api/_autosummary/fpsim.methods.ContraceptiveChoice reading sources... [ 54%] api/_autosummary/fpsim.methods.Method reading sources... [ 56%] api/_autosummary/fpsim.methods.RandomChoice reading sources... [ 57%] api/_autosummary/fpsim.methods.SimpleChoice reading sources... [ 58%] api/_autosummary/fpsim.methods.StandardChoice reading sources... [ 60%] api/_autosummary/fpsim.methods.make_contra_pars reading sources... [ 61%] api/_autosummary/fpsim.methods.make_method_list reading sources... [ 62%] api/_autosummary/fpsim.methods.make_methods reading sources... [ 64%] api/_autosummary/fpsim.parameters reading sources... [ 65%] api/_autosummary/fpsim.parameters.FPPars reading sources... [ 67%] api/_autosummary/fpsim.parameters.SimPars reading sources... [ 68%] api/_autosummary/fpsim.parameters.all_pars reading sources... [ 69%] api/_autosummary/fpsim.parameters.make_fp_pars reading sources... [ 71%] api/_autosummary/fpsim.parameters.make_sim_pars reading sources... [ 72%] api/_autosummary/fpsim.scenarios reading sources... [ 74%] api/_autosummary/fpsim.scenarios.Scenario reading sources... [ 75%] api/_autosummary/fpsim.scenarios.Scenarios reading sources... [ 76%] api/_autosummary/fpsim.scenarios.make_scen reading sources... [ 78%] api/_autosummary/fpsim.settings reading sources... [ 79%] api/_autosummary/fpsim.sim reading sources... [ 81%] api/_autosummary/fpsim.sim.Sim reading sources... [ 82%] api/_autosummary/fpsim.utils reading sources... [ 83%] api/_autosummary/fpsim.utils.DuplicateNameException reading sources... [ 85%] api/index reading sources... [ 86%] index reading sources... [ 88%] overview reading sources... [ 89%] tutorials reading sources... [ 90%] tutorials/README reading sources... [ 92%] tutorials/T1_intro /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/fpsim/education.py:docstring of fpsim.education.Education.set_objective_dists:3: ERROR: Unexpected indentation. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/fpsim/education.py:docstring of fpsim.education.Education.set_objective_dists:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/fpsim/interventions.py:docstring of fpsim.interventions.change_initiation:20: ERROR: Unexpected indentation. [docutils] WARNING: Summarised items should not include the current module. Replace 'fpsim.analyzers' with 'analyzers'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.arrays' with 'arrays'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.calibration' with 'calibration'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.defaults' with 'defaults'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.demographics' with 'demographics'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.education' with 'education'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.experiment' with 'experiment'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.interventions' with 'interventions'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.methods' with 'methods'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.parameters' with 'parameters'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.scenarios' with 'scenarios'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.settings' with 'settings'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.sim' with 'sim'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.utils' with 'utils'. [autosummary.import_cycle] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/tutorials.rst:3: WARNING: toctree contains reference to nonexisting document 'tutorials/T6_scenarios' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/tutorials.rst:3: WARNING: toctree contains reference to nonexisting document 'tutorials/T7_scenarios_plotting' [toc.not_readable] Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/nbsphinx/__init__.py", line 634, in parse rststring, resources = exporter.from_notebook_node(nb, resources) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/nbsphinx/__init__.py", line 397, in from_notebook_node nb, resources = pp.preprocess(nb, resources) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/nbconvert/preprocessors/execute.py", line 100, in preprocess self.preprocess_cell(cell, resources, index) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/nbconvert/preprocessors/execute.py", line 121, in preprocess_cell cell = self.execute_cell(cell, index, store_history=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped return loop.run_until_complete(inner) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.asdf/installs/python/3.11.12/lib/python3.11/asyncio/base_events.py", line 654, in run_until_complete return future.result() ^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import fpsim as fp sim = fp.Sim() sim.run() fig = sim.plot() ------------------ ----- stderr ----- /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html from .autonotebook import tqdm as notebook_tqdm ----- stdout ----- Location not supplied: using parameters from Senegal ------------------ --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) Cell In[1], line 3  1 import fpsim as fp ----> 3 sim = fp.Sim()  4 sim.run()  5 fig = sim.plot() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/fpsim/sim.py:127, in Sim.__init__(self, pars, sim_pars, fp_pars, contra_pars, edu_pars, fp_module, contraception_module, empowerment_module, education_module, label, people, demographics, diseases, networks, interventions, analyzers, connectors, copy_inputs, **kwargs)  125 default_contra = fpm.StandardChoice(location=self.pars.location, pars=self.contra_pars)  126 default_edu = fped.Education(location=self.pars.location, pars=self.edu_pars) --> 127 default_fp = fp.FPmod(location=self.pars.location, pars=self.fp_pars)  128 contraception_module = contraception_module or sc.dcp(default_contra)  129 education_module = education_module or sc.dcp(default_edu) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/fpsim/fpmod.py:31, in FPmod.__init__(self, pars, location, name, **kwargs)  29 self.define_pars(**default_pars)  30 self.update_pars(pars, **kwargs) ---> 31 self.define_states(*fp.fpmod_states)  33 # Distributions: binary outcomes  34 self._p_fertile = ss.bernoulli(p=1-self.pars['primary_infertility']) # Probability that a woman is fertile, i.e. 1 - primary infertility File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/starsim/modules.py:521, in Module.define_states(self, check, reset, lock, *args)  519 errormsg += f'New states being added:\n{new}\n'  520 errormsg += f'Conflicting states:\n{set(present) & set(new)}\n' --> 521 raise AttributeError(errormsg)  522 setattr(self, attr, state)  523 if lock: AttributeError: Cannot add "lam" to "fp" ( since already present in module. Did you mean to use define_states(reset=True) (skip inherited states) or define_states(check=False) (skip this check)? States already in module: ['on_contra', 'method', 'ti_contra', 'barrier', 'ever_used_contra', 'rel_sus', 'lam', 'pregnant', 'fertile', 'sexually_active', 'sexual_debut', 'lactating', 'postpartum'] New states being added: ['on_contra', 'method', 'ti_contra', 'barrier', 'ever_used_contra', 'rel_sus', 'lam', 'pregnant', 'fertile', 'sexually_active', 'sexual_debut', 'lactating', 'postpartum', 'lam', 'pregnant', 'fertile', 'sexually_active', 'sexual_debut', 'lactating', 'postpartum', 'sexual_debut_age', 'fated_debut', 'first_birth_age', 'parity', 'n_births', 'n_stillbirths', 'n_miscarriages', 'n_abortions', 'n_pregnancies', 'months_inactive', 'short_interval', 'gestation', 'remainder_months', 'dur_pregnancy', 'dur_postpartum', 'dur_breastfeed', 'dur_breastfeed_total', 'ti_conceived', 'ti_pregnant', 'ti_delivery', 'ti_last_delivery', 'ti_live_birth', 'ti_stillbirth', 'ti_postpartum', 'ti_miscarriage', 'ti_abortion', 'ti_stop_postpartum', 'ti_stop_breastfeeding', 'ti_debut', 'ti_dead', 'parity', 'n_births', 'n_stillbirths', 'n_miscarriages', 'n_abortions', 'n_pregnancies', 'months_inactive', 'short_interval', 'gestation', 'remainder_months', 'dur_pregnancy', 'dur_postpartum', 'dur_breastfeed', 'dur_breastfeed_total', 'ti_conceived', 'ti_pregnant', 'ti_delivery', 'ti_last_delivery', 'ti_live_birth', 'ti_stillbirth', 'ti_postpartum', 'ti_miscarriage', 'ti_abortion', 'ti_stop_postpartum', 'ti_stop_breastfeeding', 'ti_debut', 'ti_dead', 'personal_fecundity', 'birth_ages', 'stillborn_ages', 'miscarriage_ages', 'abortion_ages', 'partnered', 'partnership_age', 'partnered', 'partnership_age'] Conflicting states: {'on_contra', 'method', 'fertile', 'lam', 'ti_contra', 'sexual_debut', 'lactating', 'postpartum', 'sexually_active', 'rel_sus', 'barrier', 'ever_used_contra', 'pregnant'} During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/sphinx/cmd/build.py", line 514, in build_main app.build(args.force_all, args.filenames) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/sphinx/application.py", line 381, in build self.builder.build_update() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 352, in build_update self.build( File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 379, in build updated_docnames = set(self.read()) ^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 496, in read self._read_serial(docnames) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 561, in _read_serial self.read_doc(docname) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 624, in read_doc publisher.publish() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/docutils/core.py", line 234, in publish self.document = self.reader.read(self.source, self.parser, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/sphinx/io.py", line 106, in read self.parse() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/docutils/readers/__init__.py", line 76, in parse self.parser.parse(self.input, document) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/nbsphinx/__init__.py", line 641, in parse raise NotebookError('\n'.join(lines)) nbsphinx.NotebookError: CellExecutionError in tutorials/T1_intro.ipynb: ------------------ import fpsim as fp sim = fp.Sim() sim.run() fig = sim.plot() ------------------ ----- stderr ----- /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html from .autonotebook import tqdm as notebook_tqdm ----- stdout ----- Location not supplied: using parameters from Senegal ------------------ --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) Cell In[1], line 3  1 import fpsim as fp ----> 3 sim = fp.Sim()  4 sim.run()  5 fig = sim.plot() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/fpsim/sim.py:127, in Sim.__init__(self, pars, sim_pars, fp_pars, contra_pars, edu_pars, fp_module, contraception_module, empowerment_module, education_module, label, people, demographics, diseases, networks, interventions, analyzers, connectors, copy_inputs, **kwargs)  125 default_contra = fpm.StandardChoice(location=self.pars.location, pars=self.contra_pars)  126 default_edu = fped.Education(location=self.pars.location, pars=self.edu_pars) --> 127 default_fp = fp.FPmod(location=self.pars.location, pars=self.fp_pars)  128 contraception_module = contraception_module or sc.dcp(default_contra)  129 education_module = education_module or sc.dcp(default_edu) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/fpsim/fpmod.py:31, in FPmod.__init__(self, pars, location, name, **kwargs)  29 self.define_pars(**default_pars)  30 self.update_pars(pars, **kwargs) ---> 31 self.define_states(*fp.fpmod_states)  33 # Distributions: binary outcomes  34 self._p_fertile = ss.bernoulli(p=1-self.pars['primary_infertility']) # Probability that a woman is fertile, i.e. 1 - primary infertility File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/starsim/modules.py:521, in Module.define_states(self, check, reset, lock, *args)  519 errormsg += f'New states being added:\n{new}\n'  520 errormsg += f'Conflicting states:\n{set(present) & set(new)}\n' --> 521 raise AttributeError(errormsg)  522 setattr(self, attr, state)  523 if lock: AttributeError: Cannot add "lam" to "fp" ( since already present in module. Did you mean to use define_states(reset=True) (skip inherited states) or define_states(check=False) (skip this check)? States already in module: ['on_contra', 'method', 'ti_contra', 'barrier', 'ever_used_contra', 'rel_sus', 'lam', 'pregnant', 'fertile', 'sexually_active', 'sexual_debut', 'lactating', 'postpartum'] New states being added: ['on_contra', 'method', 'ti_contra', 'barrier', 'ever_used_contra', 'rel_sus', 'lam', 'pregnant', 'fertile', 'sexually_active', 'sexual_debut', 'lactating', 'postpartum', 'lam', 'pregnant', 'fertile', 'sexually_active', 'sexual_debut', 'lactating', 'postpartum', 'sexual_debut_age', 'fated_debut', 'first_birth_age', 'parity', 'n_births', 'n_stillbirths', 'n_miscarriages', 'n_abortions', 'n_pregnancies', 'months_inactive', 'short_interval', 'gestation', 'remainder_months', 'dur_pregnancy', 'dur_postpartum', 'dur_breastfeed', 'dur_breastfeed_total', 'ti_conceived', 'ti_pregnant', 'ti_delivery', 'ti_last_delivery', 'ti_live_birth', 'ti_stillbirth', 'ti_postpartum', 'ti_miscarriage', 'ti_abortion', 'ti_stop_postpartum', 'ti_stop_breastfeeding', 'ti_debut', 'ti_dead', 'parity', 'n_births', 'n_stillbirths', 'n_miscarriages', 'n_abortions', 'n_pregnancies', 'months_inactive', 'short_interval', 'gestation', 'remainder_months', 'dur_pregnancy', 'dur_postpartum', 'dur_breastfeed', 'dur_breastfeed_total', 'ti_conceived', 'ti_pregnant', 'ti_delivery', 'ti_last_delivery', 'ti_live_birth', 'ti_stillbirth', 'ti_postpartum', 'ti_miscarriage', 'ti_abortion', 'ti_stop_postpartum', 'ti_stop_breastfeeding', 'ti_debut', 'ti_dead', 'personal_fecundity', 'birth_ages', 'stillborn_ages', 'miscarriage_ages', 'abortion_ages', 'partnered', 'partnership_age', 'partnered', 'partnership_age'] Conflicting states: {'on_contra', 'method', 'fertile', 'lam', 'ti_contra', 'sexual_debut', 'lactating', 'postpartum', 'sexually_active', 'rel_sus', 'barrier', 'ever_used_contra', 'pregnant'} You can ignore this error by setting the following in conf.py: nbsphinx_allow_errors = True Notebook error: CellExecutionError in tutorials/T1_intro.ipynb: ------------------ import fpsim as fp sim = fp.Sim() sim.run() fig = sim.plot() ------------------ ----- stderr ----- /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html from .autonotebook import tqdm as notebook_tqdm ----- stdout ----- Location not supplied: using parameters from Senegal ------------------ --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) Cell In[1], line 3  1 import fpsim as fp ----> 3 sim = fp.Sim()  4 sim.run()  5 fig = sim.plot() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/fpsim/sim.py:127, in Sim.__init__(self, pars, sim_pars, fp_pars, contra_pars, edu_pars, fp_module, contraception_module, empowerment_module, education_module, label, people, demographics, diseases, networks, interventions, analyzers, connectors, copy_inputs, **kwargs)  125 default_contra = fpm.StandardChoice(location=self.pars.location, pars=self.contra_pars)  126 default_edu = fped.Education(location=self.pars.location, pars=self.edu_pars) --> 127 default_fp = fp.FPmod(location=self.pars.location, pars=self.fp_pars)  128 contraception_module = contraception_module or sc.dcp(default_contra)  129 education_module = education_module or sc.dcp(default_edu) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/fpsim/fpmod.py:31, in FPmod.__init__(self, pars, location, name, **kwargs)  29 self.define_pars(**default_pars)  30 self.update_pars(pars, **kwargs) ---> 31 self.define_states(*fp.fpmod_states)  33 # Distributions: binary outcomes  34 self._p_fertile = ss.bernoulli(p=1-self.pars['primary_infertility']) # Probability that a woman is fertile, i.e. 1 - primary infertility File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/starsim/modules.py:521, in Module.define_states(self, check, reset, lock, *args)  519 errormsg += f'New states being added:\n{new}\n'  520 errormsg += f'Conflicting states:\n{set(present) & set(new)}\n' --> 521 raise AttributeError(errormsg)  522 setattr(self, attr, state)  523 if lock: AttributeError: Cannot add "lam" to "fp" ( since already present in module. Did you mean to use define_states(reset=True) (skip inherited states) or define_states(check=False) (skip this check)? States already in module: ['on_contra', 'method', 'ti_contra', 'barrier', 'ever_used_contra', 'rel_sus', 'lam', 'pregnant', 'fertile', 'sexually_active', 'sexual_debut', 'lactating', 'postpartum'] New states being added: ['on_contra', 'method', 'ti_contra', 'barrier', 'ever_used_contra', 'rel_sus', 'lam', 'pregnant', 'fertile', 'sexually_active', 'sexual_debut', 'lactating', 'postpartum', 'lam', 'pregnant', 'fertile', 'sexually_active', 'sexual_debut', 'lactating', 'postpartum', 'sexual_debut_age', 'fated_debut', 'first_birth_age', 'parity', 'n_births', 'n_stillbirths', 'n_miscarriages', 'n_abortions', 'n_pregnancies', 'months_inactive', 'short_interval', 'gestation', 'remainder_months', 'dur_pregnancy', 'dur_postpartum', 'dur_breastfeed', 'dur_breastfeed_total', 'ti_conceived', 'ti_pregnant', 'ti_delivery', 'ti_last_delivery', 'ti_live_birth', 'ti_stillbirth', 'ti_postpartum', 'ti_miscarriage', 'ti_abortion', 'ti_stop_postpartum', 'ti_stop_breastfeeding', 'ti_debut', 'ti_dead', 'parity', 'n_births', 'n_stillbirths', 'n_miscarriages', 'n_abortions', 'n_pregnancies', 'months_inactive', 'short_interval', 'gestation', 'remainder_months', 'dur_pregnancy', 'dur_postpartum', 'dur_breastfeed', 'dur_breastfeed_total', 'ti_conceived', 'ti_pregnant', 'ti_delivery', 'ti_last_delivery', 'ti_live_birth', 'ti_stillbirth', 'ti_postpartum', 'ti_miscarriage', 'ti_abortion', 'ti_stop_postpartum', 'ti_stop_breastfeeding', 'ti_debut', 'ti_dead', 'personal_fecundity', 'birth_ages', 'stillborn_ages', 'miscarriage_ages', 'abortion_ages', 'partnered', 'partnership_age', 'partnered', 'partnership_age'] Conflicting states: {'on_contra', 'method', 'fertile', 'lam', 'ti_contra', 'sexual_debut', 'lactating', 'postpartum', 'sexually_active', 'rel_sus', 'barrier', 'ever_used_contra', 'pregnant'} You can ignore this error by setting the following in conf.py: nbsphinx_allow_errors = True