Read the Docs build information Build id: 3939383 Project: institute-for-disease-modeling-hpvsim Version: latest Commit: 5cfba773272e48cb736284031471a88215c14879 Date: 2026-04-17T22:35:16.569047Z State: finished Success: True [rtd-command-info] start-time: 2026-04-17T22:35:45.913030Z, end-time: 2026-04-17T22:35:46.357434Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/starsimhub/hpvsim.git . Cloning into '.'... [rtd-command-info] start-time: 2026-04-17T22:35:46.445928Z, end-time: 2026-04-17T22:35:47.665178Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main From https://github.com/starsimhub/hpvsim * [new tag] v0.4.16 -> v0.4.16 * [new tag] v0.4.5 -> v0.4.5 * [new tag] v1.0.0 -> v1.0.0 * [new tag] v1.1.1 -> v1.1.1 * [new tag] v1.2.0 -> v1.2.0 * [new tag] v1.2.2 -> v1.2.2 * [new tag] v1.2.3 -> v1.2.3 * [new tag] v1.2.4 -> v1.2.4 * [new tag] v1.2.5 -> v1.2.5 * [new tag] v1.2.6 -> v1.2.6 * [new tag] v1.2.7 -> v1.2.7 * [new tag] v2.0.0 -> v2.0.0 * [new tag] v2.1.0 -> v2.1.0 [rtd-command-info] start-time: 2026-04-17T22:35:48.381260Z, end-time: 2026-04-17T22:35:48.431693Z, 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 5cfba77 Merge pull request #75 from starsimhub/v2.2.6 [rtd-command-info] start-time: 2026-04-17T22:35:48.518909Z, end-time: 2026-04-17T22:35:48.555358Z, 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-24.04 tools: python: "3.13" jobs: post_install: - hpvsim-download-data # 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: 2026-04-17T22:35:53.348529Z, end-time: 2026-04-17T22:35:53.399121Z, duration: 0, exit-code: 0 asdf global python 3.13.3 [rtd-command-info] start-time: 2026-04-17T22:35:53.734967Z, end-time: 2026-04-17T22:35:54.350431Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.13.3.final.0-64 in 392ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/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: 2026-04-17T22:35:54.439536Z, end-time: 2026-04-17T22:35:59.669470Z, duration: 5, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages (23.1) Collecting pip Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/de/f0/c81e05b613866b76d2d1066490adf1a3dbc4ee9d9c839961c3fc8a6997af/pip-26.0.1-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 12.8 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages (67.6.1) Collecting setuptools Downloading 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[rtd-command-info] start-time: 2026-04-17T22:36:06.738554Z, end-time: 2026-04-17T22:36:42.678457Z, duration: 35, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Collecting pandoc (from -r docs/requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/10/9a/e3186e760c57ee5f1c27ea5cea577a0ff9abfca51eefcb4d9a4cd39aff2e/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 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kiwisolver, jupyterlab-pygments, ipython-pygments-lexers, greenlet, fonttools, executing, defusedxml, decorator, debugpy, cycler, comm, colorlog, bleach, attrs, asttokens, accessible-pygments, stack_data, sqlalchemy, referencing, python-dateutil, prompt_toolkit, plantweb, pandoc, matplotlib-inline, jupyter-core, jedi, contourpy, beautifulsoup4, sphinx-design, sphinx-autodoc-typehints, pydata-sphinx-theme, pandas, matplotlib, jupyter-client, jsonschema-specifications, ipython, alembic, seaborn, optuna, jsonschema, ipykernel, nbformat, nbclient, nbconvert, nbsphinx Successfully installed Mako-1.3.11 PyYAML-6.0.3 accessible-pygments-0.0.5 alembic-1.18.4 asttokens-3.0.1 attrs-26.1.0 beautifulsoup4-4.14.3 bleach-6.3.0 colorlog-6.10.1 comm-0.2.3 contourpy-1.3.3 cycler-0.12.1 debugpy-1.8.20 decorator-5.2.1 defusedxml-0.7.1 executing-2.2.1 fastjsonschema-2.21.2 fonttools-4.62.1 greenlet-3.4.0 ipykernel-7.2.0 ipython-9.12.0 ipython-pygments-lexers-1.1.1 jedi-0.19.2 jsonschema-4.26.0 jsonschema-specifications-2025.9.1 jupyter-client-8.8.0 jupyter-core-5.9.1 jupyterlab-pygments-0.3.0 kiwisolver-1.5.0 matplotlib-3.10.8 matplotlib-inline-0.2.1 mistune-3.2.0 nbclient-0.10.4 nbconvert-7.17.0 nbformat-5.10.4 nbsphinx-0.9.8 nest-asyncio-1.6.0 numpy-2.4.4 optuna-4.8.0 pandas-3.0.2 pandoc-2.4 pandocfilters-1.5.1 parso-0.8.6 pexpect-4.9.0 pillow-12.2.0 plantweb-1.3.0 platformdirs-4.9.6 plumbum-1.10.0 ply-3.11 prompt_toolkit-3.0.52 psutil-7.2.2 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.17.0 pypandoc-1.17 pyparsing-3.3.2 python-dateutil-2.9.0.post0 pyzmq-27.1.0 readthedocs-sphinx-search-0.3.2 referencing-0.37.0 rpds-py-0.30.0 seaborn-0.13.2 six-1.17.0 soupsieve-2.8.3 sphinx-autodoc-typehints-3.10.2 sphinx-design-0.7.0 sqlalchemy-2.0.49 stack_data-0.6.3 tinycss2-1.4.0 tornado-6.5.5 tqdm-4.67.3 traitlets-5.14.3 typing-extensions-4.15.0 wcwidth-0.6.0 webencodings-0.5.1 [rtd-command-info] start-time: 2026-04-17T22:36:42.775346Z, end-time: 2026-04-17T22:36:57.022783Z, duration: 14, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir . 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/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages (from matplotlib->hpvsim==2.2.6) (4.62.1) Requirement already satisfied: kiwisolver>=1.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages (from matplotlib->hpvsim==2.2.6) (1.5.0) Requirement already satisfied: pillow>=8 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages (from matplotlib->hpvsim==2.2.6) (12.2.0) Requirement already satisfied: pyparsing>=3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages (from matplotlib->hpvsim==2.2.6) (3.3.2) Collecting et-xmlfile (from openpyxl->sciris>=3.0.0->hpvsim==2.2.6) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c1/8b/5fe2cc11fee489817272089c4203e679c63b570a5aaeb18d852ae3cbba6a/et_xmlfile-2.0.0-py3-none-any.whl (18 kB) Requirement already satisfied: alembic>=1.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages (from optuna->hpvsim==2.2.6) (1.18.4) Requirement already satisfied: colorlog in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages (from optuna->hpvsim==2.2.6) (6.10.1) Requirement already satisfied: sqlalchemy>=1.4.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages (from optuna->hpvsim==2.2.6) (2.0.49) Requirement already satisfied: Mako in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages (from alembic>=1.5.0->optuna->hpvsim==2.2.6) (1.3.11) Requirement already satisfied: greenlet>=1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages (from sqlalchemy>=1.4.2->optuna->hpvsim==2.2.6) (3.4.0) Requirement already satisfied: MarkupSafe>=0.9.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages (from Mako->alembic>=1.5.0->optuna->hpvsim==2.2.6) (3.0.3) Building wheels for collected packages: hpvsim Building wheel for hpvsim (pyproject.toml): started Building wheel for hpvsim (pyproject.toml): finished with status 'done' Created wheel for hpvsim: filename=hpvsim-2.2.6-py3-none-any.whl size=198965 sha256=2f5c9c5df1a79bb3b2a5567e24ceec146fdcc95eea7273f00f2cf40f1055360e Stored in directory: /tmp/pip-ephem-wheel-cache-gsthfydw/wheels/29/de/44/1bdac70a3a61aeb142636970031996253dc29aa28dbd54a141 Successfully built hpvsim Installing collected packages: zstandard, xlsxwriter, smmap, scipy, memory_profiler, line_profiler, jsonpickle, jellyfish, et-xmlfile, dill, openpyxl, multiprocess, gitdb, gitpython, sciris, hpvsim Successfully installed dill-0.4.1 et-xmlfile-2.0.0 gitdb-4.0.12 gitpython-3.1.46 hpvsim-2.2.6 jellyfish-1.2.1 jsonpickle-4.1.1 line_profiler-5.0.2 memory_profiler-0.61.0 multiprocess-0.70.19 openpyxl-3.1.5 scipy-1.17.1 sciris-3.2.9 smmap-5.0.3 xlsxwriter-3.2.9 zstandard-0.25.0 [rtd-command-info] start-time: 2026-04-17T22:36:57.122209Z, end-time: 2026-04-17T22:37:42.417720Z, duration: 45, exit-code: 0 hpvsim-download-data Matplotlib is building the font cache; this may take a moment. HPVsim 2.2.6 (2026-04-17) — © 2023-2026 by the Gates Foundation HPVsim data: at least one file missing: {'age_dist': False, 'age_dist_sex': False, 'birth': False, 'death': False}  ———————————————————————————————————— Downloading preprocessed HPVsim data ————————————————————————————————————  Note: this automatic download only happens once, when HPVsim is first run. Downloading https://github.com/hpvsim/hpvsim_data/blob/main/hpvsim_data_v1.4.zip?raw=true... Saving to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages/hpvsim/data/files/tmp_hpvsim_data_v1.4.zip.zip... Time to download https://github.com/hpvsim/hpvsim_data/blob/main/hpvsim_data_v1.4.zip?raw=true: 2.27 s Removed "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages/hpvsim/data/files/tmp_hpvsim_data_v1.4.zip.zip" Data downloaded.  —————————————————————————————————————————————————————— Downloading HPVsim data manually, please be patient... ——————————————————————————————————————————————————————  /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages/sciris/sc_datetime.py:1092: FutureWarning: sc.toc() argument "doprint" is deprecated; use "verbose" instead output = toc(elapsed=self.elapsed, unit=self.unit, verbose=verbose, **kwargs) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages/sciris/sc_datetime.py:1092: FutureWarning: sc.toc() argument "doprint" is deprecated; use "verbose" instead output = toc(elapsed=self.elapsed, unit=self.unit, verbose=verbose, **kwargs) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages/sciris/sc_datetime.py:1092: FutureWarning: sc.toc() argument "doprint" is deprecated; use "verbose" instead output = toc(elapsed=self.elapsed, unit=self.unit, verbose=verbose, **kwargs)  ———————————————— Working on birth ————————————————  Downloading birth data... Downloading https://population.un.org/wpp/assets/Excel%20Files/1_Indicator%20(Standard)/CSV_FILES/WPP2024_Demographic_Indicators_Medium.csv.gz... Removed "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.13/site-packages/hpvsim/data/files/WPP2024_Demographic_Indicators_Medium.csv.gz" Done with "birth" for : 2.25 s Done with birth: 2.30276 Done downloading data for HPVsim: 33.7 s [rtd-command-info] start-time: 2026-04-17T22:37:42.579713Z, end-time: 2026-04-17T22:37:42.616822Z, 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 hpvsim as hpv # Set environment os.environ['SPHINX_BUILD'] = 'True' # This is used so hpv.options.set('jupyter') doesn't reset the Matplotlib renderer on_rtd = os.environ.get('READTHEDOCS') == 'True' # -- Project information ----------------------------------------------------- project = 'HPVsim' copyright = f'2020 - {sc.now().year}, Gates Foundation. All rights reserved.\nThese docs were built for HPVsim version {hpv.__version__}.\n' author = 'Institute for Disease Modeling' # The short X.Y version version = hpv.__version__ # The full version, including alpha/beta/rc tags release = hpv.__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 = ["hpvsim."] # 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://hpvsim.org", "icon": "fas fa-home"}, { "name": "GitHub", "url": "https://github.com/institutefordiseasemodeling/hpvsim", "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"], } 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/hpvsim/en/latest" html_context = { 'rtd_url': 'https://docs.idmod.org/projects/hpvsim/en/latest', "versions_dropdown": { "latest": "devel (latest)", "stable": "current (stable)", }, "default_mode": "light", } # 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 = 'HPVsim' # 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/hpvsim/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: 2026-04-17T22:37:42.707374Z, end-time: 2026-04-17T22:41:42.993991Z, duration: 240, exit-code: 0 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v9.1.0 HPVsim 2.2.6 (2026-04-17) — © 2023-2026 by the Gates Foundation 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/tut_analyzers.ipynb, tutorials/tut_calibration.ipynb, tutorials/tut_interventions.ipynb, tutorials/tut_intro.ipynb, tutorials/tut_people.ipynb, tutorials/tut_plotting.ipynb, tutorials/tut_running.ipynb, whats-new.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.analysis.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.base.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.calibration.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.data.downloaders.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.data.loaders.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.defaults.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.hiv.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.immunity.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.interventions.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.misc.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.parameters.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.people.rst, 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