Read the Docs build information Build id: 3810342 Project: institute-for-disease-modeling-hpvsim Version: latest Commit: 7b7cf705b201be6bfde770381104d6c62be32faf Date: 2026-03-07T02:22:02.945468Z State: finished Success: False [rtd-command-info] start-time: 2026-03-07T02:22:03.718460Z, end-time: 2026-03-07T02:22:04.199947Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/starsimhub/hpvsim.git . Cloning into '.'... [rtd-command-info] start-time: 2026-03-07T02:22:04.288588Z, end-time: 2026-03-07T02:22:05.372813Z, 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: 2026-03-07T02:22:06.038341Z, end-time: 2026-03-07T02:22:06.086447Z, 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 7b7cf70 Merge pull request #19 from starsimhub/JSchripsema-IDM-patch-1 [rtd-command-info] start-time: 2026-03-07T02:22:06.176274Z, end-time: 2026-03-07T02:22:06.219009Z, duration: 0, exit-code: 0 cat .readthedocs.yaml # .readthedocs.yaml # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details # Required version: 2 # Set the version of Python and other tools you might need build: os: ubuntu-20.04 tools: python: "3.9" # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py # If using Sphinx, optionally build your docs in additional formats such as PDF # formats: # Optionally declare the Python requirements required to build your docs python: install: - requirements: docs/requirements.txt - method: pip path: . [rtd-command-info] start-time: 2026-03-07T02:22:10.522838Z, end-time: 2026-03-07T02:22:10.576890Z, duration: 0, exit-code: 0 asdf global python 3.9.22 [rtd-command-info] start-time: 2026-03-07T02:22:10.972849Z, end-time: 2026-03-07T02:22:11.484689Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.22.final.0-64 in 298ms 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: 2026-03-07T02:22:11.574102Z, end-time: 2026-03-07T02:22:16.134947Z, duration: 4, 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/python3.9/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 12.5 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/python3.9/site-packages (67.6.1) Collecting setuptools Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e1/c6/76dc613121b793286a3f91621d7b75a2b493e0390ddca50f11993eadf192/setuptools-82.0.0-py3-none-any.whl 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importlib-metadata-8.7.1 packaging-26.0 requests-2.32.5 snowballstemmer-3.0.1 sphinx-7.4.7 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 tomli-2.4.0 urllib3-2.6.3 zipp-3.23.0 [rtd-command-info] start-time: 2026-03-07T02:22:22.868212Z, end-time: 2026-03-07T02:22:56.032837Z, duration: 33, 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 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kiwisolver, jupyterlab-pygments, importlib-resources, greenlet, fonttools, executing, defusedxml, decorator, debugpy, cycler, comm, colorlog, bleach, attrs, asttokens, accessible-pygments, stack-data, sqlalchemy, referencing, python-dateutil, prompt-toolkit, plantweb, pandoc, mistune, matplotlib-inline, jupyter-core, jedi, exceptiongroup, 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-1.3.10 PyYAML-6.0.3 accessible-pygments-0.0.5 alembic-1.16.5 asttokens-3.0.1 attrs-25.4.0 beautifulsoup4-4.14.3 bleach-6.2.0 colorlog-6.10.1 comm-0.2.3 contourpy-1.3.0 cycler-0.12.1 debugpy-1.8.20 decorator-5.2.1 defusedxml-0.7.1 exceptiongroup-1.3.1 executing-2.2.1 fastjsonschema-2.21.2 fonttools-4.60.2 greenlet-3.2.5 importlib-resources-6.5.2 ipykernel-6.31.0 ipython-8.18.1 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(6.0.3) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (from sciris>=3.0.0->hpvsim==2.1.0) (26.0) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (from sciris>=3.0.0->hpvsim==2.1.0) (82.0.0) Collecting gitpython (from sciris>=3.0.0->hpvsim==2.1.0) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/6a/09/e21df6aef1e1ffc0c816f0522ddc3f6dcded766c3261813131c78a704470/gitpython-3.1.46-py3-none-any.whl (208 kB) Collecting jellyfish (from sciris>=3.0.0->hpvsim==2.1.0) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/3a/ff/f9cc3182e3da6797b58451a9607575c0e3707dea171142459d4b0bb8d6e1/jellyfish-1.2.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (361 kB) Requirement already 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/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (from matplotlib->hpvsim==2.1.0) (1.3.0) Requirement already satisfied: cycler>=0.10 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (from matplotlib->hpvsim==2.1.0) (0.12.1) Requirement already satisfied: fonttools>=4.22.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (from matplotlib->hpvsim==2.1.0) (4.60.2) Requirement already satisfied: kiwisolver>=1.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (from matplotlib->hpvsim==2.1.0) (1.4.7) Requirement already satisfied: pillow>=8 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (from matplotlib->hpvsim==2.1.0) (11.3.0) Requirement already satisfied: pyparsing>=2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (from matplotlib->hpvsim==2.1.0) (3.3.2) Requirement already satisfied: importlib-resources>=3.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (from matplotlib->hpvsim==2.1.0) (6.5.2) Requirement already satisfied: zipp>=3.1.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (from importlib-resources>=3.2.0->matplotlib->hpvsim==2.1.0) (3.23.0) Collecting et-xmlfile (from openpyxl->sciris>=3.0.0->hpvsim==2.1.0) 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/python3.9/site-packages (from optuna->hpvsim==2.1.0) (1.16.5) Requirement already satisfied: colorlog in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (from optuna->hpvsim==2.1.0) (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/python3.9/site-packages (from optuna->hpvsim==2.1.0) (2.0.48) Requirement already satisfied: Mako in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (from alembic>=1.5.0->optuna->hpvsim==2.1.0) (1.3.10) Requirement already satisfied: greenlet>=1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (from sqlalchemy>=1.4.2->optuna->hpvsim==2.1.0) (3.2.5) Requirement already satisfied: MarkupSafe>=0.9.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (from Mako->alembic>=1.5.0->optuna->hpvsim==2.1.0) (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-2.1.0-py3-none-any.whl size=198188 sha256=9b5d3019da2a146176138ca64375ec03f789ce68587a1744afecb0f3d7cb6268 Stored in directory: /tmp/pip-ephem-wheel-cache-6613ivpr/wheels/51/35/6f/df976332f8d726e8d5b6219b83a0569f551e10d63ed39a50fb 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-2.1.0 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-1.13.1 sciris-3.2.9 smmap-5.0.2 xlsxwriter-3.2.9 zstandard-0.25.0 [rtd-command-info] start-time: 2026-03-07T02:23:09.009847Z, end-time: 2026-03-07T02:23:09.043840Z, 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", } # 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 = '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: 2026-03-07T02:23:09.420873Z, end-time: 2026-03-07T02:23:22.383948Z, duration: 12, exit-code: 2 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v7.4.7 HPVsim 2.1.0 (2025-03-25) — © 2023-2025 by IDM 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... Quick download failed (HTTP Error 429: Too Many Requests), trying manual download ...  —————————————————————————————————————————————————————— Downloading HPVsim data manually, please be patient... ——————————————————————————————————————————————————————  Warning: couldn't download data: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/__init__.py", line 30, in data.quick_download(init=True) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/downloaders.py", line 193, in quick_download sc.download(url=quick_url, filename=filepath, convert=False, verbose=verbose) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_utils.py", line 877, in download raise E File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_utils.py", line 874, in download output = urlopen(url=url, filename=key, **func_kwargs) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_utils.py", line 749, in urlopen resp = ur.urlopen(request) # Actually open the URL File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 214, in urlopen return opener.open(url, data, timeout) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 523, in open response = meth(req, response) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 632, in http_response response = self.parent.error( File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 561, in error return self._call_chain(*args) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 494, in _call_chain result = func(*args) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 641, in http_error_default raise HTTPError(req.full_url, code, msg, hdrs, fp) urllib.error.HTTPError: HTTP Error 429: Too Many Requests 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-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/__init__.py", line 34, in data.download_data(serial=True) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/downloaders.py", line 168, in download_data raise ValueError(errormsg) ValueError: Invalid selection "-T": must be all, ages, births, or deaths Proceeding anyway... 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, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.plotting.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.population.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.run.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.settings.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.utils.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.analysis.Analyzer.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.analysis.age_causal_infection.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.analysis.age_pyramid.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.analysis.age_results.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.analysis.cancer_detection.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.analysis.dalys.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.analysis.snapshot.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.base.BasePeople.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.base.BaseSim.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.base.Contacts.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.utils.n_binomial.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.utils.n_multinomial.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.utils.n_neg_binomial.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.utils.n_poisson.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.utils.participation_filter.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.utils.poisson.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.utils.sample.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.utils.set_seed.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.utils.true.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/latest/docs/api/_autosummary/hpvsim.utils.undefined.rst building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 13 source files that are out of date updating environment: [new config] 163 added, 0 changed, 0 removed reading sources... 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WARNING: Summarised items should not include the current module. Replace 'hpvsim.base' with 'base'. WARNING: Summarised items should not include the current module. Replace 'hpvsim.calibration' with 'calibration'. WARNING: Summarised items should not include the current module. Replace 'hpvsim.defaults' with 'defaults'. WARNING: Summarised items should not include the current module. Replace 'hpvsim.hiv' with 'hiv'. WARNING: Summarised items should not include the current module. Replace 'hpvsim.immunity' with 'immunity'. WARNING: Summarised items should not include the current module. Replace 'hpvsim.interventions' with 'interventions'. WARNING: Summarised items should not include the current module. Replace 'hpvsim.misc' with 'misc'. WARNING: Summarised items should not include the current module. Replace 'hpvsim.parameters' with 'parameters'. WARNING: Summarised items should not include the current module. Replace 'hpvsim.people' with 'people'. WARNING: Summarised items should not include the current module. Replace 'hpvsim.plotting' with 'plotting'. WARNING: Summarised items should not include the current module. Replace 'hpvsim.population' with 'population'. WARNING: Summarised items should not include the current module. Replace 'hpvsim.run' with 'run'. WARNING: Summarised items should not include the current module. Replace 'hpvsim.settings' with 'settings'. WARNING: Summarised items should not include the current module. Replace 'hpvsim.sim' with 'sim'. WARNING: Summarised items should not include the current module. Replace 'hpvsim.utils' with 'utils'. WARNING: Summarised items should not include the current module. Replace 'hpvsim.data.downloaders' with 'data.downloaders'. WARNING: Summarised items should not include the current module. Replace 'hpvsim.data.loaders' with 'data.loaders'. Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 154, in wrapped asyncio.get_running_loop() RuntimeError: no running event loop 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-hpvsim/envs/latest/lib/python3.9/site-packages/nbsphinx/__init__.py", line 653, in parse rststring, resources = exporter.from_notebook_node(nb, resources) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/nbsphinx/__init__.py", line 416, in from_notebook_node nb, resources = pp.preprocess(nb, resources) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/nbconvert/preprocessors/execute.py", line 103, in preprocess self.preprocess_cell(cell, resources, index) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/nbconvert/preprocessors/execute.py", line 124, in preprocess_cell cell = self.execute_cell(cell, index, store_history=True) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 158, in wrapped return loop.run_until_complete(inner) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete return future.result() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/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-hpvsim/envs/latest/lib/python3.9/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 numpy as np import sciris as sc import hpvsim as hpv # Create some parameters, setting beta (per-contact transmission probability) higher # to create more cancers for illutration pars = dict(beta=0.5, n_agents=50e3, start=1970, n_years=50, dt=1., location='tanzania') # Also set initial HPV prevalence to be high, again to generate more cancers pars['init_hpv_prev'] = { 'age_brackets' : np.array([ 12, 17, 24, 34, 44, 64, 80, 150]), 'm' : np.array([ 0.0, 0.75, 0.9, 0.45, 0.1, 0.05, 0.005, 0]), 'f' : np.array([ 0.0, 0.75, 0.9, 0.45, 0.1, 0.05, 0.005, 0]), } # Create the age analyzers. az1 = hpv.age_results( result_args=sc.objdict( hpv_prevalence=sc.objdict( # The keys of this dictionary are any results you want by age, and can be any key of sim.results years=2019, # List the years that you want to generate results for edges=np.array([0., 15., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ), hpv_incidence=sc.objdict( years=2019, edges=np.array([0., 15., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ), cancer_incidence=sc.objdict( years=2019, edges=np.array([0.,20.,25.,30.,40.,45.,50.,55.,65.,100.]), ), cancer_mortality=sc.objdict( years=2019, edges=np.array([0., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ) ) ) sim = hpv.Sim(pars, genotypes=[16, 18], analyzers=[az1]) sim.run() a = sim.get_analyzer() a.plot(); ------------------ ----- stdout ----- HPVsim 2.1.0 (2025-03-25) — © 2023-2025 by IDM 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... Quick download failed (HTTP Error 429: Too Many Requests), trying manual download ...  —————————————————————————————————————————————————————— Downloading HPVsim data manually, please be patient... ——————————————————————————————————————————————————————  Warning: couldn't download data: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/__init__.py", line 30, in data.quick_download(init=True) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/downloaders.py", line 193, in quick_download sc.download(url=quick_url, filename=filepath, convert=False, verbose=verbose) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_utils.py", line 877, in download raise E File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_utils.py", line 874, in download output = urlopen(url=url, filename=key, **func_kwargs) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_utils.py", line 749, in urlopen resp = ur.urlopen(request) # Actually open the URL File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 214, in urlopen return opener.open(url, data, timeout) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 523, in open response = meth(req, response) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 632, in http_response response = self.parent.error( File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 561, in error return self._call_chain(*args) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 494, in _call_chain result = func(*args) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 641, in http_error_default raise HTTPError(req.full_url, code, msg, hdrs, fp) urllib.error.HTTPError: HTTP Error 429: Too Many Requests 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-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/__init__.py", line 34, in data.download_data(serial=True) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/downloaders.py", line 168, in download_data raise ValueError(errormsg) ValueError: Invalid selection "-f": must be all, ages, births, or deaths Proceeding anyway... Loading location-specific demographic data for "tanzania" ------------------ --------------------------------------------------------------------------- FileNotFoundError Traceback (most recent call last) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/loaders.py:271, in get_death_rates(location, by_sex, overall)  270 try: --> 271 df = load_file(files.death)  272 except Exception as E: File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/loaders.py:53, in load_file(path)  52 if strpath not in cache: ---> 53 obj = sc.load(path)  54 cache[strpath] = obj File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_fileio.py:180, in load(filename, folder, verbose, die, remapping, method, auto_remap, **kwargs)  179 # Load the file --> 180 filestr = _load_filestr(filename, folder, verbose=verbose)  182 # Unpickle it File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_fileio.py:107, in _load_filestr(filename, folder, verbose)  106 if exc == FileNotFoundError: # This is simple, just raise directly --> 107 raise E  108 elif exc == gz.BadGzipFile: File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_fileio.py:102, in _load_filestr(filename, folder, verbose)  101 if verbose: print(' Reading as gzip file...') --> 102 with gz.GzipFile(**fileargs) as fileobj:  103 filestr = fileobj.read() # Convert it to a string File ~/.asdf/installs/python/3.9.22/lib/python3.9/gzip.py:173, in GzipFile.__init__(self, filename, mode, compresslevel, fileobj, mtime)  172 if fileobj is None: --> 173 fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')  174 if filename is None: FileNotFoundError: [Errno 2] No such file or directory: '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/files/mx.obj' The above exception was the direct cause of the following exception: ValueError Traceback (most recent call last) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/parameters.py:252, in get_births_deaths(location, verbose, by_sex, overall, die)  251 try: --> 252 death_rates = hpdata.get_death_rates(location=location, by_sex=by_sex, overall=overall)  253 birth_rates = hpdata.get_birth_rates(location=location) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/loaders.py:274, in get_death_rates(location, by_sex, overall)  273 errormsg = f'Could not locate datafile with age-specific death rates by country. {download_tip}' --> 274 raise ValueError(errormsg) from E  276 raw_df = map_entries(df, location) ValueError: Could not locate datafile with age-specific death rates by country. Please run hpv.download_data() first. During handling of the above exception, another exception occurred: RuntimeWarning Traceback (most recent call last) Cell In[1], line 38  16 # Create the age analyzers.  17 az1 = hpv.age_results(  18 result_args=sc.objdict(  19 hpv_prevalence=sc.objdict( # The keys of this dictionary are any results you want by age, and can be any key of sim.results  (...)  35 )  36 ) ---> 38 sim = hpv.Sim(pars, genotypes=[16, 18], analyzers=[az1])  39 sim.run()  40 a = sim.get_analyzer() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/sim.py:65, in Sim.__init__(self, pars, datafile, label, popfile, popdict, people, version, hiv_datafile, art_datafile, **kwargs)  62 if not pars.get('location') or pars['location'] is None:  63 pars['location'] = default_location ---> 65 self.update_pars(pars, **kwargs) # Update the parameters  67 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/base.py:298, in BaseSim.update_pars(self, pars, create, **kwargs)  296 if pars.get('location'):  297 location = pars['location'] --> 298 pars['birth_rates'], pars['death_rates'] = hppar.get_births_deaths(location=location) # Set birth and death rates  299 if pars.get('n_clusters'):  300 hppar.add_mixing(pars) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/parameters.py:257, in get_births_deaths(location, verbose, by_sex, overall, die)  255 except ValueError as E:  256 warnmsg = f'Could not load demographic data for requested location "{location}" ({str(E)})' --> 257 hpm.warn(warnmsg, die=die) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/misc.py:726, in warn(msg, category, verbose, die)  724 # Handle the different options  725 if warnopt in ['error', 'errors']: # Include alias since hard to remember --> 726 raise category(msg)  727 elif warnopt == 'warn':  728 msg = '\n' + msg RuntimeWarning: Could not load demographic data for requested location "tanzania" (Could not locate datafile with age-specific death rates by country. Please run hpv.download_data() first.) 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-hpvsim/envs/latest/lib/python3.9/site-packages/sphinx/cmd/build.py", line 337, in build_main app.build(args.force_all, args.filenames) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sphinx/application.py", line 378, in build self.builder.build_update() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 297, in build_update self.build(to_build, File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 318, in build updated_docnames = set(self.read()) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 425, in read self._read_serial(docnames) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 477, in _read_serial self.read_doc(docname) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 536, in read_doc publisher.publish() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/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-hpvsim/envs/latest/lib/python3.9/site-packages/sphinx/io.py", line 106, in read self.parse() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/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-hpvsim/envs/latest/lib/python3.9/site-packages/nbsphinx/__init__.py", line 660, in parse raise NotebookError('\n'.join(lines)) nbsphinx.NotebookError: CellExecutionError in tutorials/tut_analyzers.ipynb: ------------------ import numpy as np import sciris as sc import hpvsim as hpv # Create some parameters, setting beta (per-contact transmission probability) higher # to create more cancers for illutration pars = dict(beta=0.5, n_agents=50e3, start=1970, n_years=50, dt=1., location='tanzania') # Also set initial HPV prevalence to be high, again to generate more cancers pars['init_hpv_prev'] = { 'age_brackets' : np.array([ 12, 17, 24, 34, 44, 64, 80, 150]), 'm' : np.array([ 0.0, 0.75, 0.9, 0.45, 0.1, 0.05, 0.005, 0]), 'f' : np.array([ 0.0, 0.75, 0.9, 0.45, 0.1, 0.05, 0.005, 0]), } # Create the age analyzers. az1 = hpv.age_results( result_args=sc.objdict( hpv_prevalence=sc.objdict( # The keys of this dictionary are any results you want by age, and can be any key of sim.results years=2019, # List the years that you want to generate results for edges=np.array([0., 15., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ), hpv_incidence=sc.objdict( years=2019, edges=np.array([0., 15., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ), cancer_incidence=sc.objdict( years=2019, edges=np.array([0.,20.,25.,30.,40.,45.,50.,55.,65.,100.]), ), cancer_mortality=sc.objdict( years=2019, edges=np.array([0., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ) ) ) sim = hpv.Sim(pars, genotypes=[16, 18], analyzers=[az1]) sim.run() a = sim.get_analyzer() a.plot(); ------------------ ----- stdout ----- HPVsim 2.1.0 (2025-03-25) — © 2023-2025 by IDM 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... Quick download failed (HTTP Error 429: Too Many Requests), trying manual download ...  —————————————————————————————————————————————————————— Downloading HPVsim data manually, please be patient... ——————————————————————————————————————————————————————  Warning: couldn't download data: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/__init__.py", line 30, in data.quick_download(init=True) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/downloaders.py", line 193, in quick_download sc.download(url=quick_url, filename=filepath, convert=False, verbose=verbose) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_utils.py", line 877, in download raise E File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_utils.py", line 874, in download output = urlopen(url=url, filename=key, **func_kwargs) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_utils.py", line 749, in urlopen resp = ur.urlopen(request) # Actually open the URL File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 214, in urlopen return opener.open(url, data, timeout) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 523, in open response = meth(req, response) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 632, in http_response response = self.parent.error( File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 561, in error return self._call_chain(*args) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 494, in _call_chain result = func(*args) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 641, in http_error_default raise HTTPError(req.full_url, code, msg, hdrs, fp) urllib.error.HTTPError: HTTP Error 429: Too Many Requests 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-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/__init__.py", line 34, in data.download_data(serial=True) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/downloaders.py", line 168, in download_data raise ValueError(errormsg) ValueError: Invalid selection "-f": must be all, ages, births, or deaths Proceeding anyway... Loading location-specific demographic data for "tanzania" ------------------ --------------------------------------------------------------------------- FileNotFoundError Traceback (most recent call last) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/loaders.py:271, in get_death_rates(location, by_sex, overall)  270 try: --> 271 df = load_file(files.death)  272 except Exception as E: File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/loaders.py:53, in load_file(path)  52 if strpath not in cache: ---> 53 obj = sc.load(path)  54 cache[strpath] = obj File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_fileio.py:180, in load(filename, folder, verbose, die, remapping, method, auto_remap, **kwargs)  179 # Load the file --> 180 filestr = _load_filestr(filename, folder, verbose=verbose)  182 # Unpickle it File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_fileio.py:107, in _load_filestr(filename, folder, verbose)  106 if exc == FileNotFoundError: # This is simple, just raise directly --> 107 raise E  108 elif exc == gz.BadGzipFile: File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_fileio.py:102, in _load_filestr(filename, folder, verbose)  101 if verbose: print(' Reading as gzip file...') --> 102 with gz.GzipFile(**fileargs) as fileobj:  103 filestr = fileobj.read() # Convert it to a string File ~/.asdf/installs/python/3.9.22/lib/python3.9/gzip.py:173, in GzipFile.__init__(self, filename, mode, compresslevel, fileobj, mtime)  172 if fileobj is None: --> 173 fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')  174 if filename is None: FileNotFoundError: [Errno 2] No such file or directory: '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/files/mx.obj' The above exception was the direct cause of the following exception: ValueError Traceback (most recent call last) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/parameters.py:252, in get_births_deaths(location, verbose, by_sex, overall, die)  251 try: --> 252 death_rates = hpdata.get_death_rates(location=location, by_sex=by_sex, overall=overall)  253 birth_rates = hpdata.get_birth_rates(location=location) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/loaders.py:274, in get_death_rates(location, by_sex, overall)  273 errormsg = f'Could not locate datafile with age-specific death rates by country. {download_tip}' --> 274 raise ValueError(errormsg) from E  276 raw_df = map_entries(df, location) ValueError: Could not locate datafile with age-specific death rates by country. Please run hpv.download_data() first. During handling of the above exception, another exception occurred: RuntimeWarning Traceback (most recent call last) Cell In[1], line 38  16 # Create the age analyzers.  17 az1 = hpv.age_results(  18 result_args=sc.objdict(  19 hpv_prevalence=sc.objdict( # The keys of this dictionary are any results you want by age, and can be any key of sim.results  (...)  35 )  36 ) ---> 38 sim = hpv.Sim(pars, genotypes=[16, 18], analyzers=[az1])  39 sim.run()  40 a = sim.get_analyzer() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/sim.py:65, in Sim.__init__(self, pars, datafile, label, popfile, popdict, people, version, hiv_datafile, art_datafile, **kwargs)  62 if not pars.get('location') or pars['location'] is None:  63 pars['location'] = default_location ---> 65 self.update_pars(pars, **kwargs) # Update the parameters  67 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/base.py:298, in BaseSim.update_pars(self, pars, create, **kwargs)  296 if pars.get('location'):  297 location = pars['location'] --> 298 pars['birth_rates'], pars['death_rates'] = hppar.get_births_deaths(location=location) # Set birth and death rates  299 if pars.get('n_clusters'):  300 hppar.add_mixing(pars) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/parameters.py:257, in get_births_deaths(location, verbose, by_sex, overall, die)  255 except ValueError as E:  256 warnmsg = f'Could not load demographic data for requested location "{location}" ({str(E)})' --> 257 hpm.warn(warnmsg, die=die) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/misc.py:726, in warn(msg, category, verbose, die)  724 # Handle the different options  725 if warnopt in ['error', 'errors']: # Include alias since hard to remember --> 726 raise category(msg)  727 elif warnopt == 'warn':  728 msg = '\n' + msg RuntimeWarning: Could not load demographic data for requested location "tanzania" (Could not locate datafile with age-specific death rates by country. Please run hpv.download_data() first.) You can ignore this error by setting the following in conf.py: nbsphinx_allow_errors = True Notebook error: CellExecutionError in tutorials/tut_analyzers.ipynb: ------------------ import numpy as np import sciris as sc import hpvsim as hpv # Create some parameters, setting beta (per-contact transmission probability) higher # to create more cancers for illutration pars = dict(beta=0.5, n_agents=50e3, start=1970, n_years=50, dt=1., location='tanzania') # Also set initial HPV prevalence to be high, again to generate more cancers pars['init_hpv_prev'] = { 'age_brackets' : np.array([ 12, 17, 24, 34, 44, 64, 80, 150]), 'm' : np.array([ 0.0, 0.75, 0.9, 0.45, 0.1, 0.05, 0.005, 0]), 'f' : np.array([ 0.0, 0.75, 0.9, 0.45, 0.1, 0.05, 0.005, 0]), } # Create the age analyzers. az1 = hpv.age_results( result_args=sc.objdict( hpv_prevalence=sc.objdict( # The keys of this dictionary are any results you want by age, and can be any key of sim.results years=2019, # List the years that you want to generate results for edges=np.array([0., 15., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ), hpv_incidence=sc.objdict( years=2019, edges=np.array([0., 15., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ), cancer_incidence=sc.objdict( years=2019, edges=np.array([0.,20.,25.,30.,40.,45.,50.,55.,65.,100.]), ), cancer_mortality=sc.objdict( years=2019, edges=np.array([0., 20., 25., 30., 40., 45., 50., 55., 65., 100.]), ) ) ) sim = hpv.Sim(pars, genotypes=[16, 18], analyzers=[az1]) sim.run() a = sim.get_analyzer() a.plot(); ------------------ ----- stdout ----- HPVsim 2.1.0 (2025-03-25) — © 2023-2025 by IDM 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... Quick download failed (HTTP Error 429: Too Many Requests), trying manual download ...  —————————————————————————————————————————————————————— Downloading HPVsim data manually, please be patient... ——————————————————————————————————————————————————————  Warning: couldn't download data: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/__init__.py", line 30, in data.quick_download(init=True) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/downloaders.py", line 193, in quick_download sc.download(url=quick_url, filename=filepath, convert=False, verbose=verbose) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_utils.py", line 877, in download raise E File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_utils.py", line 874, in download output = urlopen(url=url, filename=key, **func_kwargs) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_utils.py", line 749, in urlopen resp = ur.urlopen(request) # Actually open the URL File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 214, in urlopen return opener.open(url, data, timeout) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 523, in open response = meth(req, response) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 632, in http_response response = self.parent.error( File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 561, in error return self._call_chain(*args) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 494, in _call_chain result = func(*args) File "/home/docs/.asdf/installs/python/3.9.22/lib/python3.9/urllib/request.py", line 641, in http_error_default raise HTTPError(req.full_url, code, msg, hdrs, fp) urllib.error.HTTPError: HTTP Error 429: Too Many Requests 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-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/__init__.py", line 34, in data.download_data(serial=True) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/downloaders.py", line 168, in download_data raise ValueError(errormsg) ValueError: Invalid selection "-f": must be all, ages, births, or deaths Proceeding anyway... Loading location-specific demographic data for "tanzania" ------------------ --------------------------------------------------------------------------- FileNotFoundError Traceback (most recent call last) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/loaders.py:271, in get_death_rates(location, by_sex, overall)  270 try: --> 271 df = load_file(files.death)  272 except Exception as E: File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/loaders.py:53, in load_file(path)  52 if strpath not in cache: ---> 53 obj = sc.load(path)  54 cache[strpath] = obj File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_fileio.py:180, in load(filename, folder, verbose, die, remapping, method, auto_remap, **kwargs)  179 # Load the file --> 180 filestr = _load_filestr(filename, folder, verbose=verbose)  182 # Unpickle it File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_fileio.py:107, in _load_filestr(filename, folder, verbose)  106 if exc == FileNotFoundError: # This is simple, just raise directly --> 107 raise E  108 elif exc == gz.BadGzipFile: File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/sciris/sc_fileio.py:102, in _load_filestr(filename, folder, verbose)  101 if verbose: print(' Reading as gzip file...') --> 102 with gz.GzipFile(**fileargs) as fileobj:  103 filestr = fileobj.read() # Convert it to a string File ~/.asdf/installs/python/3.9.22/lib/python3.9/gzip.py:173, in GzipFile.__init__(self, filename, mode, compresslevel, fileobj, mtime)  172 if fileobj is None: --> 173 fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')  174 if filename is None: FileNotFoundError: [Errno 2] No such file or directory: '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/files/mx.obj' The above exception was the direct cause of the following exception: ValueError Traceback (most recent call last) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/parameters.py:252, in get_births_deaths(location, verbose, by_sex, overall, die)  251 try: --> 252 death_rates = hpdata.get_death_rates(location=location, by_sex=by_sex, overall=overall)  253 birth_rates = hpdata.get_birth_rates(location=location) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/data/loaders.py:274, in get_death_rates(location, by_sex, overall)  273 errormsg = f'Could not locate datafile with age-specific death rates by country. {download_tip}' --> 274 raise ValueError(errormsg) from E  276 raw_df = map_entries(df, location) ValueError: Could not locate datafile with age-specific death rates by country. Please run hpv.download_data() first. During handling of the above exception, another exception occurred: RuntimeWarning Traceback (most recent call last) Cell In[1], line 38  16 # Create the age analyzers.  17 az1 = hpv.age_results(  18 result_args=sc.objdict(  19 hpv_prevalence=sc.objdict( # The keys of this dictionary are any results you want by age, and can be any key of sim.results  (...)  35 )  36 ) ---> 38 sim = hpv.Sim(pars, genotypes=[16, 18], analyzers=[az1])  39 sim.run()  40 a = sim.get_analyzer() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/sim.py:65, in Sim.__init__(self, pars, datafile, label, popfile, popdict, people, version, hiv_datafile, art_datafile, **kwargs)  62 if not pars.get('location') or pars['location'] is None:  63 pars['location'] = default_location ---> 65 self.update_pars(pars, **kwargs) # Update the parameters  67 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/base.py:298, in BaseSim.update_pars(self, pars, create, **kwargs)  296 if pars.get('location'):  297 location = pars['location'] --> 298 pars['birth_rates'], pars['death_rates'] = hppar.get_births_deaths(location=location) # Set birth and death rates  299 if pars.get('n_clusters'):  300 hppar.add_mixing(pars) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/parameters.py:257, in get_births_deaths(location, verbose, by_sex, overall, die)  255 except ValueError as E:  256 warnmsg = f'Could not load demographic data for requested location "{location}" ({str(E)})' --> 257 hpm.warn(warnmsg, die=die) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages/hpvsim/misc.py:726, in warn(msg, category, verbose, die)  724 # Handle the different options  725 if warnopt in ['error', 'errors']: # Include alias since hard to remember --> 726 raise category(msg)  727 elif warnopt == 'warn':  728 msg = '\n' + msg RuntimeWarning: Could not load demographic data for requested location "tanzania" (Could not locate datafile with age-specific death rates by country. Please run hpv.download_data() first.) You can ignore this error by setting the following in conf.py: nbsphinx_allow_errors = True