Read the Docs build information Build id: 3810359 Project: institute-for-disease-modeling-hpvsim Version: 31 Commit: 9603d13725e227e4b5317fb661230416e07cdc4f Date: 2026-03-07T02:44:58.622341Z State: finished Success: False [rtd-command-info] start-time: 2026-03-07T02:44:59.340365Z, end-time: 2026-03-07T02:44:59.826039Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/starsimhub/hpvsim.git . Cloning into '.'... [rtd-command-info] start-time: 2026-03-07T02:44:59.904933Z, end-time: 2026-03-07T02:45:01.246023Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/31/head:external-31 From https://github.com/starsimhub/hpvsim * [new ref] refs/pull/31/head -> external-31 * [new tag] v0.4.16 -> v0.4.16 * [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: 2026-03-07T02:45:01.895934Z, end-time: 2026-03-07T02:45:01.952565Z, duration: 0, exit-code: 0 git checkout --force 9603d13725e227e4b5317fb661230416e07cdc4f Note: switching to '9603d13725e227e4b5317fb661230416e07cdc4f'. 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 9603d13 update readthedocs [rtd-command-info] start-time: 2026-03-07T02:45:02.038681Z, end-time: 2026-03-07T02:45:02.079147Z, 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: - python -c "import hpvsim" # 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: 2026-03-07T02:45:07.001963Z, end-time: 2026-03-07T02:45:07.056870Z, duration: 0, exit-code: 0 asdf global python 3.13.3 [rtd-command-info] start-time: 2026-03-07T02:45:07.435765Z, end-time: 2026-03-07T02:45:07.936433Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.13.3.final.0-64 in 281ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31, 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: 2026-03-07T02:45:08.019879Z, end-time: 2026-03-07T02:45:11.749354Z, duration: 3, exit-code: 0 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Installing collected packages: urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, roman-numerals, 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-2.18.0 certifi-2026.2.25 charset_normalizer-3.4.5 docutils-0.22.4 idna-3.11 imagesize-2.0.0 packaging-26.0 requests-2.32.5 roman-numerals-4.1.0 snowballstemmer-3.0.1 sphinx-9.1.0 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 urllib3-2.6.3 [rtd-command-info] start-time: 2026-03-07T02:45:18.106778Z, end-time: 2026-03-07T02:45:50.241374Z, duration: 32, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r 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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-1.3.10 PyYAML-6.0.3 accessible-pygments-0.0.5 alembic-1.18.4 asttokens-3.0.1 attrs-25.4.0 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-4.61.1 greenlet-3.3.2 ipykernel-7.2.0 ipython-9.11.0 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-1.4.9 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-2.4.2 optuna-4.7.0 pandas-3.0.1 pandoc-2.4 pandocfilters-1.5.1 parso-0.8.6 pexpect-4.9.0 pillow-12.1.1 plantweb-1.3.0 platformdirs-4.9.4 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-0.16.1 pypandoc-1.16.2 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-3.9.7 sphinx-design-0.7.0 sqlalchemy-2.0.48 stack_data-0.6.3 tinycss2-1.4.0 tornado-6.5.4 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: 2026-03-07T02:45:50.344708Z, end-time: 2026-03-07T02:46:02.967827Z, duration: 12, 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/31/lib/python3.13/site-packages (from matplotlib->hpvsim==2.1.0) (4.61.1) Requirement already satisfied: kiwisolver>=1.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31/lib/python3.13/site-packages (from matplotlib->hpvsim==2.1.0) (1.4.9) Requirement already satisfied: pillow>=8 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31/lib/python3.13/site-packages (from matplotlib->hpvsim==2.1.0) (12.1.1) Requirement already satisfied: pyparsing>=3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31/lib/python3.13/site-packages (from matplotlib->hpvsim==2.1.0) (3.3.2) 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/31/lib/python3.13/site-packages (from optuna->hpvsim==2.1.0) (1.18.4) Requirement already satisfied: colorlog in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/site-packages (from sqlalchemy>=1.4.2->optuna->hpvsim==2.1.0) (3.3.2) Requirement already satisfied: MarkupSafe>=0.9.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31/lib/python3.13/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=cad2070ba59f0ba1ded75d4f2e0cef61058df2585f8c248b19ad299e994b8c3a Stored in directory: /tmp/pip-ephem-wheel-cache-sdlvsskz/wheels/4a/3d/7a/4164043fd10604ccd26c7cb8cb7bea44386438c0ddea4197d9 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-1.17.1 sciris-3.2.9 smmap-5.0.2 xlsxwriter-3.2.9 zstandard-0.25.0 [rtd-command-info] start-time: 2026-03-07T02:46:03.054373Z, end-time: 2026-03-07T02:46:58.757587Z, duration: 55, exit-code: 0 python -c "import hpvsim" /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31/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) 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... ——————————————————————————————————————————————————————   —————————————— Working on age ——————————————  Downloading age data... Downloading https://population.un.org/wpp/assets/Excel%20Files/1_Indicator%20(Standard)/CSV_FILES/WPP2024_Population1JanuaryBySingleAgeSex_Medium_1950-2023.csv.gz... Removed "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/hpvsim/data/files/WPP2024_Population1JanuaryBySingleAgeSex_Medium_1950-2023.csv.gz" Done with "age" for 1950-2023: 5.30 s Downloading https://population.un.org/wpp/assets/Excel%20Files/1_Indicator%20(Standard)/CSV_FILES/WPP2024_Population1JanuaryBySingleAgeSex_Medium_2024-2100.csv.gz... Removed "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/hpvsim/data/files/WPP2024_Population1JanuaryBySingleAgeSex_Medium_2024-2100.csv.gz" Done with "age" for 2024-2100: 5.09 s Done with age: 13.4118 Downloading age data... Downloading https://population.un.org/wpp/assets/Excel%20Files/1_Indicator%20(Standard)/CSV_FILES/WPP2024_Population1JanuaryBySingleAgeSex_Medium_1950-2023.csv.gz... Removed "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/hpvsim/data/files/WPP2024_Population1JanuaryBySingleAgeSex_Medium_1950-2023.csv.gz" Done with "age" for 1950-2023: 5.74 s Downloading https://population.un.org/wpp/assets/Excel%20Files/1_Indicator%20(Standard)/CSV_FILES/WPP2024_Population1JanuaryBySingleAgeSex_Medium_2024-2100.csv.gz... Removed "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/hpvsim/data/files/WPP2024_Population1JanuaryBySingleAgeSex_Medium_2024-2100.csv.gz" Done with "age" for 2024-2100: 5.98 s Done with age: 15.8425  ———————————————— 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/checkouts/31/hpvsim/data/files/WPP2024_Demographic_Indicators_Medium.csv.gz" Done with "birth" for : 1.92 s Done with birth: 1.962  ———————————————— Working on death ————————————————  Downloading death data... Downloading https://population.un.org/wpp/assets/Excel%20Files/1_Indicator%20(Standard)/CSV_FILES/WPP2024_Life_Table_Abridged_Medium_1950-2023.csv.gz... Removed "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/hpvsim/data/files/WPP2024_Life_Table_Abridged_Medium_1950-2023.csv.gz" Done with "death" for 1950-2023: 8.32 s Downloading https://population.un.org/wpp/assets/Excel%20Files/1_Indicator%20(Standard)/CSV_FILES/WPP2024_Life_Table_Abridged_Medium_2024-2100.csv.gz... Removed "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/hpvsim/data/files/WPP2024_Life_Table_Abridged_Medium_2024-2100.csv.gz" Done with "death" for 2024-2100: 8.19 s Done with death: 18.5731 Done downloading data for HPVsim: 49.9 s [rtd-command-info] start-time: 2026-03-07T02:46:58.904328Z, end-time: 2026-03-07T02:46:58.942924Z, 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: 2026-03-07T02:46:59.024349Z, end-time: 2026-03-07T02:47:08.590246Z, duration: 9, exit-code: 2 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v9.1.0 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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/site-packages/sciris/sc_utils.py", line 749, in urlopen resp = ur.urlopen(request) # Actually open the URL File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 189, in urlopen return opener.open(url, data, timeout) ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 495, in open response = meth(req, response) File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 604, in http_response response = self.parent.error( 'http', request, response, code, msg, hdrs) File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 533, in error return self._call_chain(*args) ~~~~~~~~~~~~~~~~^^^^^^^ File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 466, in _call_chain result = func(*args) File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 613, 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/31/lib/python3.13/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/31/lib/python3.13/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/31/docs/api/_autosummary/hpvsim.analysis.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.base.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.calibration.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.data.downloaders.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.data.loaders.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.defaults.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.hiv.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.immunity.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.interventions.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.misc.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.parameters.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.people.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.plotting.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.population.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.run.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.settings.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.utils.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.analysis.Analyzer.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.analysis.age_causal_infection.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.analysis.age_pyramid.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.analysis.age_results.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.analysis.cancer_detection.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.analysis.dalys.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.analysis.snapshot.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.base.BasePeople.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.base.BaseSim.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.base.Contacts.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.utils.n_binomial.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.utils.n_multinomial.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.utils.n_neg_binomial.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.utils.n_poisson.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.utils.participation_filter.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.utils.poisson.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.utils.sample.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.utils.set_seed.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.utils.true.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/docs/api/_autosummary/hpvsim.utils.undefined.rst Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/checkouts/31/_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 13 source files that are out of date updating environment: [new config] 163 added, 0 changed, 0 removed reading 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[docutils] WARNING: :1: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. [docutils] WARNING: Summarised items should not include the current module. Replace 'hpvsim.analysis' with 'analysis'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.base' with 'base'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.calibration' with 'calibration'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.defaults' with 'defaults'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.hiv' with 'hiv'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.immunity' with 'immunity'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.interventions' with 'interventions'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.misc' with 'misc'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.parameters' with 'parameters'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.people' with 'people'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.plotting' with 'plotting'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.population' with 'population'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.run' with 'run'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.settings' with 'settings'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.sim' with 'sim'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.utils' with 'utils'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.data.downloaders' with 'data.downloaders'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'hpvsim.data.loaders' with 'data.loaders'. [autosummary.import_cycle] Notebook error! Versions ======== * Platform: linux; (Linux-6.17.0-1007-aws-x86_64-with-glibc2.39) * Python version: 3.13.3 (CPython) * Sphinx version: 9.1.0 * Docutils version: 0.22.4 * Jinja2 version: 3.1.6 * Pygments version: 2.19.2 Last Messages ============= reading sources... [ 94%] tutorials reading sources... [ 95%] tutorials/README reading sources... [ 96%] tutorials/tut_analyzers Loaded Extensions ================= * sphinx.ext.mathjax (9.1.0) * alabaster (1.0.0) * sphinxcontrib.applehelp (2.0.0) * sphinxcontrib.devhelp (2.0.0) * sphinxcontrib.htmlhelp (2.1.0) * sphinxcontrib.serializinghtml (2.0.0) * sphinxcontrib.qthelp (2.0.0) * sphinx.ext.autodoc (9.1.0) * sphinx.ext.autosummary (9.1.0) * sphinx.ext.intersphinx (9.1.0) * sphinx.ext.viewcode (9.1.0) * sphinx.ext.napoleon (9.1.0) * sphinx.ext.autosectionlabel (9.1.0) * sphinx_autodoc_typehints (unknown version) * sphinx_design (0.7.0) * sphinx_search.extension (0.3.2) * nbsphinx (0.9.8) * pydata_sphinx_theme (unknown version) Traceback ========= Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped return loop.run_until_complete(inner) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^ File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/asyncio/base_events.py", line 719, in run_until_complete return future.result() ~~~~~~~~~~~~~^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/site-packages/sciris/sc_utils.py", line 749, in urlopen resp = ur.urlopen(request) # Actually open the URL File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 189, in urlopen return opener.open(url, data, timeout) ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 495, in open response = meth(req, response) File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 604, in http_response response = self.parent.error( 'http', request, response, code, msg, hdrs) File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 533, in error return self._call_chain(*args) ~~~~~~~~~~~~~~~~^^^^^^^ File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 466, in _call_chain result = func(*args) File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 613, 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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/3.13.3/lib/python3.13/gzip.py:203, in GzipFile.__init__(self, filename, mode, compresslevel, fileobj, mtime)  202 if fileobj is None: --> 203 fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')  204 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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/site-packages/sphinx/cmd/build.py", line 432, in build_main app.build(args.force_all, args.filenames) ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31/lib/python3.13/site-packages/sphinx/application.py", line 442, in build self.builder.build_update() ~~~~~~~~~~~~~~~~~~~~~~~~~^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31/lib/python3.13/site-packages/sphinx/builders/__init__.py", line 381, in build_update self.build( ~~~~~~~~~~^ to_build, ^^^^^^^^^ ...<2 lines>... method='update', ^^^^^^^^^^^^^^^^ ) ^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31/lib/python3.13/site-packages/sphinx/builders/__init__.py", line 409, in build updated_docnames = set(self.read()) ~~~~~~~~~^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31/lib/python3.13/site-packages/sphinx/builders/__init__.py", line 525, in read self._read_serial(docnames) ~~~~~~~~~~~~~~~~~^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31/lib/python3.13/site-packages/sphinx/builders/__init__.py", line 590, in _read_serial self.read_doc(docname) ~~~~~~~~~~~~~^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31/lib/python3.13/site-packages/sphinx/builders/__init__.py", line 653, in read_doc doctree = _parse_str_to_doctree( content, ...<6 lines>... transforms=self._registry.get_transforms(), ) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31/lib/python3.13/site-packages/sphinx/util/docutils.py", line 902, in _parse_str_to_doctree parser.parse(content, document) ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/site-packages/sciris/sc_utils.py", line 749, in urlopen resp = ur.urlopen(request) # Actually open the URL File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 189, in urlopen return opener.open(url, data, timeout) ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 495, in open response = meth(req, response) File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 604, in http_response response = self.parent.error( 'http', request, response, code, msg, hdrs) File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 533, in error return self._call_chain(*args) ~~~~~~~~~~~~~~~~^^^^^^^ File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 466, in _call_chain result = func(*args) File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/urllib/request.py", line 613, 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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/3.13.3/lib/python3.13/gzip.py:203, in GzipFile.__init__(self, filename, mode, compresslevel, fileobj, mtime)  202 if fileobj is None: --> 203 fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')  204 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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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/31/lib/python3.13/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 The full traceback has been saved in: /tmp/sphinx-err-98feo3qv.log To report this error to the developers, please open an issue at . Thanks! Please also report this if it was a user error, so that a better error message can be provided next time.