Read the Docs build information Build id: 2904725 Project: institute-for-disease-modeling-starsim Version: 847 Commit: e81a1840af09ada219dc061ac89db77a430e1598 Date: 2025-03-24T14:01:56.276221Z State: finished Success: True [rtd-command-info] start-time: 2025-03-24T14:01:57.165161Z, end-time: 2025-03-24T14:01:57.667676Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/starsimhub/starsim.git . Cloning into '.'... [rtd-command-info] start-time: 2025-03-24T14:01:57.733338Z, end-time: 2025-03-24T14:01:59.036284Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/847/head:external-847 From https://github.com/starsimhub/starsim * [new ref] refs/pull/847/head -> external-847 * [new tag] v0.5.0 -> v0.5.0 * [new tag] v1.0.0 -> v1.0.0 * [new tag] v1.0.2 -> v1.0.2 * [new tag] v1.0.3 -> v1.0.3 * [new tag] v2.0.0 -> v2.0.0 * [new tag] v2.1.0 -> v2.1.0 * [new tag] v2.1.1 -> v2.1.1 * [new tag] v2.2.0 -> v2.2.0 [rtd-command-info] start-time: 2025-03-24T14:01:59.147106Z, end-time: 2025-03-24T14:01:59.200192Z, duration: 0, exit-code: 0 git checkout --force e81a1840af09ada219dc061ac89db77a430e1598 Note: switching to 'e81a1840af09ada219dc061ac89db77a430e1598'. 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 e81a184 Fix where sim repr draws simulation timespan from after initialisation [rtd-command-info] start-time: 2025-03-24T14:01:59.259148Z, end-time: 2025-03-24T14:01:59.300881Z, duration: 0, exit-code: 0 cat .readthedocs.yaml # .readthedocs.yaml # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details # Required version: 2 # Set the version of Python and other tools you might need build: os: ubuntu-22.04 tools: python: "3.11" # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py # If using Sphinx, optionally build your docs in additional formats such as PDF #formats: # - htmlzip # Optionally declare the Python requirements required to build your docs python: install: - requirements: docs/requirements.txt - method: pip path: . [rtd-command-info] start-time: 2025-03-24T14:02:03.484588Z, end-time: 2025-03-24T14:02:03.540395Z, duration: 0, exit-code: 0 asdf global python 3.11.10 [rtd-command-info] start-time: 2025-03-24T14:02:03.876228Z, end-time: 2025-03-24T14:02:04.708178Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.11.10.final.0-64 in 567ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2025-03-24T14:02:04.776319Z, end-time: 2025-03-24T14:02:13.630849Z, duration: 8, exit-code: 0 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installed Jinja2-3.1.6 MarkupSafe-3.0.2 Pygments-2.19.1 alabaster-1.0.0 babel-2.17.0 certifi-2025.1.31 charset-normalizer-3.4.1 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-24.2 requests-2.32.3 roman-numerals-py-3.1.0 snowballstemmer-2.2.0 sphinx-8.2.3 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.3.0 [rtd-command-info] start-time: 2025-03-24T14:02:20.375705Z, end-time: 2025-03-24T14:02:46.149066Z, duration: 25, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting pandoc (from -r docs/requirements.txt (line 1)) Downloading pandoc-2.4.tar.gz (34 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pypandoc (from -r docs/requirements.txt (line 2)) Downloading pypandoc-1.15-py3-none-any.whl.metadata (16 kB) Collecting 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pytz, pure-eval, ptyprocess, ply, fastjsonschema, widgetsnbextension, tzdata, typing-extensions, traitlets, tqdm, tornado, tinycss2, soupsieve, six, rpds-py, readthedocs-sphinx-search, pyzmq, PyYAML, pyparsing, pypandoc, psutil, prompt_toolkit, plumbum, platformdirs, pillow, pexpect, parso, pandocfilters, numpy, nest-asyncio, mistune, Mako, kiwisolver, jupyterlab-widgets, jupyterlab-pygments, ipython-pygments-lexers, greenlet, fonttools, executing, defusedxml, decorator, debugpy, cycler, colorlog, bleach, attrs, asttokens, accessible-pygments, stack_data, sqlalchemy, sphinx, referencing, python-dateutil, pockets, plantweb, pandoc, matplotlib-inline, jupyter-core, jedi, contourpy, comm, beautifulsoup4, sphinxcontrib-napoleon, sphinx-design, sphinx-autodoc-typehints, pydata-sphinx-theme, pandas, matplotlib, jupyter-client, jsonschema-specifications, ipython, alembic, seaborn, optuna, jsonschema, ipywidgets, ipykernel, nbformat, nbclient, nbconvert, nbsphinx Attempting uninstall: sphinx Found existing installation: Sphinx 8.2.3 Uninstalling Sphinx-8.2.3: Successfully uninstalled Sphinx-8.2.3 Successfully installed Mako-1.3.9 PyYAML-6.0.2 accessible-pygments-0.0.5 alembic-1.15.1 asttokens-3.0.0 attrs-25.3.0 beautifulsoup4-4.13.3 bleach-6.2.0 colorlog-6.9.0 comm-0.2.2 contourpy-1.3.1 cycler-0.12.1 debugpy-1.8.13 decorator-5.2.1 defusedxml-0.7.1 executing-2.2.0 fastjsonschema-2.21.1 fonttools-4.56.0 greenlet-3.1.1 ipykernel-6.29.5 ipython-9.0.2 ipython-pygments-lexers-1.1.1 ipywidgets-8.1.5 jedi-0.19.2 jsonschema-4.23.0 jsonschema-specifications-2024.10.1 jupyter-client-8.6.3 jupyter-core-5.7.2 jupyterlab-pygments-0.3.0 jupyterlab-widgets-3.0.13 kiwisolver-1.4.8 matplotlib-3.10.1 matplotlib-inline-0.1.7 mistune-3.1.3 nbclient-0.10.2 nbconvert-7.16.6 nbformat-5.10.4 nbsphinx-0.9.7 nest-asyncio-1.6.0 numpy-2.2.4 optuna-4.2.1 pandas-2.2.3 pandoc-2.4 pandocfilters-1.5.1 parso-0.8.4 pexpect-4.9.0 pillow-11.1.0 plantweb-1.3.0 platformdirs-4.3.7 plumbum-1.9.0 ply-3.11 pockets-0.9.1 prompt_toolkit-3.0.50 psutil-7.0.0 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.16.1 pypandoc-1.15 pyparsing-3.2.2 python-dateutil-2.9.0.post0 pytz-2025.1 pyzmq-26.3.0 readthedocs-sphinx-search-0.3.2 referencing-0.36.2 rpds-py-0.23.1 seaborn-0.13.2 six-1.17.0 soupsieve-2.6 sphinx-8.1.3 sphinx-autodoc-typehints-3.0.1 sphinx-design-0.6.1 sphinxcontrib-napoleon-0.7 sqlalchemy-2.0.39 stack_data-0.6.3 tinycss2-1.4.0 tornado-6.4.2 tqdm-4.67.1 traitlets-5.14.3 typing-extensions-4.12.2 tzdata-2025.2 wcwidth-0.2.13 webencodings-0.5.1 widgetsnbextension-4.0.13 [rtd-command-info] start-time: 2025-03-24T14:02:46.243248Z, end-time: 2025-03-24T14:03:02.670220Z, duration: 16, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir . 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et_xmlfile-2.0.0-py3-none-any.whl (18 kB) Downloading smmap-5.0.2-py3-none-any.whl (24 kB) Building wheels for collected packages: starsim Building wheel for starsim (pyproject.toml): started Building wheel for starsim (pyproject.toml): finished with status 'done' Created wheel for starsim: filename=starsim-2.3.1-py3-none-any.whl size=161926 sha256=239ce8f85ea6e0fa76184288471ba311144de0ca67e1f7dff6b67b5d81f92d49 Stored in directory: /tmp/pip-ephem-wheel-cache-e8h9sy3a/wheels/cb/99/0f/d958ceab7a04e26e1853a33cfc76f63f7f7366c15aa5301c90 Successfully built starsim Installing collected packages: zstandard, xlsxwriter, smmap, numpy, networkx, memory-profiler, llvmlite, line-profiler, jsonpickle, jellyfish, et-xmlfile, dill, scipy, openpyxl, numba, multiprocess, gitdb, gitpython, sciris, starsim Attempting uninstall: numpy Found existing installation: numpy 2.2.4 Uninstalling numpy-2.2.4: Successfully uninstalled numpy-2.2.4 Successfully installed dill-0.3.9 et-xmlfile-2.0.0 gitdb-4.0.12 gitpython-3.1.44 jellyfish-1.1.3 jsonpickle-4.0.2 line-profiler-4.2.0 llvmlite-0.44.0 memory-profiler-0.61.0 multiprocess-0.70.17 networkx-3.4.2 numba-0.61.0 numpy-2.1.3 openpyxl-3.1.5 scipy-1.15.2 sciris-3.2.0 smmap-5.0.2 starsim-2.3.1 xlsxwriter-3.2.2 zstandard-0.23.0 [rtd-command-info] start-time: 2025-03-24T14:03:02.859353Z, end-time: 2025-03-24T14:03:02.900987Z, 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 starsim as ss on_rtd = os.environ.get('READTHEDOCS') == 'True' # -- Project information ----------------------------------------------------- project = 'Starsim' copyright = f'2023 - {sc.now().year}, Gates Foundation. All rights reserved. These docs were built for Starsim v{ss.__version__}' author = 'Starsim Collective' # The short X.Y version version = ss.__version__ # The full version, including alpha/beta/rc tags release = ss.__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 = ["starsim."] # 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://starsim.org", "icon": "fas fa-home"}, { "name": "GitHub", "url": "https://github.com/starsimhub/starsim", "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/starsim/en/latest" html_context = { 'rtd_url': 'https://docs.idmod.org/projects/starsim/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 = 'Starsim' # 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 nbsphinx_execute = 'always' nbsphinx_timeout = 300 # OpenSearch options html_use_opensearch = 'docs.idmod.org/projects/starsim/en/latest' # -- RTD Sphinx search for searching across the entire domain, default child ------------- if os.environ.get('READTHEDOCS') == 'True': search_project_parent = "institute-for-disease-modeling-idm" search_project = os.environ["READTHEDOCS_PROJECT"] search_version = os.environ["READTHEDOCS_VERSION"] rtd_sphinx_search_default_filter = f"subprojects:{search_project}/{search_version}" rtd_sphinx_search_filters = { "Search this project": f"project:{search_project}/{search_version}", "Search all IDM docs": f"subprojects:{search_project_parent}/{search_version}", } [rtd-command-info] start-time: 2025-03-24T14:03:02.974981Z, end-time: 2025-03-24T14:06:18.791427Z, duration: 195, exit-code: 0 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v8.1.3 loading translations [en]... done making output directory... done [autosummary] generating autosummary for: api/index.rst, conduct.rst, contributing.rst, index.rst, tutorials.rst, tutorials/README.rst, tutorials/dev_tut_analyzers.ipynb, tutorials/dev_tut_diseases.ipynb, tutorials/dev_tut_nonstandard.ipynb, tutorials/dev_tut_pars.ipynb, tutorials/tut_buildsim.ipynb, tutorials/tut_calibration.ipynb, tutorials/tut_demographics.ipynb, tutorials/tut_diseases.ipynb, tutorials/tut_interventions.ipynb, tutorials/tut_intro.ipynb, tutorials/tut_transmission.ipynb, whatsnew.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.arrays.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.calibration.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.demographics.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.disease.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.distributions.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.interventions.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.loop.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.modules.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.networks.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.parameters.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.people.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.products.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.results.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.run.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.samples.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.settings.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.time.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.arrays.Arr.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.arrays.BaseArr.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.arrays.BoolArr.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.arrays.FloatArr.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.arrays.IndexArr.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.arrays.State.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.arrays.uids.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.calibration.Calibration.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.demographics.Births.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.demographics.Deaths.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.find_contacts.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.load.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.ndict.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.return_fig.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.save.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.set_seed.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.standardize_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.standardize_netkey.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.validate_sim_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.warn.rst Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/_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 18 source files that are out of date updating environment: [new config] 163 added, 0 changed, 0 removed reading sources... 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