Read the Docs build information Build id: 3095289 Project: institute-for-disease-modeling-fpsim Version: 555 Commit: 8e788dc75c0090e6eebb18b95594c40b9b134a07 Date: 2025-06-04T20:18:33.931482Z State: cancelled Success: False [rtd-command-info] start-time: 2025-06-04T20:18:34.615476Z, end-time: 2025-06-04T20:18:35.276033Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/fpsim/fpsim.git . Cloning into '.'... [rtd-command-info] start-time: 2025-06-04T20:18:35.315271Z, end-time: 2025-06-04T20:18:36.783066Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/555/head:external-555 From https://github.com/fpsim/fpsim * [new ref] refs/pull/555/head -> external-555 * [new tag] v.1.latest -> v.1.latest * [new tag] v0.24.0 -> v0.24.0 * [new tag] v0.28.1 -> v0.28.1 * [new tag] v1.0.4 -> v1.0.4 * [new tag] v2.0.0 -> v2.0.0 [rtd-command-info] start-time: 2025-06-04T20:18:36.862397Z, end-time: 2025-06-04T20:18:36.926177Z, duration: 0, exit-code: 0 git checkout --force 8e788dc75c0090e6eebb18b95594c40b9b134a07 Note: switching to '8e788dc75c0090e6eebb18b95594c40b9b134a07'. 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 8e788dc unittest for stockout module [rtd-command-info] start-time: 2025-06-04T20:18:36.959584Z, end-time: 2025-06-04T20:18:36.996619Z, 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: 2025-06-04T20:18:40.727287Z, end-time: 2025-06-04T20:18:40.782109Z, duration: 0, exit-code: 0 asdf global python 3.9.22 [rtd-command-info] start-time: 2025-06-04T20:18:41.150638Z, end-time: 2025-06-04T20:18:41.854654Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.22.final.0-64 in 444ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/555, 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: 2025-06-04T20:18:41.891929Z, end-time: 2025-06-04T20:18:46.231696Z, duration: 4, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/555/lib/python3.9/site-packages (23.1) Collecting pip Downloading pip-25.1.1-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 37.4 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/555/lib/python3.9/site-packages (67.6.1) Collecting setuptools Downloading setuptools-80.9.0-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 160.0 MB/s eta 0:00:00 Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 67.6.1 Uninstalling setuptools-67.6.1: Successfully uninstalled setuptools-67.6.1 Attempting uninstall: pip Found existing installation: pip 23.1 Uninstalling pip-23.1: Successfully 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sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, sphinx Successfully installed Jinja2-3.1.6 MarkupSafe-3.0.2 Pygments-2.19.1 alabaster-0.7.16 babel-2.17.0 certifi-2025.4.26 charset-normalizer-3.4.2 docutils-0.21.2 idna-3.10 imagesize-1.4.1 importlib-metadata-8.7.0 packaging-25.0 requests-2.32.3 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-2.2.1 urllib3-2.4.0 zipp-3.22.0 [rtd-command-info] start-time: 2025-06-04T20:18:50.950332Z, end-time: 2025-06-04T20:19:03.245189Z, duration: 12, 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)) 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Discussion can be found at https://github.com/pypa/pip/issues/6334 Building wheel for pandoc (setup.py): started Building wheel for pandoc (setup.py): finished with status 'done' Created wheel for pandoc: filename=pandoc-2.4-py3-none-any.whl size=34871 sha256=d362d5d9388ce806049c1cb81b8f1d82fc061672875681ddb3980419feff7042 Stored in directory: /tmp/pip-ephem-wheel-cache-zccwcek5/wheels/10/f8/26/ddf077e60385563a3fef3afad369a40b22e59603a700ec23e4 Successfully built pandoc Installing collected packages: webencodings, wcwidth, pure-eval, ptyprocess, ply, fastjsonschema, typing-extensions, traitlets, tqdm, tornado, tinycss2, soupsieve, six, rpds-py, readthedocs-sphinx-search, pyzmq, PyYAML, pypandoc, psutil, prompt-toolkit, plumbum, platformdirs, pexpect, parso, pandocfilters, numpy, nest-asyncio, Mako, jupyterlab-pygments, greenlet, executing, defusedxml, decorator, debugpy, colorlog, bleach, attrs, asttokens, accessible-pygments, stack-data, sqlalchemy, referencing, python-dateutil, plantweb, pandoc, mistune, matplotlib-inline, jupyter-core, jedi, exceptiongroup, comm, beautifulsoup4, sphinx-design, sphinx-autodoc-typehints, pydata-sphinx-theme, jupyter-client, jsonschema-specifications, ipython, alembic, optuna, jsonschema, ipykernel, nbformat, nbclient, nbconvert, nbsphinx Successfully installed Mako-1.3.10 PyYAML-6.0.2 accessible-pygments-0.0.5 alembic-1.16.1 asttokens-3.0.0 attrs-25.3.0 beautifulsoup4-4.13.4 bleach-6.2.0 colorlog-6.9.0 comm-0.2.2 debugpy-1.8.14 decorator-5.2.1 defusedxml-0.7.1 exceptiongroup-1.3.0 executing-2.2.0 fastjsonschema-2.21.1 greenlet-3.2.2 ipykernel-6.29.5 ipython-8.18.1 jedi-0.19.2 jsonschema-4.24.0 jsonschema-specifications-2025.4.1 jupyter-client-8.6.3 jupyter-core-5.8.1 jupyterlab-pygments-0.3.0 matplotlib-inline-0.1.7 mistune-3.1.3 nbclient-0.10.2 nbconvert-7.13.0 nbformat-5.10.4 nbsphinx-0.9.7 nest-asyncio-1.6.0 numpy-2.0.2 optuna-4.3.0 pandoc-2.4 pandocfilters-1.5.1 parso-0.8.4 pexpect-4.9.0 plantweb-1.3.0 platformdirs-4.3.8 plumbum-1.9.0 ply-3.11 prompt-toolkit-3.0.51 psutil-7.0.0 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.16.1 pypandoc-1.15 python-dateutil-2.9.0.post0 pyzmq-26.4.0 readthedocs-sphinx-search-0.3.2 referencing-0.36.2 rpds-py-0.25.1 six-1.17.0 soupsieve-2.7 sphinx-autodoc-typehints-2.3.0 sphinx-design-0.6.1 sqlalchemy-2.0.41 stack-data-0.6.3 tinycss2-1.4.0 tornado-6.5.1 tqdm-4.67.1 traitlets-5.14.3 typing-extensions-4.14.0 wcwidth-0.2.13 webencodings-0.5.1 [rtd-command-info] start-time: 2025-06-04T20:19:03.301662Z, end-time: 2025-06-04T20:19:24.868000Z, duration: 21, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir . 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A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'fpsim'. Discussion can be found at https://github.com/pypa/pip/issues/6334 Building wheel for fpsim (setup.py): started Building wheel for fpsim (setup.py): finished with status 'done' Created wheel for fpsim: filename=fpsim-2.0.1-py3-none-any.whl size=491262 sha256=e03f17813a9cb6c3c7a7a8963a06568050418def0a0cf45e039e1a678e0614a3 Stored in directory: /tmp/pip-ephem-wheel-cache-0cahegzu/wheels/60/25/f4/704a9f63004b8a5b6537339f26abce6eabfa78f4eae1331137 Successfully built fpsim Installing collected packages: pytz, zstandard, xlsxwriter, tzdata, smmap, scipy, pyparsing, pyarrow, pillow, patsy, networkx, memory_profiler, llvmlite, line_profiler, kiwisolver, jsonpickle, jellyfish, importlib-resources, fonttools, et-xmlfile, dill, cycler, contourpy, pandas, openpyxl, numba, multiprocess, matplotlib, gitdb, statsmodels, seaborn, mizani, gitpython, sciris, plotnine, starsim, fpsim Successfully installed contourpy-1.3.0 cycler-0.12.1 dill-0.4.0 et-xmlfile-2.0.0 fonttools-4.58.1 fpsim-2.0.1 gitdb-4.0.12 gitpython-3.1.44 importlib-resources-6.5.2 jellyfish-1.2.0 jsonpickle-4.1.1 kiwisolver-1.4.7 line_profiler-4.2.0 llvmlite-0.43.0 matplotlib-3.9.4 memory_profiler-0.61.0 mizani-0.11.4 multiprocess-0.70.18 networkx-3.2.1 numba-0.60.0 openpyxl-3.1.5 pandas-2.2.3 patsy-1.0.1 pillow-11.2.1 plotnine-0.13.6 pyarrow-20.0.0 pyparsing-3.2.3 pytz-2025.2 scipy-1.13.1 sciris-3.2.1 seaborn-0.13.2 smmap-5.0.2 starsim-2.3.1 statsmodels-0.14.4 tzdata-2025.2 xlsxwriter-3.2.3 zstandard-0.23.0 [rtd-command-info] start-time: 2025-06-04T20:19:24.994863Z, end-time: 2025-06-04T20:19:25.034298Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Configuration file for the Sphinx documentation builder. import os import sys import sciris as sc import fpsim as fp # Set environment os.environ['SPHINX_BUILD'] = 'True' # This is used so fp.options.set('jupyter') doesn't reset the Matplotlib renderer os.environ['FPSIM_WARNINGS'] = 'error' # Don't let warnings pass in the tutorials on_rtd = os.environ.get('READTHEDOCS') == 'True' # -- Project information ----------------------------------------------------- project = 'FPsim' copyright = f'2019 - {sc.now().year}, Gates Foundation. All rights reserved.\nThese docs were built for FPsim version {fp.__version__}\n' author = 'Institute for Disease Modeling' # The short X.Y version version = fp.__version__ # The full version, including alpha/beta/rc tags release = fp.__version__ # -- General configuration --------------------------------------------------- # Add any Sphinx extension module names here extensions = [ "sphinx.ext.autodoc", # Core Sphinx library for auto html doc generation from docstrings "sphinx.ext.autosummary", # Create neat summary tables for modules/classes/methods etc -- causes warnings with Napoleon however "sphinx.ext.intersphinx", "sphinx.ext.viewcode", # Add a link to the Python source code for classes, functions etc. "sphinx.ext.napoleon", "sphinx.ext.autosectionlabel", "sphinx_autodoc_typehints", # Automatically document param types (less noise in class signature) "sphinx_design", # Add e.g. grid layout 'sphinx_search.extension', # search across multiple docsets in domain "nbsphinx", ] # Use Google docstrings napoleon_google_docstring = True # Configure autosummary autosummary_generate = True # Turn on sphinx.ext.autosummary autosummary_ignore_module_all = False # Respect __all__ autodoc_member_order = 'bysource' # Keep original ordering add_module_names = False # NB, does not work autodoc_inherit_docstrings = False # Stops sublcasses from including docs from parent classes # Add any paths that contain templates here, relative to this directory. templates_path = ["_templates"] # Syntax highlighting style pygments_style = "sphinx" modindex_common_prefix = ["fpsim."] # List of patterns, relative to source directory, to exclude exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"] # Suppress certain warnings suppress_warnings = ['autosectionlabel.*'] # -- Options for HTML output ------------------------------------------------- html_theme = "pydata_sphinx_theme" html_theme_options = { "collapse_navigation": False, "navigation_depth": 3, "show_prev_next": True, "icon_links": [ {"name": "Web", "url": "https://fpsim.org", "icon": "fas fa-home"}, { "name": "GitHub", "url": "https://github.com/fpsim/fpsim", "icon": "fab fa-github-square", }, ], "navbar_end": ["theme-switcher", "navbar-icon-links"], "secondary_sidebar_items": ["navbar-side"], "header_links_before_dropdown": 5, "footer_start": ["copyright", "footer_start"], "footer_end": ["theme-version", "footer_end"], "logo": { "text": "FPsim", }, } html_sidebars = { "**": ["sidebar-nav-bs", "page-toc"], } html_logo = "images/idm-logo-transparent.png" html_favicon = "images/favicon.ico" html_static_path = ['_static'] html_baseurl = "https://docs.idmod.org/projects/fpsim/en/latest" html_context = { 'rtd_url': 'https://docs.idmod.org/projects/fpsim/en/latest', "versions_dropdown": { "latest": "devel (latest)", "stable": "current (stable)", }, "default_mode": "light", } # Add any extra paths that contain custom files if not on_rtd: html_extra_path = ['robots.txt'] # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. html_last_updated_fmt = '%Y-%b-%d' html_show_sourcelink = True html_show_sphinx = False html_copy_source = False htmlhelp_basename = 'FPsim' # Add customizations def setup(app): app.add_css_file("theme_overrides.css") # Modify this to not rerun the Jupyter notebook cells -- usually set by build_docs nb_ex_default = ['auto', 'never'][0] nb_ex = os.getenv('NBSPHINX_EXECUTE') if not nb_ex: nb_ex = nb_ex_default print(f'\n\nBuilding Jupyter notebooks with build option: {nb_ex}\n\n') nbsphinx_execute = nb_ex # OpenSearch options html_use_opensearch = 'docs.idmod.org/projects/fpsim/en/latest' # -- RTD Sphinx search for searching across the entire domain, default child ------------- if os.environ.get('READTHEDOCS') == 'True': search_project_parent = "institute-for-disease-modeling-idm" search_project = os.environ["READTHEDOCS_PROJECT"] search_version = os.environ["READTHEDOCS_VERSION"] rtd_sphinx_search_default_filter = f"subprojects:{search_project}/{search_version}" rtd_sphinx_search_filters = { "Search this project": f"project:{search_project}/{search_version}", "Search all IDM docs": f"subprojects:{search_project_parent}/{search_version}", }