Read the Docs build information Build id: 3482484 Project: institute-for-disease-modeling-fpsim Version: 653 Commit: 5e8a6b64477327c5642687138bad0f02947017be Date: 2025-10-29T16:54:54.334913Z State: finished Success: False [rtd-command-info] start-time: 2025-10-29T16:54:55.227188Z, end-time: 2025-10-29T16:54:55.849497Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/fpsim/fpsim.git . Cloning into '.'... [rtd-command-info] start-time: 2025-10-29T16:54:55.945986Z, end-time: 2025-10-29T16:54:57.644709Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/653/head:external-653 From https://github.com/fpsim/fpsim * [new ref] refs/pull/653/head -> external-653 * [new tag] v.1.latest -> v.1.latest * [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: 2025-10-29T16:54:58.337891Z, end-time: 2025-10-29T16:54:58.413095Z, duration: 0, exit-code: 0 git checkout --force 5e8a6b64477327c5642687138bad0f02947017be Note: switching to '5e8a6b64477327c5642687138bad0f02947017be'. 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 5e8a6b6 Update defaults.py [rtd-command-info] start-time: 2025-10-29T16:54:58.500612Z, end-time: 2025-10-29T16:54:58.532992Z, 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: # Optionally declare the Python requirements required to build your docs python: install: - requirements: docs/requirements.txt - method: pip path: . [rtd-command-info] start-time: 2025-10-29T16:55:03.081185Z, end-time: 2025-10-29T16:55:03.132720Z, duration: 0, exit-code: 0 asdf global python 3.11.12 [rtd-command-info] start-time: 2025-10-29T16:55:03.527100Z, end-time: 2025-10-29T16:55:04.244846Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.11.12.final.0-64 in 477ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653, 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: 2025-10-29T16:55:04.350990Z, end-time: 2025-10-29T16:55:08.920164Z, 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/653/lib/python3.11/site-packages (23.1) Collecting pip Downloading pip-25.3-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 51.7 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages (67.6.1) Collecting setuptools Downloading setuptools-80.9.0-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 207.5 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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alabaster, requests, Jinja2, sphinx Successfully installed Jinja2-3.1.6 MarkupSafe-3.0.3 Pygments-2.19.2 alabaster-1.0.0 babel-2.17.0 certifi-2025.10.5 charset_normalizer-3.4.4 docutils-0.21.2 idna-3.11 imagesize-1.4.1 packaging-25.0 requests-2.32.5 roman-numerals-py-3.1.0 snowballstemmer-3.0.1 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 urllib3-2.5.0 [rtd-command-info] start-time: 2025-10-29T16:55:12.882719Z, end-time: 2025-10-29T16:55:25.840361Z, 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)) Downloading pandoc-2.4.tar.gz (34 kB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with 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packages: webencodings, pure-eval, ptyprocess, ply, fastjsonschema, wcwidth, typing-extensions, traitlets, tqdm, tornado, tinycss2, soupsieve, six, rpds-py, readthedocs-sphinx-search, pyzmq, PyYAML, pypandoc, psutil, plumbum, platformdirs, pexpect, parso, pandocfilters, numpy, nest-asyncio, mistune, Mako, jupyterlab-pygments, ipython-pygments-lexers, greenlet, executing, defusedxml, decorator, debugpy, comm, colorlog, bleach, attrs, asttokens, accessible-pygments, stack_data, sqlalchemy, sphinx, referencing, python-dateutil, prompt_toolkit, plantweb, pandoc, matplotlib-inline, jupyter-core, jedi, beautifulsoup4, sphinx-design, sphinx-autodoc-typehints, pydata-sphinx-theme, jupyter-client, jsonschema-specifications, ipython, alembic, optuna, jsonschema, 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-1.3.10 PyYAML-6.0.3 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sqlalchemy-2.0.44 stack_data-0.6.3 tinycss2-1.4.0 tornado-6.5.2 tqdm-4.67.1 traitlets-5.14.3 typing-extensions-4.15.0 wcwidth-0.2.14 webencodings-0.5.1 [rtd-command-info] start-time: 2025-10-29T16:55:25.931369Z, end-time: 2025-10-29T16:55:50.485130Z, duration: 24, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir . 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zstandard, xlsxwriter, tzdata, smmap, scipy, pyparsing, pyarrow, pillow, patsy, networkx, memory_profiler, llvmlite, line_profiler, kiwisolver, jsonpickle, jellyfish, fonttools, et-xmlfile, dill, cycler, contourpy, pandas, openpyxl, numba, multiprocess, matplotlib, gitdb, statsmodels, seaborn, mizani, gitpython, sciris, plotnine, starsim, fpsim Successfully installed contourpy-1.3.3 cycler-0.12.1 dill-0.4.0 et-xmlfile-2.0.0 fonttools-4.60.1 fpsim-3.3.1 gitdb-4.0.12 gitpython-3.1.45 jellyfish-1.2.1 jsonpickle-4.1.1 kiwisolver-1.4.9 line_profiler-5.0.0 llvmlite-0.45.1 matplotlib-3.10.7 memory_profiler-0.61.0 mizani-0.14.2 multiprocess-0.70.18 networkx-3.5 numba-0.62.1 openpyxl-3.1.5 pandas-2.3.3 patsy-1.0.2 pillow-12.0.0 plotnine-0.15.0 pyarrow-22.0.0 pyparsing-3.2.5 pytz-2025.2 scipy-1.16.3 sciris-3.2.4 seaborn-0.13.2 smmap-5.0.2 starsim-3.0.4 statsmodels-0.14.5 tzdata-2025.2 xlsxwriter-3.2.9 zstandard-0.25.0 [rtd-command-info] start-time: 2025-10-29T16:55:50.634025Z, end-time: 2025-10-29T16:55:50.667964Z, 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}", } [rtd-command-info] start-time: 2025-10-29T16:55:50.760109Z, end-time: 2025-10-29T16:55:55.937538Z, duration: 5, exit-code: 2 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v8.1.0 Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/sphinx/config.py", line 529, in eval_config_file exec(code, namespace) # NoQA: S102 ^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/653/docs/conf.py", line 8, in import fpsim as fp File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/fpsim/__init__.py", line 3, in from .utils import * File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/fpsim/utils.py", line 9, in from . import defaults as fpd File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/fpsim/defaults.py", line 71 fpmod_states = [ ^ SyntaxError: invalid syntax. Maybe you meant '==' or ':=' instead of '='? The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/sphinx/cmd/build.py", line 496, in build_main app = Sphinx( ^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/sphinx/application.py", line 238, in __init__ self.config = Config.read(self.confdir, confoverrides or {}, self.tags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/sphinx/config.py", line 316, in read namespace = eval_config_file(filename, tags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/653/lib/python3.11/site-packages/sphinx/config.py", line 532, in eval_config_file raise ConfigError(msg % err) from err sphinx.errors.ConfigError: There is a syntax error in your configuration file: invalid syntax. Maybe you meant '==' or ':=' instead of '='? (defaults.py, line 71) Configuration error: There is a syntax error in your configuration file: invalid syntax. Maybe you meant '==' or ':=' instead of '='? (defaults.py, line 71)