Read the Docs build information Build id: 3750446 Project: institute-for-disease-modeling-fpsim Version: 690 Commit: 0f8f1fae110c2a9a0536a05a5e76c9ec9adb4094 Date: 2026-02-13T20:08:44.628966Z State: finished Success: False [rtd-command-info] start-time: 2026-02-13T20:08:45.423344Z, end-time: 2026-02-13T20:08:46.499508Z, duration: 1, exit-code: 0 git clone --depth 1 https://github.com/fpsim/fpsim.git . Cloning into '.'... [rtd-command-info] start-time: 2026-02-13T20:08:46.592326Z, end-time: 2026-02-13T20:08:48.870201Z, duration: 2, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/690/head:external-690 From https://github.com/fpsim/fpsim * [new ref] refs/pull/690/head -> external-690 * [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: 2026-02-13T20:08:49.754578Z, end-time: 2026-02-13T20:08:49.834256Z, duration: 0, exit-code: 0 git checkout --force 0f8f1fae110c2a9a0536a05a5e76c9ec9adb4094 Note: switching to '0f8f1fae110c2a9a0536a05a5e76c9ec9adb4094'. 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 0f8f1fa Merge branch 'rc3.5' into rc3.6 [rtd-command-info] start-time: 2026-02-13T20:08:49.929486Z, end-time: 2026-02-13T20:08:49.972946Z, 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: 2026-02-13T20:08:55.565813Z, end-time: 2026-02-13T20:08:55.627789Z, duration: 0, exit-code: 0 asdf global python 3.11.12 [rtd-command-info] start-time: 2026-02-13T20:08:56.077517Z, end-time: 2026-02-13T20:08:57.171733Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.11.12.final.0-64 in 789ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690, 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: 2026-02-13T20:08:57.258331Z, end-time: 2026-02-13T20:09:08.708262Z, duration: 11, 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/690/lib/python3.11/site-packages (23.1) Collecting pip Downloading pip-26.0.1-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 9.8 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages (67.6.1) Collecting setuptools Downloading setuptools-82.0.0-py3-none-any.whl (1.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 25.6 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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idna-3.11-py3-none-any.whl (71 kB) Downloading urllib3-2.6.3-py3-none-any.whl (131 kB) Downloading certifi-2026.1.4-py3-none-any.whl (152 kB) Downloading roman_numerals-4.1.0-py3-none-any.whl (7.7 kB) Downloading snowballstemmer-3.0.1-py3-none-any.whl (103 kB) Downloading sphinxcontrib_applehelp-2.0.0-py3-none-any.whl (119 kB) Downloading sphinxcontrib_devhelp-2.0.0-py3-none-any.whl (82 kB) Downloading sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl (98 kB) Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Downloading sphinxcontrib_qthelp-2.0.0-py3-none-any.whl (88 kB) Downloading sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl (92 kB) 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-2026.1.4 charset_normalizer-3.4.4 docutils-0.22.4 idna-3.11 imagesize-1.4.1 packaging-26.0 requests-2.32.5 roman-numerals-4.1.0 snowballstemmer-3.0.1 sphinx-9.0.4 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: 2026-02-13T20:09:17.946278Z, end-time: 2026-02-13T20:09:34.815463Z, duration: 16, 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 status 'done' 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Created wheel for pandoc: filename=pandoc-2.4-py3-none-any.whl size=34873 sha256=2fc60f77a02a1c971a018d04c13fa9d3a54fd0ab5fe82eb263f39a09eb65fb42 Stored in directory: /tmp/pip-ephem-wheel-cache-jf6xk56p/wheels/4f/d7/32/c6c9b7b05e852e920fd72174487be3a0f18e633a7adcc303be Successfully built pandoc Installing collected 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, docutils, 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: docutils Found existing installation: docutils 0.22.4 Uninstalling docutils-0.22.4: Successfully uninstalled docutils-0.22.4 Attempting uninstall: sphinx Found existing installation: Sphinx 9.0.4 Uninstalling Sphinx-9.0.4: Successfully uninstalled Sphinx-9.0.4 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 debugpy-1.8.20 decorator-5.2.1 defusedxml-0.7.1 docutils-0.21.2 executing-2.2.1 fastjsonschema-2.21.2 greenlet-3.3.1 ipykernel-7.2.0 ipython-9.10.0 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 matplotlib-inline-0.2.1 mistune-3.2.0 nbclient-0.10.4 nbconvert-7.13.0 nbformat-5.10.4 nbsphinx-0.9.8 nest-asyncio-1.6.0 numpy-2.4.2 optuna-4.7.0 pandoc-2.4 pandocfilters-1.5.1 parso-0.8.6 pexpect-4.9.0 plantweb-1.3.0 platformdirs-4.7.1 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 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 six-1.17.0 soupsieve-2.8.3 sphinx-8.1.0 sphinx-autodoc-typehints-2.5.0 sphinx-design-0.7.0 sqlalchemy-2.0.46 stack_data-0.6.3 tinycss2-1.5.1 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: 2026-02-13T20:09:34.913003Z, end-time: 2026-02-13T20:10:06.754092Z, duration: 31, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir . 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llvmlite, line_profiler, kiwisolver, jsonpickle, jellyfish, fonttools, et-xmlfile, dill, cycler, scipy, patsy, pandas, openpyxl, numba, multiprocess, gitdb, contourpy, statsmodels, mizani, matplotlib, gitpython, seaborn, sciris, plotnine, starsim, fpsim Attempting uninstall: numpy Found existing installation: numpy 2.4.2 Uninstalling numpy-2.4.2: Successfully uninstalled numpy-2.4.2 Successfully installed contourpy-1.3.3 cycler-0.12.1 dill-0.4.1 et-xmlfile-2.0.0 fonttools-4.61.1 fpsim-3.6.0 gitdb-4.0.12 gitpython-3.1.46 jellyfish-1.2.1 jsonpickle-4.1.1 kiwisolver-1.4.9 line_profiler-5.0.1 llvmlite-0.46.0 matplotlib-3.10.8 memory_profiler-0.61.0 mizani-0.14.4 multiprocess-0.70.19 networkx-3.6.1 numba-0.63.1 numpy-2.3.5 openpyxl-3.1.5 pandas-3.0.0 patsy-1.0.2 pillow-12.1.1 plotnine-0.15.3 pyarrow-23.0.0 pyparsing-3.3.2 scipy-1.17.0 sciris-3.2.6 seaborn-0.13.2 smmap-5.0.2 starsim-3.1.0 statsmodels-0.14.6 xlsxwriter-3.2.9 zstandard-0.25.0 [rtd-command-info] start-time: 2026-02-13T20:10:06.916029Z, end-time: 2026-02-13T20:10:06.962262Z, 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: 2026-02-13T20:10:07.082942Z, end-time: 2026-02-13T20:10:33.202795Z, duration: 26, exit-code: 2 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v8.1.0 Rebuilding font cache, please be patient... Font cache rebuilt in folder: /home/docs/.cache/matplotlib Note: rebuilding the font cache only happens once on first import, or set the environment variable STARSIM_INSTALL_FONTS=0 to disable. 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/T1_intro.ipynb, tutorials/T2_intro_to_new_features.ipynb, tutorials/T3_interventions_methods.ipynb, tutorials/T4_intervention_eligibility.ipynb, tutorials/T5_new_method.ipynb, whatsnew.rst /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/starsim/arrays.py:380: RuntimeWarning: Trying to access non-initialized Arr object; in most cases, Arr objects need to be initialized with a Sim object, but set skip_init=True if this is intentional. ss.warn('Trying to access non-initialized Arr object; in most cases, Arr objects need to be initialized with a Sim object, but set skip_init=True if this is intentional.') [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.analyzers.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.arrays.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.calibration.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.defaults.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.demographics.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.education.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.experiment.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.interventions.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.methods.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.parameters.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.scenarios.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.settings.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.utils.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.analyzers.age_pyramids.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.analyzers.cpr_by_age.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.analyzers.education_recorder.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.analyzers.lifeof_recorder.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.analyzers.method_mix_by_age.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.analyzers.method_mix_over_time.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.analyzers.snapshot.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.analyzers.state_tracker.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.analyzers.track_as.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.arrays.TwoDimensionalArr.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.parameters.all_pars.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.parameters.make_fp_pars.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.parameters.make_sim_pars.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.parameters.mergepars.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.scenarios.Scenario.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.scenarios.Scenarios.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.scenarios.make_scen.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.sim.Sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.utils.DuplicateNameException.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/api/_autosummary/fpsim.utils.data2interp.rst Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/_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 11 source files that are out of date updating environment: [new config] 78 added, 0 changed, 0 removed reading sources... 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[ 94%] tutorials/T1_intro reading sources... [ 95%] tutorials/T2_intro_to_new_features /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/fpsim/education.py:docstring of fpsim.education.Education.set_objective_dists:3: ERROR: Unexpected indentation. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/fpsim/education.py:docstring of fpsim.education.Education.set_objective_dists:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/fpsim/interventions.py:docstring of fpsim.interventions.change_initiation:20: ERROR: Unexpected indentation. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/fpsim/methods.py:docstring of fpsim.methods.ContraceptiveChoice.copy_switching_probs:3: ERROR: Unexpected indentation. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/fpsim/methods.py:docstring of fpsim.methods.ContraceptiveChoice.copy_switching_to_method:3: ERROR: Unexpected indentation. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/fpsim/methods.py:docstring of fpsim.methods.ContraceptiveChoice.copy_switching_from_method:3: ERROR: Unexpected indentation. [docutils] WARNING: Summarised items should not include the current module. Replace 'fpsim.analyzers' with 'analyzers'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.arrays' with 'arrays'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.calibration' with 'calibration'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.defaults' with 'defaults'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.demographics' with 'demographics'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.education' with 'education'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.experiment' with 'experiment'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.interventions' with 'interventions'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.methods' with 'methods'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.parameters' with 'parameters'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.scenarios' with 'scenarios'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.settings' with 'settings'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.sim' with 'sim'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'fpsim.utils' with 'utils'. [autosummary.import_cycle] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/tutorials.rst:3: WARNING: toctree contains reference to nonexisting document 'tutorials/T6_scenarios' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/tutorials.rst:3: WARNING: toctree contains reference to nonexisting document 'tutorials/T7_scenarios_plotting' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/checkouts/690/docs/tutorials/T1_intro.ipynb:1: WARNING: Each notebook should have at least one section title [nbsphinx.notebooktitle] Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/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-fpsim/envs/690/lib/python3.11/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-fpsim/envs/690/lib/python3.11/site-packages/nbconvert/preprocessors/execute.py", line 100, in preprocess self.preprocess_cell(cell, resources, index) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/nbconvert/preprocessors/execute.py", line 121, in preprocess_cell cell = self.execute_cell(cell, index, store_history=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped return loop.run_until_complete(inner) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.asdf/installs/python/3.11.12/lib/python3.11/asyncio/base_events.py", line 654, in run_until_complete return future.result() ^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/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-fpsim/envs/690/lib/python3.11/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 FPsim and define the baseline parameters import fpsim as fp location = 'kenya' pars = dict(location=location, n_agents=500, start_year=1980, end_year=2020, seed=1) # Define the contraceptive choice module and the education module. choice = fp.StandardChoice(location=location) edu = fp.Education(location=location) # Make and run sim s = fp.Sim(pars, contraception_module=choice, education_module=edu) s.run() ------------------ ----- stderr ----- /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html from .autonotebook import tqdm as notebook_tqdm ----- stdout ----- Loading data from files in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/fpsim/locations/kenya/data... Applying calibration parameters for kenya... ----- stdout ----- Initializing sim with 500 agents ------------------ --------------------------------------------------------------------------- NameError Traceback (most recent call last) Cell In[1], line 12  10 # Make and run sim  11 s = fp.Sim(pars, contraception_module=choice, education_module=edu) ---> 12 s.run() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/starsim/sim.py:356, in Sim.run(self, until, verbose, check_method_calls)  347 """  348 Run the model -- the main method for running a simulation.  349  (...) 353  check_method_calls (bool): whether to check that all required methods were called  354 """  355 # Initialization steps --> 356 if not self.initialized: self.init() # Automatically initialize if not initialized  357 if verbose is not None:  358 self._orig_verbose = self.verbose File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/fpsim/sim.py:250, in Sim.init(self, force)  247 self.pars['people'] = people  249 if force or not self.initialized: --> 250 super().init(force=force)  252 return self File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/starsim/sim.py:169, in Sim.init(self, force, timer, **kwargs)  167 self.init_dists() # Initialize distributions  168 self.init_people_vals() # Initialize the values in all the states and networks --> 169 self.init_modules_post() # Initialize the module values  170 self.init_results() # Initialize the results  171 self.init_data() # Initialize the data File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/starsim/sim.py:280, in Sim.init_modules_post(self)  278 """ Initialize values in other modules, including networks and time parameters, and do any other post-processing """  279 for mod in self.module_list: --> 280 mod.init_post()  281 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/starsim/demographics.py:579, in Pregnancy.init_post(self)  577 def init_post(self):  578 super().init_post() --> 579 self.updates_pre()  581 # Burn-in  582 if self.ti == 0 and self.pars.burnin: # TODO: refactor File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/fpsim/fpmod.py:378, in FPmod.updates_pre(self, uids, upper_age)  376 # Initialize fertility intent for women who just turned 15 (entered the 15-49 age range this timestep)  377 ppl = self.sim.people --> 378 just_15 = nonpreg[(ppl.age[nonpreg] > fpd.min_age) & (ppl.age[nonpreg] <= fpd.min_age + self.t.dt_year)]  379 if len(just_15) > 0:  380 self.init_intent_states(just_15) NameError: name 'nonpreg' is not defined 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-fpsim/envs/690/lib/python3.11/site-packages/sphinx/cmd/build.py", line 514, in build_main app.build(args.force_all, args.filenames) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/sphinx/application.py", line 381, in build self.builder.build_update() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 352, in build_update self.build( File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 379, in build updated_docnames = set(self.read()) ^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 496, in read self._read_serial(docnames) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 561, in _read_serial self.read_doc(docname) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 624, in read_doc publisher.publish() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/docutils/core.py", line 234, in publish self.document = self.reader.read(self.source, self.parser, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/sphinx/io.py", line 106, in read self.parse() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/docutils/readers/__init__.py", line 76, in parse self.parser.parse(self.input, document) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/nbsphinx/__init__.py", line 660, in parse raise NotebookError('\n'.join(lines)) nbsphinx.NotebookError: CellExecutionError in tutorials/T2_intro_to_new_features.ipynb: ------------------ # Import FPsim and define the baseline parameters import fpsim as fp location = 'kenya' pars = dict(location=location, n_agents=500, start_year=1980, end_year=2020, seed=1) # Define the contraceptive choice module and the education module. choice = fp.StandardChoice(location=location) edu = fp.Education(location=location) # Make and run sim s = fp.Sim(pars, contraception_module=choice, education_module=edu) s.run() ------------------ ----- stderr ----- /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html from .autonotebook import tqdm as notebook_tqdm ----- stdout ----- Loading data from files in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/fpsim/locations/kenya/data... Applying calibration parameters for kenya... ----- stdout ----- Initializing sim with 500 agents ------------------ --------------------------------------------------------------------------- NameError Traceback (most recent call last) Cell In[1], line 12  10 # Make and run sim  11 s = fp.Sim(pars, contraception_module=choice, education_module=edu) ---> 12 s.run() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/starsim/sim.py:356, in Sim.run(self, until, verbose, check_method_calls)  347 """  348 Run the model -- the main method for running a simulation.  349  (...) 353  check_method_calls (bool): whether to check that all required methods were called  354 """  355 # Initialization steps --> 356 if not self.initialized: self.init() # Automatically initialize if not initialized  357 if verbose is not None:  358 self._orig_verbose = self.verbose File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/fpsim/sim.py:250, in Sim.init(self, force)  247 self.pars['people'] = people  249 if force or not self.initialized: --> 250 super().init(force=force)  252 return self File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/starsim/sim.py:169, in Sim.init(self, force, timer, **kwargs)  167 self.init_dists() # Initialize distributions  168 self.init_people_vals() # Initialize the values in all the states and networks --> 169 self.init_modules_post() # Initialize the module values  170 self.init_results() # Initialize the results  171 self.init_data() # Initialize the data File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/starsim/sim.py:280, in Sim.init_modules_post(self)  278 """ Initialize values in other modules, including networks and time parameters, and do any other post-processing """  279 for mod in self.module_list: --> 280 mod.init_post()  281 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/starsim/demographics.py:579, in Pregnancy.init_post(self)  577 def init_post(self):  578 super().init_post() --> 579 self.updates_pre()  581 # Burn-in  582 if self.ti == 0 and self.pars.burnin: # TODO: refactor File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/fpsim/fpmod.py:378, in FPmod.updates_pre(self, uids, upper_age)  376 # Initialize fertility intent for women who just turned 15 (entered the 15-49 age range this timestep)  377 ppl = self.sim.people --> 378 just_15 = nonpreg[(ppl.age[nonpreg] > fpd.min_age) & (ppl.age[nonpreg] <= fpd.min_age + self.t.dt_year)]  379 if len(just_15) > 0:  380 self.init_intent_states(just_15) NameError: name 'nonpreg' is not defined You can ignore this error by setting the following in conf.py: nbsphinx_allow_errors = True Notebook error: CellExecutionError in tutorials/T2_intro_to_new_features.ipynb: ------------------ # Import FPsim and define the baseline parameters import fpsim as fp location = 'kenya' pars = dict(location=location, n_agents=500, start_year=1980, end_year=2020, seed=1) # Define the contraceptive choice module and the education module. choice = fp.StandardChoice(location=location) edu = fp.Education(location=location) # Make and run sim s = fp.Sim(pars, contraception_module=choice, education_module=edu) s.run() ------------------ ----- stderr ----- /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html from .autonotebook import tqdm as notebook_tqdm ----- stdout ----- Loading data from files in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/fpsim/locations/kenya/data... Applying calibration parameters for kenya... ----- stdout ----- Initializing sim with 500 agents ------------------ --------------------------------------------------------------------------- NameError Traceback (most recent call last) Cell In[1], line 12  10 # Make and run sim  11 s = fp.Sim(pars, contraception_module=choice, education_module=edu) ---> 12 s.run() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/starsim/sim.py:356, in Sim.run(self, until, verbose, check_method_calls)  347 """  348 Run the model -- the main method for running a simulation.  349  (...) 353  check_method_calls (bool): whether to check that all required methods were called  354 """  355 # Initialization steps --> 356 if not self.initialized: self.init() # Automatically initialize if not initialized  357 if verbose is not None:  358 self._orig_verbose = self.verbose File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/fpsim/sim.py:250, in Sim.init(self, force)  247 self.pars['people'] = people  249 if force or not self.initialized: --> 250 super().init(force=force)  252 return self File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/starsim/sim.py:169, in Sim.init(self, force, timer, **kwargs)  167 self.init_dists() # Initialize distributions  168 self.init_people_vals() # Initialize the values in all the states and networks --> 169 self.init_modules_post() # Initialize the module values  170 self.init_results() # Initialize the results  171 self.init_data() # Initialize the data File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/starsim/sim.py:280, in Sim.init_modules_post(self)  278 """ Initialize values in other modules, including networks and time parameters, and do any other post-processing """  279 for mod in self.module_list: --> 280 mod.init_post()  281 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/starsim/demographics.py:579, in Pregnancy.init_post(self)  577 def init_post(self):  578 super().init_post() --> 579 self.updates_pre()  581 # Burn-in  582 if self.ti == 0 and self.pars.burnin: # TODO: refactor File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-fpsim/envs/690/lib/python3.11/site-packages/fpsim/fpmod.py:378, in FPmod.updates_pre(self, uids, upper_age)  376 # Initialize fertility intent for women who just turned 15 (entered the 15-49 age range this timestep)  377 ppl = self.sim.people --> 378 just_15 = nonpreg[(ppl.age[nonpreg] > fpd.min_age) & (ppl.age[nonpreg] <= fpd.min_age + self.t.dt_year)]  379 if len(just_15) > 0:  380 self.init_intent_states(just_15) NameError: name 'nonpreg' is not defined You can ignore this error by setting the following in conf.py: nbsphinx_allow_errors = True