Read the Docs build information
Build id: 3782067
Project: institute-for-disease-modeling-laser-measles
Version: 122
Commit: 10570e769669ac082fc526de9d2104b886980ee9
Date: 2026-02-25T21:57:26.274821Z
State: cancelled
Success: False


[rtd-command-info] start-time: 2026-02-25T21:57:27.088125Z, end-time: 2026-02-25T21:57:27.745694Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/InstituteforDiseaseModeling/laser-measles.git .
Cloning into '.'...

[rtd-command-info] start-time: 2026-02-25T21:57:27.836159Z, end-time: 2026-02-25T21:57:28.998349Z, duration: 1, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/122/head:external-122
From https://github.com/InstituteforDiseaseModeling/laser-measles
 * [new ref]         refs/pull/122/head -> external-122
 * [new tag]         v0.7.2-dev3        -> v0.7.2-dev3
 * [new tag]         v0.8.0-dev1        -> v0.8.0-dev1
 * [new tag]         v0.9.0             -> v0.9.0

[rtd-command-info] start-time: 2026-02-25T21:57:29.777374Z, end-time: 2026-02-25T21:57:29.817474Z, duration: 0, exit-code: 0
git checkout --force 10570e769669ac082fc526de9d2104b886980ee9
Note: switching to '10570e769669ac082fc526de9d2104b886980ee9'.

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 <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 10570e7 pin rastertools version

[rtd-command-info] start-time: 2026-02-25T21:57:29.934610Z, end-time: 2026-02-25T21:57:29.968042Z, duration: 0, exit-code: 0
cat .readthedocs.yml
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
version: 2
sphinx:
  configuration: docs/conf.py
formats:
  - htmlzip
  - epub
  - pdf

build:
  os: ubuntu-22.04
  tools:
    python: "3.12"
  jobs:
    post_install:
      - python docs/tutorials/convert_tutorials.py
python:
  install:
    - requirements: docs/requirements.txt
    - method: pip
      path: .

[rtd-command-info] start-time: 2026-02-25T21:57:34.241720Z, end-time: 2026-02-25T21:57:34.291856Z, duration: 0, exit-code: 0
asdf global python 3.12.10


[rtd-command-info] start-time: 2026-02-25T21:57:34.898966Z, end-time: 2026-02-25T21:57:35.401589Z, duration: 0, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.12.10.final.0-64 in 292ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/122, 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: 2026-02-25T21:57:35.552260Z, end-time: 2026-02-25T21:57:41.330537Z, duration: 5, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
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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 uninstalled pip-23.1
Successfully installed pip-26.0.1 setuptools-82.0.0

[rtd-command-info] start-time: 2026-02-25T21:57:41.422232Z, end-time: 2026-02-25T21:57:47.727707Z, duration: 6, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx
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Installing collected packages: urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, roman-numerals, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset_normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx

Successfully installed Jinja2-3.1.6 MarkupSafe-3.0.3 Pygments-2.19.2 alabaster-1.0.0 babel-2.18.0 certifi-2026.2.25 charset_normalizer-3.4.4 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-9.1.0 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.6.3

[rtd-command-info] start-time: 2026-02-25T21:57:47.817421Z, end-time: 2026-02-25T21:58:31.507087Z, duration: 43, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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Successfully installed accessible-pygments-0.0.5 annotated-types-0.7.0 asttokens-3.0.1 attrs-25.4.0 autodoc_pydantic-2.2.0 beautifulsoup4-4.14.3 bleach-6.3.0 comm-0.2.3 contourpy-1.3.3 cycler-0.12.1 debugpy-1.8.20 decorator-5.2.1 defusedxml-0.7.1 dill-0.4.1 et-xmlfile-2.0.0 executing-2.2.1 fastjsonschema-2.21.2 fonttools-4.61.1 gitdb-4.0.12 gitpython-3.1.46 ipykernel-7.2.0 ipython-9.10.0 ipython-pygments-lexers-1.1.1 ipywidgets-8.1.8 jedi-0.19.2 jellyfish-1.2.1 jsonpickle-4.1.1 jsonschema-4.26.0 jsonschema-specifications-2025.9.1 jupyter-client-8.8.0 jupyter-core-5.9.1 jupyterlab-pygments-0.3.0 jupyterlab_widgets-3.0.16 jupytext-1.19.1 kiwisolver-1.4.9 line_profiler-5.0.2 markdown-it-py-4.0.0 matplotlib-3.10.8 matplotlib-inline-0.2.1 mdit-py-plugins-0.5.0 mdurl-0.1.2 memory_profiler-0.61.0 mistune-3.2.0 multiprocess-0.70.19 nbclient-0.10.4 nbconvert-7.17.0 nbformat-5.10.4 nbsphinx-0.9.8 nest-asyncio-1.6.0 numpy-2.4.2 openpyxl-3.1.5 pandas-3.0.1 pandoc-2.4 pandocfilters-1.5.1 parso-0.8.6 pexpect-4.9.0 pillow-12.1.1 plantweb-1.3.0 platformdirs-4.9.2 plumbum-1.10.0 ply-3.11 pockets-0.9.1 prompt_toolkit-3.0.52 psutil-7.2.2 ptyprocess-0.7.0 pure-eval-0.2.3 pydantic-2.12.5 pydantic-core-2.41.5 pydantic-settings-2.13.1 pydata-sphinx-theme-0.16.1 pypandoc-1.16.2 pyparsing-3.3.2 python-dateutil-2.9.0.post0 python-dotenv-1.2.1 pyyaml-6.0.3 pyzmq-27.1.0 readthedocs-sphinx-search-0.3.2 referencing-0.37.0 rpds-py-0.30.0 scipy-1.17.1 sciris-3.2.6 seaborn-0.13.2 six-1.17.0 smmap-5.0.2 soupsieve-2.8.3 sphinx-autodoc-typehints-3.8.0 sphinx-design-0.7.0 sphinxcontrib-napoleon-0.7 stack_data-0.6.3 tinycss2-1.4.0 tornado-6.5.4 tqdm-4.67.3 traitlets-5.14.3 typing-extensions-4.15.0 typing-inspection-0.4.2 wcwidth-0.6.0 webencodings-0.5.1 widgetsnbextension-4.0.15 xlsxwriter-3.2.9 zstandard-0.25.0

[rtd-command-info] start-time: 2026-02-25T21:58:31.606590Z, end-time: 2026-02-25T21:59:03.934607Z, duration: 32, exit-code: 0
python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .
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Collecting shellingham>=1.3.0 (from typer>=0.12.0->laser.measles==0.9.0)
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e0/f9/0595336914c5619e5f28a1fb793285925a8cd4b432c9da0a987836c7f822/shellingham-1.5.4-py2.py3-none-any.whl (9.8 kB)
Collecting rich>=12.3.0 (from typer>=0.12.0->laser.measles==0.9.0)
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/14/25/b208c5683343959b670dc001595f2f3737e051da617f66c31f7c4fa93abc/rich-14.3.3-py3-none-any.whl (310 kB)
Collecting annotated-doc>=0.0.2 (from typer>=0.12.0->laser.measles==0.9.0)
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1e/d3/26bf1008eb3d2daa8ef4cacc7f3bfdc11818d111f7e2d0201bc6e3b49d45/annotated_doc-0.0.4-py3-none-any.whl (5.3 kB)
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Collecting pyogrio>=0.7.2 (from geopandas->laser-core>=1.0.0->laser.measles==0.9.0)
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/36/f7/cf8bec9024625947e1a71441906f60a5fa6f9e4c441c4428037e73b1fcc8/pyogrio-0.12.1-cp312-cp312-manylinux_2_28_x86_64.whl (32.5 MB)
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Building wheels for collected packages: laser.measles
  Building wheel for laser.measles (pyproject.toml): started
  Building wheel for laser.measles (pyproject.toml): finished with status 'done'
  Created wheel for laser.measles: filename=laser_measles-0.9.0-py3-none-any.whl size=132379 sha256=cca39d6b2a0a7489828e7d65813e1419a850213c80e4155e0e172250cb75d407
  Stored in directory: /tmp/pip-ephem-wheel-cache-mkf47iqf/wheels/d4/ee/a8/c5314a433d237e2ab2bf0c76c7eff5f59a2cc8301f0f29bee6
Successfully built laser.measles
Installing collected packages: appdirs, threadpoolctl, shellingham, shapely, pyvd, pyshp, pyproj, pyogrio, pycountry, pyarrow, polars-runtime-32, llvmlite, joblib, h5py, graphemeu, diskcache, click, annotated-doc, about-time, scikit-learn, rich, polars, numba, alive-progress, typer, rastertoolkit, patito, geopandas, laser-core, laser.measles

Successfully installed about-time-4.2.1 alive-progress-3.3.0 annotated-doc-0.0.4 appdirs-1.4.4 click-8.3.1 diskcache-5.6.3 geopandas-1.1.2 graphemeu-0.7.2 h5py-3.15.1 joblib-1.5.3 laser-core-1.0.0 laser.measles-0.9.0 llvmlite-0.46.0 numba-0.64.0 patito-0.8.6 polars-1.38.1 polars-runtime-32-1.38.1 pyarrow-23.0.1 pycountry-26.2.16 pyogrio-0.12.1 pyproj-3.7.2 pyshp-2.3.1 pyvd-1.0.1 rastertoolkit-0.3.12 rich-14.3.3 scikit-learn-1.8.0 shapely-2.1.2 shellingham-1.5.4 threadpoolctl-3.6.0 typer-0.24.1

[rtd-command-info] start-time: 2026-02-25T21:59:04.045225Z, end-time: 2026-02-25T21:59:10.459631Z, duration: 6, exit-code: 0
python docs/tutorials/convert_tutorials.py
[jupytext] Reading tut_spatial_mixing.py in format py
[jupytext] Writing tut_spatial_mixing.ipynb
[jupytext] Reading tut_basic_model.py in format py
[jupytext] Writing tut_basic_model.ipynb
[jupytext] Reading tut_vaccination.py in format py
[jupytext] Writing tut_vaccination.ipynb
[jupytext] Reading tut_model_structure.py in format py
[jupytext] Writing tut_model_structure.ipynb
[jupytext] Reading tut_traveling_waves.py in format py
[jupytext] Writing tut_traveling_waves.ipynb
[jupytext] Reading tut_scenarios.py in format py
[jupytext] Writing tut_scenarios.ipynb
[jupytext] Reading tut_state_arrays.py in format py
[jupytext] Writing tut_state_arrays.ipynb
[jupytext] Reading tut_creating_component.py in format py
[jupytext] Writing tut_creating_component.ipynb
[jupytext] Reading tut_pydantic_component_parameters.py in format py
[jupytext] Writing tut_pydantic_component_parameters.ipynb
[jupytext] Reading tut_random_numbers.py in format py
[jupytext] Writing tut_random_numbers.ipynb
[jupytext] Reading tut_abm_vital_dynamics.py in format py
[jupytext] Writing tut_abm_vital_dynamics.ipynb
[jupytext] Reading tut_abm_intro.py in format py
[jupytext] Writing tut_abm_intro.ipynb
[jupytext] Reading tut_quickstart_hello_world.py in format py
[jupytext] Writing tut_quickstart_hello_world.ipynb
Converting tut_spatial_mixing.py to notebook...
Successfully converted tut_spatial_mixing.py
Converting tut_basic_model.py to notebook...
Successfully converted tut_basic_model.py
Converting tut_vaccination.py to notebook...
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Converting tut_model_structure.py to notebook...
Successfully converted tut_model_structure.py
Converting tut_traveling_waves.py to notebook...
Successfully converted tut_traveling_waves.py
Converting tut_scenarios.py to notebook...
Successfully converted tut_scenarios.py
Converting tut_state_arrays.py to notebook...
Successfully converted tut_state_arrays.py
Converting tut_creating_component.py to notebook...
Successfully converted tut_creating_component.py
Converting tut_pydantic_component_parameters.py to notebook...
Successfully converted tut_pydantic_component_parameters.py
Converting tut_random_numbers.py to notebook...
Successfully converted tut_random_numbers.py
Converting tut_abm_vital_dynamics.py to notebook...
Successfully converted tut_abm_vital_dynamics.py
Converting tut_abm_intro.py to notebook...
Successfully converted tut_abm_intro.py
Converting tut_quickstart_hello_world.py to notebook...
Successfully converted tut_quickstart_hello_world.py
Successfully converted 13 tutorial files to notebooks

[rtd-command-info] start-time: 2026-02-25T21:59:10.643595Z, end-time: 2026-02-25T21:59:10.682853Z, duration: 0, exit-code: 0
cat docs/conf.py
#
# Configuration file for the Sphinx documentation builder.

import os

import sciris as sc

on_rtd = os.environ.get("READTHEDOCS") == "True"


# -- Project information -----------------------------------------------------

project = "laser-measles"
copyright = f"2024 - {sc.now().year}, Bill & Melinda Gates Foundation. All rights reserved."

# The short X.Y version
version = release = "0.9.0"


# -- 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.ext.doctest",  # Enable doctest builder
    "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",
    "sphinxcontrib.autodoc_pydantic",
]

# 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 = True  # Allow subclasses to inherit 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 = ["laser.measles."]

# List of patterns, relative to source directory, to exclude
exclude_patterns = [
    "_build",
    "Thumbs.db",
    ".DS_Store",
    "**.ipynb_checkpoints",
    "tutorials/not_ready/**",
    "tutorials/convert_tutorials.ipynb",
]

# Suppress certain warnings
suppress_warnings = ["autosectionlabel.*"]

# Configure pydantic


# -- 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://laser-measles.readthedocs.io/en/latest/", "icon": "fas fa-home"},
        {
            "name": "GitHub",
            "url": "https://github.com/InstituteforDiseaseModeling/laser-measles",
            "icon": "fab fa-github-square",
        },
    ],
    "navbar_end": ["theme-switcher", "navbar-icon-links"],
    "secondary_sidebar_items": [],
    "header_links_before_dropdown": 5,
    "footer_start": ["copyright", "footer_start"],
    "footer_end": ["theme-version", "footer_end"],
}
html_sidebars = {
    "**": ["page-toc"],
}
html_logo = "images/idm-logo-transparent.png"
html_favicon = "images/favicon.ico"
html_static_path = ["_static"]
html_baseurl = "https://docs.idmod.org/"
html_context = {
    "rtd_url": "https://docs.idmod.org/",
    "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 = "laser-measles"


# 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 = "auto"
nbsphinx_timeout = 600
nbsphinx_allow_errors = True
nbsphinx_execute_arguments = [
    "--InlineBackend.figure_formats={'svg', 'pdf'}",
    "--InlineBackend.rc={'figure.dpi': 96}",
]

# OpenSearch options
html_use_opensearch = "docs.idmod.org/projects/laser-measles/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_parent}/{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}",
    }

# -- Linkcheck configuration -------------------------------------------------
# Configuration for sphinx-build -b linkcheck

# URLs that should be ignored during link checking
linkcheck_ignore = [
    r"https://chatgpt\.com/g/g-674f5fd33aec8191bcdc1a2736fb7c8d-laser-gpt-jenner",  # Requires authentication
    r"https://.*\.idmod\.org/.*",  # Internal IDM links that may require auth
    r"https://.*\.gatesfoundation\.org/.*",  # Gates Foundation internal links
]

# HTTP status codes that should be considered as "working" (not broken)
# 403 = Forbidden (requires authentication)
# 401 = Unauthorized (requires authentication)
linkcheck_allowed_redirects = {
    r"https://.*\.idmod\.org/.*": r".*",
    r"https://.*\.gatesfoundation\.org/.*": r".*",
}

# Timeout for link checking (in seconds)
linkcheck_timeout = 30

# Number of workers for parallel link checking
linkcheck_workers = 5

# Whether to check anchors in links
linkcheck_anchors = False

# Whether to check anchors in relative links
linkcheck_anchors_ignore = [
    r"#.*",  # Ignore all anchor links
]

# Retry count for failed links
linkcheck_retries = 2

[rtd-command-info] start-time: None, end-time: None, duration: None, exit-code: None
python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html