Read the Docs build information
Build id: 3702807
Project: institute-for-disease-modeling-laser
Version: 352
Commit: bc1bb7736a5c8af6b6a97fda6794a86ad7338100
Date: 2026-01-29T00:02:06.331778Z
State: finished
Success: True


[rtd-command-info] start-time: 2026-01-29T00:02:07.642124Z, end-time: 2026-01-29T00:02:08.101971Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/InstituteforDiseaseModeling/laser.git .
Cloning into '.'...

[rtd-command-info] start-time: 2026-01-29T00:02:08.282482Z, end-time: 2026-01-29T00:02:09.169444Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/352/head:external-352
From https://github.com/InstituteforDiseaseModeling/laser
 * [new ref]         refs/pull/352/head -> external-352
 * [new tag]         v0.7.0             -> v0.7.0
 * [new tag]         v0.8.0             -> v0.8.0
 * [new tag]         v0.8.1             -> v0.8.1
 * [new tag]         v0.9.0             -> v0.9.0
 * [new tag]         v0.9.1             -> v0.9.1
 * [new tag]         v1.0.0             -> v1.0.0

[rtd-command-info] start-time: 2026-01-29T00:02:09.886046Z, end-time: 2026-01-29T00:02:09.929174Z, duration: 0, exit-code: 0
git checkout --force bc1bb7736a5c8af6b6a97fda6794a86ad7338100
Note: switching to 'bc1bb7736a5c8af6b6a97fda6794a86ad7338100'.

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 bc1bb77 Bump uv from 0.8.18 to 0.9.6

[rtd-command-info] start-time: 2026-01-29T00:02:10.072737Z, end-time: 2026-01-29T00:02:10.109220Z, duration: 0, exit-code: 0
cat .readthedocs.yml
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
version: 2

build:
  os: ubuntu-22.04
  tools:
    python: "3.13"

sphinx:
  configuration: docs/conf.py
  fail_on_warning: false

formats:
  - htmlzip
  - pdf

python:
  install:
    - requirements: docs/requirements.txt
    - method: pip
      path: .
      extra_requirements:
        - test

search:
  ranking:
    installation.html: 3
    laser.core.html: 2

[rtd-command-info] start-time: 2026-01-29T00:02:14.111177Z, end-time: 2026-01-29T00:02:14.154133Z, duration: 0, exit-code: 0
asdf global python 3.13.3


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python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.13.3.final.0-64 in 496ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/352, 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: 2026-01-29T00:02:15.452797Z, end-time: 2026-01-29T00:02:25.319839Z, duration: 9, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
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Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/352/lib/python3.13/site-packages (23.1)
Collecting pip
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Collecting 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-25.3 setuptools-80.10.2

[rtd-command-info] start-time: 2026-01-29T00:02:25.484560Z, end-time: 2026-01-29T00:02:32.609848Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx
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Collecting 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-2.17.0 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-9.1.0 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

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python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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Installing collected packages: sphinxcontrib-jquery, sphinx-rtd-theme

Successfully installed sphinx-rtd-theme-3.1.0 sphinxcontrib-jquery-4.1

[rtd-command-info] start-time: 2026-01-29T00:02:34.516352Z, end-time: 2026-01-29T00:03:19.178080Z, duration: 44, exit-code: 0
python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[test]
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple
Processing /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/352
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  Preparing metadata (pyproject.toml): started
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Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas->laser-core==1.0.0)
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Collecting kiwisolver>=1.3.1 (from matplotlib->laser-core==1.0.0)
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Collecting pillow>=8 (from matplotlib->laser-core==1.0.0)
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Building wheels for collected packages: laser-core
  Building wheel for laser-core (pyproject.toml): started
  Building wheel for laser-core (pyproject.toml): finished with status 'done'
  Created wheel for laser-core: filename=laser_core-1.0.0-cp313-cp313-linux_x86_64.whl size=47194 sha256=aa59cd3a9b00c88e50bf3b982a72043cc85a972517b09d24a52b64cd0f21fe1f
  Stored in directory: /tmp/pip-ephem-wheel-cache-huevqlg_/wheels/1e/9a/8c/1656b2e25d9860b41003f3e83b5b4c5b8d0bd4c4cc1f2327a4
Successfully built laser-core
Installing collected packages: uv, six, pyproj, pyparsing, pluggy, pillow, numpy, llvmlite, kiwisolver, iniconfig, fonttools, cycler, coverage, click, shapely, scipy, python-dateutil, pytest, pyogrio, numba, h5py, contourpy, pytest-cov, pandas, matplotlib, geopandas, laser-core

Successfully installed click-8.3.1 contourpy-1.3.3 coverage-7.13.2 cycler-0.12.1 fonttools-4.61.1 geopandas-1.1.2 h5py-3.15.1 iniconfig-2.3.0 kiwisolver-1.4.9 laser-core-1.0.0 llvmlite-0.46.0 matplotlib-3.10.8 numba-0.63.1 numpy-2.3.5 pandas-3.0.0 pillow-12.1.0 pluggy-1.6.0 pyogrio-0.12.1 pyparsing-3.3.2 pyproj-3.7.2 pytest-9.0.2 pytest-cov-7.0.0 python-dateutil-2.9.0.post0 scipy-1.17.0 shapely-2.1.2 six-1.17.0 uv-0.9.27

[rtd-command-info] start-time: 2026-01-29T00:03:19.527320Z, end-time: 2026-01-29T00:03:19.561160Z, duration: 0, exit-code: 0
cat docs/conf.py
import os

extensions = [
    "sphinx.ext.autodoc",
    "sphinx.ext.autosummary",
    "sphinx.ext.coverage",
    "sphinx.ext.doctest",
    "sphinx.ext.extlinks",
    "sphinx.ext.ifconfig",
    "sphinx.ext.napoleon",
    "sphinx.ext.todo",
    "sphinx.ext.viewcode",
    "sphinx.ext.mathjax",
]
source_suffix = {".rst": "restructuredtext"}
master_doc = "index"
project = "LASER"
year = "2023-2024"
author = "Institute for Disease Modeling"
copyright = f"{year}, {author}"
version = release = "1.0.0"

pygments_style = "trac"
templates_path = ["."]
extlinks = {
    "issue": ("https://github.com/InstituteforDiseaseModeling/laser/issues/%s", "#"),
    "pr": ("https://github.com/InstituteforDiseaseModeling/laser/pull/%s", "PR #"),
}
# on_rtd is whether we are on readthedocs.org
on_rtd = os.environ.get("READTHEDOCS", None) == "True"

if not on_rtd:  # only set the theme if we are building docs locally
    html_theme = "sphinx_rtd_theme"

html_use_smartypants = True
html_last_updated_fmt = "%b %d, %Y"
html_split_index = False
html_sidebars = {
    "**": ["searchbox.html", "globaltoc.html", "sourcelink.html"],
}
html_short_title = f"{project}-{version}"

# Napoleon settings (Napolean converts Google-style docstrings to reStructuredText)
napoleon_google_docstring = True
napoleon_numpy_docstring = True
napoleon_include_init_with_doc = False
napoleon_include_private_with_doc = False
napoleon_include_special_with_doc = True
napoleon_use_admonition_for_examples = False
napoleon_use_admonition_for_notes = False
napoleon_use_admonition_for_references = False
napoleon_use_ivar = True  # from Cookiecutter template, False is the default
napoleon_use_param = False  # from Cookiecutter template, True is the default
napoleon_use_rtype = False  # from Cookiecutter template, True is the default
napoleon_preprocess_types = False
napoleon_type_aliases = None
napoleon_attr_annotations = True

mathjax3_config = {"TeX": {"Macros": {"small": ["{\\scriptstyle #1}", 1]}}}

# Prevent the following warning:
# sphinx/builders/linkcheck.py:86: RemovedInSphinx80Warning: The default value for 'linkcheck_report_timeouts_as_broken' will change to False in Sphinx 8, meaning that request timeouts will be reported with a new 'timeout' status, instead of as 'broken'. This is intended to provide more detail as to the failure mode. See https://github.com/sphinx-doc/sphinx/issues/11868 for details.
#   warnings.warn(deprecation_msg, RemovedInSphinx80Warning, stacklevel=1)

linkcheck_ignore = [r"https://www\.populationpyramid\.net/nigeria/2024/"]
linkcheck_report_timeouts_as_broken = False

[rtd-command-info] start-time: 2026-01-29T00:03:19.757310Z, end-time: 2026-01-29T00:03:29.201492Z, duration: 9, exit-code: 0
python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v9.1.0
loading translations [en]... done
making output directory... done
[autosummary] generating autosummary for: architecture.rst, authors.rst, calibration.rst, changelog.rst, contributing.rst, eula.rst, example.rst, index.rst, installation.rst, kmestimator.rst, migration.rst, performance.rst, pyramids.rst, readme.rst, source/laser.core.demographics.rst, source/laser.core.rst, source/modules.rst, spatialexample.rst, usage.rst, vdexample.rst
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 20 source files that are out of date
updating environment: [new config] 20 added, 0 changed, 0 removed
reading sources... [  5%] architecture
reading sources... [ 10%] authors
reading sources... [ 15%] calibration
reading sources... [ 20%] changelog
reading sources... [ 25%] contributing
reading sources... [ 30%] eula
reading sources... [ 35%] example
reading sources... [ 40%] index
reading sources... [ 45%] installation
reading sources... [ 50%] kmestimator
reading sources... [ 55%] migration
reading sources... [ 60%] performance
reading sources... [ 65%] pyramids
reading sources... [ 70%] readme
reading sources... [ 75%] source/laser.core
reading sources... [ 80%] source/laser.core.demographics
reading sources... [ 85%] source/modules
reading sources... [ 90%] spatialexample
reading sources... [ 95%] usage
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/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/352/lib/python3.13/site-packages/laser/core/propertyset.py:docstring of laser.core.propertyset.PropertySet:57: WARNING: Inline substitution_reference start-string without end-string. [docutils]
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