Read the Docs build information
Build id: 4024188
Project: institute-for-disease-modeling-laser
Version: 400
Commit: dca9762c1df49ed195e968ce589fb86d0fda1cc6
Date: 2026-05-19T02:28:41.031039Z
State: finished
Success: True


[rtd-command-info] start-time: 2026-05-19T02:30:50.419195Z, end-time: 2026-05-19T02:30:50.921711Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/InstituteforDiseaseModeling/laser.git .
Cloning into '.'...

[rtd-command-info] start-time: 2026-05-19T02:30:51.005104Z, end-time: 2026-05-19T02:30:51.981866Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/400/head:external-400
From https://github.com/InstituteforDiseaseModeling/laser
 * [new ref]         refs/pull/400/head -> external-400
 * [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
 * [new tag]         v1.0.1             -> v1.0.1

[rtd-command-info] start-time: 2026-05-19T02:30:52.633015Z, end-time: 2026-05-19T02:30:52.687558Z, duration: 0, exit-code: 0
git checkout --force dca9762c1df49ed195e968ce589fb86d0fda1cc6
Note: switching to 'dca9762c1df49ed195e968ce589fb86d0fda1cc6'.

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 dca9762 Bump pytest from 8.4.2 to 9.0.3

[rtd-command-info] start-time: 2026-05-19T02:30:52.762807Z, end-time: 2026-05-19T02:30:52.800829Z, 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: 2026-05-19T02:30:57.460275Z, end-time: 2026-05-19T02:30:57.515380Z, duration: 0, exit-code: 0
asdf global python 3.13.9


[rtd-command-info] start-time: 2026-05-19T02:30:57.849992Z, end-time: 2026-05-19T02:30:58.487329Z, duration: 0, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.13.9.final.0-64 in 392ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400, 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: 2026-05-19T02:30:58.570011Z, end-time: 2026-05-19T02:31:05.140978Z, duration: 6, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (23.1)
Collecting pip
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/3a/eb/fea4d1d51c49832120f7f285d07306db3960f423a2612c6057caf3e8196f/pip-26.1.1-py3-none-any.whl (1.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 14.8 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (67.6.1)
Collecting setuptools
  Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9d/76/f789f7a86709c6b087c5a2f52f911838cad707cc613162401badc665acfe/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 16.3 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 uninstalled pip-23.1
Successfully installed pip-26.1.1 setuptools-82.0.1

[rtd-command-info] start-time: 2026-05-19T02:31:05.220682Z, end-time: 2026-05-19T02:31:12.048112Z, duration: 6, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple
Collecting sphinx
  Downloading sphinx-9.1.0-py3-none-any.whl (3.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.9/3.9 MB 15.2 MB/s  0:00:00
Collecting sphinxcontrib-applehelp>=1.0.7 (from sphinx)
  Downloading sphinxcontrib_applehelp-2.0.0-py3-none-any.whl (119 kB)
Collecting sphinxcontrib-devhelp>=1.0.6 (from sphinx)
  Downloading sphinxcontrib_devhelp-2.0.0-py3-none-any.whl (82 kB)
Collecting sphinxcontrib-htmlhelp>=2.0.6 (from sphinx)
  Downloading sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl (98 kB)
Collecting sphinxcontrib-jsmath>=1.0.1 (from sphinx)
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting sphinxcontrib-qthelp>=1.0.6 (from sphinx)
  Downloading sphinxcontrib_qthelp-2.0.0-py3-none-any.whl (88 kB)
Collecting sphinxcontrib-serializinghtml>=1.1.9 (from sphinx)
  Downloading sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl (92 kB)
Collecting Jinja2>=3.1 (from sphinx)
  Downloading jinja2-3.1.6-py3-none-any.whl (134 kB)
Collecting Pygments>=2.17 (from sphinx)
  Downloading pygments-2.20.0-py3-none-any.whl (1.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 15.5 MB/s  0:00:00
Collecting docutils<0.23,>=0.21 (from sphinx)
  Downloading docutils-0.22.4-py3-none-any.whl (633 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 633.2/633.2 kB 20.3 MB/s  0:00:00
Collecting snowballstemmer>=2.2 (from sphinx)
  Downloading snowballstemmer-3.0.1-py3-none-any.whl (103 kB)
Collecting babel>=2.13 (from sphinx)
  Downloading babel-2.18.0-py3-none-any.whl (10.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.2/10.2 MB 15.0 MB/s  0:00:00
Collecting alabaster>=0.7.14 (from sphinx)
  Downloading alabaster-1.0.0-py3-none-any.whl (13 kB)
Collecting imagesize>=1.3 (from sphinx)
  Downloading imagesize-2.0.0-py2.py3-none-any.whl (9.4 kB)
Collecting requests>=2.30.0 (from sphinx)
  Downloading requests-2.34.2-py3-none-any.whl (73 kB)
Collecting roman-numerals>=1.0.0 (from sphinx)
  Downloading roman_numerals-4.1.0-py3-none-any.whl (7.7 kB)
Collecting packaging>=23.0 (from sphinx)
  Downloading packaging-26.2-py3-none-any.whl (100 kB)
Collecting MarkupSafe>=2.0 (from Jinja2>=3.1->sphinx)
  Downloading markupsafe-3.0.3-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
Collecting charset_normalizer<4,>=2 (from requests>=2.30.0->sphinx)
  Downloading charset_normalizer-3.4.7-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (215 kB)
Collecting idna<4,>=2.5 (from requests>=2.30.0->sphinx)
  Downloading idna-3.15-py3-none-any.whl (72 kB)
Collecting urllib3<3,>=1.26 (from requests>=2.30.0->sphinx)
  Downloading urllib3-2.7.0-py3-none-any.whl (131 kB)
Collecting certifi>=2023.5.7 (from requests>=2.30.0->sphinx)
  Downloading certifi-2026.4.22-py3-none-any.whl (135 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-2.20.0 alabaster-1.0.0 babel-2.18.0 certifi-2026.4.22 charset_normalizer-3.4.7 docutils-0.22.4 idna-3.15 imagesize-2.0.0 packaging-26.2 requests-2.34.2 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 urllib3-2.7.0

[rtd-command-info] start-time: 2026-05-19T02:31:12.128645Z, end-time: 2026-05-19T02:31:13.699241Z, duration: 1, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple
Requirement already satisfied: sphinx>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from -r docs/requirements.txt (line 1)) (9.1.0)
Collecting sphinx-rtd-theme (from -r docs/requirements.txt (line 2))
  Downloading sphinx_rtd_theme-3.1.0-py2.py3-none-any.whl (7.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.7/7.7 MB 15.0 MB/s  0:00:00
Requirement already satisfied: sphinxcontrib-applehelp>=1.0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.0.0)
Requirement already satisfied: sphinxcontrib-devhelp>=1.0.6 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.0.0)
Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.6 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.1.0)
Requirement already satisfied: sphinxcontrib-jsmath>=1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (1.0.1)
Requirement already satisfied: sphinxcontrib-qthelp>=1.0.6 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.0.0)
Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.9 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.0.0)
Requirement already satisfied: Jinja2>=3.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (3.1.6)
Requirement already satisfied: Pygments>=2.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.20.0)
Requirement already satisfied: docutils<0.23,>=0.21 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (0.22.4)
Requirement already satisfied: snowballstemmer>=2.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (3.0.1)
Requirement already satisfied: babel>=2.13 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.18.0)
Requirement already satisfied: alabaster>=0.7.14 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (1.0.0)
Requirement already satisfied: imagesize>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.0.0)
Requirement already satisfied: requests>=2.30.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.34.2)
Requirement already satisfied: roman-numerals>=1.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (4.1.0)
Requirement already satisfied: packaging>=23.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (26.2)
Collecting sphinxcontrib-jquery<5,>=4 (from sphinx-rtd-theme->-r docs/requirements.txt (line 2))
  Downloading sphinxcontrib_jquery-4.1-py2.py3-none-any.whl (121 kB)
Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from Jinja2>=3.1->sphinx>=1.3->-r docs/requirements.txt (line 1)) (3.0.3)
Requirement already satisfied: charset_normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from requests>=2.30.0->sphinx>=1.3->-r docs/requirements.txt (line 1)) (3.4.7)
Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from requests>=2.30.0->sphinx>=1.3->-r docs/requirements.txt (line 1)) (3.15)
Requirement already satisfied: urllib3<3,>=1.26 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from requests>=2.30.0->sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.7.0)
Requirement already satisfied: certifi>=2023.5.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from requests>=2.30.0->sphinx>=1.3->-r docs/requirements.txt (line 1)) (2026.4.22)
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: 2026-05-19T02:31:13.783803Z, end-time: 2026-05-19T02:32:01.790378Z, duration: 48, 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 ./.
  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'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting click (from laser-core==1.0.1)
  Downloading click-8.4.0-py3-none-any.whl (116 kB)
Collecting numpy (from laser-core==1.0.1)
  Downloading numpy-2.4.6-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.6/16.6 MB 14.9 MB/s  0:00:01
Collecting numba (from laser-core==1.0.1)
  Downloading numba-0.65.1-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.8/3.8 MB 14.6 MB/s  0:00:00
Collecting matplotlib (from laser-core==1.0.1)
  Downloading matplotlib-3.10.9-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (8.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.8/8.8 MB 14.9 MB/s  0:00:00
Collecting pandas (from laser-core==1.0.1)
  Downloading pandas-3.0.3-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (10.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.9/10.9 MB 14.8 MB/s  0:00:00
Collecting h5py (from laser-core==1.0.1)
  Downloading h5py-3.16.0-cp313-cp313-manylinux_2_28_x86_64.whl (5.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.4/5.4 MB 14.7 MB/s  0:00:00
Collecting geopandas (from laser-core==1.0.1)
  Downloading geopandas-1.1.3-py3-none-any.whl (342 kB)
Collecting shapely (from laser-core==1.0.1)
  Downloading shapely-2.1.2-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 15.2 MB/s  0:00:00
Collecting uv>=0.10.5 (from laser-core==1.0.1)
  Downloading uv-0.11.15-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (24.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 24.4/24.4 MB 14.6 MB/s  0:00:01
Collecting pytest>=6.0 (from laser-core==1.0.1)
  Downloading pytest-9.0.3-py3-none-any.whl (375 kB)
Collecting pytest-cov (from laser-core==1.0.1)
  Downloading pytest_cov-7.1.0-py3-none-any.whl (22 kB)
Collecting scipy (from laser-core==1.0.1)
  Downloading scipy-1.17.1-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (35.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 35.2/35.2 MB 14.8 MB/s  0:00:02
Collecting tox (from laser-core==1.0.1)
  Downloading tox-4.54.0-py3-none-any.whl (214 kB)
Collecting tox-uv (from laser-core==1.0.1)
  Downloading tox_uv-1.35.2-py3-none-any.whl (6.6 kB)
Collecting iniconfig>=1.0.1 (from pytest>=6.0->laser-core==1.0.1)
  Downloading iniconfig-2.3.0-py3-none-any.whl (7.5 kB)
Requirement already satisfied: packaging>=22 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from pytest>=6.0->laser-core==1.0.1) (26.2)
Collecting pluggy<2,>=1.5 (from pytest>=6.0->laser-core==1.0.1)
  Downloading pluggy-1.6.0-py3-none-any.whl (20 kB)
Requirement already satisfied: pygments>=2.7.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from pytest>=6.0->laser-core==1.0.1) (2.20.0)
Collecting pyogrio>=0.7.2 (from geopandas->laser-core==1.0.1)
  Downloading pyogrio-0.12.1-cp313-cp313-manylinux_2_28_x86_64.whl (32.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 32.5/32.5 MB 14.8 MB/s  0:00:02
Collecting pyproj>=3.5.0 (from geopandas->laser-core==1.0.1)
  Downloading pyproj-3.7.2-cp313-cp313-manylinux_2_28_x86_64.whl (9.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 14.9 MB/s  0:00:00
Collecting python-dateutil>=2.8.2 (from pandas->laser-core==1.0.1)
  Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Requirement already satisfied: certifi in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/400/lib/python3.13/site-packages (from pyogrio>=0.7.2->geopandas->laser-core==1.0.1) (2026.4.22)
Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas->laser-core==1.0.1)
  Downloading six-1.17.0-py2.py3-none-any.whl (11 kB)
Collecting contourpy>=1.0.1 (from matplotlib->laser-core==1.0.1)
  Downloading contourpy-1.3.3-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (362 kB)
Collecting cycler>=0.10 (from matplotlib->laser-core==1.0.1)
  Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB)
Collecting fonttools>=4.22.0 (from matplotlib->laser-core==1.0.1)
  Downloading fonttools-4.63.0-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (5.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.0/5.0 MB 14.7 MB/s  0:00:00
Collecting kiwisolver>=1.3.1 (from matplotlib->laser-core==1.0.1)
  Downloading kiwisolver-1.5.0-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (1.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.5/1.5 MB 15.3 MB/s  0:00:00
Collecting pillow>=8 (from matplotlib->laser-core==1.0.1)
  Downloading pillow-12.2.0-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (7.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.1/7.1 MB 14.9 MB/s  0:00:00
Collecting pyparsing>=3 (from matplotlib->laser-core==1.0.1)
  Downloading pyparsing-3.3.2-py3-none-any.whl (122 kB)
Collecting llvmlite<0.48,>=0.47.0dev0 (from numba->laser-core==1.0.1)
  Downloading llvmlite-0.47.0-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (56.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.3/56.3 MB 14.8 MB/s  0:00:03
Collecting coverage>=7.10.6 (from coverage[toml]>=7.10.6->pytest-cov->laser-core==1.0.1)
  Downloading coverage-7.14.0-cp313-cp313-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (253 kB)
Collecting cachetools>=7.0.3 (from tox->laser-core==1.0.1)
  Downloading cachetools-7.1.3-py3-none-any.whl (16 kB)
Collecting colorama>=0.4.6 (from tox->laser-core==1.0.1)
  Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Collecting filelock>=3.25 (from tox->laser-core==1.0.1)
  Downloading filelock-3.29.0-py3-none-any.whl (39 kB)
Collecting platformdirs>=4.9.4 (from tox->laser-core==1.0.1)
  Downloading platformdirs-4.9.6-py3-none-any.whl (21 kB)
Collecting pyproject-api>=1.10 (from tox->laser-core==1.0.1)
  Downloading pyproject_api-1.10.0-py3-none-any.whl (13 kB)
Collecting python-discovery>=1.2.2 (from tox->laser-core==1.0.1)
  Downloading python_discovery-1.3.1-py3-none-any.whl (33 kB)
Collecting tomli-w>=1.2 (from tox->laser-core==1.0.1)
  Downloading tomli_w-1.2.0-py3-none-any.whl (6.7 kB)
Collecting virtualenv>=21.1 (from tox->laser-core==1.0.1)
  Downloading virtualenv-21.3.3-py3-none-any.whl (7.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.6/7.6 MB 14.9 MB/s  0:00:00
Collecting distlib<1,>=0.3.7 (from virtualenv>=21.1->tox->laser-core==1.0.1)
  Downloading distlib-0.4.0-py2.py3-none-any.whl (469 kB)
Collecting tox-uv-bare==1.35.2 (from tox-uv->laser-core==1.0.1)
  Downloading tox_uv_bare-1.35.2-py3-none-any.whl (22 kB)
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-1.0.1-py3-none-any.whl size=36638 sha256=ad05044d7059ebd560958150d6d2f7e69e8bc448992cf1c6c4013f07c3db9e1a
  Stored in directory: /tmp/pip-ephem-wheel-cache-xdp_r8jg/wheels/41/42/20/8bd806a83b3827cceb780e9694d52fdf7f16347fe7988922dc
Successfully built laser-core
Installing collected packages: distlib, uv, tomli-w, six, pyproject-api, pyproj, pyparsing, pluggy, platformdirs, pillow, numpy, llvmlite, kiwisolver, iniconfig, fonttools, filelock, cycler, coverage, colorama, click, cachetools, shapely, scipy, python-discovery, python-dateutil, pytest, pyogrio, numba, h5py, contourpy, virtualenv, pytest-cov, pandas, matplotlib, tox, geopandas, tox-uv-bare, laser-core, tox-uv

Successfully installed cachetools-7.1.3 click-8.4.0 colorama-0.4.6 contourpy-1.3.3 coverage-7.14.0 cycler-0.12.1 distlib-0.4.0 filelock-3.29.0 fonttools-4.63.0 geopandas-1.1.3 h5py-3.16.0 iniconfig-2.3.0 kiwisolver-1.5.0 laser-core-1.0.1 llvmlite-0.47.0 matplotlib-3.10.9 numba-0.65.1 numpy-2.4.6 pandas-3.0.3 pillow-12.2.0 platformdirs-4.9.6 pluggy-1.6.0 pyogrio-0.12.1 pyparsing-3.3.2 pyproj-3.7.2 pyproject-api-1.10.0 pytest-9.0.3 pytest-cov-7.1.0 python-dateutil-2.9.0.post0 python-discovery-1.3.1 scipy-1.17.1 shapely-2.1.2 six-1.17.0 tomli-w-1.2.0 tox-4.54.0 tox-uv-1.35.2 tox-uv-bare-1.35.2 uv-0.11.15 virtualenv-21.3.3

[rtd-command-info] start-time: 2026-05-19T02:32:01.919856Z, end-time: 2026-05-19T02:32:01.959081Z, 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 = "1.0.1"

pygments_style = "trac"
templates_path = ["."]
extlinks = {
    "issue": ("https://github.com/laser-base/laser-core/issues/%s", "#"),
    "pr": ("https://github.com/laser-base/laser-core/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: 2026-05-19T02:32:02.039114Z, end-time: 2026-05-19T02:32:06.315561Z, duration: 4, 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
reading sources... [100%] vdexample

../CHANGELOG.rst:76: WARNING: Inline substitution_reference start-string without end-string. [docutils]
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
copying assets... 
copying static files... 
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/400/_readthedocs/html/_static/language_data.js
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/400/_readthedocs/html/_static/basic.css
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/400/_readthedocs/html/_static/documentation_options.js
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/400/_readthedocs/html/_static/alabaster.css
copying static files: done
copying extra files... 
copying extra files: done
copying assets: done
writing output... [  5%] architecture
writing output... [ 10%] authors
writing output... [ 15%] calibration
writing output... [ 20%] changelog
writing output... [ 25%] contributing
writing output... [ 30%] eula
writing output... [ 35%] example
writing output... [ 40%] index
writing output... [ 45%] installation
writing output... [ 50%] kmestimator
writing output... [ 55%] migration
writing output... [ 60%] performance
writing output... [ 65%] pyramids
writing output... [ 70%] readme
writing output... [ 75%] source/laser.core
writing output... [ 80%] source/laser.core.demographics
writing output... [ 85%] source/modules
writing output... [ 90%] spatialexample
writing output... [ 95%] usage
writing output... [100%] vdexample

generating indices... genindex py-modindex done
highlighting module code... [ 10%] laser.core.demographics.kmestimator
highlighting module code... [ 20%] laser.core.demographics.pyramid
highlighting module code... [ 30%] laser.core.demographics.spatialpops
highlighting module code... [ 40%] laser.core.distributions
highlighting module code... [ 50%] laser.core.laserframe
highlighting module code... [ 60%] laser.core.migration
highlighting module code... [ 70%] laser.core.propertyset
highlighting module code... [ 80%] laser.core.random
highlighting module code... [ 90%] laser.core.sortedqueue
highlighting module code... [100%] laser.core.utils

writing additional pages... search done
copying images... [ 25%] media/squash_save_load.png
copying images... [ 50%] media/Nigeria-NDD.png
copying images... [ 75%] media/Nigeria-2024.png
copying images... [100%] media/Nigeria-Sampled.png

dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 1 warning.

The HTML pages are in ../_readthedocs/html.