Read the Docs build information Build id: 3948928 Project: institute-for-disease-modeling-laser-cholera Version: latest Commit: 38595969c17136446cfda0840cc2e5a76e108ebe Date: 2026-04-21T22:53:50.927206Z State: finished Success: True [rtd-command-info] start-time: 2026-04-21T22:53:51.775280Z, end-time: 2026-04-21T22:53:52.838965Z, duration: 1, exit-code: 0 git clone --depth 1 https://github.com/InstituteforDiseaseModeling/laser-cholera.git . Cloning into '.'... [rtd-command-info] start-time: 2026-04-21T22:53:52.930947Z, end-time: 2026-04-21T22:53:54.137775Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main From https://github.com/InstituteforDiseaseModeling/laser-cholera * [new tag] v0.10.0 -> v0.10.0 * [new tag] v0.10.1 -> v0.10.1 * [new tag] v0.11.1 -> v0.11.1 * [new tag] v0.12.0 -> v0.12.0 * [new tag] v0.12.1 -> v0.12.1 * [new tag] v0.9.1 -> v0.9.1 [rtd-command-info] start-time: 2026-04-21T22:53:54.990143Z, end-time: 2026-04-21T22:53:55.239855Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: switching to 'origin/main'. 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 3859596 Bump version: 0.12.2 → 0.12.3 [rtd-command-info] start-time: 2026-04-21T22:53:55.325281Z, end-time: 2026-04-21T22:53:55.363834Z, 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: all build: os: ubuntu-22.04 tools: python: "3.12" python: install: - requirements: docs/requirements.txt - method: pip path: . # Optionally build your docs in additional formats such as PDF and ePub # formats: # - pdf # - epub [rtd-command-info] start-time: 2026-04-21T22:53:59.782269Z, end-time: 2026-04-21T22:53:59.835495Z, duration: 0, exit-code: 0 asdf global python 3.12.10 [rtd-command-info] start-time: 2026-04-21T22:54:00.182267Z, end-time: 2026-04-21T22:54:00.792629Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.12.10.final.0-64 in 384ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest, 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: 2026-04-21T22:54:00.874892Z, end-time: 2026-04-21T22:54:06.619354Z, duration: 5, 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 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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-2026.2.25 charset_normalizer-3.4.7 docutils-0.22.4 idna-3.12 imagesize-2.0.0 packaging-26.1 requests-2.33.1 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: 2026-04-21T22:54:14.021861Z, end-time: 2026-04-21T22:54:15.636875Z, 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-cholera/envs/latest/lib/python3.12/site-packages (from -r 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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 laser-core~=1.0 (from laser.cholera==0.12.3) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/40/c1/b132127dd83d1f09bf2b1d24597d6fa25e72b94617d72735db9a382481e8/laser_core-1.0.1-cp312-cp312-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (48 kB) Collecting geopandas>=1.1.2 (from laser.cholera==0.12.3) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/3c/78/6a04792ace63a93e162f1305392d500ae8ddcb620e7eb88a22fd622b35bb/geopandas-1.1.3-py3-none-any.whl (342 kB) Collecting h5py (from laser.cholera==0.12.3) Downloading 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pyproj>=3.5.0 (from geopandas>=1.1.2->laser.cholera==0.12.3) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/b8/be/212882c450bba74fc8d7d35cbd57e4af84792f0a56194819d98106b075af/pyproj-3.7.2-cp312-cp312-manylinux_2_28_x86_64.whl (9.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.6/9.6 MB 17.5 MB/s 0:00:00 Collecting python-dateutil>=2.8.2 (from pandas->laser-core~=1.0->laser.cholera==0.12.3) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ec/57/56b9bcc3c9c6a792fcbaf139543cee77261f3651ca9da0c93f5c1221264b/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-cholera/envs/latest/lib/python3.12/site-packages (from pyogrio>=0.7.2->geopandas>=1.1.2->laser.cholera==0.12.3) (2026.2.25) Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas->laser-core~=1.0->laser.cholera==0.12.3) Downloading 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━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.1/7.1 MB 17.5 MB/s 0:00:00 Collecting pyparsing>=3 (from matplotlib->laser-core~=1.0->laser.cholera==0.12.3) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/10/bd/c038d7cc38edc1aa5bf91ab8068b63d4308c66c4c8bb3cbba7dfbc049f9c/pyparsing-3.3.2-py3-none-any.whl (122 kB) Collecting llvmlite<0.48,>=0.47.0dev0 (from numba->laser-core~=1.0->laser.cholera==0.12.3) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e6/4b/e3f2cd17822cf772a4a51a0a8080b0032e6d37b2dbe8cfb724eac4e31c52/llvmlite-0.47.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (56.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.3/56.3 MB 17.4 MB/s 0:00:03 Building wheels for collected packages: laser.cholera Building wheel for laser.cholera (pyproject.toml): started Building wheel for laser.cholera (pyproject.toml): finished with status 'done' Created wheel for laser.cholera: filename=laser_cholera-0.12.3-py3-none-any.whl size=24914941 sha256=65a575960e2ee23f7b71c775b4e3342a4319d5acc53c388c250271f6318f69a9 Stored in directory: /tmp/pip-ephem-wheel-cache-gjifrap1/wheels/e4/41/c4/e967a23ddfd8af9e99deb8dc754220f53ccbffc4fec8d1d152 Successfully built laser.cholera Installing collected packages: uv, tqdm, six, pyproj, pyparsing, pillow, numpy, llvmlite, kiwisolver, fonttools, cycler, click, shapely, scipy, python-dateutil, pyogrio, numba, h5py, contourpy, pandas, matplotlib, geopandas, laser-core, laser.cholera Successfully installed click-8.3.2 contourpy-1.3.3 cycler-0.12.1 fonttools-4.62.1 geopandas-1.1.3 h5py-3.16.0 kiwisolver-1.5.0 laser-core-1.0.1 laser.cholera-0.12.3 llvmlite-0.47.0 matplotlib-3.10.8 numba-0.65.0 numpy-2.4.4 pandas-3.0.2 pillow-12.2.0 pyogrio-0.12.1 pyparsing-3.3.2 pyproj-3.7.2 python-dateutil-2.9.0.post0 scipy-1.17.1 shapely-2.1.2 six-1.17.0 tqdm-4.67.3 uv-0.11.7 [rtd-command-info] start-time: 2026-04-21T22:54:59.727448Z, end-time: 2026-04-21T22:54:59.764667Z, duration: 0, exit-code: 0 cat docs/conf.py extensions = [ "sphinx.ext.autodoc", "sphinx.ext.autosummary", "sphinx.ext.coverage", "sphinx.ext.doctest", "sphinx.ext.extlinks", "sphinx.ext.ifconfig", "sphinx.ext.mathjax", "sphinx.ext.napoleon", "sphinx.ext.todo", "sphinx.ext.viewcode", ] source_suffix = {".rst": "restructuredtext"} master_doc = "index" project = "LASER Cholera (LASIK)" year = "2024-2025" author = "Institute for Disease Modeling" copyright = f"{year}, Bill & Melinda Gates Foundation" version = release = "0.12.3" pygments_style = "trac" templates_path = ["."] extlinks = { "issue": ("https://github.com/InstituteforDiseaseModeling/laser-cholera/issues/%s", "#%s"), "pr": ("https://github.com/InstituteforDiseaseModeling/laser-cholera/pull/%s", "PR #%s"), } html_theme = "furo" html_theme_options = { # "githuburl": "https://github.com/InstituteforDiseaseModeling/laser-cholera/", } html_use_smartypants = True html_last_updated_fmt = "%b %d, %Y" html_split_index = False 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_report_timeouts_as_broken = False [rtd-command-info] start-time: 2026-04-21T22:54:59.847342Z, end-time: 2026-04-21T22:55:12.311043Z, duration: 12, 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: authors.rst, changelog.rst, contributing.rst, index.rst, installation.rst, readme.rst, reference/index.rst, reference/laser.cholera.metapop.rst, reference/laser.cholera.rst, reference/laser.rst, usage.rst Matplotlib is building the font cache; this may take a moment. 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] 11 added, 0 changed, 0 removed reading sources... 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[ 65%] laser.cholera.metapop.params highlighting module code... [ 70%] laser.cholera.metapop.recorder highlighting module code... [ 75%] laser.cholera.metapop.recovered highlighting module code... [ 80%] laser.cholera.metapop.susceptible highlighting module code... [ 85%] laser.cholera.metapop.utils highlighting module code... [ 90%] laser.cholera.metapop.vaccinated highlighting module code... [ 95%] laser.cholera.test highlighting module code... [100%] laser.cholera.utils writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded. The HTML pages are in ../_readthedocs/html. [rtd-command-info] start-time: 2026-04-21T22:55:12.405821Z, end-time: 2026-04-21T22:55:15.908423Z, duration: 3, exit-code: 0 python -m sphinx -T -b singlehtml -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v9.1.0 loading translations [en]... done making output directory... done loading pickled environment... The configuration has changed (1 option: 'pygments_dark_style') done [autosummary] generating autosummary for: authors.rst, changelog.rst, contributing.rst, index.rst, installation.rst, readme.rst, reference/index.rst, reference/laser.cholera.metapop.rst, reference/laser.cholera.rst, reference/laser.rst, usage.rst building [mo]: targets for 0 po files that are out of date writing output... building [singlehtml]: all documents updating environment: 0 added, 0 changed, 0 removed reading sources... looking for now-outdated files... none found preparing documents... done copying assets... copying static files... 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[rtd-command-info] start-time: 2026-04-21T22:55:16.158590Z, end-time: 2026-04-21T22:55:21.875780Z, duration: 5, exit-code: 0 python -m sphinx -T -b latex -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/pdf Running Sphinx v9.1.0 loading translations [en]... done making output directory... done loading pickled environment... The configuration has changed (1 option: 'pygments_dark_style') done [autosummary] generating autosummary for: authors.rst, changelog.rst, contributing.rst, index.rst, installation.rst, readme.rst, reference/index.rst, reference/laser.cholera.metapop.rst, reference/laser.cholera.rst, reference/laser.rst, usage.rst building [mo]: targets for 0 po files that are out of date writing output... building [latex]: all documents updating environment: 0 added, 0 changed, 0 removed reading sources... looking for now-outdated files... none found preparing documents... done copying assets... copying TeX support files... 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The LaTeX files are in ../_readthedocs/pdf. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). [rtd-command-info] start-time: 2026-04-21T22:55:21.967076Z, end-time: 2026-04-21T22:55:22.004568Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2026-04-21T22:55:22.111322Z, end-time: 2026-04-21T22:55:26.101988Z, duration: 3, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-laser-cholera -interaction=nonstopmode Use of uninitialized value in concatenation (.) or string at (eval 10) line 1. Use of uninitialized value in concatenation (.) or string at (eval 10) line 2. Use of uninitialized value in concatenation (.) or string at (eval 10) line 3. Use of uninitialized value in concatenation (.) or string at (eval 10) line 4. Subroutine makeglo redefined at (eval 11) line 7. Use of uninitialized value in concatenation (.) or string at (eval 11) line 1. Use of uninitialized value in concatenation (.) or string at (eval 11) line 2. 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec-sc.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.en c}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt.pfb> Output written on institute-for-disease-modeling-laser-cholera.pdf (35 pages, 3 09831 bytes). Transcript written on institute-for-disease-modeling-laser-cholera.log. Latexmk: Index file 'institute-for-disease-modeling-laser-cholera.idx' was written Latexmk: Missing input file 'institute-for-disease-modeling-laser-cholera.ind' (or dependence on it) from following: 'No file institute-for-disease-modeling-laser-cholera.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-laser-cholera.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-laser-cholera.pdf' Latexmk: List of undefined refs and citations: Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop' on page 31 undefined on input line 3194 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.analyzer' on page 31 undefined on input line 3195 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.census' on page 31 undefined on input line 3196 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.derivedvalues' on page 31 undefined on input line 3197 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.environmental' on page 31 undefined on input line 3198 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.envtohuman' on page 31 undefined on input line 3199 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.exposed' on page 31 undefined on input line 3200 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.humantohuman' on page 31 undefined on input line 3201 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.infectious' on page 31 undefined on input line 3202 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.logsetup' on page 31 undefined on input line 3203 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.model' on page 31 undefined on input line 3204 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.params' on page 31 undefined on input line 3205 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.recorder' on page 31 undefined on input line 3206 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.recovered' on page 31 undefined on input line 3207 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.scenario' on page 31 undefined on input line 3208 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.susceptible' on page 31 undefined on input line 3209 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.utils' on page 31 undefined on input line 3210 Reference `reference/laser.cholera.metapop:module-laser.cholera.metapop.vaccinated' on page 31 undefined on input line 3211 Reference `reference/laser.cholera:module-laser.cholera' on page 31 undefined on input line 3189 Reference `reference/laser.cholera:module-laser.cholera.cli' on page 31 undefined on input line 3190 Reference `reference/laser.cholera:module-laser.cholera.core' on page 31 undefined on input line 3191 Reference `reference/laser.cholera:module-laser.cholera.iso_codes' on page 31 undefined on input line 3192 Reference `reference/laser.cholera:module-laser.cholera.likelihood' on page 31 undefined on input line 3193 Reference `reference/laser.cholera:module-laser.cholera.test' on page 31 undefined on input line 3212 Reference `reference/laser.cholera:module-laser.cholera.utils' on page 31 undefined on input line 3213 Reference `reference/laser:module-laser' on page 31 undefined on input line 3188 Rule 'makeindex institute-for-disease-modeling-laser-cholera.idx': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-laser-cholera.idx' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-laser-cholera.idx' ------------ Latexmk: Examining 'institute-for-disease-modeling-laser-cholera.log' === TeX engine is 'pdfTeX' Latexmk: applying rule 'makeindex institute-for-disease-modeling-laser-cholera.idx'... ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-laser-cholera.ind" "institute-for-disease-modeling-laser-cholera.idx"' ------------ This is makeindex, version 2.15 [TeX Live 2022/dev] (kpathsea + Thai support). 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec-sc.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.en c}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt.pfb> Output written on institute-for-disease-modeling-laser-cholera.pdf (40 pages, 3 35404 bytes). Transcript written on institute-for-disease-modeling-laser-cholera.log. Latexmk: Index file 'institute-for-disease-modeling-laser-cholera.idx' was written Latexmk: References changed. 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