Read the Docs build information Build id: 3663619 Project: institute-for-disease-modeling-laser-cholera Version: latest Commit: a47d3becc6e73000277fa75e655af873e4ac8cb1 Date: 2026-01-15T00:36:16.190681Z State: finished Success: True [rtd-command-info] start-time: 2026-01-15T00:36:17.223271Z, end-time: 2026-01-15T00:36:18.314046Z, duration: 1, exit-code: 0 git clone --depth 1 https://github.com/InstituteforDiseaseModeling/laser-cholera.git . Cloning into '.'... [rtd-command-info] start-time: 2026-01-15T00:36:18.436431Z, end-time: 2026-01-15T00:36:19.551053Z, 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] v0.7.10 -> v0.7.10 * [new tag] v0.7.11 -> v0.7.11 * [new tag] v0.7.3 -> v0.7.3 * [new tag] v0.7.4 -> v0.7.4 * [new tag] v0.7.5 -> v0.7.5 * [new tag] v0.7.6 -> v0.7.6 * [new tag] v0.7.7 -> v0.7.7 * [new tag] v0.7.8 -> v0.7.8 * [new tag] v0.7.9 -> v0.7.9 * [new tag] v0.8.0 -> v0.8.0 * [new tag] v0.9.0 -> v0.9.0 * [new tag] v0.9.1 -> v0.9.1 [rtd-command-info] start-time: 2026-01-15T00:36:20.459298Z, end-time: 2026-01-15T00:36:20.678335Z, 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 a47d3be Remove MacOS x86_64 from test matrix [rtd-command-info] start-time: 2026-01-15T00:36:20.757108Z, end-time: 2026-01-15T00:36:20.800216Z, 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: "3.9" 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: 2026-01-15T00:36:25.451082Z, end-time: 2026-01-15T00:36:25.514964Z, duration: 0, exit-code: 0 asdf global python 3.9.22 [rtd-command-info] start-time: 2026-01-15T00:36:25.941003Z, end-time: 2026-01-15T00:36:27.212183Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.22.final.0-64 in 964ms 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: 2026-01-15T00:36:27.298516Z, end-time: 2026-01-15T00:36:35.215330Z, duration: 7, 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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tomli-2.4.0 urllib3-2.6.3 zipp-3.23.0 [rtd-command-info] start-time: 2026-01-15T00:36:43.163215Z, end-time: 2026-01-15T00:36:45.028386Z, 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/python3.9/site-packages (from -r docs/requirements.txt (line 1)) (7.4.7) Collecting furo (from -r docs/requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f4/b2/50e9b292b5cac13e9e81272c7171301abc753a60460d21505b606e15cf21/furo-2025.12.19-py3-none-any.whl (339 kB) Requirement already satisfied: sphinxcontrib-applehelp in 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requests>=2.30.0->sphinx>=1.3->-r docs/requirements.txt (line 1)) (3.4.4) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.9/site-packages (from requests>=2.30.0->sphinx>=1.3->-r docs/requirements.txt (line 1)) (3.11) Requirement already satisfied: urllib3<3,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.9/site-packages (from requests>=2.30.0->sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.6.3) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.9/site-packages (from requests>=2.30.0->sphinx>=1.3->-r docs/requirements.txt (line 1)) (2026.1.4) Collecting soupsieve>=1.6.1 (from beautifulsoup4->furo->-r docs/requirements.txt (line 2)) Downloading 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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-cholera/checkouts/latest 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==0.4.0 (from laser-cholera==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c1/ab/37c7068274df5475e98f729f29d4736c76b00d65ccce02e477760fe14d64/laser_core-0.4.0-py3-none-any.whl (28 kB) Collecting geopandas (from laser-cholera==0.9.1) Downloading 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12.8/12.8 MB 13.9 MB/s 0:00:00 Collecting pyogrio>=0.7.2 (from geopandas->laser-cholera==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/88/f6/0df5c6f370752acb9a649a5c8ebb626952fd7fc5cfc0da215181dbbc3601/pyogrio-0.11.1-cp39-cp39-manylinux_2_28_x86_64.whl (27.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 27.5/27.5 MB 13.9 MB/s 0:00:01 Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.9/site-packages (from geopandas->laser-cholera==0.9.1) (25.0) Collecting pyproj>=3.3.0 (from geopandas->laser-cholera==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/97/0a/b1525be9680369cc06dd288e12c59d24d5798b4afcdcf1b0915836e1caa6/pyproj-3.6.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.3/8.3 MB 13.9 MB/s 0:00:00 Collecting shapely>=2.0.0 (from geopandas->laser-cholera==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ab/f0/befc440a6c90c577300f5f84361bad80919e7c7ac381ae4960ce3195cedc/shapely-2.0.7-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.5/2.5 MB 14.0 MB/s 0:00:00 Collecting python-dateutil>=2.8.2 (from pandas->laser-core==0.4.0->laser-cholera==0.9.1) 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) Collecting pytz>=2020.1 (from pandas->laser-core==0.4.0->laser-cholera==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/81/c4/34e93fe5f5429d7570ec1fa436f1986fb1f00c3e0f43a589fe2bbcd22c3f/pytz-2025.2-py2.py3-none-any.whl (509 kB) Collecting tzdata>=2022.7 (from pandas->laser-core==0.4.0->laser-cholera==0.9.1) Downloading 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matplotlib->laser-core==0.4.0->laser-cholera==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a4/ed/1f1afb2e9e7f38a545d628f864d562a5ae64fe6f7a10e28ffb9b185b4e89/importlib_resources-6.5.2-py3-none-any.whl (37 kB) Requirement already satisfied: zipp>=3.1.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.9/site-packages (from importlib-resources>=3.2.0->matplotlib->laser-core==0.4.0->laser-cholera==0.9.1) (3.23.0) Collecting llvmlite<0.44,>=0.43.0dev0 (from numba->laser-core==0.4.0->laser-cholera==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e0/d0/889e9705107db7b1ec0767b03f15d7b95b4c4f9fdf91928ab1c7e9ffacf6/llvmlite-0.43.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (43.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.9/43.9 MB 13.9 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-0.9.1-py3-none-any.whl size=23044771 sha256=2c012b2364a073348571327aea46eea294a9b39dfe584356d7c0e25f82d59b74 Stored in directory: /tmp/pip-ephem-wheel-cache-8nfsuuyi/wheels/1b/0f/7b/74575a95d73415b690356a84d8e4acd186a7ab4685a6a42455 Successfully built laser-cholera Installing collected packages: pytz, tzdata, tqdm, six, pyproj, pyparsing, pillow, numpy, llvmlite, kiwisolver, importlib-resources, fonttools, cycler, click, shapely, scipy, python-dateutil, pyogrio, numba, h5py, contourpy, pandas, matplotlib, laser-core, geopandas, laser-cholera Successfully installed click-8.1.8 contourpy-1.3.0 cycler-0.12.1 fonttools-4.60.2 geopandas-1.0.1 h5py-3.14.0 importlib-resources-6.5.2 kiwisolver-1.4.7 laser-cholera-0.9.1 laser-core-0.4.0 llvmlite-0.43.0 matplotlib-3.9.4 numba-0.60.0 numpy-2.0.2 pandas-2.3.3 pillow-11.3.0 pyogrio-0.11.1 pyparsing-3.3.1 pyproj-3.6.1 python-dateutil-2.9.0.post0 pytz-2025.2 scipy-1.13.1 shapely-2.0.7 six-1.17.0 tqdm-4.67.1 tzdata-2025.3 [rtd-command-info] start-time: 2026-01-15T00:37:31.435655Z, end-time: 2026-01-15T00:37:31.479159Z, 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 = "0.9.1" 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: 2026-01-15T00:37:31.580611Z, end-time: 2026-01-15T00:37:44.375738Z, duration: 12, exit-code: 0 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v7.4.7 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, usage.rst building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 10 source files that are out of date updating environment: [new config] 10 added, 0 changed, 0 removed reading sources... [ 10%] authors reading sources... [ 20%] changelog reading sources... [ 30%] contributing reading sources... [ 40%] index reading sources... [ 50%] installation reading sources... [ 60%] readme reading sources... [ 70%] reference/index reading sources... [ 80%] reference/laser_cholera reading sources... [ 90%] reference/laser_cholera.metapop reading sources... [100%] usage looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... done copying extra files... done copying assets: done writing output... [ 10%] authors writing output... [ 20%] changelog writing output... [ 30%] contributing writing output... [ 40%] index writing output... [ 50%] installation writing output... [ 60%] readme writing output... [ 70%] reference/index writing output... [ 80%] reference/laser_cholera writing output... [ 90%] reference/laser_cholera.metapop writing output... [100%] usage generating indices... genindex py-modindex done highlighting module code... [ 5%] laser_cholera.core highlighting module code... [ 9%] laser_cholera.likelihood highlighting module code... [ 14%] laser_cholera.metapop.analyzer highlighting module code... [ 18%] laser_cholera.metapop.census highlighting module code... [ 23%] laser_cholera.metapop.derivedvalues highlighting module code... [ 27%] laser_cholera.metapop.environmental highlighting module code... [ 32%] laser_cholera.metapop.envtohuman highlighting module code... [ 36%] laser_cholera.metapop.envtohumanvax highlighting module code... [ 41%] laser_cholera.metapop.exposed highlighting module code... [ 45%] laser_cholera.metapop.humantohuman highlighting module code... [ 50%] laser_cholera.metapop.humantohumanvax highlighting module code... [ 55%] laser_cholera.metapop.infectious highlighting module code... [ 59%] laser_cholera.metapop.logsetup highlighting module code... [ 64%] laser_cholera.metapop.model highlighting module code... [ 68%] laser_cholera.metapop.params highlighting module code... [ 73%] laser_cholera.metapop.recorder highlighting module code... [ 77%] laser_cholera.metapop.recovered highlighting module code... [ 82%] laser_cholera.metapop.susceptible highlighting module code... [ 86%] laser_cholera.metapop.utils highlighting module code... [ 91%] 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: 2026-01-15T00:37:44.578050Z, end-time: 2026-01-15T00:37:47.857943Z, duration: 3, exit-code: 0 python -m sphinx -T -b singlehtml -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v7.4.7 loading translations [en]... done making output directory... done loading pickled environment... 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, 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 assembling single document... readme installation usage reference/index reference/laser_cholera reference/laser_cholera.metapop contributing authors changelog done writing... done writing additional files... done copying static files... done copying extra files... done dumping object inventory... done build succeeded. The HTML page is in ../_readthedocs/htmlzip. [rtd-command-info] start-time: 2026-01-15T00:37:48.184233Z, end-time: 2026-01-15T00:37:54.061092Z, duration: 5, exit-code: 0 python -m sphinx -T -b latex -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/pdf Running Sphinx v7.4.7 loading translations [en]... done making output directory... done loading pickled environment... 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, 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 copying TeX support files... copying TeX support files... done processing lasercholeralasik.tex... index readme installation usage reference/index reference/laser_cholera reference/laser_cholera.metapop contributing authors changelog resolving references... /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/README.rst:16: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://readthedocs.org/projects/laser-cholera/badge/?style=flat) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/README.rst:20: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://github.com/InstituteforDiseaseModeling/laser-cholera/actions/workflows/github-actions.yml/badge.svg) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/README.rst:24: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://codecov.io/gh/InstituteforDiseaseModeling/laser-cholera/branch/main/graphs/badge.svg?branch=main) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/README.rst:28: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/pypi/v/laser-cholera.svg) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/README.rst:32: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/pypi/wheel/laser-cholera.svg) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/README.rst:36: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/pypi/pyversions/laser-cholera.svg) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/README.rst:40: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/pypi/implementation/laser-cholera.svg) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/README.rst:44: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/github/commits-since/InstituteforDiseaseModeling/laser-cholera/v0.9.1.svg) done writing... done build succeeded, 8 warnings. 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: 2026-01-15T00:37:54.176079Z, end-time: 2026-01-15T00:37:54.218402Z, 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: 2026-01-15T00:37:54.312093Z, end-time: 2026-01-15T00:37:58.393411Z, duration: 4, 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. Use of uninitialized value in concatenation (.) or string at (eval 11) line 3. Use of uninitialized value in concatenation (.) or string at (eval 11) line 4. Rc files read: /etc/LatexMk latexmkrc latexmkrc Latexmk: This is Latexmk, John Collins, 20 November 2021, version: 4.76. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'lasercholeralasik.tex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-laser-cholera" "lasercholeralasik.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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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-ts1.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmex10.pfb> Output written on institute-for-disease-modeling-laser-cholera.pdf (33 pages, 3 04742 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 29 undefined on input line 2571 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.analyzer' on page 29 undefined on input line 2572 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.census' on page 29 undefined on input line 2573 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.derivedvalues' on page 29 undefined on input line 2574 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.environmental' on page 29 undefined on input line 2575 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.envtohuman' on page 29 undefined on input line 2576 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.envtohumanvax' on page 29 undefined on input line 2577 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.exposed' on page 29 undefined on input line 2578 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.humantohuman' on page 29 undefined on input line 2579 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.humantohumanvax' on page 29 undefined on input line 2580 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.infectious' on page 29 undefined on input line 2581 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.logsetup' on page 29 undefined on input line 2582 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.model' on page 29 undefined on input line 2583 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.params' on page 29 undefined on input line 2584 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.recorder' on page 29 undefined on input line 2585 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.recovered' on page 29 undefined on input line 2586 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.scenario' on page 29 undefined on input line 2587 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.susceptible' on page 29 undefined on input line 2588 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.utils' on page 29 undefined on input line 2589 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.vaccinated' on page 29 undefined on input line 2590 Reference `reference/laser_cholera:module-laser_cholera' on page 29 undefined on input line 2566 Reference `reference/laser_cholera:module-laser_cholera.cli' on page 29 undefined on input line 2567 Reference `reference/laser_cholera:module-laser_cholera.core' on page 29 undefined on input line 2568 Reference `reference/laser_cholera:module-laser_cholera.iso_codes' on page 29 undefined on input line 2569 Reference `reference/laser_cholera:module-laser_cholera.likelihood' on page 29 undefined on input line 2570 Reference `reference/laser_cholera:module-laser_cholera.test' on page 29 undefined on input line 2591 Reference `reference/laser_cholera:module-laser_cholera.utils' on page 29 undefined on input line 2592 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' ------------ ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-laser-cholera.ind" "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'... This is makeindex, version 2.15 [TeX Live 2022/dev] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file institute-for-disease-modeling-laser-cholera.idx....done (202 entries accepted, 0 rejected). Sorting entries.....done (1602 comparisons). Generating output file institute-for-disease-modeling-laser-cholera.ind....done (347 lines written, 0 warnings). Output written in institute-for-disease-modeling-laser-cholera.ind. Transcript written in institute-for-disease-modeling-laser-cholera.ilg. 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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-ts1.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmex10.pfb> Output written on institute-for-disease-modeling-laser-cholera.pdf (38 pages, 3 29271 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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