Read the Docs build information Build id: 2993923 Project: institute-for-disease-modeling-laser-cholera Version: v0.7.1 Commit: 1e26eb3fe5787a19d3802f24d7b05e11944319c9 Date: 2025-04-24T06:03:33.402019Z State: finished Success: True [rtd-command-info] start-time: 2025-04-24T06:05:03.563383Z, end-time: 2025-04-24T06:05:04.685310Z, duration: 1, exit-code: 0 git clone --depth 1 https://github.com/InstituteforDiseaseModeling/laser-cholera.git . Cloning into '.'... [rtd-command-info] start-time: 2025-04-24T06:05:04.745157Z, end-time: 2025-04-24T06:05:05.945841Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/tags/v0.7.1:refs/tags/v0.7.1 From https://github.com/InstituteforDiseaseModeling/laser-cholera * [new tag] v0.0.0 -> v0.0.0 * [new tag] v0.7.0 -> v0.7.0 [rtd-command-info] start-time: 2025-04-24T06:05:06.049389Z, end-time: 2025-04-24T06:05:06.250141Z, duration: 0, exit-code: 0 git checkout --force 1e26eb3fe5787a19d3802f24d7b05e11944319c9 Note: switching to '1e26eb3fe5787a19d3802f24d7b05e11944319c9'. 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 1e26eb3 Bump version: 0.7.0 → 0.7.1 [rtd-command-info] start-time: 2025-04-24T06:05:06.305935Z, end-time: 2025-04-24T06:05:06.347385Z, 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: 2025-04-24T06:05:10.514456Z, end-time: 2025-04-24T06:05:10.577065Z, duration: 0, exit-code: 0 asdf global python 3.9.20 [rtd-command-info] start-time: 2025-04-24T06:05:10.980384Z, end-time: 2025-04-24T06:05:12.153324Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.20.final.0-64 in 864ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/v0.7.1, 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: 2025-04-24T06:05:12.206749Z, end-time: 2025-04-24T06:05:21.252817Z, duration: 9, 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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sphinxcontrib-serializinghtml-2.0.0 tomli-2.2.1 urllib3-2.4.0 zipp-3.21.0 [rtd-command-info] start-time: 2025-04-24T06:05:29.447669Z, end-time: 2025-04-24T06:05:30.738017Z, 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/v0.7.1/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/27/48/e791a7ed487dbb9729ef32bb5d1af16693d8925f4366befef54119b2e576/furo-2024.8.6-py3-none-any.whl (341 kB) Requirement already satisfied: sphinxcontrib-applehelp in 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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/v0.7.1 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==0.7.1) 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==0.7.1) Downloading 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shapely>=2.0.0 (from geopandas->laser-cholera==0.7.1) 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 16.3 MB/s eta 0:00:00 Collecting python-dateutil>=2.8.2 (from pandas->laser-core==0.4.0->laser-cholera==0.7.1) 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==0.7.1) 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==0.7.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/5c/23/c7abc0ca0a1526a0774eca151daeb8de62ec457e77262b66b359c3c7679e/tzdata-2025.2-py2.py3-none-any.whl (347 kB) Requirement already satisfied: certifi in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/v0.7.1/lib/python3.9/site-packages (from pyogrio>=0.7.2->geopandas->laser-cholera==0.7.1) (2025.1.31) Collecting contourpy>=1.0.1 (from matplotlib->laser-core==0.4.0->laser-cholera==0.7.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/05/11/57335544a3027e9b96a05948c32e566328e3a2f84b7b99a325b7a06d2b06/contourpy-1.3.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (321 kB) Collecting cycler>=0.10 (from matplotlib->laser-core==0.4.0->laser-cholera==0.7.1) Downloading 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matplotlib->laser-core==0.4.0->laser-cholera==0.7.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/be/0b/532e31abc7389617ddff12551af625a9b03cd61d2989fa595e43c470ec67/pillow-11.2.1-cp39-cp39-manylinux_2_28_x86_64.whl (4.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 16.2 MB/s eta 0:00:00 Collecting pyparsing>=2.3.1 (from matplotlib->laser-core==0.4.0->laser-cholera==0.7.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/05/e7/df2285f3d08fee213f2d041540fa4fc9ca6c2d44cf36d3a035bf2a8d2bcc/pyparsing-3.2.3-py3-none-any.whl (111 kB) Collecting importlib-resources>=3.2.0 (from matplotlib->laser-core==0.4.0->laser-cholera==0.7.1) 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) Collecting llvmlite<0.44,>=0.43.0dev0 (from numba->laser-core==0.4.0->laser-cholera==0.7.1) 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 16.1 MB/s eta 0:00:00 Requirement already satisfied: zipp>=3.1.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/v0.7.1/lib/python3.9/site-packages (from importlib-resources>=3.2.0->matplotlib->laser-core==0.4.0->laser-cholera==0.7.1) (3.21.0) Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas->laser-core==0.4.0->laser-cholera==0.7.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/six-1.17.0-py2.py3-none-any.whl (11 kB) 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-0.7.1-py3-none-any.whl size=22902713 sha256=6ff92ec45afcb82fae846ee82a291b268e72e4508a4f732f52796715a7f7fc9f Stored in directory: /tmp/pip-ephem-wheel-cache-ckoq9enb/wheels/50/bc/2a/de222cbec63c1bb53bf4900e19c2b99c10902f8ce122b1ee4c 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-4.57.0 geopandas-1.0.1 h5py-3.13.0 importlib-resources-6.5.2 kiwisolver-1.4.7 laser-cholera-0.7.1 laser-core-0.4.0 llvmlite-0.43.0 matplotlib-3.9.4 numba-0.60.0 numpy-2.0.2 pandas-2.2.3 pillow-11.2.1 pyogrio-0.10.0 pyparsing-3.2.3 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-2025.2 [rtd-command-info] start-time: 2025-04-24T06:06:09.235680Z, end-time: 2025-04-24T06:06:09.279624Z, 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.napoleon", "sphinx.ext.todo", "sphinx.ext.viewcode", ] source_suffix = {".rst": "restructuredtext"} master_doc = "index" project = "LASER Cholera (LASIK)" year = "2024" author = "Institute for Disease Modeling" copyright = f"{year}, Bill & Melinda Gates Foundation" version = release = "0.7.1" 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: 2025-04-24T06:06:09.334180Z, end-time: 2025-04-24T06:06:23.810913Z, duration: 14, 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 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 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... [ 10%] laser_cholera.metapop.analyzer highlighting module code... [ 14%] laser_cholera.metapop.census highlighting module code... [ 19%] laser_cholera.metapop.derivedvalues highlighting module code... [ 24%] laser_cholera.metapop.environmental highlighting module code... [ 29%] laser_cholera.metapop.envtohuman highlighting module code... [ 33%] laser_cholera.metapop.envtohumanvax highlighting module code... [ 38%] laser_cholera.metapop.exposed highlighting module code... [ 43%] laser_cholera.metapop.humantohuman highlighting module code... [ 48%] laser_cholera.metapop.humantohumanvax highlighting module code... [ 52%] laser_cholera.metapop.infectious highlighting module code... [ 57%] laser_cholera.metapop.model highlighting module code... [ 62%] laser_cholera.metapop.params highlighting module code... [ 67%] laser_cholera.metapop.recorder highlighting module code... [ 71%] laser_cholera.metapop.recovered highlighting module code... [ 76%] laser_cholera.metapop.susceptible highlighting module code... [ 81%] laser_cholera.metapop.utils highlighting module code... [ 86%] laser_cholera.metapop.vaccinated highlighting module code... [ 90%] laser_cholera.sc 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: 2025-04-24T06:06:23.869471Z, end-time: 2025-04-24T06:06:27.108599Z, 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: 2025-04-24T06:06:27.394994Z, end-time: 2025-04-24T06:06:31.797873Z, duration: 4, 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/v0.7.1/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/v0.7.1/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/v0.7.1/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/v0.7.1/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/v0.7.1/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/v0.7.1/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/v0.7.1/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/v0.7.1/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/v0.7.1.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: 2025-04-24T06:06:31.858825Z, end-time: 2025-04-24T06:06:31.900497Z, 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: 2025-04-24T06:06:31.960075Z, end-time: 2025-04-24T06:06:46.810737Z, duration: 14, 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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See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 \end{tabulary} (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) Underfull \hbox (badness 10000) in paragraph at lines 173--175 []|\T1/qhv/m/n/10 Win- [1] [2] Chapter 2. [3] [4] Chapter 3. [5] [6] Chapter 4. [7] [8] LaTeX Warning: Hyper reference `reference/laser_cholera.metapop:laser_cholera.m etapop.susceptible.Component' on page 9 undefined on input line 668. [9] [10] [11] [12] [13] LaTeX Warning: Hyper reference `reference/laser_cholera.metapop:laser_cholera.m etapop.susceptible.Component' on page 14 undefined on input line 1534. [14] [15] [16] Chapter 5. [17] [18] Chapter 6. [19] [20] Chapter 7. [21] [22] Chapter 8. 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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/cmsy10.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb> Output written on institute-for-disease-modeling-laser-cholera.pdf (29 pages, 2 05456 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 25 undefined on input line 2062 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.analyzer' on page 25 undefined on input line 2063 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.census' on page 25 undefined on input line 2064 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.derivedvalues' on page 25 undefined on input line 2065 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.environmental' on page 25 undefined on input line 2066 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.envtohuman' on page 25 undefined on input line 2067 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.envtohumanvax' on page 25 undefined on input line 2068 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.exposed' on page 25 undefined on input line 2069 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.humantohuman' on page 25 undefined on input line 2070 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.humantohumanvax' on page 25 undefined on input line 2071 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.infectious' on page 25 undefined on input line 2072 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.model' on page 25 undefined on input line 2073 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.params' on page 25 undefined on input line 2074 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.recorder' on page 25 undefined on input line 2075 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.recovered' on page 25 undefined on input line 2076 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.scenario' on page 25 undefined on input line 2077 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.susceptible' on page 25 undefined on input line 2078 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.utils' on page 25 undefined on input line 2079 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.vaccinated' on page 25 undefined on input line 2080 Reference `reference/laser_cholera:module-laser_cholera' on page 25 undefined on input line 2058 Reference `reference/laser_cholera:module-laser_cholera.cli' on page 25 undefined on input line 2059 Reference `reference/laser_cholera:module-laser_cholera.core' on page 25 undefined on input line 2060 Reference `reference/laser_cholera:module-laser_cholera.iso_codes' on page 25 undefined on input line 2061 Reference `reference/laser_cholera:module-laser_cholera.sc' on page 25 undefined on input line 2081 Reference `reference/laser_cholera:module-laser_cholera.test' on page 25 undefined on input line 2082 Reference `reference/laser_cholera:module-laser_cholera.utils' on page 25 undefined on input line 2083 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). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file institute-for-disease-modeling-laser-cholera.idx....done (183 entries accepted, 0 rejected). Sorting entries....done (1370 comparisons). Generating output file institute-for-disease-modeling-laser-cholera.ind....done (312 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/cmsy10.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb> Output written on institute-for-disease-modeling-laser-cholera.pdf (34 pages, 2 29909 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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HumanToHumanVax Overfull \hbox (62.25238pt too wide) in paragraph at lines 253--255 []\T1/txtt/m/n/10 plot() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser_cholera.metapop. humantohumanvax.HumanToHumanVax Underfull \hbox (badness 10000) in paragraph at lines 256--258 []\T1/txtt/m/n/10 plot() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser_cholera.metapop. infectious.Infectious Underfull \hbox (badness 10000) in paragraph at lines 260--261 []\T1/txtt/m/n/10 plot() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser_cholera.metapop. params.Parameters Underfull \hbox (badness 10000) in paragraph at lines 262--264 []\T1/txtt/m/n/10 plot() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser_cholera.metapop. recovered.Recovered Underfull \hbox (badness 10000) in paragraph at lines 265--267 []\T1/txtt/m/n/10 plot() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser_cholera.metapop. susceptible.Susceptible Underfull \hbox (badness 10000) in paragraph at lines 268--270 []\T1/txtt/m/n/10 plot() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser_cholera.metapop. vaccinated.Vaccinated Underfull \hbox (badness 10000) in paragraph at lines 271--273 []\T1/txtt/m/n/10 plot_helper() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 271--273 \T1/qtm/m/it/10 laser_cholera.metapop.envtohumanvax\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 273--275 []\T1/txtt/m/n/10 plot_helper() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 290--292 []\T1/txtt/m/n/10 sanitize_json() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule [29] Underfull \hbox (badness 10000) in paragraph at lines 292--294 []\T1/txtt/m/n/10 save_compressed_hdf5_parameters() \T1/qtm/m/n/10 (\T1/qtm/m/i t/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 294--295 []\T1/txtt/m/n/10 save_hdf5() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 295--297 []\T1/txtt/m/n/10 save_hdf5_parameters() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule Underfull \hbox (badness 10000) in paragraph at lines 299--301 []\T1/txtt/m/n/10 Susceptible \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Overfull \hbox (2.33733pt too wide) in paragraph at lines 305--306 []\T1/txtt/m/n/10 Vaccinated \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in laser_cho lera.metapop.vaccinated\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 306--307 []\T1/txtt/m/n/10 validate_parameters() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 307--309 []\T1/txtt/m/n/10 validate_parameters() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 309--310 []\T1/txtt/m/n/10 verbose() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser_cholera.metap op.model.Model Underfull \hbox (badness 10000) in paragraph at lines 310--311 []\T1/txtt/m/n/10 visualize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser_cholera.met apop.model.Model [30]) (./institute-for-disease-modeling-laser-cholera.aux) ) (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/cmsy10.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb> Output written on institute-for-disease-modeling-laser-cholera.pdf (34 pages, 2 29923 bytes). 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Latexmk: Index file 'institute-for-disease-modeling-laser-cholera.idx' was written 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: Examining 'institute-for-disease-modeling-laser-cholera.log' === TeX engine is 'pdfTeX' Latexmk: Errors, in force_mode: so I tried finishing targets Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 1 Refer to 'institute-for-disease-modeling-laser-cholera.log' for details [rtd-command-info] start-time: 2025-04-24T06:06:47.087483Z, end-time: 2025-04-24T06:06:51.723671Z, duration: 4, exit-code: 0 python -m sphinx -T -b epub -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/epub 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 [epub]: targets for 10 source files that are out of date 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... done copying extra files... done copying assets: done writing output... 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