Read the Docs build information Build id: 2996629 Project: institute-for-disease-modeling-laser-cholera Version: v0.7.2 Commit: 076c19fbef21f07db9adde63727ac48bca35e859 Date: 2025-04-24T21:16:46.127040Z State: finished Success: True [rtd-command-info] start-time: 2025-04-24T21:16:47.001096Z, end-time: 2025-04-24T21:16:48.120995Z, duration: 1, exit-code: 0 git clone --depth 1 https://github.com/InstituteforDiseaseModeling/laser-cholera.git . Cloning into '.'... [rtd-command-info] start-time: 2025-04-24T21:16:48.175856Z, end-time: 2025-04-24T21:16:49.380566Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/tags/v0.7.2:refs/tags/v0.7.2 From https://github.com/InstituteforDiseaseModeling/laser-cholera * [new tag] v0.0.0 -> v0.0.0 * [new tag] v0.7.0 -> v0.7.0 * [new tag] v0.7.1 -> v0.7.1 [rtd-command-info] start-time: 2025-04-24T21:16:49.479846Z, end-time: 2025-04-24T21:16:49.674361Z, duration: 0, exit-code: 0 git checkout --force 076c19fbef21f07db9adde63727ac48bca35e859 Note: switching to '076c19fbef21f07db9adde63727ac48bca35e859'. 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 076c19f Bump version: 0.7.1 → 0.7.2 [rtd-command-info] start-time: 2025-04-24T21:16:49.735326Z, end-time: 2025-04-24T21:16:49.779162Z, 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: 2025-04-24T21:16:54.055611Z, end-time: 2025-04-24T21:16:54.119884Z, duration: 0, exit-code: 0 asdf global python 3.9.20 [rtd-command-info] start-time: 2025-04-24T21:16:54.534883Z, end-time: 2025-04-24T21:16:55.651534Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.20.final.0-64 in 797ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/v0.7.2, 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: 2025-04-24T21:16:55.716218Z, end-time: 2025-04-24T21:17:05.080034Z, 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: 2025-04-24T21:17:13.390756Z, end-time: 2025-04-24T21:17:14.730886Z, 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/v0.7.2/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/v0.7.2 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==0.7.2) 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==0.7.2) Downloading 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shapely>=2.0.0 (from geopandas->laser-cholera==0.7.2) 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 13.1 MB/s eta 0:00:00 Collecting python-dateutil>=2.8.2 (from pandas->laser-core==0.4.0->laser-cholera==0.7.2) 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==0.7.2) 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==0.7.2) 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/v0.7.2/lib/python3.9/site-packages (from pyogrio>=0.7.2->geopandas->laser-cholera==0.7.2) (2025.1.31) Collecting contourpy>=1.0.1 (from matplotlib->laser-core==0.4.0->laser-cholera==0.7.2) 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==0.7.2) Downloading 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matplotlib->laser-core==0.4.0->laser-cholera==0.7.2) 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 13.0 MB/s eta 0:00:00 Collecting pyparsing>=2.3.1 (from matplotlib->laser-core==0.4.0->laser-cholera==0.7.2) 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==0.7.2) 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==0.7.2) 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 12.9 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/v0.7.2/lib/python3.9/site-packages (from importlib-resources>=3.2.0->matplotlib->laser-core==0.4.0->laser-cholera==0.7.2) (3.21.0) Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas->laser-core==0.4.0->laser-cholera==0.7.2) 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-0.7.2-py3-none-any.whl size=22903095 sha256=56bc9141184be3847d724ca1e9277a34e39866fb574a373e1a120da73e4210d6 Stored in directory: /tmp/pip-ephem-wheel-cache-qpgjdc8s/wheels/14/19/24/63324310deb8cb76f22241817df8a2bfc8178697c350e67f15 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-0.7.2 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: 2025-04-24T21:17:57.069283Z, end-time: 2025-04-24T21:17:57.112793Z, 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 = "0.7.2" 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: 2025-04-24T21:17:57.171465Z, end-time: 2025-04-24T21:18:07.951126Z, duration: 10, 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... [ 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: 2025-04-24T21:18:08.007470Z, end-time: 2025-04-24T21:18:11.392985Z, 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: 2025-04-24T21:18:11.649481Z, end-time: 2025-04-24T21:18:16.411761Z, 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/v0.7.2/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/v0.7.2/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/v0.7.2/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/v0.7.2/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/v0.7.2/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/v0.7.2/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/v0.7.2/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/v0.7.2/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/v0.7.2.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: 2025-04-24T21:18:16.465603Z, end-time: 2025-04-24T21:18:16.509771Z, 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: 2025-04-24T21:18:16.567703Z, end-time: 2025-04-24T21:18:20.508813Z, 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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LaTeX Warning: Reference `reference/laser_cholera:module-laser_cholera.utils' o n page 25 undefined on input line 2143. [25] No file institute-for-disease-modeling-laser-cholera.ind. (./institute-for-disease-modeling-laser-cholera.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `institute-for-disease-modeling-laser-chol era.out' has changed. (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 08853 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 2122 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.analyzer' on page 25 undefined on input line 2123 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.census' on page 25 undefined on input line 2124 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.derivedvalues' on page 25 undefined on input line 2125 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.environmental' on page 25 undefined on input line 2126 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.envtohuman' on page 25 undefined on input line 2127 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.envtohumanvax' on page 25 undefined on input line 2128 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.exposed' on page 25 undefined on input line 2129 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.humantohuman' on page 25 undefined on input line 2130 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.humantohumanvax' on page 25 undefined on input line 2131 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.infectious' on page 25 undefined on input line 2132 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.model' on page 25 undefined on input line 2133 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.params' on page 25 undefined on input line 2134 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.recorder' on page 25 undefined on input line 2135 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.recovered' on page 25 undefined on input line 2136 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.scenario' on page 25 undefined on input line 2137 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.susceptible' on page 25 undefined on input line 2138 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.utils' on page 25 undefined on input line 2139 Reference `reference/laser_cholera.metapop:module-laser_cholera.metapop.vaccinated' on page 25 undefined on input line 2140 Reference `reference/laser_cholera:module-laser_cholera' on page 25 undefined on input line 2118 Reference `reference/laser_cholera:module-laser_cholera.cli' on page 25 undefined on input line 2119 Reference `reference/laser_cholera:module-laser_cholera.core' on page 25 undefined on input line 2120 Reference `reference/laser_cholera:module-laser_cholera.iso_codes' on page 25 undefined on input line 2121 Reference `reference/laser_cholera:module-laser_cholera.sc' on page 25 undefined on input line 2141 Reference `reference/laser_cholera:module-laser_cholera.test' on page 25 undefined on input line 2142 Reference `reference/laser_cholera:module-laser_cholera.utils' on page 25 undefined on input line 2143 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 (186 entries accepted, 0 rejected). Sorting entries....done (1469 comparisons). Generating output file institute-for-disease-modeling-laser-cholera.ind....done (317 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 33429 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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