Read the Docs build information Build id: 3183189 Project: institute-for-disease-modeling-laser-measles Version: latest Commit: cde02283c0f1d2aa25f5c142f6883ad30a387f93 Date: 2025-07-09T17:55:41.003094Z State: finished Success: True [rtd-command-info] start-time: 2025-07-09T17:55:41.928627Z, end-time: 2025-07-09T17:55:42.430828Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/InstituteforDiseaseModeling/laser-measles.git . Cloning into '.'... [rtd-command-info] start-time: 2025-07-09T17:55:42.541657Z, end-time: 2025-07-09T17:55:43.537178Z, duration: 0, 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-measles * [new tag] v0.6.1 -> v0.6.1 * [new tag] v0.6.2 -> v0.6.2 * [new tag] v0.6.3 -> v0.6.3 [rtd-command-info] start-time: 2025-07-09T17:55:44.560413Z, end-time: 2025-07-09T17:55:44.616391Z, 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 cde0228 remove sidebar, add server for devcontainer [rtd-command-info] start-time: 2025-07-09T17:55:44.711329Z, end-time: 2025-07-09T17:55:44.755018Z, duration: 0, exit-code: 0 cat .readthedocs.yml # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details version: 2 sphinx: configuration: docs/conf.py formats: all build: os: ubuntu-22.04 tools: python: "3.12" python: install: - requirements: docs/requirements.txt - method: pip path: . # Optionally build your docs in additional formats such as PDF and ePub # formats: # - pdf # - epub [rtd-command-info] start-time: 2025-07-09T17:55:49.910749Z, end-time: 2025-07-09T17:55:49.975249Z, duration: 0, exit-code: 0 asdf global python 3.12.10 [rtd-command-info] start-time: 2025-07-09T17:55:50.429511Z, end-time: 2025-07-09T17:55:51.474969Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.12.10.final.0-64 in 748ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/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: 2025-07-09T17:55:51.557710Z, end-time: 2025-07-09T17:56:00.964784Z, 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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alabaster, requests, Jinja2, sphinx Successfully installed Jinja2-3.1.6 MarkupSafe-3.0.2 Pygments-2.19.2 alabaster-1.0.0 babel-2.17.0 certifi-2025.7.9 charset_normalizer-3.4.2 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-25.0 requests-2.32.4 roman-numerals-py-3.1.0 snowballstemmer-3.0.1 sphinx-8.2.3 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.5.0 [rtd-command-info] start-time: 2025-07-09T17:56:08.001873Z, end-time: 2025-07-09T17:56:56.683256Z, duration: 48, 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 Collecting pandoc (from -r docs/requirements.txt (line 1)) Downloading 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A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'pandoc'. Discussion can be found at https://github.com/pypa/pip/issues/6334 Building wheel for pandoc (setup.py): started Building wheel for pandoc (setup.py): finished with status 'done' Created wheel for pandoc: filename=pandoc-2.4-py3-none-any.whl size=34871 sha256=d9464ee626f926e8466d93126a9c54b87f3fb95881569415e6fe105f0dcccaa9 Stored in directory: /tmp/pip-ephem-wheel-cache-89j8kv04/wheels/48/c9/1f/4e719eb39abdab7e13324bc447609284c7bb8a5ce5836dc838 Successfully built pandoc Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, ply, fastjsonschema, zstandard, xlsxwriter, widgetsnbextension, tzdata, typing-extensions, traitlets, tqdm, tornado, tinycss2, soupsieve, smmap, six, rpds-py, readthedocs-sphinx-search, pyzmq, pyyaml, python-dotenv, pyparsing, pypandoc, psutil, prompt_toolkit, plumbum, platformdirs, pillow, pexpect, parso, pandocfilters, numpy, nest-asyncio, mistune, mdurl, line_profiler, kiwisolver, jupyterlab_widgets, jupyterlab-pygments, jsonpickle, jellyfish, ipython-pygments-lexers, fonttools, executing, et-xmlfile, dill, defusedxml, decorator, debugpy, cycler, bleach, attrs, asttokens, annotated-types, accessible-pygments, typing-inspection, stack_data, scipy, referencing, python-dateutil, pydantic-core, pockets, plantweb, pandoc, openpyxl, multiprocess, memory_profiler, matplotlib-inline, markdown-it-py, jupyter-core, jedi, gitdb, contourpy, comm, beautifulsoup4, sphinxcontrib-napoleon, sphinx-design, sphinx-autodoc-typehints, pydata-sphinx-theme, pydantic, pandas, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, ipython, gitpython, seaborn, sciris, pydantic-settings, jsonschema, ipywidgets, ipykernel, nbformat, autodoc_pydantic, nbclient, jupytext, nbconvert, nbsphinx Successfully installed accessible-pygments-0.0.5 annotated-types-0.7.0 asttokens-3.0.0 attrs-25.3.0 autodoc_pydantic-2.2.0 beautifulsoup4-4.13.4 bleach-6.2.0 comm-0.2.2 contourpy-1.3.2 cycler-0.12.1 debugpy-1.8.14 decorator-5.2.1 defusedxml-0.7.1 dill-0.4.0 et-xmlfile-2.0.0 executing-2.2.0 fastjsonschema-2.21.1 fonttools-4.58.5 gitdb-4.0.12 gitpython-3.1.44 ipykernel-6.29.5 ipython-9.4.0 ipython-pygments-lexers-1.1.1 ipywidgets-8.1.7 jedi-0.19.2 jellyfish-1.2.0 jsonpickle-4.1.1 jsonschema-4.24.0 jsonschema-specifications-2025.4.1 jupyter-client-8.6.3 jupyter-core-5.8.1 jupyterlab-pygments-0.3.0 jupyterlab_widgets-3.0.15 jupytext-1.17.2 kiwisolver-1.4.8 line_profiler-4.2.0 markdown-it-py-3.0.0 matplotlib-3.10.3 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.2 mdurl-0.1.2 memory_profiler-0.61.0 mistune-3.1.3 multiprocess-0.70.18 nbclient-0.10.2 nbconvert-7.16.6 nbformat-5.10.4 nbsphinx-0.9.6 nest-asyncio-1.6.0 numpy-2.3.1 openpyxl-3.1.5 pandas-2.3.1 pandoc-2.4 pandocfilters-1.5.1 parso-0.8.4 pexpect-4.9.0 pillow-11.3.0 plantweb-1.3.0 platformdirs-4.3.8 plumbum-1.9.0 ply-3.11 pockets-0.9.1 prompt_toolkit-3.0.51 psutil-7.0.0 ptyprocess-0.7.0 pure-eval-0.2.3 pydantic-2.11.7 pydantic-core-2.33.2 pydantic-settings-2.10.1 pydata-sphinx-theme-0.16.1 pypandoc-1.15 pyparsing-3.2.3 python-dateutil-2.9.0.post0 python-dotenv-1.1.1 pytz-2025.2 pyyaml-6.0.2 pyzmq-27.0.0 readthedocs-sphinx-search-0.3.2 referencing-0.36.2 rpds-py-0.26.0 scipy-1.16.0 sciris-3.2.3 seaborn-0.13.2 six-1.17.0 smmap-5.0.2 soupsieve-2.7 sphinx-autodoc-typehints-3.2.0 sphinx-design-0.6.1 sphinxcontrib-napoleon-0.7 stack_data-0.6.3 tinycss2-1.4.0 tornado-6.5.1 tqdm-4.67.1 traitlets-5.14.3 typing-extensions-4.14.1 typing-inspection-0.4.1 tzdata-2025.2 wcwidth-0.2.13 webencodings-0.5.1 widgetsnbextension-4.0.14 xlsxwriter-3.2.5 zstandard-0.23.0 [rtd-command-info] start-time: 2025-07-09T17:56:56.793829Z, end-time: 2025-07-09T17:57:29.144380Z, duration: 32, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir . 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gitdb<5,>=4.0.1->gitpython->sciris>=3.2.1->laser-measles==0.7.0.dev0) (5.0.2) Collecting llvmlite<0.45,>=0.44.0dev0 (from numba->laser-core>=0.5.1->laser-measles==0.7.0.dev0) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/cb/da/8341fd3056419441286c8e26bf436923021005ece0bff5f41906476ae514/llvmlite-0.44.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (42.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.4/42.4 MB 16.1 MB/s eta 0:00:00 Collecting numpy (from laser-core>=0.5.1->laser-measles==0.7.0.dev0) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/8c/3d/1e1db36cfd41f895d266b103df00ca5b3cbe965184df824dec5c08c6b803/numpy-2.2.6-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.5/16.5 MB 16.3 MB/s eta 0:00:00 Requirement already satisfied: et-xmlfile in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages (from openpyxl->sciris>=3.2.1->laser-measles==0.7.0.dev0) (2.0.0) Requirement already satisfied: pytz>=2020.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages (from pandas->laser-core>=0.5.1->laser-measles==0.7.0.dev0) (2025.2) Requirement already satisfied: tzdata>=2022.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages (from pandas->laser-core>=0.5.1->laser-measles==0.7.0.dev0) (2025.2) Building wheels for collected packages: laser-measles, grapheme Building wheel for laser-measles (pyproject.toml): started Building wheel for laser-measles (pyproject.toml): finished with status 'done' Created wheel for laser-measles: filename=laser_measles-0.7.0.dev0-cp312-cp312-linux_x86_64.whl size=126373 sha256=065271653dd6edf0649771fb5ea156f2b13b5a0083a8d711f71756455d7ea187 Stored in directory: /tmp/pip-ephem-wheel-cache-dl9t4527/wheels/62/3a/36/ef67797e01da7b9b6a2f5625cf489f3ab1d1bec0d42e59cb70 DEPRECATION: Building 'grapheme' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'grapheme'. Discussion can be found at https://github.com/pypa/pip/issues/6334 Building wheel for grapheme (setup.py): started Building wheel for grapheme (setup.py): finished with status 'done' Created wheel for grapheme: filename=grapheme-0.6.0-py3-none-any.whl size=210136 sha256=4f051642e8a366ce6acdbf6a048ad31028f7ca808f17e2c1c7cc2723d825af30 Stored in directory: /tmp/pip-ephem-wheel-cache-dl9t4527/wheels/79/3e/d7/a2aee5a2aaef471aaf680602ef8734c9eca78ab158ad47a4c7 Successfully built laser-measles grapheme Installing collected packages: grapheme, appdirs, threadpoolctl, shellingham, pyshp, pyproj, pycountry, pyarrow, polars, numpy, llvmlite, joblib, diskcache, click, about-time, shapely, rich, numba, h5py, alive-progress, typer, scikit-learn, patito, rastertoolkit, laser-core, laser-measles Attempting uninstall: numpy Found existing installation: numpy 2.3.1 Uninstalling numpy-2.3.1: Successfully uninstalled numpy-2.3.1 Successfully installed about-time-4.2.1 alive-progress-3.2.0 appdirs-1.4.4 click-8.2.1 diskcache-5.6.3 grapheme-0.6.0 h5py-3.14.0 joblib-1.5.1 laser-core-0.5.1 laser-measles-0.7.0.dev0 llvmlite-0.44.0 numba-0.61.2 numpy-2.2.6 patito-0.8.3 polars-1.31.0 pyarrow-20.0.0 pycountry-24.6.1 pyproj-3.7.1 pyshp-2.3.1 rastertoolkit-0.3.12 rich-14.0.0 scikit-learn-1.7.0 shapely-2.1.1 shellingham-1.5.4 threadpoolctl-3.6.0 typer-0.16.0 [rtd-command-info] start-time: 2025-07-09T17:57:29.363334Z, end-time: 2025-07-09T17:57:29.405414Z, duration: 0, exit-code: 0 cat docs/conf.py # # Configuration file for the Sphinx documentation builder. import os import sciris as sc on_rtd = os.environ.get("READTHEDOCS") == "True" # -- Project information ----------------------------------------------------- project = "laser-measles" copyright = f"2024 - {sc.now().year}, Bill & Melinda Gates Foundation. All rights reserved." # The short X.Y version version = release = "0.7.0-dev0" # -- General configuration --------------------------------------------------- # Add any Sphinx extension module names here extensions = [ "sphinx.ext.autodoc", # Core Sphinx library for auto html doc generation from docstrings "sphinx.ext.autosummary", # Create neat summary tables for modules/classes/methods etc -- causes warnings with Napoleon however "sphinx.ext.intersphinx", "sphinx.ext.viewcode", # Add a link to the Python source code for classes, functions etc. "sphinx.ext.napoleon", "sphinx.ext.autosectionlabel", # "sphinx.ext.doctest", # Enable doctest builder "sphinx_autodoc_typehints", # Automatically document param types (less noise in class signature) "sphinx_design", # Add e.g. grid layout "sphinx_search.extension", # search across multiple docsets in domain "nbsphinx", "sphinxcontrib.autodoc_pydantic", ] # Use Google docstrings napoleon_google_docstring = True # Configure autosummary autosummary_generate = True # Turn on sphinx.ext.autosummary autosummary_ignore_module_all = False # Respect __all__ autodoc_member_order = "bysource" # Keep original ordering add_module_names = False # NB, does not work autodoc_inherit_docstrings = False # Stops sublcasses from including docs from parent classes # Add any paths that contain templates here, relative to this directory. templates_path = ["_templates"] # Syntax highlighting style pygments_style = "sphinx" modindex_common_prefix = ["laser_measles."] # List of patterns, relative to source directory, to exclude exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints", "tutorials/not_ready/**"] # Suppress certain warnings suppress_warnings = ["autosectionlabel.*"] # Configure pydantic # -- Options for HTML output ------------------------------------------------- html_theme = "pydata_sphinx_theme" html_theme_options = { "collapse_navigation": False, "navigation_depth": 3, "show_prev_next": True, "icon_links": [ {"name": "Web", "url": "https://laser-measles.readthedocs.io/en/latest/", "icon": "fas fa-home"}, { "name": "GitHub", "url": "https://github.com/InstituteforDiseaseModeling/laser-measles", "icon": "fab fa-github-square", }, ], "navbar_end": ["theme-switcher", "navbar-icon-links"], "secondary_sidebar_items": [], "header_links_before_dropdown": 5, "footer_start": ["copyright", "footer_start"], "footer_end": ["theme-version", "footer_end"], } html_sidebars = { "**": ["page-toc"], } html_logo = "images/idm-logo-transparent.png" html_favicon = "images/favicon.ico" html_static_path = ["_static"] html_baseurl = "https://docs.idmod.org/" html_context = { "rtd_url": "https://docs.idmod.org/", "versions_dropdown": { "latest": "devel (latest)", "stable": "current (stable)", }, "default_mode": "light", } # Add any extra paths that contain custom files if not on_rtd: html_extra_path = ["robots.txt"] # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. html_last_updated_fmt = "%Y-%b-%d" html_show_sourcelink = True html_show_sphinx = False html_copy_source = False htmlhelp_basename = "laser-measles" # Add customizations def setup(app): app.add_css_file("theme_overrides.css") # Modify this to not rerun the Jupyter notebook cells -- usually set by build_docs nbsphinx_execute = "auto" nbsphinx_timeout = 600 nbsphinx_allow_errors = True nbsphinx_execute_arguments = [ "--InlineBackend.figure_formats={'svg', 'pdf'}", "--InlineBackend.rc={'figure.dpi': 96}", ] # OpenSearch options html_use_opensearch = "docs.idmod.org/projects/laser-measles/en/latest" # -- RTD Sphinx search for searching across the entire domain, default child ------------- if os.environ.get("READTHEDOCS") == "True": search_project_parent = "institute-for-disease-modeling-idm" search_project = os.environ["READTHEDOCS_PROJECT"] search_version = os.environ["READTHEDOCS_VERSION"] rtd_sphinx_search_default_filter = f"subprojects:{search_project_parent}/{search_version}" rtd_sphinx_search_filters = { "Search this project": f"project:{search_project}/{search_version}", "Search all IDM docs": f"subprojects:{search_project_parent}/{search_version}", } # -- Linkcheck configuration ------------------------------------------------- # Configuration for sphinx-build -b linkcheck # URLs that should be ignored during link checking linkcheck_ignore = [ r"https://chatgpt\.com/g/g-674f5fd33aec8191bcdc1a2736fb7c8d-laser-gpt-jenner", # Requires authentication r"https://.*\.idmod\.org/.*", # Internal IDM links that may require auth r"https://.*\.gatesfoundation\.org/.*", # Gates Foundation internal links ] # HTTP status codes that should be considered as "working" (not broken) # 403 = Forbidden (requires authentication) # 401 = Unauthorized (requires authentication) linkcheck_allowed_redirects = { r"https://.*\.idmod\.org/.*": r".*", r"https://.*\.gatesfoundation\.org/.*": r".*", } # Timeout for link checking (in seconds) linkcheck_timeout = 30 # Number of workers for parallel link checking linkcheck_workers = 5 # Whether to check anchors in links linkcheck_anchors = False # Whether to check anchors in relative links linkcheck_anchors_ignore = [ r"#.*", # Ignore all anchor links ] # Retry count for failed links linkcheck_retries = 2 [rtd-command-info] start-time: 2025-07-09T17:57:29.507742Z, end-time: 2025-07-09T17:57:54.037273Z, duration: 24, exit-code: 0 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v8.2.3 loading translations [en]... done making output directory... done [autosummary] generating autosummary for: api/index.rst, authors.rst, changelog.rst, contributing.rst, index.rst, installation.rst, reference/laser_measles.biweekly.rst, reference/laser_measles.demographics.rst, reference/laser_measles.nigeria.rst, reference/laser_measles.rst, reference/modules.rst, tutorials.rst, tutorials/README.rst, usage.rst WARNING: Failed to import laser_measles.nigeria. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: Failed to import laser_measles.nigeria.lgas. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: Failed to import laser_measles.nigeria.metapop. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: Failed to import laser_measles.nigeria.model. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: Failed to import laser_measles.nigeria.params. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: [autosummary] failed to import laser_measles.abm.cli. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.abm.cli' * ImportError: * AttributeError: module 'laser_measles.abm' has no attribute 'cli' WARNING: [autosummary] failed to import laser_measles.abm.components.StatesTracker. Possible hints: * ImportError: * ModuleNotFoundError: No module named 'laser_measles.abm.components.StatesTracker' * AttributeError: module 'laser_measles.abm.components' has no attribute 'StatesTracker' WARNING: [autosummary] failed to import laser_measles.pretty_laserframe. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.pretty_laserframe' * AttributeError: module 'laser_measles' has no attribute 'pretty_laserframe' * ImportError: [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.abm.components.ConstantPopProcess.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.abm.components.InfectionProcess.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.abm.components.PopulationTracker.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.abm.core.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.abm.model.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.abm.params.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.abm.utils.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.base.BaseComponent.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.base.BaseLaserModel.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.biweekly.base.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.biweekly.components.VitalDynamicsProcess.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.biweekly.mixing.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.biweekly.model.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.biweekly.params.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.create_component.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.demographics.GADMShapefile.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.demographics.RasterPatchGenerator.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.demographics.RasterPatchParams.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.demographics.get_shapefile_dataframe.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/_autosummary/laser_measles.demographics.plot_shapefile_dataframe.rst Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/html/_static/nbsphinx-code-cells.css building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 14 source files that are out of date updating environment: [new config] 40 added, 0 changed, 0 removed reading sources... [ 2%] api/_autosummary/laser_measles.abm.components.ConstantPopProcess reading sources... [ 5%] api/_autosummary/laser_measles.abm.components.InfectionProcess reading sources... [ 8%] api/_autosummary/laser_measles.abm.components.PopulationTracker reading sources... [ 10%] api/_autosummary/laser_measles.abm.core reading sources... [ 12%] api/_autosummary/laser_measles.abm.model reading sources... [ 15%] api/_autosummary/laser_measles.abm.params reading sources... [ 18%] api/_autosummary/laser_measles.abm.utils reading sources... [ 20%] api/_autosummary/laser_measles.base.BaseComponent reading sources... [ 22%] api/_autosummary/laser_measles.base.BaseLaserModel reading sources... [ 25%] api/_autosummary/laser_measles.biweekly.base reading sources... [ 28%] api/_autosummary/laser_measles.biweekly.components.CaseSurveillanceTracker reading sources... [ 30%] api/_autosummary/laser_measles.biweekly.components.FadeOutTracker reading sources... [ 32%] api/_autosummary/laser_measles.biweekly.components.ImportationPressureProcess reading sources... [ 35%] api/_autosummary/laser_measles.biweekly.components.InfectionProcess reading sources... [ 38%] api/_autosummary/laser_measles.biweekly.components.SIACalendarProcess reading sources... [ 40%] api/_autosummary/laser_measles.biweekly.components.StateTracker reading sources... [ 42%] api/_autosummary/laser_measles.biweekly.components.VitalDynamicsProcess reading sources... [ 45%] api/_autosummary/laser_measles.biweekly.mixing reading sources... [ 48%] api/_autosummary/laser_measles.biweekly.model reading sources... [ 50%] api/_autosummary/laser_measles.biweekly.params reading sources... [ 52%] api/_autosummary/laser_measles.create_component reading sources... [ 55%] api/_autosummary/laser_measles.demographics.GADMShapefile reading sources... [ 57%] api/_autosummary/laser_measles.demographics.RasterPatchGenerator reading sources... [ 60%] api/_autosummary/laser_measles.demographics.RasterPatchParams reading sources... [ 62%] api/_autosummary/laser_measles.demographics.get_shapefile_dataframe reading sources... [ 65%] api/_autosummary/laser_measles.demographics.plot_shapefile_dataframe reading sources... [ 68%] api/index reading sources... [ 70%] authors reading sources... [ 72%] changelog reading sources... [ 75%] contributing reading sources... [ 78%] index reading sources... [ 80%] installation reading sources... [ 82%] reference/laser_measles reading sources... [ 85%] reference/laser_measles.biweekly reading sources... [ 88%] reference/laser_measles.demographics reading sources... [ 90%] reference/laser_measles.nigeria reading sources... [ 92%] reference/modules reading sources... [ 95%] tutorials reading sources... [ 98%] tutorials/README reading sources... [100%] usage WARNING: Failed to get a function signature for laser_measles.abm.core: is not a callable object WARNING: Failed to get a function signature for laser_measles.abm.model: is not a callable object WARNING: Failed to get a function signature for laser_measles.abm.params: is not a callable object WARNING: Failed to get a function signature for laser_measles.abm.utils: is not a callable object WARNING: Failed to get a function signature for laser_measles.biweekly.base: is not a callable object /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/biweekly/components/process_infection.py:docstring of laser_measles.biweekly.components.process_infection.InfectionProcess:9: ERROR: Unexpected indentation. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/biweekly/components/process_infection.py:docstring of laser_measles.biweekly.components.process_infection.InfectionProcess:13: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] WARNING: Failed to get a function signature for laser_measles.biweekly.mixing: is not a callable object WARNING: Failed to get a function signature for laser_measles.biweekly.model: is not a callable object WARNING: Failed to get a function signature for laser_measles.biweekly.params: is not a callable object /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/index.rst:31: WARNING: autosummary: failed to import pretty_laserframe. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.pretty_laserframe' * ModuleNotFoundError: No module named 'pretty_laserframe' * ValueError: not enough values to unpack (expected 2, got 1) * KeyError: 'pretty_laserframe' * AttributeError: module 'laser_measles' has no attribute 'pretty_laserframe' /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/index.rst:52: WARNING: autosummary: failed to import cli. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.abm.cli' * AttributeError: module 'laser_measles.abm' has no attribute 'cli' * KeyError: 'cli' * ValueError: not enough values to unpack (expected 2, got 1) * ModuleNotFoundError: No module named 'cli' /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/index.rst:82: WARNING: autosummary: failed to import components.StatesTracker. Possible hints: * ImportError: * AttributeError: module 'laser_measles.abm.components' has no attribute 'StatesTracker' * ModuleNotFoundError: No module named 'components' * ModuleNotFoundError: No module named 'laser_measles.abm.components.StatesTracker' * KeyError: 'components' /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/index.rst:171::1: ERROR: Content block expected for the "raw" directive; none found. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/api/index.rst:183::1: ERROR: Content block expected for the "raw" directive; none found. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/installation.rst:1: WARNING: Title overline too short. ======================================== Installation and Development Instructions ======================================== [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/installation.rst:19: WARNING: Title underline too short. Optional Dependencies ==================== [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/installation.rst:38: WARNING: Title underline too short. Dependency Groups ---------------- [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/__init__.py:docstring of laser_measles.components.utils.create_component:1: WARNING: duplicate object description of laser_measles.create_component, other instance in api/_autosummary/laser_measles.create_component, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.abm' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.compartmental' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.components' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.scenarios' [toc.not_readable] WARNING: Cannot handle as a local function: "laser_measles.base.BasePatchLaserFrame.create_resized_copy" (use @functools.wraps) WARNING: Cannot resolve forward reference in type annotations of "laser_measles.base.BasePatchLaserFrame.create_resized_copy": name 'WrappedClass' is not defined WARNING: Cannot handle as a local function: "laser_measles.base.BasePeopleLaserFrame.create_resized_copy" (use @functools.wraps) WARNING: Cannot resolve forward reference in type annotations of "laser_measles.base.BasePeopleLaserFrame.create_resized_copy": name 'WrappedClass' is not defined /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/base.py:docstring of laser_measles.base.BaseLaserModel:1: WARNING: duplicate object description of laser_measles.base.BaseLaserModel, other instance in api/_autosummary/laser_measles.base.BaseLaserModel, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/base.py:docstring of laser_measles.base.BaseLaserModel.get_instance:14: ERROR: Unexpected indentation. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/base.py:docstring of laser_measles.base.BaseComponent:1: WARNING: duplicate object description of laser_measles.base.BaseComponent, other instance in api/_autosummary/laser_measles.base.BaseComponent, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.biweekly.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.biweekly.components' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/biweekly/base.py:docstring of laser_measles.biweekly.base:1: WARNING: duplicate object description of laser_measles.biweekly.base, other instance in api/_autosummary/laser_measles.biweekly.base, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/biweekly/mixing.py:docstring of laser_measles.biweekly.mixing:1: WARNING: duplicate object description of laser_measles.biweekly.mixing, other instance in api/_autosummary/laser_measles.biweekly.mixing, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/biweekly/model.py:docstring of laser_measles.biweekly.model:1: WARNING: duplicate object description of laser_measles.biweekly.model, other instance in api/_autosummary/laser_measles.biweekly.model, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/biweekly/params.py:docstring of laser_measles.biweekly.params:1: WARNING: duplicate object description of laser_measles.biweekly.params, other instance in api/_autosummary/laser_measles.biweekly.params, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/demographics/__init__.py:docstring of laser_measles.demographics.gadm.GADMShapefile:1: WARNING: duplicate object description of laser_measles.demographics.GADMShapefile, other instance in api/_autosummary/laser_measles.demographics.GADMShapefile, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/demographics/__init__.py:docstring of laser_measles.demographics.raster_patch.RasterPatchGenerator:1: WARNING: duplicate object description of laser_measles.demographics.RasterPatchGenerator, other instance in api/_autosummary/laser_measles.demographics.RasterPatchGenerator, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/demographics/__init__.py:docstring of laser_measles.demographics.raster_patch.RasterPatchParams:1: WARNING: duplicate object description of laser_measles.demographics.RasterPatchParams, other instance in api/_autosummary/laser_measles.demographics.RasterPatchParams, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/demographics/__init__.py:docstring of laser_measles.demographics.shapefiles.get_shapefile_dataframe:1: WARNING: duplicate object description of laser_measles.demographics.get_shapefile_dataframe, other instance in api/_autosummary/laser_measles.demographics.get_shapefile_dataframe, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/demographics/__init__.py:docstring of laser_measles.demographics.shapefiles.plot_shapefile_dataframe:1: WARNING: duplicate object description of laser_measles.demographics.plot_shapefile_dataframe, other instance in api/_autosummary/laser_measles.demographics.plot_shapefile_dataframe, use :no-index: for one of them WARNING: autodoc: failed to import module 'nigeria' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'nigeria.lgas' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'nigeria.metapop' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'nigeria.model' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'nigeria.params' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:7: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_basic_model' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:7: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_model_structure' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:7: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_abm_intro' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:7: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_scenarios' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:20: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_random_numbers' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:20: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_creating_component' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:20: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_pydantic_component_parameters' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:20: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_state_arrays' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:29: WARNING: Title underline too short. AI Assistance ------------ [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:29: WARNING: Title underline too short. AI Assistance ------------ [docutils] looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/authors.rst: WARNING: document isn't included in any toctree [toc.not_included] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/changelog.rst: WARNING: document isn't included in any toctree [toc.not_included] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/contributing.rst: WARNING: document isn't included in any toctree [toc.not_included] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/installation.rst: WARNING: document isn't included in any toctree [toc.not_included] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.nigeria.rst: WARNING: document isn't included in any toctree [toc.not_included] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/modules.rst: WARNING: document isn't included in any toctree [toc.not_included] done preparing documents... done copying assets... copying static files... Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/html/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/html/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/html/_static/documentation_options.js copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 2%] api/_autosummary/laser_measles.abm.components.ConstantPopProcess writing output... [ 5%] api/_autosummary/laser_measles.abm.components.InfectionProcess writing output... [ 8%] api/_autosummary/laser_measles.abm.components.PopulationTracker writing output... 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[ 72%] changelog writing output... [ 75%] contributing writing output... [ 78%] index writing output... [ 80%] installation writing output... [ 82%] reference/laser_measles writing output... [ 85%] reference/laser_measles.biweekly writing output... [ 88%] reference/laser_measles.demographics writing output... [ 90%] reference/laser_measles.nigeria writing output... [ 92%] reference/modules writing output... [ 95%] tutorials writing output... [ 98%] tutorials/README writing output... [100%] usage /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.biweekly.rst:37: WARNING: more than one target found for cross-reference 'BiweeklyParams': laser_measles.biweekly.BiweeklyParams, laser_measles.biweekly.params.BiweeklyParams [ref.python] generating indices... genindex py-modindex done copying linked files... copying notebooks ... highlighting module code... 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[100%] laser_measles.wrapper writing additional pages... search opensearch done dumping search index in English (code: en)... done dumping object inventory... done Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/html/_static/js/rtd_search_config.js build succeeded, 70 warnings. The HTML pages are in ../_readthedocs/html. [rtd-command-info] start-time: 2025-07-09T17:57:54.134343Z, end-time: 2025-07-09T17:58:12.092095Z, duration: 17, exit-code: 0 python -m sphinx -T -b singlehtml -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v8.2.3 loading translations [en]... done making output directory... done loading pickled environment... The configuration has changed (6 options: 'html_permalinks_icon', 'html_static_path', 'html_theme_options', 'nbsphinx_requirejs_options', 'nbsphinx_requirejs_path', ...) done [autosummary] generating autosummary for: api/_autosummary/laser_measles.abm.components.ConstantPopProcess.rst, api/_autosummary/laser_measles.abm.components.InfectionProcess.rst, api/_autosummary/laser_measles.abm.components.PopulationTracker.rst, api/_autosummary/laser_measles.abm.core.rst, api/_autosummary/laser_measles.abm.model.rst, api/_autosummary/laser_measles.abm.params.rst, api/_autosummary/laser_measles.abm.utils.rst, api/_autosummary/laser_measles.base.BaseComponent.rst, api/_autosummary/laser_measles.base.BaseLaserModel.rst, api/_autosummary/laser_measles.biweekly.base.rst, ..., index.rst, installation.rst, reference/laser_measles.biweekly.rst, reference/laser_measles.demographics.rst, reference/laser_measles.nigeria.rst, reference/laser_measles.rst, reference/modules.rst, tutorials.rst, tutorials/README.rst, usage.rst WARNING: Failed to import laser_measles.nigeria. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: Failed to import laser_measles.nigeria.lgas. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: Failed to import laser_measles.nigeria.metapop. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: Failed to import laser_measles.nigeria.model. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: Failed to import laser_measles.nigeria.params. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: [autosummary] failed to import laser_measles.abm.cli. Possible hints: * AttributeError: module 'laser_measles.abm' has no attribute 'cli' * ModuleNotFoundError: No module named 'laser_measles.abm.cli' * ImportError: WARNING: [autosummary] failed to import laser_measles.abm.components.StatesTracker. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.abm.components.StatesTracker' * AttributeError: module 'laser_measles.abm.components' has no attribute 'StatesTracker' * ImportError: WARNING: [autosummary] failed to import laser_measles.pretty_laserframe. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.pretty_laserframe' * AttributeError: module 'laser_measles' has no attribute 'pretty_laserframe' * ImportError: Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/htmlzip/_static/nbsphinx-code-cells.css building [mo]: targets for 0 po files that are out of date writing output... building [singlehtml]: all documents updating environment: 0 added, 4 changed, 0 removed reading sources... [ 25%] reference/laser_measles reading sources... [ 50%] reference/laser_measles.biweekly reading sources... [ 75%] reference/laser_measles.nigeria reading sources... [100%] tutorials /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.abm' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.compartmental' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.components' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.scenarios' [toc.not_readable] WARNING: Cannot handle as a local function: "laser_measles.base.BasePatchLaserFrame.create_resized_copy" (use @functools.wraps) WARNING: Cannot resolve forward reference in type annotations of "laser_measles.base.BasePatchLaserFrame.create_resized_copy": name 'WrappedClass' is not defined WARNING: Cannot handle as a local function: "laser_measles.base.BasePeopleLaserFrame.create_resized_copy" (use @functools.wraps) WARNING: Cannot resolve forward reference in type annotations of "laser_measles.base.BasePeopleLaserFrame.create_resized_copy": name 'WrappedClass' is not defined /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/base.py:docstring of laser_measles.base.BaseLaserModel.get_instance:14: ERROR: Unexpected indentation. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.biweekly.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.biweekly.components' [toc.not_readable] WARNING: autodoc: failed to import module 'nigeria' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'nigeria.lgas' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'nigeria.metapop' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'nigeria.model' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'nigeria.params' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:7: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_basic_model' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:7: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_model_structure' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:7: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_abm_intro' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:7: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_scenarios' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:20: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_random_numbers' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:20: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_creating_component' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:20: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_pydantic_component_parameters' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:20: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_state_arrays' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:29: WARNING: Title underline too short. AI Assistance ------------ [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:29: WARNING: Title underline too short. AI Assistance ------------ [docutils] looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/authors.rst: WARNING: document isn't included in any toctree [toc.not_included] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/changelog.rst: WARNING: document isn't included in any toctree [toc.not_included] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/contributing.rst: WARNING: document isn't included in any toctree [toc.not_included] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/installation.rst: WARNING: document isn't included in any toctree [toc.not_included] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.nigeria.rst: WARNING: document isn't included in any toctree [toc.not_included] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/modules.rst: WARNING: document isn't included in any toctree [toc.not_included] done preparing documents... done copying assets... copying static files... Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/htmlzip/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/htmlzip/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/htmlzip/_static/documentation_options.js copying static files: done copying extra files... copying extra files: done copying assets: done assembling single document... index usage tutorials api/index api/_autosummary/laser_measles.base.BaseComponent api/_autosummary/laser_measles.base.BaseLaserModel api/_autosummary/laser_measles.create_component api/_autosummary/laser_measles.abm.model api/_autosummary/laser_measles.abm.params api/_autosummary/laser_measles.abm.core api/_autosummary/laser_measles.abm.utils api/_autosummary/laser_measles.abm.components.InfectionProcess api/_autosummary/laser_measles.abm.components.ConstantPopProcess api/_autosummary/laser_measles.abm.components.PopulationTracker api/_autosummary/laser_measles.biweekly.model api/_autosummary/laser_measles.biweekly.params api/_autosummary/laser_measles.biweekly.base api/_autosummary/laser_measles.biweekly.components.InfectionProcess api/_autosummary/laser_measles.biweekly.components.VitalDynamicsProcess api/_autosummary/laser_measles.biweekly.components.ImportationPressureProcess api/_autosummary/laser_measles.biweekly.components.SIACalendarProcess api/_autosummary/laser_measles.biweekly.components.StateTracker api/_autosummary/laser_measles.biweekly.components.FadeOutTracker api/_autosummary/laser_measles.biweekly.components.CaseSurveillanceTracker api/_autosummary/laser_measles.biweekly.mixing api/_autosummary/laser_measles.demographics.get_shapefile_dataframe api/_autosummary/laser_measles.demographics.plot_shapefile_dataframe api/_autosummary/laser_measles.demographics.GADMShapefile api/_autosummary/laser_measles.demographics.RasterPatchParams api/_autosummary/laser_measles.demographics.RasterPatchGenerator assembling single document: done writing... done writing additional files... opensearchdone copying static files... Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/htmlzip/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/htmlzip/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/htmlzip/_static/documentation_options.js copying static files: done copying extra files... copying extra files: done dumping object inventory... done Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/htmlzip/_static/js/rtd_search_config.js build succeeded, 39 warnings. The HTML page is in ../_readthedocs/htmlzip. [rtd-command-info] start-time: 2025-07-09T17:58:12.693299Z, end-time: 2025-07-09T17:58:30.960444Z, duration: 18, exit-code: 0 python -m sphinx -T -b latex -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/pdf Running Sphinx v8.2.3 loading translations [en]... done making output directory... done loading pickled environment... The configuration has changed (6 options: 'html_permalinks_icon', 'html_static_path', 'html_theme_options', 'nbsphinx_requirejs_options', 'nbsphinx_requirejs_path', ...) done [autosummary] generating autosummary for: api/_autosummary/laser_measles.abm.components.ConstantPopProcess.rst, api/_autosummary/laser_measles.abm.components.InfectionProcess.rst, api/_autosummary/laser_measles.abm.components.PopulationTracker.rst, api/_autosummary/laser_measles.abm.core.rst, api/_autosummary/laser_measles.abm.model.rst, api/_autosummary/laser_measles.abm.params.rst, api/_autosummary/laser_measles.abm.utils.rst, api/_autosummary/laser_measles.base.BaseComponent.rst, api/_autosummary/laser_measles.base.BaseLaserModel.rst, api/_autosummary/laser_measles.biweekly.base.rst, ..., index.rst, installation.rst, reference/laser_measles.biweekly.rst, reference/laser_measles.demographics.rst, reference/laser_measles.nigeria.rst, reference/laser_measles.rst, reference/modules.rst, tutorials.rst, tutorials/README.rst, usage.rst WARNING: Failed to import laser_measles.nigeria. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: Failed to import laser_measles.nigeria.lgas. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: Failed to import laser_measles.nigeria.metapop. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: Failed to import laser_measles.nigeria.model. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: Failed to import laser_measles.nigeria.params. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: [autosummary] failed to import laser_measles.abm.cli. Possible hints: * AttributeError: module 'laser_measles.abm' has no attribute 'cli' * ModuleNotFoundError: No module named 'laser_measles.abm.cli' * ImportError: WARNING: [autosummary] failed to import laser_measles.abm.components.StatesTracker. Possible hints: * ImportError: * AttributeError: module 'laser_measles.abm.components' has no attribute 'StatesTracker' * ModuleNotFoundError: No module named 'laser_measles.abm.components.StatesTracker' WARNING: [autosummary] failed to import laser_measles.pretty_laserframe. Possible hints: * AttributeError: module 'laser_measles' has no attribute 'pretty_laserframe' * ModuleNotFoundError: No module named 'laser_measles.pretty_laserframe' * ImportError: building [mo]: targets for 0 po files that are out of date writing output... building [latex]: all documents updating environment: 0 added, 4 changed, 0 removed reading sources... [ 25%] reference/laser_measles reading sources... [ 50%] reference/laser_measles.biweekly reading sources... [ 75%] reference/laser_measles.nigeria reading sources... [100%] tutorials /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.abm' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.compartmental' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.components' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.scenarios' [toc.not_readable] WARNING: Cannot handle as a local function: "laser_measles.base.BasePatchLaserFrame.create_resized_copy" (use @functools.wraps) WARNING: Cannot resolve forward reference in type annotations of "laser_measles.base.BasePatchLaserFrame.create_resized_copy": name 'WrappedClass' is not defined WARNING: Cannot handle as a local function: "laser_measles.base.BasePeopleLaserFrame.create_resized_copy" (use @functools.wraps) WARNING: Cannot resolve forward reference in type annotations of "laser_measles.base.BasePeopleLaserFrame.create_resized_copy": name 'WrappedClass' is not defined /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/base.py:docstring of laser_measles.base.BaseLaserModel.get_instance:14: ERROR: Unexpected indentation. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.biweekly.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.biweekly.components' [toc.not_readable] WARNING: autodoc: failed to import module 'nigeria' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'nigeria.lgas' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'nigeria.metapop' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'nigeria.model' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'nigeria.params' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:7: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_basic_model' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:7: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_model_structure' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:7: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_abm_intro' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:7: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_scenarios' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:20: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_random_numbers' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:20: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_creating_component' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:20: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_pydantic_component_parameters' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:20: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_state_arrays' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:29: WARNING: Title underline too short. 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The LaTeX files are in ../_readthedocs/pdf. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). [rtd-command-info] start-time: 2025-07-09T17:58:31.044029Z, end-time: 2025-07-09T17:58:31.085968Z, 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: 2025-07-09T17:58:31.174501Z, end-time: 2025-07-09T17:58:34.133952Z, duration: 2, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-laser-measles -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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No file institute-for-disease-modeling-laser-measles.ind. Package longtable Warning: Table widths have changed. Rerun LaTeX. [17] (./institute-for-disease-modeling-laser-measles.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-meas les.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-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}< /usr/share/texmf/fonts/type1/public/tex-gyre/qhvb.pfb> Output written on institute-for-disease-modeling-laser-measles.pdf (21 pages, 1 84627 bytes). Transcript written on institute-for-disease-modeling-laser-measles.log. Latexmk: Index file 'institute-for-disease-modeling-laser-measles.idx' was written Latexmk: Missing input file 'institute-for-disease-modeling-laser-measles.ind' (or dependence on it) from following: 'No file institute-for-disease-modeling-laser-measles.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-laser-measles.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-laser-measles.pdf' Rule 'makeindex institute-for-disease-modeling-laser-measles.idx': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-laser-measles.idx' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-laser-measles.idx' ------------ Latexmk: Examining 'institute-for-disease-modeling-laser-measles.log' === TeX engine is 'pdfTeX' Latexmk: applying rule 'makeindex institute-for-disease-modeling-laser-measles.idx'... ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-laser-measles.ind" "institute-for-disease-modeling-laser-measles.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-measles.idx....done (31 entries accepted, 0 rejected). Sorting entries....done (164 comparisons). Generating output file institute-for-disease-modeling-laser-measles.ind....done (85 lines written, 0 warnings). Output written in institute-for-disease-modeling-laser-measles.ind. Transcript written in institute-for-disease-modeling-laser-measles.ilg. 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(/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] (./institute-for-disease-modeling-laser-measles.ind [17] [18] Underfull \hbox (badness 10000) in paragraph at lines 14--16 []\T1/txtt/m/n/10 CaseSurveillanceTracker() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/txtt/m/n/10 ConstantPopProcess() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 23--25 []\T1/txtt/m/n/10 fade_out_tracker \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 25--27 []\T1/txtt/m/n/10 FadeOutTracker() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 30--31 []\T1/txtt/m/n/10 GADMShapefile() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 31--33 []\T1/txtt/m/n/10 get_shapefile_dataframe() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 36--38 []\T1/txtt/m/n/10 ImportationPressureProcess() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 38--40 []\T1/txtt/m/n/10 InfectionProcess() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 40--42 []\T1/txtt/m/n/10 InfectionProcess() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 42--43 []\T1/txtt/m/n/10 initializers \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 56--58 []\T1/txtt/m/n/10 plot_shapefile_dataframe() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 58--60 []\T1/txtt/m/n/10 PopulationTracker() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 63--65 []\T1/txtt/m/n/10 RasterPatchGenerator() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule Underfull \hbox (badness 10000) in paragraph at lines 65--67 []\T1/txtt/m/n/10 RasterPatchParams() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 70--72 []\T1/txtt/m/n/10 SIACalendarProcess() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 72--74 []\T1/txtt/m/n/10 StateTracker() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 82--84 []\T1/txtt/m/n/10 VitalDynamicsProcess() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule [19]) (./institute-for-disease-modeling-laser-measles.aux) Package rerunfilecheck Warning: File `institute-for-disease-modeling-laser-meas les.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-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}< /usr/share/texmf/fonts/type1/public/tex-gyre/qhvb.pfb> Output written on institute-for-disease-modeling-laser-measles.pdf (23 pages, 2 12296 bytes). Transcript written on institute-for-disease-modeling-laser-measles.log. Latexmk: Index file 'institute-for-disease-modeling-laser-measles.idx' was written Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-laser-measles.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-laser-measles.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-laser-measles.aux' 'institute-for-disease-modeling-laser-measles.out' 'institute-for-disease-modeling-laser-measles.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-laser-measles" "laser-measles.tex"' ------------ Latexmk: Examining 'institute-for-disease-modeling-laser-measles.log' === TeX engine is 'pdfTeX' Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./laser-measles.tex LaTeX2e <2021-11-15> patch level 1 L3 programming layer <2022-01-21> (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2021/10/04 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.88 ...8a2926cdbe6a2a7678178/laser-measles}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.88 ...8a2926cdbe6a2a7678178/laser-measles}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.90 ...d45b5424ab76a1132e798/laser-measles}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.90 ...d45b5424ab76a1132e798/laser-measles}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.92 ...0b55d921bff7f3630dfdcad5a3a2871704e}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. 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(/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] (./institute-for-disease-modeling-laser-measles.ind [17] [18] Underfull \hbox (badness 10000) in paragraph at lines 14--16 []\T1/txtt/m/n/10 CaseSurveillanceTracker() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/txtt/m/n/10 ConstantPopProcess() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 23--25 []\T1/txtt/m/n/10 fade_out_tracker \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 25--27 []\T1/txtt/m/n/10 FadeOutTracker() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 30--31 []\T1/txtt/m/n/10 GADMShapefile() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 31--33 []\T1/txtt/m/n/10 get_shapefile_dataframe() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 36--38 []\T1/txtt/m/n/10 ImportationPressureProcess() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 38--40 []\T1/txtt/m/n/10 InfectionProcess() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 40--42 []\T1/txtt/m/n/10 InfectionProcess() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 42--43 []\T1/txtt/m/n/10 initializers \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 56--58 []\T1/txtt/m/n/10 plot_shapefile_dataframe() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 58--60 []\T1/txtt/m/n/10 PopulationTracker() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 63--65 []\T1/txtt/m/n/10 RasterPatchGenerator() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule Underfull \hbox (badness 10000) in paragraph at lines 65--67 []\T1/txtt/m/n/10 RasterPatchParams() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 70--72 []\T1/txtt/m/n/10 SIACalendarProcess() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 72--74 []\T1/txtt/m/n/10 StateTracker() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 82--84 []\T1/txtt/m/n/10 VitalDynamicsProcess() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule [19]) (./institute-for-disease-modeling-laser-measles.aux) ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}< /usr/share/texmf/fonts/type1/public/tex-gyre/qhvb.pfb> Output written on institute-for-disease-modeling-laser-measles.pdf (23 pages, 2 12709 bytes). Transcript written on institute-for-disease-modeling-laser-measles.log. Latexmk: Index file 'institute-for-disease-modeling-laser-measles.idx' was written Latexmk: Log file says output to 'institute-for-disease-modeling-laser-measles.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-laser-measles.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 1 Refer to 'institute-for-disease-modeling-laser-measles.log' for details Latexmk: Examining 'institute-for-disease-modeling-laser-measles.log' === TeX engine is 'pdfTeX' Latexmk: Errors, in force_mode: so I tried finishing targets [rtd-command-info] start-time: 2025-07-09T17:58:34.403822Z, end-time: 2025-07-09T17:58:54.910527Z, duration: 20, exit-code: 0 python -m sphinx -T -b epub -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/epub Running Sphinx v8.2.3 loading translations [en]... done making output directory... done loading pickled environment... The configuration has changed (4 options: 'html_static_path', 'latex_documents', 'nbsphinx_requirejs_options', 'nbsphinx_requirejs_path') done [autosummary] generating autosummary for: api/_autosummary/laser_measles.abm.components.ConstantPopProcess.rst, api/_autosummary/laser_measles.abm.components.InfectionProcess.rst, api/_autosummary/laser_measles.abm.components.PopulationTracker.rst, api/_autosummary/laser_measles.abm.core.rst, api/_autosummary/laser_measles.abm.model.rst, api/_autosummary/laser_measles.abm.params.rst, api/_autosummary/laser_measles.abm.utils.rst, api/_autosummary/laser_measles.base.BaseComponent.rst, api/_autosummary/laser_measles.base.BaseLaserModel.rst, api/_autosummary/laser_measles.biweekly.base.rst, ..., index.rst, installation.rst, reference/laser_measles.biweekly.rst, reference/laser_measles.demographics.rst, reference/laser_measles.nigeria.rst, reference/laser_measles.rst, reference/modules.rst, tutorials.rst, tutorials/README.rst, usage.rst WARNING: Failed to import laser_measles.nigeria. Possible hints: * AttributeError: module 'laser_measles' has no attribute 'nigeria' * ModuleNotFoundError: No module named 'laser_measles.nigeria' WARNING: Failed to import laser_measles.nigeria.lgas. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: Failed to import laser_measles.nigeria.metapop. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: Failed to import laser_measles.nigeria.model. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: Failed to import laser_measles.nigeria.params. Possible hints: * ModuleNotFoundError: No module named 'laser_measles.nigeria' * AttributeError: module 'laser_measles' has no attribute 'nigeria' WARNING: [autosummary] failed to import laser_measles.abm.cli. Possible hints: * AttributeError: module 'laser_measles.abm' has no attribute 'cli' * ModuleNotFoundError: No module named 'laser_measles.abm.cli' * ImportError: WARNING: [autosummary] failed to import laser_measles.abm.components.StatesTracker. Possible hints: * ImportError: * AttributeError: module 'laser_measles.abm.components' has no attribute 'StatesTracker' * ModuleNotFoundError: No module named 'laser_measles.abm.components.StatesTracker' WARNING: [autosummary] failed to import laser_measles.pretty_laserframe. Possible hints: * AttributeError: module 'laser_measles' has no attribute 'pretty_laserframe' * ModuleNotFoundError: No module named 'laser_measles.pretty_laserframe' * ImportError: Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/_readthedocs/epub/_static/nbsphinx-code-cells.css building [mo]: targets for 0 po files that are out of date writing output... building [epub]: targets for 40 source files that are out of date updating environment: 0 added, 4 changed, 0 removed reading sources... [ 25%] reference/laser_measles reading sources... [ 50%] reference/laser_measles.biweekly reading sources... [ 75%] reference/laser_measles.nigeria reading sources... [100%] tutorials /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.abm' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.compartmental' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.components' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.scenarios' [toc.not_readable] WARNING: Cannot handle as a local function: "laser_measles.base.BasePatchLaserFrame.create_resized_copy" (use @functools.wraps) WARNING: Cannot resolve forward reference in type annotations of "laser_measles.base.BasePatchLaserFrame.create_resized_copy": name 'WrappedClass' is not defined WARNING: Cannot handle as a local function: "laser_measles.base.BasePeopleLaserFrame.create_resized_copy" (use @functools.wraps) WARNING: Cannot resolve forward reference in type annotations of "laser_measles.base.BasePeopleLaserFrame.create_resized_copy": name 'WrappedClass' is not defined /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/laser_measles/base.py:docstring of laser_measles.base.BaseLaserModel.get_instance:14: ERROR: Unexpected indentation. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/reference/laser_measles.biweekly.rst:12: WARNING: toctree contains reference to nonexisting document 'reference/laser_measles.biweekly.components' [toc.not_readable] WARNING: autodoc: failed to import module 'nigeria' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'nigeria.lgas' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'nigeria.metapop' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'nigeria.model' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] WARNING: autodoc: failed to import module 'nigeria.params' from module 'laser_measles'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', ' File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/envs/latest/lib/python3.12/site-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'laser_measles.nigeria'\n"] [autodoc.import_object] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:7: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_basic_model' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:7: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_model_structure' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:7: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_abm_intro' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:7: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_scenarios' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:20: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_random_numbers' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:20: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_creating_component' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:20: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_pydantic_component_parameters' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:20: WARNING: toctree contains reference to nonexisting document 'tutorials/tut_state_arrays' [toc.not_readable] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-measles/checkouts/latest/docs/tutorials.rst:29: WARNING: Title underline too short. 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