Read the Docs build information Build id: 3588910 Project: institute-for-disease-modeling-laser Version: v0.9.1 Commit: ceeba8654909d2ed9fc3b9ce3aa84d59dfd93061 Date: 2025-12-10T01:15:48.126073Z State: finished Success: True [rtd-command-info] start-time: 2025-12-10T01:15:49.294697Z, end-time: 2025-12-10T01:15:49.777435Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/InstituteforDiseaseModeling/laser.git . Cloning into '.'... [rtd-command-info] start-time: 2025-12-10T01:15:49.897875Z, end-time: 2025-12-10T01:15:50.750670Z, duration: 0, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/tags/v0.9.1:refs/tags/v0.9.1 From https://github.com/InstituteforDiseaseModeling/laser * [new tag] v0.9.1 -> v0.9.1 * [new tag] v0.7.0 -> v0.7.0 * [new tag] v0.8.0 -> v0.8.0 * [new tag] v0.8.1 -> v0.8.1 [rtd-command-info] start-time: 2025-12-10T01:15:51.489758Z, end-time: 2025-12-10T01:15:51.547902Z, duration: 0, exit-code: 0 git checkout --force ceeba8654909d2ed9fc3b9ce3aa84d59dfd93061 Note: switching to 'ceeba8654909d2ed9fc3b9ce3aa84d59dfd93061'. 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 ceeba86 🔖 Bump patch version 0.9.0 -> 0.9.1 [rtd-command-info] start-time: 2025-12-10T01:15:51.649515Z, end-time: 2025-12-10T01:15:51.694368Z, duration: 0, exit-code: 0 cat .readthedocs.yml # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details version: 2 build: os: ubuntu-22.04 tools: python: "3.13" sphinx: configuration: docs/conf.py fail_on_warning: false formats: - htmlzip - pdf python: install: - requirements: docs/requirements.txt - method: pip path: . extra_requirements: - test search: ranking: installation.html: 3 laser.core.html: 2 [rtd-command-info] start-time: 2025-12-10T01:15:57.341338Z, end-time: 2025-12-10T01:15:57.406618Z, duration: 0, exit-code: 0 asdf global python 3.13.3 [rtd-command-info] start-time: 2025-12-10T01:15:57.827739Z, end-time: 2025-12-10T01:15:58.997902Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.13.3.final.0-64 in 850ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.9.1, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2025-12-10T01:15:59.133366Z, end-time: 2025-12-10T01:16:08.409625Z, 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-3.0.3 Pygments-2.19.2 alabaster-1.0.0 babel-2.17.0 certifi-2025.11.12 charset_normalizer-3.4.4 docutils-0.22.3 idna-3.11 imagesize-1.4.1 packaging-25.0 requests-2.32.5 roman-numerals-3.1.0 snowballstemmer-3.0.1 sphinx-9.0.4 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.6.1 [rtd-command-info] start-time: 2025-12-10T01:16:15.817228Z, end-time: 2025-12-10T01:16:19.466727Z, duration: 3, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Requirement already satisfied: sphinx>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.9.1/lib/python3.13/site-packages (from -r 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satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.9.1/lib/python3.13/site-packages (from requests>=2.30.0->sphinx>=1.3->-r docs/requirements.txt (line 1)) (2025.11.12) Installing collected packages: roman-numerals-py, docutils, sphinx, sphinxcontrib-jquery, sphinx-rtd-theme Attempting uninstall: docutils Found existing installation: docutils 0.22.3 Uninstalling docutils-0.22.3: Successfully uninstalled docutils-0.22.3 Attempting uninstall: sphinx Found existing installation: Sphinx 9.0.4 Uninstalling Sphinx-9.0.4: Successfully uninstalled Sphinx-9.0.4 Successfully installed docutils-0.21.2 roman-numerals-py-3.1.0 sphinx-8.2.3 sphinx-rtd-theme-3.0.2 sphinxcontrib-jquery-4.1 [rtd-command-info] start-time: 2025-12-10T01:16:19.560018Z, end-time: 2025-12-10T01:17:09.838924Z, duration: 50, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[test] Looking in indexes: 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Collecting pyproj>=3.5.0 (from geopandas->laser-core==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f8/85/c2b1706e51942de19076eff082f8495e57d5151364e78b5bef4af4a1d94a/pyproj-3.7.2-cp313-cp313-manylinux_2_28_x86_64.whl (9.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 13.4 MB/s 0:00:00 Collecting python-dateutil>=2.8.2 (from pandas->laser-core==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ec/57/56b9bcc3c9c6a792fcbaf139543cee77261f3651ca9da0c93f5c1221264b/python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) Collecting pytz>=2020.1 (from pandas->laser-core==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/81/c4/34e93fe5f5429d7570ec1fa436f1986fb1f00c3e0f43a589fe2bbcd22c3f/pytz-2025.2-py2.py3-none-any.whl (509 kB) Collecting tzdata>=2022.7 (from pandas->laser-core==0.9.1) Downloading 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cycler>=0.10 (from matplotlib->laser-core==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e7/05/c19819d5e3d95294a6f5947fb9b9629efb316b96de511b418c53d245aae6/cycler-0.12.1-py3-none-any.whl (8.3 kB) Collecting fonttools>=4.22.0 (from matplotlib->laser-core==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/4e/80/c87bc524a90dbeb2a390eea23eae448286983da59b7e02c67fa0ca96a8c5/fonttools-4.61.0-cp313-cp313-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl (4.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.9/4.9 MB 13.6 MB/s 0:00:00 Collecting kiwisolver>=1.3.1 (from matplotlib->laser-core==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e9/e9/f218a2cb3a9ffbe324ca29a9e399fa2d2866d7f348ec3a88df87fc248fc5/kiwisolver-1.4.9-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (1.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.5/1.5 MB 13.9 MB/s 0:00:00 Collecting pillow>=8 (from matplotlib->laser-core==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/38/57/755dbd06530a27a5ed74f8cb0a7a44a21722ebf318edbe67ddbd7fb28f88/pillow-12.0.0-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (7.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.0/7.0 MB 13.6 MB/s 0:00:00 Collecting pyparsing>=3 (from matplotlib->laser-core==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/10/5e/1aa9a93198c6b64513c9d7752de7422c06402de6600a8767da1524f9570b/pyparsing-3.2.5-py3-none-any.whl (113 kB) Collecting llvmlite<0.47,>=0.46.0dev0 (from numba->laser-core==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/0e/54/737755c0a91558364b9200702c3c9c15d70ed63f9b98a2c32f1c2aa1f3ba/llvmlite-0.46.0-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (56.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.3/56.3 MB 13.4 MB/s 0:00:04 Collecting coverage>=7.10.6 (from coverage[toml]>=7.10.6->pytest-cov->laser-core==0.9.1) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/90/3a/9bfd4de2ff191feb37ef9465855ca56a6f2f30a3bca172e474130731ac3d/coverage-7.13.0-cp313-cp313-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (252 kB) Building wheels for collected packages: laser-core Building wheel for laser-core (pyproject.toml): started Building wheel for laser-core (pyproject.toml): finished with status 'done' Created wheel for laser-core: filename=laser_core-0.9.1-cp313-cp313-linux_x86_64.whl size=47192 sha256=86e57552b8fbb82cb04c54a47dcb9477990a34465e23b746095186a0e8e81607 Stored in directory: /tmp/pip-ephem-wheel-cache-axi6kobs/wheels/b6/a4/94/54c126eb9344406d10dd23d0a627c7db5010d1252311ccf90c Successfully built laser-core Installing collected packages: pytz, uv, tzdata, six, pyproj, pyparsing, pluggy, pillow, numpy, llvmlite, kiwisolver, iniconfig, fonttools, cycler, coverage, click, shapely, scipy, python-dateutil, pytest, pyogrio, numba, h5py, contourpy, pytest-cov, pandas, matplotlib, geopandas, laser-core Successfully installed click-8.3.1 contourpy-1.3.3 coverage-7.13.0 cycler-0.12.1 fonttools-4.61.0 geopandas-1.1.1 h5py-3.15.1 iniconfig-2.3.0 kiwisolver-1.4.9 laser-core-0.9.1 llvmlite-0.46.0 matplotlib-3.10.7 numba-0.63.0 numpy-2.3.5 pandas-2.3.3 pillow-12.0.0 pluggy-1.6.0 pyogrio-0.12.1 pyparsing-3.2.5 pyproj-3.7.2 pytest-9.0.2 pytest-cov-7.0.0 python-dateutil-2.9.0.post0 pytz-2025.2 scipy-1.16.3 shapely-2.1.2 six-1.17.0 tzdata-2025.2 uv-0.9.17 [rtd-command-info] start-time: 2025-12-10T01:17:09.997380Z, end-time: 2025-12-10T01:17:10.040838Z, duration: 0, exit-code: 0 cat docs/conf.py import os extensions = [ "sphinx.ext.autodoc", "sphinx.ext.autosummary", "sphinx.ext.coverage", "sphinx.ext.doctest", "sphinx.ext.extlinks", "sphinx.ext.ifconfig", "sphinx.ext.napoleon", "sphinx.ext.todo", "sphinx.ext.viewcode", "sphinx.ext.mathjax", ] source_suffix = {".rst": "restructuredtext"} master_doc = "index" project = "LASER" year = "2023-2024" author = "Institute for Disease Modeling" copyright = f"{year}, {author}" version = release = "0.9.1" pygments_style = "trac" templates_path = ["."] extlinks = { "issue": ("https://github.com/InstituteforDiseaseModeling/laser/issues/%s", "#"), "pr": ("https://github.com/InstituteforDiseaseModeling/laser/pull/%s", "PR #"), } # on_rtd is whether we are on readthedocs.org on_rtd = os.environ.get("READTHEDOCS", None) == "True" if not on_rtd: # only set the theme if we are building docs locally html_theme = "sphinx_rtd_theme" html_use_smartypants = True html_last_updated_fmt = "%b %d, %Y" html_split_index = False html_sidebars = { "**": ["searchbox.html", "globaltoc.html", "sourcelink.html"], } html_short_title = f"{project}-{version}" # Napoleon settings (Napolean converts Google-style docstrings to reStructuredText) napoleon_google_docstring = True napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_include_private_with_doc = False napoleon_include_special_with_doc = True napoleon_use_admonition_for_examples = False napoleon_use_admonition_for_notes = False napoleon_use_admonition_for_references = False napoleon_use_ivar = True # from Cookiecutter template, False is the default napoleon_use_param = False # from Cookiecutter template, True is the default napoleon_use_rtype = False # from Cookiecutter template, True is the default napoleon_preprocess_types = False napoleon_type_aliases = None napoleon_attr_annotations = True mathjax3_config = {"TeX": {"Macros": {"small": ["{\\scriptstyle #1}", 1]}}} # Prevent the following warning: # sphinx/builders/linkcheck.py:86: RemovedInSphinx80Warning: The default value for 'linkcheck_report_timeouts_as_broken' will change to False in Sphinx 8, meaning that request timeouts will be reported with a new 'timeout' status, instead of as 'broken'. This is intended to provide more detail as to the failure mode. See https://github.com/sphinx-doc/sphinx/issues/11868 for details. # warnings.warn(deprecation_msg, RemovedInSphinx80Warning, stacklevel=1) linkcheck_ignore = [r"https://www\.populationpyramid\.net/nigeria/2024/"] linkcheck_report_timeouts_as_broken = False [rtd-command-info] start-time: 2025-12-10T01:17:10.145054Z, end-time: 2025-12-10T01:17:22.321790Z, duration: 12, 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: architecture.rst, authors.rst, calibration.rst, changelog.rst, contributing.rst, eula.rst, example.rst, index.rst, installation.rst, kmestimator.rst, migration.rst, performance.rst, pyramids.rst, readme.rst, source/laser.core.demographics.rst, source/laser.core.rst, source/modules.rst, spatialexample.rst, usage.rst, vdexample.rst building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 20 source files that are out of date updating environment: [new config] 20 added, 0 changed, 0 removed reading sources... [ 5%] architecture reading sources... [ 10%] authors reading sources... [ 15%] calibration reading sources... [ 20%] changelog reading sources... [ 25%] contributing reading sources... [ 30%] eula reading sources... [ 35%] example reading sources... [ 40%] index reading sources... [ 45%] installation reading sources... [ 50%] kmestimator reading sources... [ 55%] migration reading sources... [ 60%] performance reading sources... [ 65%] pyramids reading sources... [ 70%] readme reading sources... [ 75%] source/laser.core reading sources... [ 80%] source/laser.core.demographics reading sources... [ 85%] source/modules reading sources... [ 90%] spatialexample reading sources... [ 95%] usage reading sources... [100%] vdexample /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.9.1/lib/python3.13/site-packages/laser/core/propertyset.py:docstring of laser.core.propertyset.PropertySet:57: WARNING: Inline substitution_reference start-string without end-string. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.9.1/lib/python3.13/site-packages/laser/core/__init__.py:docstring of laser.core.propertyset.PropertySet:57: WARNING: Inline substitution_reference start-string without end-string. [docutils] looking for now-outdated files... none found pickling environment... done checking consistency... 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/checkouts/v0.9.1/_readthedocs/html/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/_readthedocs/html/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/_readthedocs/html/_static/documentation_options.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/_readthedocs/html/_static/alabaster.css copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 5%] architecture writing output... [ 10%] authors writing output... [ 15%] calibration writing output... [ 20%] changelog writing output... [ 25%] contributing writing output... [ 30%] eula writing output... [ 35%] example writing output... [ 40%] index writing output... [ 45%] installation writing output... [ 50%] kmestimator writing output... [ 55%] migration writing output... [ 60%] performance writing output... [ 65%] pyramids writing output... [ 70%] readme writing output... [ 75%] source/laser.core writing output... [ 80%] source/laser.core.demographics writing output... [ 85%] source/modules writing output... [ 90%] spatialexample writing output... [ 95%] usage writing output... [100%] vdexample generating indices... genindex py-modindex done highlighting module code... [ 9%] laser.core.demographics.kmestimator highlighting module code... [ 18%] laser.core.demographics.pyramid highlighting module code... [ 27%] laser.core.demographics.spatialpops highlighting module code... [ 36%] laser.core.distributions highlighting module code... [ 45%] laser.core.extension highlighting module code... [ 55%] laser.core.laserframe highlighting module code... [ 64%] laser.core.migration highlighting module code... [ 73%] laser.core.propertyset highlighting module code... [ 82%] laser.core.random highlighting module code... [ 91%] laser.core.sortedqueue highlighting module code... [100%] laser.core.utils writing additional pages... search done copying images... [ 25%] media/workflow.png copying images... [ 50%] media/Nigeria-NDD.png copying images... [ 75%] media/Nigeria-2024.png copying images... [100%] media/Nigeria-Sampled.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 2 warnings. The HTML pages are in ../_readthedocs/html. [rtd-command-info] start-time: 2025-12-10T01:17:22.435024Z, end-time: 2025-12-10T01:17:33.635904Z, duration: 11, 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... done [autosummary] generating autosummary for: architecture.rst, authors.rst, calibration.rst, changelog.rst, contributing.rst, eula.rst, example.rst, index.rst, installation.rst, kmestimator.rst, migration.rst, performance.rst, pyramids.rst, readme.rst, source/laser.core.demographics.rst, source/laser.core.rst, source/modules.rst, spatialexample.rst, usage.rst, vdexample.rst building [mo]: targets for 0 po files that are out of date writing output... building [singlehtml]: all documents updating environment: 0 added, 0 changed, 0 removed reading sources... looking for now-outdated files... none found preparing documents... done copying assets... copying static files... Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/_readthedocs/htmlzip/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/_readthedocs/htmlzip/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/_readthedocs/htmlzip/_static/documentation_options.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/_readthedocs/htmlzip/_static/alabaster.css copying static files: done copying extra files... copying extra files: done copying assets: done assembling single document... index readme installation usage architecture source/modules source/laser.core source/laser.core.demographics migration pyramids kmestimator example vdexample spatialexample eula performance calibration contributing authors changelog assembling single document: done writing... done writing additional files... done copying images... [ 25%] media/Nigeria-2024.png copying images... [ 50%] media/Nigeria-Sampled.png copying images... [ 75%] media/Nigeria-NDD.png copying images... [100%] media/workflow.png copying static files... Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/_readthedocs/htmlzip/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/_readthedocs/htmlzip/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/_readthedocs/htmlzip/_static/documentation_options.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/_readthedocs/htmlzip/_static/alabaster.css copying static files: done copying extra files... copying extra files: done dumping object inventory... done build succeeded. The HTML page is in ../_readthedocs/htmlzip. [rtd-command-info] start-time: 2025-12-10T01:17:33.952794Z, end-time: 2025-12-10T01:17:46.819769Z, duration: 12, 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... done [autosummary] generating autosummary for: architecture.rst, authors.rst, calibration.rst, changelog.rst, contributing.rst, eula.rst, example.rst, index.rst, installation.rst, kmestimator.rst, migration.rst, performance.rst, pyramids.rst, readme.rst, source/laser.core.demographics.rst, source/laser.core.rst, source/modules.rst, spatialexample.rst, usage.rst, vdexample.rst building [mo]: targets for 0 po files that are out of date writing output... building [latex]: all documents updating environment: 0 added, 0 changed, 0 removed reading sources... looking for now-outdated files... none found preparing documents... done copying assets... copying TeX support files... Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/_readthedocs/pdf/latexmkrc Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/_readthedocs/pdf/Makefile Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/_readthedocs/pdf/make.bat Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/_readthedocs/pdf/latexmkjarc done copying assets: done processing laser.tex... index readme installation usage architecture source/modules source/laser.core source/laser.core.demographics migration pyramids kmestimator example vdexample spatialexample eula performance calibration contributing authors changelog resolving references... /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/README.rst:18: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://readthedocs.org/projects/idmlaser/badge/?style=flat) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/README.rst:22: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://github.com/InstituteforDiseaseModeling/laser/actions/workflows/github-actions.yml/badge.svg) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/README.rst:26: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://codecov.io/gh/InstituteforDiseaseModeling/laser/branch/main/graphs/badge.svg?branch=main) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/README.rst:30: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/pypi/v/laser-core.svg) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/README.rst:34: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/pypi/wheel/laser-core.svg) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/README.rst:38: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/pypi/pyversions/laser-core.svg) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/README.rst:42: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/pypi/implementation/laser-core.svg) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/README.rst:46: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/github/commits-since/InstituteforDiseaseModeling/laser/v0.9.1.svg) processing laser.tex: done writing... done copying images... [ 25%] media/Nigeria-2024.png copying images... [ 50%] media/Nigeria-Sampled.png copying images... [ 75%] media/Nigeria-NDD.png copying images... [100%] media/workflow.png Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.9.1/_readthedocs/pdf/sphinxmessages.sty build succeeded, 8 warnings. The LaTeX files are in ../_readthedocs/pdf. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). [rtd-command-info] start-time: 2025-12-10T01:17:47.274407Z, end-time: 2025-12-10T01:17:47.318481Z, 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: 2025-12-10T01:17:47.407504Z, end-time: 2025-12-10T01:17:55.164935Z, duration: 7, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-laser -interaction=nonstopmode Use of uninitialized value in concatenation (.) or string at (eval 10) line 1. Use of uninitialized value in concatenation (.) or string at (eval 10) line 2. Use of uninitialized value in concatenation (.) or string at (eval 10) line 3. Use of uninitialized value in concatenation (.) or string at (eval 10) line 4. Subroutine makeglo redefined at (eval 11) line 7. Use of uninitialized value in concatenation (.) or string at (eval 11) line 1. Use of uninitialized value in concatenation (.) or string at (eval 11) line 2. Use of uninitialized value in concatenation (.) or string at (eval 11) line 3. Use of uninitialized value in concatenation (.) or string at (eval 11) line 4. Rc files read: /etc/LatexMk latexmkrc latexmkrc Latexmk: This is Latexmk, John Collins, 20 November 2021, version: 4.76. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'laser.tex' ------------ Run number 1 of rule 'pdflatex' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-laser" "laser.tex"' ------------ 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.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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(/usr/share/texlive/texmf-dist/tex/latex/l3packages/xparse/xparse.sty) (/usr/share/texlive/texmf-dist/tex/latex/fontawesome5/fontawesome5-generic-help er.sty (/usr/share/texlive/texmf-dist/tex/latex/fontawesome5/fontawesome5-mapping.def) )) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texmf/tex/latex/tex-gyre/t1qhv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2] Chapter 1. ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.103 ...62f58a094fd24530e38e6ec2a3b74c80d6}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.103 ...62f58a094fd24530e38e6ec2a3b74c80d6}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.110 ...3c549516b73dbf0272675ae1f060/badge}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.110 ...3c549516b73dbf0272675ae1f060/badge}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.111 ...94971c314e5f1279160af86f4a7a/badge}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.111 ...94971c314e5f1279160af86f4a7a/badge}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.119 ...dc2a18f7ca17366865a50d5/laser-core}.svg}} \sphinxhref{https://pypi.... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.119 ...dc2a18f7ca17366865a50d5/laser-core}.svg}} \sphinxhref{https://pypi.... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.119 ...c1126b9416f0393ff0e844b/laser-core}.svg}} \sphinxhref{https://pypi.... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.119 ...c1126b9416f0393ff0e844b/laser-core}.svg}} \sphinxhref{https://pypi.... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.119 ...88315d41abbadebeb500983/laser-core}.svg}} \sphinxhref{https://pypi.... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.119 ...88315d41abbadebeb500983/laser-core}.svg}} \sphinxhref{https://pypi.... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.119 ...e6b32b94148f6d243fd13d3/laser-core}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.119 ...e6b32b94148f6d243fd13d3/laser-core}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 ...6e2c8a8c501bb2cd3e47b7ee828/v0.9.1}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 ...6e2c8a8c501bb2cd3e47b7ee828/v0.9.1}.svg}} (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) Underfull \hbox (badness 10000) in paragraph at lines 177--179 []|\T1/qhv/m/n/10 Win- [1] [2] Chapter 2. [3] [4] Chapter 3. [5] [6] Chapter 4. [7] Underfull \hbox (badness 7558) in paragraph at lines 288--290 []\T1/qtm/b/n/10 Laser-Frame\T1/qtm/m/n/10 : A cus-tom dataframe class with ad- di-tional meth-ods tai-lored for LASER, such as [8] [9] [10] [11] [12] Chapter 5. (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) Underfull \hbox (badness 10000) in paragraph at lines 629--635 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 estimator = KaplanMeierEstimator(cumulative_ deaths=np.array([...])) year_of_death Underfull \hbox (badness 10000) in paragraph at lines 629--635 \T1/txtt/m/n/10 = estimator.predict_year_of_death(np.array([40, 50, 60]), max_y ear=80) age_at_death [13] Underfull \hbox (badness 10000) in paragraph at lines 693--697 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 predict_age_at_death(np.array([40*365, 50*36 5, 60*365]), max_year=80) # Underfull \hbox (badness 10000) in paragraph at lines 731--735 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 predict_year_of_death(np.array([40, 50, 60]) , max_year=80) # returns something [14] [15] [16] [17] Underfull \hbox (badness 10000) in paragraph at lines 1242--1246 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 predict_age_at_death(np.array([40*365, 50*36 5, 60*365]), max_year=80) # Underfull \hbox (badness 10000) in paragraph at lines 1280--1284 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 predict_year_of_death(np.array([40, 50, 60]) , max_year=80) # returns something [18] [19] [20] [21] Overfull \hbox (1.49371pt too wide) in paragraph at lines 1876--1885 \TS1/txtt/m/n/10 `\T1/txtt/m/n/10 python laser_frame = LaserFrame(capacity=100) laser_frame.add_scalar_property(\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 age\TS1/txtt /m/n/10 '\T1/txtt/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1876--1885 \T1/txtt/m/n/10 dtype=np.int32, default=0) laser_frame.add_vector_property(\TS1 /txtt/m/n/10 '\T1/txtt/m/n/10 position\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 , lengt h=3, Underfull \hbox (badness 10000) in paragraph at lines 1876--1885 \T1/txtt/m/n/10 dtype=np.float32, default=0.0) start, end = laser_frame.add(10) laser_frame.sort(np. Underfull \hbox (badness 10000) in paragraph at lines 1876--1885 \T1/txtt/m/n/10 arange(10)[::[]1]) laser_frame.squash(np.array([True, False, Tr ue, False, True, (/usr/share/texlive/texmf-dist/tex/latex/fontawesome5/ufontawesomefree1.fd) [22] [23] [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 2395--2397 \T1/txtt/m/n/10 row_sums = np.sum(competition_matrix, axis=1) [] np. Underfull \hbox (badness 10000) in paragraph at lines 2402--2404 \T1/txtt/m/n/10 network[i][j] = network[i][j] * (row_sums[i] [] competition_mat rix[i][j]) [26] [27] [28] [29] LaTeX Warning: Hyper reference `source/laser.core:laser.core.propertyset.Proper tySet' on page 30 undefined on input line 2879. Underfull \hbox (badness 5302) in paragraph at lines 2917--2923 []\T1/qtm/m/n/10 ps = Prop-er-ty-Set({`mything': 0.4, `that_other_thing': 42}) print(ps.mything) # Out-puts: [30] [31] [32] [33] [34] ! LaTeX Error: Unicode character ≈ (U+2248) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.3588 ... in decimal degrees (default 0.08983 ≈ 10km at the equator). [35] [36] [37] LaTeX Warning: Hyper reference `source/laser.core:laser.core.propertyset.Proper tySet' on page 38 undefined on input line 4069. Underfull \hbox (badness 5302) in paragraph at lines 4107--4113 []\T1/qtm/m/n/10 ps = Prop-er-ty-Set({`mything': 0.4, `that_other_thing': 42}) print(ps.mything) # Out-puts: [38] [39] [40] [41] [42] [43] [44] Chapter 6. [45] [46] [47] [48] Chapter 7. [49] [50] [51 <./Nigeria-2024.png>] [52 <./Nigeria-Sampled.png>] Chapter 8. [53] [54 <./Nigeria-NDD.png>] Chapter 9. [55] [56] [57] [58] Chapter 10. [59] [60] Underfull \vbox (badness 10000) detected at line 5629 Underfull \vbox (badness 10000) detected at line 5629 [61] Overfull \vbox (0.80812pt too high) detected at line 5676 [62] Overfull \vbox (0.80812pt too high) detected at line 5717 [63] [64] [65] [66] Chapter 11. [67] Underfull \vbox (badness 10000) detected at line 5981 [68] Underfull \vbox (badness 10000) detected at line 5981 Underfull \vbox (badness 10000) detected at line 5981 [69] [70] Underfull \vbox (badness 10000) detected at line 6073 Underfull \vbox (badness 10000) detected at line 6073 [71] [72] [73] [74] Underfull \vbox (badness 10000) detected at line 6290 Underfull \vbox (badness 10000) detected at line 6290 [75] [76] Chapter 12. [77] [78] Underfull \vbox (badness 7397) detected at line 6492 [79] Underfull \vbox (badness 10000) detected at line 6492 Underfull \vbox (badness 10000) detected at line 6492 [80] [81] [82] Chapter 13. [83] [84] Chapter 14. [85] [86] Chapter 15. [87] Underfull \vbox (badness 10000) detected at line 6891 Underfull \vbox (badness 10000) detected at line 6891 [88] Underfull \vbox (badness 10000) detected at line 6891 Underfull \vbox (badness 10000) detected at line 6891 [89] Underfull \vbox (badness 10000) detected at line 6891 Underfull \vbox (badness 10000) detected at line 6891 [90] [91] [92] Chapter 16. [93] [94] [95] [96] Chapter 17. [97] [98] [99] [100 <./workflow.png>] [101] [102] Chapter 18. [103] [104] Chapter 19. [105] [106] Chapter 20. [107] [108] Chapter 21. [109] [110] LaTeX Warning: Reference `source/laser.core:module-laser.core' on page 111 unde fined on input line 7788. LaTeX Warning: Reference `source/laser.core:module-laser.core.cli' on page 111 undefined on input line 7789. LaTeX Warning: Reference `source/laser.core.demographics:module-laser.core.demo graphics' on page 111 undefined on input line 7790. 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LaTeX Warning: Reference `source/laser.core:module-laser.core.propertyset' on p age 111 undefined on input line 7798. LaTeX Warning: Reference `source/laser.core:module-laser.core.random' on page 1 11 undefined on input line 7799. LaTeX Warning: Reference `source/laser.core:module-laser.core.utils' on page 11 1 undefined on input line 7800. [111] No file institute-for-disease-modeling-laser.ind. (./institute-for-disease-modeling-laser.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.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ts1.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/fontaw esome5/fa5free1.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} {/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb> Output written on institute-for-disease-modeling-laser.pdf (115 pages, 685965 b ytes). Transcript written on institute-for-disease-modeling-laser.log. Latexmk: Index file 'institute-for-disease-modeling-laser.idx' was written Latexmk: Missing input file 'institute-for-disease-modeling-laser.ind' (or dependence on it) from following: 'No file institute-for-disease-modeling-laser.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-laser.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-laser.pdf' Latexmk: List of undefined refs and citations: Reference `source/laser.core.demographics:module-laser.core.demographics' on page 111 undefined on input line 7790 Reference `source/laser.core.demographics:module-laser.core.demographics.kmestimator' on page 111 undefined on input line 7791 Reference `source/laser.core.demographics:module-laser.core.demographics.pyramid' on page 111 undefined on input line 7792 Reference `source/laser.core.demographics:module-laser.core.demographics.spatialpops' on page 111 undefined on input line 7793 Reference `source/laser.core:module-laser.core' on page 111 undefined on input line 7788 Reference `source/laser.core:module-laser.core.cli' on page 111 undefined on input line 7789 Reference `source/laser.core:module-laser.core.distributions' on page 111 undefined on input line 7794 Reference `source/laser.core:module-laser.core.extension' on page 111 undefined on input line 7795 Reference `source/laser.core:module-laser.core.laserframe' on page 111 undefined on input line 7796 Reference `source/laser.core:module-laser.core.migration' on page 111 undefined on input line 7797 Reference `source/laser.core:module-laser.core.propertyset' on page 111 undefined on input line 7798 Reference `source/laser.core:module-laser.core.random' on page 111 undefined on input line 7799 Reference `source/laser.core:module-laser.core.utils' on page 111 undefined on input line 7800 Rule 'makeindex institute-for-disease-modeling-laser.idx': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-laser.idx' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-laser.idx' ------------ ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-laser.ind" "institute-for-disease-modeling-laser.idx"' ------------ Latexmk: Examining 'institute-for-disease-modeling-laser.log' === TeX engine is 'pdfTeX' Latexmk: applying rule 'makeindex institute-for-disease-modeling-laser.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.idx....done (147 entries accepted, 0 rejected). Sorting entries....done (1108 comparisons). Generating output file institute-for-disease-modeling-laser.ind....done (262 lines written, 0 warnings). Output written in institute-for-disease-modeling-laser.ind. Transcript written in institute-for-disease-modeling-laser.ilg. 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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.103 ...62f58a094fd24530e38e6ec2a3b74c80d6}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.103 ...62f58a094fd24530e38e6ec2a3b74c80d6}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.110 ...3c549516b73dbf0272675ae1f060/badge}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.110 ...3c549516b73dbf0272675ae1f060/badge}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.111 ...94971c314e5f1279160af86f4a7a/badge}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.111 ...94971c314e5f1279160af86f4a7a/badge}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.119 ...dc2a18f7ca17366865a50d5/laser-core}.svg}} \sphinxhref{https://pypi.... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.119 ...dc2a18f7ca17366865a50d5/laser-core}.svg}} \sphinxhref{https://pypi.... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.119 ...c1126b9416f0393ff0e844b/laser-core}.svg}} \sphinxhref{https://pypi.... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.119 ...c1126b9416f0393ff0e844b/laser-core}.svg}} \sphinxhref{https://pypi.... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.119 ...88315d41abbadebeb500983/laser-core}.svg}} \sphinxhref{https://pypi.... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.119 ...88315d41abbadebeb500983/laser-core}.svg}} \sphinxhref{https://pypi.... ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.119 ...e6b32b94148f6d243fd13d3/laser-core}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.119 ...e6b32b94148f6d243fd13d3/laser-core}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 ...6e2c8a8c501bb2cd3e47b7ee828/v0.9.1}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 ...6e2c8a8c501bb2cd3e47b7ee828/v0.9.1}.svg}} (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) Underfull \hbox (badness 10000) in paragraph at lines 177--179 []|\T1/qhv/m/n/10 Win- [1] [2] Chapter 2. [3] [4] Chapter 3. [5] [6] Chapter 4. [7] Underfull \hbox (badness 7558) in paragraph at lines 288--290 []\T1/qtm/b/n/10 Laser-Frame\T1/qtm/m/n/10 : A cus-tom dataframe class with ad- di-tional meth-ods tai-lored for LASER, such as [8] [9] [10] [11] [12] Chapter 5. (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) Underfull \hbox (badness 10000) in paragraph at lines 629--635 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 estimator = KaplanMeierEstimator(cumulative_ deaths=np.array([...])) year_of_death Underfull \hbox (badness 10000) in paragraph at lines 629--635 \T1/txtt/m/n/10 = estimator.predict_year_of_death(np.array([40, 50, 60]), max_y ear=80) age_at_death [13] Underfull \hbox (badness 10000) in paragraph at lines 693--697 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 predict_age_at_death(np.array([40*365, 50*36 5, 60*365]), max_year=80) # Underfull \hbox (badness 10000) in paragraph at lines 731--735 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 predict_year_of_death(np.array([40, 50, 60]) , max_year=80) # returns something [14] [15] [16] [17] Underfull \hbox (badness 10000) in paragraph at lines 1242--1246 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 predict_age_at_death(np.array([40*365, 50*36 5, 60*365]), max_year=80) # Underfull \hbox (badness 10000) in paragraph at lines 1280--1284 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 predict_year_of_death(np.array([40, 50, 60]) , max_year=80) # returns something [18] [19] [20] [21] Overfull \hbox (1.49371pt too wide) in paragraph at lines 1876--1885 \TS1/txtt/m/n/10 `\T1/txtt/m/n/10 python laser_frame = LaserFrame(capacity=100) laser_frame.add_scalar_property(\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 age\TS1/txtt /m/n/10 '\T1/txtt/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1876--1885 \T1/txtt/m/n/10 dtype=np.int32, default=0) laser_frame.add_vector_property(\TS1 /txtt/m/n/10 '\T1/txtt/m/n/10 position\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 , lengt h=3, Underfull \hbox (badness 10000) in paragraph at lines 1876--1885 \T1/txtt/m/n/10 dtype=np.float32, default=0.0) start, end = laser_frame.add(10) laser_frame.sort(np. Underfull \hbox (badness 10000) in paragraph at lines 1876--1885 \T1/txtt/m/n/10 arange(10)[::[]1]) laser_frame.squash(np.array([True, False, Tr ue, False, True, (/usr/share/texlive/texmf-dist/tex/latex/fontawesome5/ufontawesomefree1.fd) [22] [23] [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 2395--2397 \T1/txtt/m/n/10 row_sums = np.sum(competition_matrix, axis=1) [] np. Underfull \hbox (badness 10000) in paragraph at lines 2402--2404 \T1/txtt/m/n/10 network[i][j] = network[i][j] * (row_sums[i] [] competition_mat rix[i][j]) [26] [27] [28] [29] Underfull \hbox (badness 5302) in paragraph at lines 2917--2923 []\T1/qtm/m/n/10 ps = Prop-er-ty-Set({`mything': 0.4, `that_other_thing': 42}) print(ps.mything) # Out-puts: [30] [31] [32] [33] [34] ! LaTeX Error: Unicode character ≈ (U+2248) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.3588 ... in decimal degrees (default 0.08983 ≈ 10km at the equator). [35] [36] [37] Underfull \hbox (badness 5302) in paragraph at lines 4107--4113 []\T1/qtm/m/n/10 ps = Prop-er-ty-Set({`mything': 0.4, `that_other_thing': 42}) print(ps.mything) # Out-puts: [38] [39] [40] [41] [42] [43] [44] Chapter 6. [45] [46] [47] [48] Chapter 7. [49] [50] [51 <./Nigeria-2024.png>] [52 <./Nigeria-Sampled.png>] Chapter 8. [53] [54 <./Nigeria-NDD.png>] Chapter 9. [55] [56] [57] [58] Chapter 10. [59] [60] Underfull \vbox (badness 10000) detected at line 5629 Underfull \vbox (badness 10000) detected at line 5629 [61] Overfull \vbox (0.80812pt too high) detected at line 5676 [62] Overfull \vbox (0.80812pt too high) detected at line 5717 [63] [64] [65] [66] Chapter 11. 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ts1.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/fontaw esome5/fa5free1.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} {/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb> Output written on institute-for-disease-modeling-laser.pdf (121 pages, 716476 b ytes). Transcript written on institute-for-disease-modeling-laser.log. Latexmk: Index file 'institute-for-disease-modeling-laser.idx' was written Latexmk: References changed. 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See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 ...6e2c8a8c501bb2cd3e47b7ee828/v0.9.1}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 ...6e2c8a8c501bb2cd3e47b7ee828/v0.9.1}.svg}} (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) Underfull \hbox (badness 10000) in paragraph at lines 177--179 []|\T1/qhv/m/n/10 Win- [1] [2] Chapter 2. [3] [4] Chapter 3. [5] [6] Chapter 4. [7] Underfull \hbox (badness 7558) in paragraph at lines 288--290 []\T1/qtm/b/n/10 Laser-Frame\T1/qtm/m/n/10 : A cus-tom dataframe class with ad- di-tional meth-ods tai-lored for LASER, such as [8] [9] [10] [11] [12] Chapter 5. (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) Underfull \hbox (badness 10000) in paragraph at lines 629--635 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 estimator = KaplanMeierEstimator(cumulative_ deaths=np.array([...])) year_of_death Underfull \hbox (badness 10000) in paragraph at lines 629--635 \T1/txtt/m/n/10 = estimator.predict_year_of_death(np.array([40, 50, 60]), max_y ear=80) age_at_death [13] Underfull \hbox (badness 10000) in paragraph at lines 693--697 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 predict_age_at_death(np.array([40*365, 50*36 5, 60*365]), max_year=80) # Underfull \hbox (badness 10000) in paragraph at lines 731--735 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 predict_year_of_death(np.array([40, 50, 60]) , max_year=80) # returns something [14] [15] [16] [17] Underfull \hbox (badness 10000) in paragraph at lines 1242--1246 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 predict_age_at_death(np.array([40*365, 50*36 5, 60*365]), max_year=80) # Underfull \hbox (badness 10000) in paragraph at lines 1280--1284 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 predict_year_of_death(np.array([40, 50, 60]) , max_year=80) # returns something [18] [19] [20] [21] Overfull \hbox (1.49371pt too wide) in paragraph at lines 1876--1885 \TS1/txtt/m/n/10 `\T1/txtt/m/n/10 python laser_frame = LaserFrame(capacity=100) laser_frame.add_scalar_property(\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 age\TS1/txtt /m/n/10 '\T1/txtt/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1876--1885 \T1/txtt/m/n/10 dtype=np.int32, default=0) laser_frame.add_vector_property(\TS1 /txtt/m/n/10 '\T1/txtt/m/n/10 position\TS1/txtt/m/n/10 '\T1/txtt/m/n/10 , lengt h=3, Underfull \hbox (badness 10000) in paragraph at lines 1876--1885 \T1/txtt/m/n/10 dtype=np.float32, default=0.0) start, end = laser_frame.add(10) laser_frame.sort(np. Underfull \hbox (badness 10000) in paragraph at lines 1876--1885 \T1/txtt/m/n/10 arange(10)[::[]1]) laser_frame.squash(np.array([True, False, Tr ue, False, True, (/usr/share/texlive/texmf-dist/tex/latex/fontawesome5/ufontawesomefree1.fd) [22] [23] [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 2395--2397 \T1/txtt/m/n/10 row_sums = np.sum(competition_matrix, axis=1) [] np. Underfull \hbox (badness 10000) in paragraph at lines 2402--2404 \T1/txtt/m/n/10 network[i][j] = network[i][j] * (row_sums[i] [] competition_mat rix[i][j]) [26] [27] [28] [29] Underfull \hbox (badness 5302) in paragraph at lines 2917--2923 []\T1/qtm/m/n/10 ps = Prop-er-ty-Set({`mything': 0.4, `that_other_thing': 42}) print(ps.mything) # Out-puts: [30] [31] [32] [33] [34] ! LaTeX Error: Unicode character ≈ (U+2248) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.3588 ... in decimal degrees (default 0.08983 ≈ 10km at the equator). [35] [36] [37] Underfull \hbox (badness 5302) in paragraph at lines 4107--4113 []\T1/qtm/m/n/10 ps = Prop-er-ty-Set({`mything': 0.4, `that_other_thing': 42}) print(ps.mything) # Out-puts: [38] [39] [40] [41] [42] [43] [44] Chapter 6. [45] [46] [47] [48] Chapter 7. [49] [50] [51 <./Nigeria-2024.png>] [52 <./Nigeria-Sampled.png>] Chapter 8. [53] [54 <./Nigeria-NDD.png>] Chapter 9. [55] [56] [57] [58] Chapter 10. [59] [60] Underfull \vbox (badness 10000) detected at line 5629 Underfull \vbox (badness 10000) detected at line 5629 [61] Overfull \vbox (0.80812pt too high) detected at line 5676 [62] Overfull \vbox (0.80812pt too high) detected at line 5717 [63] [64] [65] [66] Chapter 11. [67] Underfull \vbox (badness 10000) detected at line 5981 [68] Underfull \vbox (badness 10000) detected at line 5981 Underfull \vbox (badness 10000) detected at line 5981 [69] [70] Underfull \vbox (badness 10000) detected at line 6073 Underfull \vbox (badness 10000) detected at line 6073 [71] [72] [73] [74] Underfull \vbox (badness 10000) detected at line 6290 Underfull \vbox (badness 10000) detected at line 6290 [75] [76] Chapter 12. [77] [78] Underfull \vbox (badness 7397) detected at line 6492 [79] Underfull \vbox (badness 10000) detected at line 6492 Underfull \vbox (badness 10000) detected at line 6492 [80] [81] [82] Chapter 13. [83] [84] Chapter 14. [85] [86] Chapter 15. 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[109] [110] [111] (./institute-for-disease-modeling-laser.ind [112] Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/txtt/m/n/10 __contains__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.pro pertyset.PropertySet Underfull \hbox (badness 10000) in paragraph at lines 17--19 []\T1/txtt/m/n/10 __getitem__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.prop ertyset.PropertySet Underfull \hbox (badness 10000) in paragraph at lines 20--22 []\T1/txtt/m/n/10 __iadd__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.propert yset.PropertySet Underfull \hbox (badness 10000) in paragraph at lines 23--25 []\T1/txtt/m/n/10 __ilshift__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.prop ertyset.PropertySet Underfull \hbox (badness 10000) in paragraph at lines 33--35 []\T1/txtt/m/n/10 __lshift__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.prope rtyset.PropertySet Underfull \hbox (badness 10000) in paragraph at lines 38--40 []\T1/txtt/m/n/10 __repr__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 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paragraph at lines 60--62 []\T1/txtt/m/n/10 alias \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.demographics .AliasedDistribution Overfull \hbox (16.2324pt too wide) in paragraph at lines 62--64 []\T1/txtt/m/n/10 alias \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.demographics .pyramid.AliasedDistribution Underfull \hbox (badness 10000) in paragraph at lines 64--65 []\T1/txtt/m/n/10 AliasedDistribution \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 65--67 []\T1/txtt/m/n/10 AliasedDistribution \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 78--80 []\T1/txtt/m/n/10 competing_destinations() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule Overfull \hbox (57.43222pt too wide) in paragraph at lines 86--88 []\T1/txtt/m/n/10 cumulative_deaths \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core. demographics.KaplanMeierEstimator [113] Overfull \hbox (108.47221pt too wide) in paragraph at lines 88--90 []\T1/txtt/m/n/10 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class in Underfull \hbox (badness 10000) in paragraph at lines 153--155 []\T1/txtt/m/n/10 load() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.propertyset .PropertySet static Underfull \hbox (badness 10000) in paragraph at lines 155--156 []\T1/txtt/m/n/10 load_pyramid_csv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 156--158 []\T1/txtt/m/n/10 load_pyramid_csv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 158--159 []\T1/txtt/m/n/10 load_snapshot() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.La serFrame class Underfull \hbox (badness 10000) in paragraph at lines 159--161 []\T1/txtt/m/n/10 load_snapshot() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.la serframe.LaserFrame Underfull \hbox (badness 10000) in paragraph at lines 183--185 []\T1/txtt/m/n/10 negative_binomial() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 196--198 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paragraph at lines 205--207 []\T1/txtt/m/n/10 probs \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.demographics .AliasedDistribution Overfull \hbox (16.2324pt too wide) in paragraph at lines 207--209 []\T1/txtt/m/n/10 probs \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.demographics .pyramid.AliasedDistribution Overfull \hbox (10.18236pt too wide) in paragraph at lines 222--224 []\T1/txtt/m/n/10 sample() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.demograph ics.KaplanMeierEstimator Overfull \hbox (61.22235pt too wide) in paragraph at lines 224--226 []\T1/txtt/m/n/10 sample() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.demograph ics.kmestimator.KaplanMeierEstimator Overfull \hbox (31.98236pt too wide) in paragraph at lines 226--228 []\T1/txtt/m/n/10 sample() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.demograph ics.pyramid.AliasedDistribution Underfull \hbox (badness 10000) in paragraph at lines 233--235 []\T1/txtt/m/n/10 save_snapshot() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.la serframe.LaserFrame Underfull \hbox (badness 10000) in paragraph at lines 249--251 []\T1/txtt/m/n/10 total \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.demographics .AliasedDistribution Overfull \hbox (16.2324pt too wide) in paragraph at lines 251--253 []\T1/txtt/m/n/10 total \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.demographics .pyramid.AliasedDistribution [115]) (./institute-for-disease-modeling-laser.aux) ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ts1.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/fontaw esome5/fa5free1.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} {/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb> Output written on institute-for-disease-modeling-laser.pdf (121 pages, 716727 b ytes). Transcript written on institute-for-disease-modeling-laser.log. Latexmk: Index file 'institute-for-disease-modeling-laser.idx' was written Latexmk: Log file says output to 'institute-for-disease-modeling-laser.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-laser.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 1 Refer to 'institute-for-disease-modeling-laser.log' for details Latexmk: Examining 'institute-for-disease-modeling-laser.log' === TeX engine is 'pdfTeX' Latexmk: Errors, in force_mode: so I tried finishing targets