Read the Docs build information Build id: 3552049 Project: institute-for-disease-modeling-laser Version: v0.8.0 Commit: f4e67e62f8750affc4c24ef70651416026e3d952 Date: 2025-11-25T22:08:36.254465Z State: finished Success: True [rtd-command-info] start-time: 2025-11-25T22:08:37.133507Z, end-time: 2025-11-25T22:08:37.880135Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/InstituteforDiseaseModeling/laser.git . Cloning into '.'... [rtd-command-info] start-time: 2025-11-25T22:08:37.960954Z, end-time: 2025-11-25T22:08:39.257883Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/tags/v0.8.0:refs/tags/v0.8.0 From https://github.com/InstituteforDiseaseModeling/laser * [new tag] v0.8.0 -> v0.8.0 * [new tag] v0.5.0 -> v0.5.0 * [new tag] v0.5.1 -> v0.5.1 * [new tag] v0.6.0 -> v0.6.0 * [new tag] v0.7.0 -> v0.7.0 [rtd-command-info] start-time: 2025-11-25T22:08:40.093594Z, end-time: 2025-11-25T22:08:40.141977Z, duration: 0, exit-code: 0 git checkout --force f4e67e62f8750affc4c24ef70651416026e3d952 Note: switching to 'f4e67e62f8750affc4c24ef70651416026e3d952'. 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 f4e67e6 Bump minor version 0.7.0 -> 0.8.0 [rtd-command-info] start-time: 2025-11-25T22:08:40.241518Z, end-time: 2025-11-25T22:08:40.282692Z, 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: 2025-11-25T22:08:45.158047Z, end-time: 2025-11-25T22:08:45.215035Z, duration: 0, exit-code: 0 asdf global python 3.13.3 [rtd-command-info] start-time: 2025-11-25T22:08:45.611097Z, end-time: 2025-11-25T22:08:46.333612Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.13.3.final.0-64 in 460ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.8.0, 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: 2025-11-25T22:08:46.429106Z, end-time: 2025-11-25T22:08:52.238137Z, duration: 5, 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-0.21.2 idna-3.11 imagesize-1.4.1 packaging-25.0 requests-2.32.5 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: 2025-11-25T22:08:59.561035Z, end-time: 2025-11-25T22:09:01.057834Z, duration: 1, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Requirement already satisfied: sphinx>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.8.0/lib/python3.13/site-packages (from -r 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(line 1)) (2025.11.12) Installing collected packages: sphinxcontrib-jquery, sphinx-rtd-theme Successfully installed sphinx-rtd-theme-3.0.2 sphinxcontrib-jquery-4.1 [rtd-command-info] start-time: 2025-11-25T22:09:01.146207Z, end-time: 2025-11-25T22:09:49.106783Z, duration: 47, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[test] Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Processing /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting click (from laser-core==0.8.0) Downloading 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directory: /tmp/pip-ephem-wheel-cache-vv5ddlmd/wheels/14/cc/f8/a6f83248520ece849edc79c0a766ee7f9f70f42504b5316ebe 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-7.12.0 cycler-0.12.1 fonttools-4.60.1 geopandas-1.1.1 h5py-3.15.1 iniconfig-2.3.0 kiwisolver-1.4.9 laser-core-0.8.0 llvmlite-0.45.1 matplotlib-3.10.7 numba-0.62.1 numpy-2.3.5 pandas-2.3.3 pillow-12.0.0 pluggy-1.6.0 pyogrio-0.11.1 pyparsing-3.2.5 pyproj-3.7.2 pytest-9.0.1 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-0.9.12 [rtd-command-info] start-time: 2025-11-25T22:09:49.252843Z, end-time: 2025-11-25T22:09:49.288181Z, 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 = "0.8.0" 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_report_timeouts_as_broken = False [rtd-command-info] start-time: 2025-11-25T22:09:49.374526Z, end-time: 2025-11-25T22:09:59.574738Z, duration: 10, 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/v0.8.0/lib/python3.13/site-packages/laser/core/migration.py:docstring of laser.core.migration:10: ERROR: Unexpected indentation. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.8.0/lib/python3.13/site-packages/laser/core/migration.py:docstring of laser.core.migration:11: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.8.0/lib/python3.13/site-packages/laser/core/migration.py:docstring of laser.core.migration:13: ERROR: Unexpected indentation. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.8.0/lib/python3.13/site-packages/laser/core/migration.py:docstring of laser.core.migration:14: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.8.0/lib/python3.13/site-packages/laser/core/migration.py:docstring of laser.core.migration:16: ERROR: Unexpected indentation. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.8.0/lib/python3.13/site-packages/laser/core/migration.py:docstring of laser.core.migration.gravity:31: WARNING: Inline literal start-string without end-string. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.8.0/lib/python3.13/site-packages/laser/core/migration.py:docstring of laser.core.migration.gravity:38: ERROR: Unexpected indentation. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.8.0/lib/python3.13/site-packages/laser/core/migration.py:docstring of laser.core.migration.gravity:41: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.8.0/lib/python3.13/site-packages/laser/core/migration.py:docstring of laser.core.migration.gravity:52: WARNING: Inline literal start-string without end-string. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.8.0/lib/python3.13/site-packages/laser/core/migration.py:docstring of laser.core.migration.gravity:52: WARNING: Inline interpreted text or phrase reference start-string without end-string. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.8.0/lib/python3.13/site-packages/laser/core/utils.py:docstring of laser.core.utils.calc_capacity:3: ERROR: Unexpected indentation. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/docs/source/laser.core.demographics.rst:8: WARNING: Title underline too short. laser.core.demographics.kmestimator module ------------------------------------ [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/docs/source/laser.core.demographics.rst:8: WARNING: Title underline too short. laser.core.demographics.kmestimator module ------------------------------------ [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/docs/source/laser.core.demographics.rst:16: WARNING: Title underline too short. laser.core.demographics.pyramid module -------------------------------- [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/docs/source/laser.core.demographics.rst:16: WARNING: Title underline too short. laser.core.demographics.pyramid module -------------------------------- [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/docs/source/laser.core.demographics.rst:24: WARNING: Title underline too short. laser.core.demographics.spatialpops module ------------------------------------ [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/docs/source/laser.core.demographics.rst:24: WARNING: Title underline too short. laser.core.demographics.spatialpops module ------------------------------------ [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.8.0/lib/python3.13/site-packages/laser/core/demographics/spatialpops.py:docstring of laser.core.demographics.spatialpops.distribute_population_skewed:25: WARNING: Bullet list ends without a blank line; unexpected unindent. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/envs/v0.8.0/lib/python3.13/site-packages/laser/core/demographics/spatialpops.py:docstring of laser.core.demographics.spatialpops.distribute_population_tapered:24: WARNING: Bullet list ends without a blank line; unexpected unindent. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/docs/source/modules.rst:2: WARNING: Title underline too short. laser.core ==== [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/v0.8.0/_readthedocs/html/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/_readthedocs/html/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/_readthedocs/html/_static/documentation_options.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/_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... [ 10%] laser.core.demographics.kmestimator highlighting module code... [ 20%] laser.core.demographics.pyramid highlighting module code... [ 30%] laser.core.demographics.spatialpops highlighting module code... [ 40%] laser.core.extension highlighting module code... [ 50%] laser.core.laserframe highlighting module code... [ 60%] laser.core.migration highlighting module code... [ 70%] laser.core.propertyset highlighting module code... [ 80%] laser.core.random highlighting module code... [ 90%] 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, 20 warnings. The HTML pages are in ../_readthedocs/html. [rtd-command-info] start-time: 2025-11-25T22:09:59.672374Z, end-time: 2025-11-25T22:10:08.712572Z, duration: 9, 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/v0.8.0/_readthedocs/htmlzip/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/_readthedocs/htmlzip/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/_readthedocs/htmlzip/_static/documentation_options.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/_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/v0.8.0/_readthedocs/htmlzip/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/_readthedocs/htmlzip/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/_readthedocs/htmlzip/_static/documentation_options.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/_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: 2025-11-25T22:10:09.039485Z, end-time: 2025-11-25T22:10:21.276223Z, 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/v0.8.0/_readthedocs/pdf/latexmkrc Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/_readthedocs/pdf/Makefile Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/_readthedocs/pdf/make.bat Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser/checkouts/v0.8.0/_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/v0.8.0/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/v0.8.0/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/v0.8.0/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/v0.8.0/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/v0.8.0/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/v0.8.0/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/v0.8.0/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/v0.8.0/README.rst:46: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/github/commits-since/InstituteforDiseaseModeling/laser/v0.8.0.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/v0.8.0/_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: 2025-11-25T22:10:23.137622Z, end-time: 2025-11-25T22:10:23.171531Z, 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: 2025-11-25T22:10:23.253413Z, end-time: 2025-11-25T22:10:39.709435Z, duration: 16, 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' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-laser" "laser.tex"' ------------ 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.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 ...c9fbab316843e7f6d91335ca088/v0.8.0}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 ...c9fbab316843e7f6d91335ca088/v0.8.0}.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] Overfull \hbox (12.99374pt too wide) in paragraph at lines 1081--1087 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 >>> from laser.core.demographics.spatialpops import distribute_population_tapered [17] Underfull \hbox (badness 10000) in paragraph at lines 1246--1250 \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 1284--1288 \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] Overfull \hbox (1.49371pt too wide) in paragraph at lines 1466--1475 \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 1466--1475 \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 1466--1475 \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 1466--1475 \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) [19] [20] [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1985--1987 \T1/txtt/m/n/10 row_sums = np.sum(competition_matrix, axis=1) [] np. Underfull \hbox (badness 10000) in paragraph at lines 1992--1994 \T1/txtt/m/n/10 network[i][j] = network[i][j] * (row_sums[i] [] competition_mat rix[i][j]) [23] [24] ! LaTeX Error: Unicode character ́ (U+0301) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2252 (Simini F, Gonza ́ lez MC, Maritan A, Baraba ́si AL. A universal mod... ! LaTeX Error: Unicode character ́ (U+0301) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2252 ... F, Gonza ́lez MC, Maritan A, Baraba ́ si AL. A universal model f... [25] [26] [27] [28] [29] [30] [31] [32] ! 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.3410 ... in decimal degrees (default 0.08983 ≈ 10km at the equator). [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] Chapter 6. [43] [44] [45] [46] Chapter 7. [47] [48] [49 <./Nigeria-2024.png>] [50 <./Nigeria-Sampled.png>] Chapter 8. [51] [52 <./Nigeria-NDD.png>] Chapter 9. [53] [54] [55] [56] Chapter 10. [57] [58] Underfull \vbox (badness 10000) detected at line 5386 Underfull \vbox (badness 10000) detected at line 5386 [59] Overfull \vbox (0.80812pt too high) detected at line 5433 [60] Overfull \vbox (0.80812pt too high) detected at line 5474 [61] [62] [63] [64] Chapter 11. [65] Underfull \vbox (badness 10000) detected at line 5738 [66] Underfull \vbox (badness 10000) detected at line 5738 Underfull \vbox (badness 10000) detected at line 5738 [67] [68] Underfull \vbox (badness 10000) detected at line 5830 Underfull \vbox (badness 10000) detected at line 5830 [69] [70] [71] [72] Underfull \vbox (badness 10000) detected at line 6047 Underfull \vbox (badness 10000) detected at line 6047 [73] [74] Chapter 12. [75] [76] Underfull \vbox (badness 7397) detected at line 6249 [77] Underfull \vbox (badness 10000) detected at line 6249 Underfull \vbox (badness 10000) detected at line 6249 [78] [79] [80] Chapter 13. [81] [82] Chapter 14. [83] [84] Chapter 15. [85] Underfull \vbox (badness 10000) detected at line 6648 Underfull \vbox (badness 10000) detected at line 6648 [86] Underfull \vbox (badness 10000) detected at line 6648 Underfull \vbox (badness 10000) detected at line 6648 [87] Underfull \vbox (badness 10000) detected at line 6648 Underfull \vbox (badness 10000) detected at line 6648 [88] [89] [90] Chapter 16. [91] [92] [93] [94] Chapter 17. [95] [96] [97] [98 <./workflow.png>] [99] [100] Chapter 18. [101] [102] Chapter 19. [103] [104] Chapter 20. [105] [106] Chapter 21. [107] [108] LaTeX Warning: Reference `source/laser.core:module-laser.core' on page 109 unde fined on input line 7545. LaTeX Warning: Reference `source/laser.core:module-laser.core.cli' on page 109 undefined on input line 7546. LaTeX Warning: Reference `source/laser.core.demographics:module-laser.core.demo graphics' on page 109 undefined on input line 7547. LaTeX Warning: Reference `source/laser.core.demographics:module-laser.core.demo graphics.kmestimator' on page 109 undefined on input line 7548. LaTeX Warning: Reference `source/laser.core.demographics:module-laser.core.demo graphics.pyramid' on page 109 undefined on input line 7549. LaTeX Warning: Reference `source/laser.core.demographics:module-laser.core.demo graphics.spatialpops' on page 109 undefined on input line 7550. LaTeX Warning: Reference `source/laser.core:module-laser.core.extension' on pag e 109 undefined on input line 7551. LaTeX Warning: Reference `source/laser.core:module-laser.core.laserframe' on pa ge 109 undefined on input line 7552. LaTeX Warning: Reference `source/laser.core:module-laser.core.migration' on pag e 109 undefined on input line 7553. LaTeX Warning: Reference `source/laser.core:module-laser.core.propertyset' on p age 109 undefined on input line 7554. LaTeX Warning: Reference `source/laser.core:module-laser.core.random' on page 1 09 undefined on input line 7555. LaTeX Warning: Reference `source/laser.core:module-laser.core.sortedqueue' on p age 109 undefined on input line 7556. LaTeX Warning: Reference `source/laser.core:module-laser.core.utils' on page 10 9 undefined on input line 7557. [109] 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/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts 1.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}{/usr/share/texlive/t exmf-dist/fonts/enc/dvips/fontawesome5/fa5free1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb> Output written on institute-for-disease-modeling-laser.pdf (113 pages, 700110 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 109 undefined on input line 7547 Reference `source/laser.core.demographics:module-laser.core.demographics.kmestimator' on page 109 undefined on input line 7548 Reference `source/laser.core.demographics:module-laser.core.demographics.pyramid' on page 109 undefined on input line 7549 Reference `source/laser.core.demographics:module-laser.core.demographics.spatialpops' on page 109 undefined on input line 7550 Reference `source/laser.core:module-laser.core' on page 109 undefined on input line 7545 Reference `source/laser.core:module-laser.core.cli' on page 109 undefined on input line 7546 Reference `source/laser.core:module-laser.core.extension' on page 109 undefined on input line 7551 Reference `source/laser.core:module-laser.core.laserframe' on page 109 undefined on input line 7552 Reference `source/laser.core:module-laser.core.migration' on page 109 undefined on input line 7553 Reference `source/laser.core:module-laser.core.propertyset' on page 109 undefined on input line 7554 Reference `source/laser.core:module-laser.core.random' on page 109 undefined on input line 7555 Reference `source/laser.core:module-laser.core.sortedqueue' on page 109 undefined on input line 7556 Reference `source/laser.core:module-laser.core.utils' on page 109 undefined on input line 7557 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 (140 entries accepted, 0 rejected). Sorting entries....done (1036 comparisons). Generating output file institute-for-disease-modeling-laser.ind....done (237 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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(/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] Overfull \hbox (12.99374pt too wide) in paragraph at lines 1081--1087 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 >>> from laser.core.demographics.spatialpops import distribute_population_tapered [17] Underfull \hbox (badness 10000) in paragraph at lines 1246--1250 \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 1284--1288 \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] Overfull \hbox (1.49371pt too wide) in paragraph at lines 1466--1475 \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 1466--1475 \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 1466--1475 \T1/txtt/m/n/10 dtype=np.float32, default=0.0) start, end = laser_frame.add(10) laser_frame.sort(np. 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F, Gonza ́lez MC, Maritan A, Baraba ́ si AL. A universal model f... [25] [26] [27] [28] [29] [30] [31] [32] ! 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.3410 ... in decimal degrees (default 0.08983 ≈ 10km at the equator). [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] Chapter 6. [43] [44] [45] [46] Chapter 7. [47] [48] [49 <./Nigeria-2024.png>] [50 <./Nigeria-Sampled.png>] Chapter 8. [51] [52 <./Nigeria-NDD.png>] Chapter 9. [53] [54] [55] [56] Chapter 10. [57] [58] Underfull \vbox (badness 10000) detected at line 5386 Underfull \vbox (badness 10000) detected at line 5386 [59] Overfull \vbox (0.80812pt too high) detected at line 5433 [60] Overfull \vbox (0.80812pt too high) detected at line 5474 [61] [62] [63] [64] 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/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts 1.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}{/usr/share/texlive/t exmf-dist/fonts/enc/dvips/fontawesome5/fa5free1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb> Output written on institute-for-disease-modeling-laser.pdf (119 pages, 728922 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 ...c9fbab316843e7f6d91335ca088/v0.8.0}.svg}} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 ...c9fbab316843e7f6d91335ca088/v0.8.0}.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] Overfull \hbox (12.99374pt too wide) in paragraph at lines 1081--1087 \TS1/txtt/m/n/10 ` \T1/txtt/m/n/10 >>> from laser.core.demographics.spatialpops import distribute_population_tapered [17] Underfull \hbox (badness 10000) in paragraph at lines 1246--1250 \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 1284--1288 \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] Overfull \hbox (1.49371pt too wide) in paragraph at lines 1466--1475 \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 1466--1475 \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 1466--1475 \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 1466--1475 \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) [19] [20] [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1985--1987 \T1/txtt/m/n/10 row_sums = np.sum(competition_matrix, axis=1) [] np. Underfull \hbox (badness 10000) in paragraph at lines 1992--1994 \T1/txtt/m/n/10 network[i][j] = network[i][j] * (row_sums[i] [] competition_mat rix[i][j]) [23] [24] ! LaTeX Error: Unicode character ́ (U+0301) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2252 (Simini F, Gonza ́ lez MC, Maritan A, Baraba ́si AL. A universal mod... ! LaTeX Error: Unicode character ́ (U+0301) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2252 ... F, Gonza ́lez MC, Maritan A, Baraba ́ si AL. A universal model f... [25] [26] [27] [28] [29] [30] [31] [32] ! 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.3410 ... in decimal degrees (default 0.08983 ≈ 10km at the equator). [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] Chapter 6. [43] [44] [45] [46] Chapter 7. [47] [48] [49 <./Nigeria-2024.png>] [50 <./Nigeria-Sampled.png>] Chapter 8. [51] [52 <./Nigeria-NDD.png>] Chapter 9. [53] [54] [55] [56] Chapter 10. [57] [58] Underfull \vbox (badness 10000) detected at line 5386 Underfull \vbox (badness 10000) detected at line 5386 [59] Overfull \vbox (0.80812pt too high) detected at line 5433 [60] Overfull \vbox (0.80812pt too high) detected at line 5474 [61] [62] [63] [64] Chapter 11. [65] Underfull \vbox (badness 10000) detected at line 5738 [66] Underfull \vbox (badness 10000) detected at line 5738 Underfull \vbox (badness 10000) detected at line 5738 [67] [68] Underfull \vbox (badness 10000) detected at line 5830 Underfull \vbox (badness 10000) detected at line 5830 [69] [70] [71] [72] Underfull \vbox (badness 10000) detected at line 6047 Underfull \vbox (badness 10000) detected at line 6047 [73] [74] Chapter 12. [75] [76] Underfull \vbox (badness 7397) detected at line 6249 [77] Underfull \vbox (badness 10000) detected at line 6249 Underfull \vbox (badness 10000) detected at line 6249 [78] [79] [80] Chapter 13. [81] [82] Chapter 14. [83] [84] Chapter 15. [85] Underfull \vbox (badness 10000) detected at line 6648 Underfull \vbox (badness 10000) detected at line 6648 [86] Underfull \vbox (badness 10000) detected at line 6648 Underfull \vbox (badness 10000) detected at line 6648 [87] Underfull \vbox (badness 10000) detected at line 6648 Underfull \vbox (badness 10000) detected at line 6648 [88] [89] [90] Chapter 16. [91] [92] [93] [94] Chapter 17. [95] [96] [97] [98 <./workflow.png>] [99] [100] Chapter 18. [101] [102] Chapter 19. [103] [104] Chapter 20. [105] [106] Chapter 21. [107] [108] [109] (./institute-for-disease-modeling-laser.ind [110] 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 32--34 []\T1/txtt/m/n/10 __len__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.sortedqu eue.SortedQueue Underfull \hbox (badness 10000) in paragraph at lines 35--37 []\T1/txtt/m/n/10 __lshift__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 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laser.c ore.LaserFrame Underfull \hbox (badness 10000) in paragraph at lines 60--62 []\T1/txtt/m/n/10 add_vector_property() Underfull \hbox (badness 10000) 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 .AliasedDistribution Overfull \hbox (16.2324pt too wide) in paragraph at lines 64--66 []\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 66--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 67--69 []\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 75--77 []\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 81--83 []\T1/txtt/m/n/10 cumulative_deaths 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\T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 139--141 []\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 141--142 []\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 142--144 []\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 144--145 []\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 145--147 []\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 5161) in paragraph at lines 174--175 []\T1/txtt/m/n/10 popi() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.sortedqueue .SortedQueue method\T1/qtm/m/n/10 ), Underfull \hbox (badness 5161) in paragraph at lines 178--179 []\T1/txtt/m/n/10 popv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.sortedqueue .SortedQueue method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 179--181 []\T1/txtt/m/n/10 predict_age_at_death() Overfull \hbox (6.51248pt too wide) in paragraph at lines 179--181 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.demographics.KaplanMeierEstimator Underfull \hbox (badness 10000) in paragraph at lines 181--183 []\T1/txtt/m/n/10 predict_age_at_death() Overfull \hbox (57.55247pt too wide) in paragraph at lines 181--183 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.demographics.kmestimator.KaplanMeier Estimator Underfull \hbox (badness 10000) in paragraph at lines 183--185 []\T1/txtt/m/n/10 predict_year_of_death() Overfull \hbox (6.51248pt too wide) in paragraph at lines 183--185 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.demographics.KaplanMeierEstimator Underfull \hbox (badness 10000) in paragraph at lines 185--187 []\T1/txtt/m/n/10 predict_year_of_death() Overfull \hbox (57.55247pt too wide) in paragraph at lines 185--187 \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.demographics.kmestimator.KaplanMeier Estimator [112] Underfull \hbox (badness 10000) in paragraph at lines 188--190 []\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 190--192 []\T1/txtt/m/n/10 probs \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.demographics .pyramid.AliasedDistribution Underfull \hbox (badness 5161) in paragraph at lines 195--196 []\T1/txtt/m/n/10 push() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.sortedqueue .SortedQueue method\T1/qtm/m/n/10 ), Overfull \hbox (10.18236pt too wide) in paragraph at lines 206--208 []\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 208--210 []\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 210--212 []\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 215--217 []\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 232--234 []\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 234--236 []\T1/txtt/m/n/10 total \T1/qtm/m/n/10 (\T1/qtm/m/it/10 laser.core.demographics .pyramid.AliasedDistribution [113]) (./institute-for-disease-modeling-laser.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts 1.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}{/usr/share/texlive/t exmf-dist/fonts/enc/dvips/fontawesome5/fa5free1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb> Output written on institute-for-disease-modeling-laser.pdf (119 pages, 729073 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