Read the Docs build information Build id: 2823112 Project: institute-for-disease-modeling-synthpops-test Version: latest Commit: 5cbb07f6931960d79cced508d135248bc84360d9 Date: 2025-02-20T16:59:55.711516Z State: finished Success: True [rtd-command-info] start-time: 2025-02-20T16:59:56.746965Z, end-time: 2025-02-20T16:59:57.333881Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/InstituteforDiseaseModeling/synthpops.git . Cloning into '.'... [rtd-command-info] start-time: 2025-02-20T16:59:57.399469Z, end-time: 2025-02-20T16:59:58.594390Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main From https://github.com/InstituteforDiseaseModeling/synthpops * [new tag] v1.7.5 -> v1.7.5 * [new tag] v1.7.6 -> v1.7.6 * [new tag] v1.7.7 -> v1.7.7 * [new tag] v1.8.0 -> v1.8.0 * [new tag] v1.8.1 -> v1.8.1 * [new tag] v1.8.2 -> v1.8.2 * [new tag] v1.8.3 -> v1.8.3 * [new tag] v1.8.4 -> v1.8.4 * [new tag] v1.9.0 -> v1.9.0 [rtd-command-info] start-time: 2025-02-20T16:59:58.714672Z, end-time: 2025-02-20T16:59:58.792526Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: switching to 'origin/main'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. 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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 5cbb07f add gitignore [rtd-command-info] start-time: 2025-02-20T16:59:58.861267Z, end-time: 2025-02-20T16:59:58.910280Z, duration: 0, exit-code: 0 cat .readthedocs.yml # .readthedocs.yaml # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details # Required version: 2 # Set the version of Python and other tools you might need build: os: ubuntu-22.04 tools: python: "3.11" # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py # If using Sphinx, optionally build your docs in additional formats such as PDF #formats: # - htmlzip # Optionally declare the Python requirements required to build your docs python: install: - requirements: docs/requirements.txt - method: pip path: . [rtd-command-info] start-time: 2025-02-20T17:00:03.575665Z, end-time: 2025-02-20T17:00:03.627454Z, duration: 0, exit-code: 0 asdf global python 3.11.10 [rtd-command-info] start-time: 2025-02-20T17:00:03.954690Z, end-time: 2025-02-20T17:00:04.752094Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.11.10.final.0-64 in 539ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2025-02-20T17:00:04.828082Z, end-time: 2025-02-20T17:00:13.223447Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.11/site-packages (23.1) Collecting pip Downloading pip-25.0.1-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 9.4 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.11/site-packages (67.6.1) Collecting setuptools Downloading setuptools-75.8.0-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 20.7 MB/s eta 0:00:00 Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 67.6.1 Uninstalling setuptools-67.6.1: Successfully uninstalled setuptools-67.6.1 Attempting uninstall: pip Found existing installation: pip 23.1 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alabaster, requests, Jinja2, sphinx Successfully installed Jinja2-3.1.5 MarkupSafe-3.0.2 Pygments-2.19.1 alabaster-1.0.0 babel-2.17.0 certifi-2025.1.31 charset-normalizer-3.4.1 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-24.2 requests-2.32.3 roman-numerals-py-3.0.0 snowballstemmer-2.2.0 sphinx-8.2.0 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 urllib3-2.3.0 [rtd-command-info] start-time: 2025-02-20T17:00:18.365372Z, end-time: 2025-02-20T17:00:20.752431Z, duration: 2, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting pandoc (from -r docs/requirements.txt (line 1)) Downloading pandoc-2.4.tar.gz (34 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pypandoc (from -r docs/requirements.txt (line 2)) Downloading 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soupsieve-2.6-py3-none-any.whl (36 kB) Building wheels for collected packages: pandoc Building wheel for pandoc (setup.py): started Building wheel for pandoc (setup.py): finished with status 'done' Created wheel for pandoc: filename=pandoc-2.4-py3-none-any.whl size=34843 sha256=5c60a68d88be140675c03f5b39db452aff66b67df13ec90e8fb17e8ea48a812b Stored in directory: /tmp/pip-ephem-wheel-cache-gtgwtdlj/wheels/4f/d7/32/c6c9b7b05e852e920fd72174487be3a0f18e633a7adcc303be Successfully built pandoc Installing collected packages: ply, typing-extensions, soupsieve, six, readthedocs-sphinx-search, pypandoc, plumbum, accessible-pygments, pockets, plantweb, pandoc, beautifulsoup4, sphinxcontrib-napoleon, sphinx-design, sphinx-autodoc-typehints, pydata-sphinx-theme Successfully installed accessible-pygments-0.0.5 beautifulsoup4-4.13.3 pandoc-2.4 plantweb-1.3.0 plumbum-1.9.0 ply-3.11 pockets-0.9.1 pydata-sphinx-theme-0.16.1 pypandoc-1.15 readthedocs-sphinx-search-0.3.2 six-1.17.0 soupsieve-2.6 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Downloading gitdb-4.0.12-py3-none-any.whl (62 kB) Downloading et_xmlfile-2.0.0-py3-none-any.whl (18 kB) Downloading smmap-5.0.2-py3-none-any.whl (24 kB) Building wheels for collected packages: synthpops, jsonobject Building wheel for synthpops (setup.py): started Building wheel for synthpops (setup.py): finished with status 'done' Created wheel for synthpops: filename=synthpops-1.10.5-py3-none-any.whl size=1526980 sha256=e24c0179d03f13cb24f9cda4112fe60dff22152de8429470159239c268ff1854 Stored in directory: /tmp/pip-ephem-wheel-cache-0s1_jm88/wheels/55/96/a1/ff11c0227cb951974ca9d276ac81d2620b7907a3b2a1712829 Building wheel for jsonobject (setup.py): started Building wheel for jsonobject (setup.py): finished with status 'done' Created wheel for jsonobject: filename=jsonobject-2.2.0-cp311-cp311-linux_x86_64.whl size=1842194 sha256=1f167b193f9576b082d3c5976030f713ea9239726b172b84844c0c8d5fdc4a7d Stored in directory: /tmp/pip-ephem-wheel-cache-0s1_jm88/wheels/a4/a1/47/6c325aee0ec8b0352ef0ff9a5bbd72a3e6ba6da43cd8646661 Successfully built synthpops jsonobject Installing collected packages: pytz, jsonobject, editorconfig, zstandard, xlsxwriter, tzdata, tqdm, smmap, pyyaml, python-dateutil, pyparsing, psutil, pillow, numpy, networkx, llvmlite, line-profiler, kiwisolver, jsonpickle, jsbeautifier, jellyfish, graphviz, fonttools, et-xmlfile, dill, cycler, scipy, pydot, pandas, openpyxl, numba, multiprocess, memory-profiler, gitdb, contourpy, colorspacious, matplotlib, gitpython, seaborn, sciris, cmocean, cmasher, synthpops Successfully installed cmasher-1.9.2 cmocean-4.0.3 colorspacious-1.1.2 contourpy-1.3.1 cycler-0.12.1 dill-0.3.9 editorconfig-0.17.0 et-xmlfile-2.0.0 fonttools-4.56.0 gitdb-4.0.12 gitpython-3.1.44 graphviz-0.20.3 jellyfish-1.1.3 jsbeautifier-1.15.3 jsonobject-2.2.0 jsonpickle-4.0.2 kiwisolver-1.4.8 line-profiler-4.2.0 llvmlite-0.44.0 matplotlib-3.10.0 memory-profiler-0.61.0 multiprocess-0.70.17 networkx-3.4.2 numba-0.61.0 numpy-2.1.3 openpyxl-3.1.5 pandas-2.2.3 pillow-11.1.0 psutil-7.0.0 pydot-3.0.4 pyparsing-3.2.1 python-dateutil-2.9.0.post0 pytz-2025.1 pyyaml-6.0.2 scipy-1.15.2 sciris-3.2.0 seaborn-0.13.2 smmap-5.0.2 synthpops-1.10.5 tqdm-4.67.1 tzdata-2025.1 xlsxwriter-3.2.2 zstandard-0.23.0 [rtd-command-info] start-time: 2025-02-20T17:01:00.837760Z, end-time: 2025-02-20T17:01:00.886403Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Configuration file for the Sphinx documentation builder. import os import sys import synthpops as sp on_rtd = os.environ.get('READTHEDOCS') == 'True' # -- Project information ----------------------------------------------------- project = 'SynthPops' copyright = f'2020 - 2021, Institute for Disease Modeling. All rights reserved.\nThese docs were built for SynthPops version {sp.__version__}.\n' author = 'Institute for Disease Modeling' # The short X.Y version version = sp.__version__ # The full version, including alpha/beta/rc tags release = sp.__version__ # -- General configuration --------------------------------------------------- # Add any Sphinx extension module names here extensions = [ "sphinx.ext.autodoc", # Core Sphinx library for auto html doc generation from docstrings "sphinx.ext.autosummary", # Create neat summary tables for modules/classes/methods etc -- causes warnings with Napoleon however "sphinx.ext.intersphinx", "sphinx.ext.viewcode", # Add a link to the Python source code for classes, functions etc. "sphinx.ext.napoleon", "sphinx.ext.autosectionlabel", "sphinx_autodoc_typehints", # Automatically document param types (less noise in class signature) "sphinx_design", # Add e.g. grid layout 'sphinx_search.extension', # search across multiple docsets in domain ] # Use Google docstrings napoleon_google_docstring = True # Configure autosummary autosummary_generate = True # Turn on sphinx.ext.autosummary autosummary_ignore_module_all = False # Respect __all__ autodoc_member_order = 'bysource' # Keep original ordering add_module_names = False # NB, does not work autodoc_inherit_docstrings = False # Stops sublcasses from including docs from parent classes # Add any paths that contain templates here, relative to this directory. templates_path = ["_templates"] # Syntax highlighting style pygments_style = "sphinx" modindex_common_prefix = ["synthpops."] # List of patterns, relative to source directory, to exclude exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"] # Suppress certain warnings suppress_warnings = ['autosectionlabel.*'] # Add variable substitutions rst_epilog = "\n.. include:: /variables.txt" # -- Options for HTML output ------------------------------------------------- html_theme = "pydata_sphinx_theme" html_theme_options = { "collapse_navigation": False, "navigation_depth": 3, "show_prev_next": True, "icon_links": [ {"name": "Web", "url": "https://synthpops.org", "icon": "fas fa-home"}, { "name": "GitHub", "url": "https://github.com/synthpops/synthpops", "icon": "fab fa-github-square", }, ], "navbar_end": ["theme-switcher", "navbar-icon-links"], "secondary_sidebar_items": ["navbar-side"], "header_links_before_dropdown": 5, "footer_start": ["copyright", "footer_start"], "footer_end": ["theme-version", "footer_end"], } html_sidebars = { "**": ["sidebar-nav-bs", "page-toc"], } html_logo = "images/IDM_white.png" html_favicon = "images/favicon.ico" html_static_path = ['_static'] html_context = { 'rtd_url': 'https://docs.idmod.org/projects/synthpops/en/latest', "versions_dropdown": { "latest": "devel (latest)", "stable": "current (stable)", }, "default_mode": "light", } # Add any extra paths that contain custom files if not on_rtd: html_extra_path = ['robots.txt'] # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. html_last_updated_fmt = '%Y-%b-%d' html_show_sourcelink = True html_show_sphinx = False html_copy_source = False htmlhelp_basename = 'SynthPops' # Add customizations def setup(app): app.add_css_file("theme_overrides.css") # OpenSearch options html_use_opensearch = 'docs.idmod.org/projects/synthpops/en/latest' # -- RTD Sphinx search for searching across the entire domain, default child ------------- if os.environ.get('READTHEDOCS') == 'True': search_project_parent = "institute-for-disease-modeling-idm" search_project = os.environ["READTHEDOCS_PROJECT"] search_version = os.environ["READTHEDOCS_VERSION"] rtd_sphinx_search_default_filter = f"subprojects:{search_project}/{search_version}" rtd_sphinx_search_filters = { "Search this project": f"project:{search_project}/{search_version}", "Search all IDM docs": f"subprojects:{search_project_parent}/{search_version}", } [rtd-command-info] start-time: 2025-02-20T17:01:00.953453Z, end-time: 2025-02-20T17:01:31.600277Z, duration: 30, exit-code: 0 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v8.2.0 loading translations [en]... done making output directory... done [autosummary] generating autosummary for: algorithm.rst, api/index.rst, glossary.rst, households.rst, index.rst, input_data.rst, installation.rst, overview.rst, schools.rst, usage.rst, whatsnew.rst, workplaces.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.base.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.config.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.contact_networks.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.data.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.data_distributions.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.defaults.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.households.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.ltcfs.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.plotting.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.pop.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.sampling.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.schools.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.workplaces.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.base.LayerGroup.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.base.binned_values_dist.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.base.count_ages.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.base.count_binned_values.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.base.count_values.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.base.get_age_by_brackets.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.base.get_aggregate_ages.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.base.get_aggregate_matrix.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.base.get_asymmetric_matrix.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.base.get_bin_edges.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.schools.get_school_type_labels.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.workplaces.Workplace.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.workplaces.add_workplace.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.workplaces.count_employment_by_age.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.workplaces.get_employment_rates_by_age.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.workplaces.get_generated_workplace_size_distribution.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.workplaces.get_workplace.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.workplaces.get_workplace_sizes.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.workplaces.initialize_empty_workplaces.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/docs/api/_autosummary/synthpops.workplaces.populate_workplaces.rst building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 12 source files that are out of date updating environment: [new config] 205 added, 0 changed, 0 removed reading sources... [ 0%] algorithm reading sources... [ 1%] api/_autosummary/synthpops.base reading sources... [ 1%] api/_autosummary/synthpops.base.LayerGroup reading sources... [ 2%] api/_autosummary/synthpops.base.binned_values_dist reading sources... [ 2%] api/_autosummary/synthpops.base.count_ages reading sources... [ 3%] api/_autosummary/synthpops.base.count_binned_values reading sources... [ 3%] api/_autosummary/synthpops.base.count_values reading sources... [ 4%] api/_autosummary/synthpops.base.get_age_by_brackets reading sources... [ 4%] api/_autosummary/synthpops.base.get_aggregate_ages reading sources... [ 5%] api/_autosummary/synthpops.base.get_aggregate_matrix reading sources... [ 5%] api/_autosummary/synthpops.base.get_asymmetric_matrix reading sources... [ 6%] api/_autosummary/synthpops.base.get_bin_edges reading sources... [ 6%] api/_autosummary/synthpops.base.get_bin_labels reading sources... [ 7%] api/_autosummary/synthpops.base.get_ids_by_age reading sources... 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