Read the Docs build information Build id: 2087241 Project: institute-for-disease-modeling-starsim Version: latest Commit: 0f94497964799b63436989a592279bce675a6274 Date: 2024-03-15T04:12:06.743456Z State: finished Success: True [rtd-command-info] start-time: 2024-03-15T04:12:07.843493Z, end-time: 2024-03-15T04:12:08.409169Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/starsimhub/starsim.git . Cloning into '.'... [rtd-command-info] start-time: 2024-03-15T04:12:08.477666Z, end-time: 2024-03-15T04:12:09.582546Z, 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/starsimhub/starsim * [new tag] v0.1.6 -> v0.1.6 [rtd-command-info] start-time: 2024-03-15T04:12:09.703985Z, end-time: 2024-03-15T04:12:09.770818Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: switching to 'origin/main'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 0f94497 Merge branch 'main' of https://github.com/starsimhub/starsim [rtd-command-info] start-time: 2024-03-15T04:12:09.843049Z, end-time: 2024-03-15T04:12:09.898930Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2024-03-15T04:12:09.964727Z, end-time: 2024-03-15T04:12:10.025760Z, duration: 0, exit-code: 0 cat .readthedocs.yaml # .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: 2024-03-15T04:12:16.126776Z, end-time: 2024-03-15T04:12:16.209073Z, duration: 0, exit-code: 0 asdf global python 3.11.6 [rtd-command-info] start-time: 2024-03-15T04:12:16.628412Z, end-time: 2024-03-15T04:12:17.718671Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.11.6.final.0-64 in 790ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/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: 2024-03-15T04:12:17.784853Z, end-time: 2024-03-15T04:12:30.349507Z, duration: 12, exit-code: 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readthedocs-sphinx-ext Successfully installed Jinja2-3.1.3 MarkupSafe-2.1.5 Pygments-2.17.2 alabaster-0.7.16 babel-2.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.6 imagesize-1.4.1 packaging-24.0 readthedocs-sphinx-ext-2.2.5 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.8 sphinxcontrib-devhelp-1.0.6 sphinxcontrib-htmlhelp-2.0.5 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.7 sphinxcontrib-serializinghtml-1.1.10 urllib3-2.2.1 [rtd-command-info] start-time: 2024-03-15T04:12:37.534123Z, end-time: 2024-03-15T04:13:07.973369Z, duration: 30, 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-2.3.tar.gz (33 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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(setup.py): finished with status 'done' Created wheel for pandoc: filename=pandoc-2.3-py3-none-any.whl size=33262 sha256=f81c62ef49747aae17a70e8265c28f8c424cd6427781be89a0ddbde02db66644 Stored in directory: /tmp/pip-ephem-wheel-cache-aoxl54pt/wheels/1c/a9/c4/6254542c4e8202d52fcd69798d2507aaad1f2a4bb60f2f0fea Successfully built pandoc Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, ply, fastjsonschema, tzdata, typing-extensions, traitlets, tqdm, tornado, tinycss2, soupsieve, six, rpds-py, readthedocs-sphinx-search, pyzmq, PyYAML, pyparsing, pypandoc, psutil, prompt-toolkit, plumbum, platformdirs, pillow, pexpect, parso, pandocfilters, numpy, nest-asyncio, mistune, Mako, kiwisolver, jupyterlab-pygments, greenlet, fonttools, executing, defusedxml, decorator, debugpy, cycler, colorlog, attrs, accessible-pygments, sqlalchemy, referencing, python-dateutil, plantweb, pandoc, matplotlib-inline, jupyter-core, jedi, contourpy, comm, bleach, beautifulsoup4, asttokens, stack-data, sphinx-design, sphinx-autodoc-typehints, pydata-sphinx-theme, pandas, matplotlib, jupyter-client, jsonschema-specifications, alembic, seaborn, optuna, jsonschema, ipython, nbformat, ipykernel, nbclient, nbconvert, nbsphinx Successfully installed Mako-1.3.2 PyYAML-6.0.1 accessible-pygments-0.0.4 alembic-1.13.1 asttokens-2.4.1 attrs-23.2.0 beautifulsoup4-4.12.3 bleach-6.1.0 colorlog-6.8.2 comm-0.2.2 contourpy-1.2.0 cycler-0.12.1 debugpy-1.8.1 decorator-5.1.1 defusedxml-0.7.1 executing-2.0.1 fastjsonschema-2.19.1 fonttools-4.49.0 greenlet-3.0.3 ipykernel-6.29.3 ipython-8.22.2 jedi-0.19.1 jsonschema-4.21.1 jsonschema-specifications-2023.12.1 jupyter-client-8.6.1 jupyter-core-5.7.2 jupyterlab-pygments-0.3.0 kiwisolver-1.4.5 matplotlib-3.8.3 matplotlib-inline-0.1.6 mistune-3.0.2 nbclient-0.10.0 nbconvert-7.13.0 nbformat-5.10.2 nbsphinx-0.9.3 nest-asyncio-1.6.0 numpy-1.26.4 optuna-3.5.0 pandas-2.2.1 pandoc-2.3 pandocfilters-1.5.1 parso-0.8.3 pexpect-4.9.0 pillow-10.2.0 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et-xmlfile, dill, openpyxl, numba, multiprocess, gitdb, gitpython, sciris, starsim Successfully installed dill-0.3.8 et-xmlfile-1.1.0 gitdb-4.0.11 gitpython-3.1.42 jellyfish-1.0.3 jsonpickle-3.0.3 line-profiler-4.1.2 llvmlite-0.42.0 memory-profiler-0.61.0 multiprocess-0.70.16 networkx-3.2.1 numba-0.59.0 openpyxl-3.1.2 scipy-1.12.0 sciris-3.1.4 smmap-5.0.1 starsim-0.2.8 xlsxwriter-3.2.0 zstandard-0.22.0 [rtd-command-info] start-time: 2024-03-15T04:13:25.225260Z, end-time: 2024-03-15T04:13:25.283049Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Configuration file for the Sphinx documentation builder. import os import sys import sciris as sc import starsim as ss # Set environment os.environ['SPHINX_BUILD'] = 'True' # This is used so ss.options.set('jupyter') doesn't reset the Matplotlib renderer on_rtd = os.environ.get('READTHEDOCS') == 'True' # -- Project information ----------------------------------------------------- project = 'Starsim' copyright = f'2023 - {sc.now().year}, Bill & Melinda Gates Foundation. All rights reserved. These docs were built for Starsim v{ss.__version__}' author = 'Starsim Collective' # The short X.Y version version = ss.__version__ # The full version, including alpha/beta/rc tags release = ss.__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 "nbsphinx", ] # 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 = ["starsim."] # List of patterns, relative to source directory, to exclude exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"] # Suppress certain warnings suppress_warnings = ['autosectionlabel.*'] # -- 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://starsim.org", "icon": "fas fa-home"}, { "name": "GitHub", "url": "https://github.com/starsimhub/starsim", "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-logo-transparent.png" html_favicon = "images/favicon.ico" html_static_path = ['_static'] html_baseurl = "https://docs.idmod.org/projects/starsim/en/latest" html_context = { 'rtd_url': 'https://docs.idmod.org/projects/starsim/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 = 'Starsim' # Add customizations def setup(app): app.add_css_file("theme_overrides.css") # Modify this to not rerun the Jupyter notebook cells -- usually set by build_docs nb_ex_default = ['auto', 'never'][0] nb_ex = os.getenv('NBSPHINX_EXECUTE') if not nb_ex: nb_ex = nb_ex_default print(f'\n\nBuilding Jupyter notebooks with build option: {nb_ex}\n\n') nbsphinx_execute = nb_ex # OpenSearch options html_use_opensearch = 'docs.idmod.org/projects/starsim/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}", } ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Define this variable in case it's not defined by the user. # It defaults to `alabaster` which is the default from Sphinx. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme html_theme = globals().get('html_theme', 'alabaster') #Add project information to the template context. context = { 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-starsim', 'name': u'starsim', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': '', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'starsimhub', 'proxied_api_host': '/_', 'github_repo': 'starsim', 'github_version': 'main', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'main', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'main', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '0f944979', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): for key in context: if key not in html_context: html_context[key] = context[key] else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-starsim/builds/2087241/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2024-03-15T04:13:25.343939Z, end-time: 2024-03-15T04:15:50.770260Z, duration: 145, exit-code: 0 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v7.2.6 Matplotlib is building the font cache; this may take a moment. Starsim 0.2.8 (2024-03-13) — © 2023-2024 by IDM Building Jupyter notebooks with build option: auto making output directory... done [autosummary] generating autosummary for: api/index.rst, conduct.rst, contributing.rst, index.rst, tutorials.rst, tutorials/README.rst, tutorials/dev_tut_diseases.ipynb, tutorials/tut_buildsim.ipynb, tutorials/tut_demographics.ipynb, tutorials/tut_diseases.ipynb, tutorials/tut_interventions.ipynb, tutorials/tut_intro.ipynb, tutorials/tut_networks.ipynb, whatsnew.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.connectors.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.demographics.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.disease.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.distributions.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.interventions.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.modules.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.network.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.parameters.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.people.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.products.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.random.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.results.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.run.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.samples.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.settings.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.states.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.utils.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.connectors.Connector.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.connectors.simple_hiv_ng.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.demographics.BaseDemographics.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.demographics.Births.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.demographics.Deaths.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.demographics.Pregnancy.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.disease.Disease.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.disease.Infection.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.disease.InfectionLog.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.distributions.ScipyDistribution.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.utils.lognorm_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.utils.ndict.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.utils.omerge.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.utils.omergeleft.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.utils.set_seed.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.utils.standardize_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.utils.true.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.utils.undefined.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.utils.unique.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/latest/docs/api/_autosummary/starsim.utils.warn.rst The default value for `navigation_with_keys` will change to `False` in the next release. If you wish to preserve the old behavior for your site, set `navigation_with_keys=True` in the `html_theme_options` dict in your `conf.py` file. Be aware that `navigation_with_keys = True` has negative accessibility implications: https://github.com/pydata/pydata-sphinx-theme/issues/1492 building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 14 source files that are out of date updating environment: [new config] 118 added, 0 changed, 0 removed reading sources... [ 1%] api/_autosummary/starsim.connectors reading sources... [ 2%] api/_autosummary/starsim.connectors.Connector reading sources... [ 3%] api/_autosummary/starsim.connectors.simple_hiv_ng reading sources... [ 3%] api/_autosummary/starsim.demographics reading sources... [ 4%] api/_autosummary/starsim.demographics.BaseDemographics reading sources... [ 5%] api/_autosummary/starsim.demographics.Births reading sources... [ 6%] api/_autosummary/starsim.demographics.Deaths reading sources... [ 7%] api/_autosummary/starsim.demographics.Pregnancy reading sources... [ 8%] api/_autosummary/starsim.disease reading sources... [ 8%] api/_autosummary/starsim.disease.Disease reading sources... [ 9%] api/_autosummary/starsim.disease.Infection reading sources... [ 10%] api/_autosummary/starsim.disease.InfectionLog reading sources... [ 11%] api/_autosummary/starsim.distributions reading sources... [ 12%] api/_autosummary/starsim.distributions.ScipyDistribution reading sources... [ 13%] api/_autosummary/starsim.distributions.ScipyHistogram reading sources... [ 14%] api/_autosummary/starsim.distributions.rv_discrete reading sources... [ 14%] api/_autosummary/starsim.interventions reading sources... [ 15%] api/_autosummary/starsim.interventions.Analyzer reading sources... [ 16%] api/_autosummary/starsim.interventions.BaseScreening reading sources... [ 17%] api/_autosummary/starsim.interventions.BaseTest reading sources... [ 18%] api/_autosummary/starsim.interventions.BaseTreatment reading sources... [ 19%] api/_autosummary/starsim.interventions.BaseTriage reading sources... [ 19%] api/_autosummary/starsim.interventions.BaseVaccination reading sources... [ 20%] api/_autosummary/starsim.interventions.CampaignDelivery reading sources... [ 21%] api/_autosummary/starsim.interventions.Intervention reading sources... [ 22%] api/_autosummary/starsim.interventions.RoutineDelivery reading sources... [ 23%] api/_autosummary/starsim.interventions.campaign_screening reading sources... [ 24%] api/_autosummary/starsim.interventions.campaign_triage reading sources... [ 25%] api/_autosummary/starsim.interventions.campaign_vx reading sources... [ 25%] api/_autosummary/starsim.interventions.routine_screening reading sources... [ 26%] api/_autosummary/starsim.interventions.routine_triage reading sources... [ 27%] api/_autosummary/starsim.interventions.routine_vx reading sources... [ 28%] api/_autosummary/starsim.interventions.treat_num reading sources... [ 29%] api/_autosummary/starsim.modules reading sources... [ 30%] api/_autosummary/starsim.modules.Module reading sources... [ 31%] api/_autosummary/starsim.network reading sources... [ 31%] api/_autosummary/starsim.network.DynamicNetwork reading sources... [ 32%] api/_autosummary/starsim.network.EmbeddingNet reading sources... [ 33%] api/_autosummary/starsim.network.HPVNet reading sources... [ 34%] api/_autosummary/starsim.network.MFNet reading sources... [ 35%] api/_autosummary/starsim.network.MF_MSM reading sources... [ 36%] api/_autosummary/starsim.network.MSMNet reading sources... [ 36%] api/_autosummary/starsim.network.MaternalNet reading sources... [ 37%] api/_autosummary/starsim.network.Network reading sources... [ 38%] api/_autosummary/starsim.network.NetworkConnector reading sources... 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[ 52%] api/_autosummary/starsim.random reading sources... [ 53%] api/_autosummary/starsim.random.MultiRNG reading sources... [ 53%] api/_autosummary/starsim.random.NotReadyException reading sources... [ 54%] api/_autosummary/starsim.random.RNG reading sources... [ 55%] api/_autosummary/starsim.random.RNGContainer reading sources... [ 56%] api/_autosummary/starsim.random.SingleRNG reading sources... [ 57%] api/_autosummary/starsim.results reading sources... [ 58%] api/_autosummary/starsim.results.Result reading sources... [ 58%] api/_autosummary/starsim.results.Results reading sources... [ 59%] api/_autosummary/starsim.run reading sources... [ 60%] api/_autosummary/starsim.run.MultiSim reading sources... [ 61%] api/_autosummary/starsim.run.multi_run reading sources... [ 62%] api/_autosummary/starsim.run.parallel reading sources... [ 63%] api/_autosummary/starsim.run.single_run reading sources... [ 64%] api/_autosummary/starsim.samples reading sources... 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[ 77%] api/_autosummary/starsim.utils.false reading sources... [ 78%] api/_autosummary/starsim.utils.find_contacts reading sources... [ 79%] api/_autosummary/starsim.utils.get_subclasses reading sources... [ 80%] api/_autosummary/starsim.utils.lognorm_mean reading sources... [ 81%] api/_autosummary/starsim.utils.lognorm_params reading sources... [ 81%] api/_autosummary/starsim.utils.ndict reading sources... [ 82%] api/_autosummary/starsim.utils.omerge reading sources... [ 83%] api/_autosummary/starsim.utils.omergeleft reading sources... [ 84%] api/_autosummary/starsim.utils.set_seed reading sources... [ 85%] api/_autosummary/starsim.utils.standardize_data reading sources... [ 86%] api/_autosummary/starsim.utils.true reading sources... [ 86%] api/_autosummary/starsim.utils.undefined reading sources... [ 87%] api/_autosummary/starsim.utils.unique reading sources... [ 88%] api/_autosummary/starsim.utils.warn reading sources... [ 89%] api/index reading sources... [ 90%] conduct reading sources... [ 91%] contributing reading sources... [ 92%] index reading sources... [ 92%] tutorials reading sources... [ 93%] tutorials/README reading sources... [ 94%] tutorials/dev_tut_diseases /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/jupyter_client/localinterfaces.py:56: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long) ret = f(**kwargs) 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/jupyter_client/localinterfaces.py:56: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long) ret = f(**kwargs) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/nbsphinx/__init__.py:1058: RuntimeWarning: You are using an unsupported version of pandoc (2.9.2.1). Your version must be at least (2.14.2) but less than (4.0.0). Refer to https://pandoc.org/installing.html. Continuing with doubts... nbconvert.utils.pandoc.check_pandoc_version() reading sources... [ 95%] tutorials/tut_buildsim 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/jupyter_client/localinterfaces.py:56: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long) ret = f(**kwargs) reading sources... [ 96%] tutorials/tut_demographics 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/jupyter_client/localinterfaces.py:56: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long) ret = f(**kwargs) reading sources... [ 97%] tutorials/tut_diseases 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/jupyter_client/localinterfaces.py:56: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long) ret = f(**kwargs) reading sources... [ 97%] tutorials/tut_interventions 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/jupyter_client/localinterfaces.py:56: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long) ret = f(**kwargs) reading sources... [ 98%] tutorials/tut_intro /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/nbformat/__init__.py:96: MissingIDFieldWarning: Cell is missing an id field, this will become a hard error in future nbformat versions. You may want to use `normalize()` on your notebooks before validations (available since nbformat 5.1.4). Previous versions of nbformat are fixing this issue transparently, and will stop doing so in the future. validate(nb) 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/jupyter_client/localinterfaces.py:56: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long) ret = f(**kwargs) reading sources... [ 99%] tutorials/tut_networks 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/jupyter_client/localinterfaces.py:56: UserWarning: Unexpected error discovering local network interfaces: encoding with 'idna' codec failed (UnicodeError: label too long) ret = f(**kwargs) reading sources... [100%] whatsnew /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py:docstring of scipy.stats._distn_infrastructure.rv_discrete.rvs:1: WARNING: duplicate object description of starsim.distributions.rv_discrete.rvs, other instance in api/_autosummary/starsim.distributions.rv_discrete, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py:docstring of scipy.stats._distn_infrastructure.rv_discrete.pmf:1: WARNING: duplicate object description of starsim.distributions.rv_discrete.pmf, other instance in api/_autosummary/starsim.distributions.rv_discrete, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py:docstring of scipy.stats._distn_infrastructure.rv_discrete.logpmf:1: WARNING: duplicate object description of starsim.distributions.rv_discrete.logpmf, other instance in api/_autosummary/starsim.distributions.rv_discrete, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py:docstring of scipy.stats._distn_infrastructure.rv_discrete.cdf:1: WARNING: duplicate object description of starsim.distributions.rv_discrete.cdf, other instance in api/_autosummary/starsim.distributions.rv_discrete, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py:docstring of scipy.stats._distn_infrastructure.rv_discrete.logcdf:1: WARNING: duplicate object description of starsim.distributions.rv_discrete.logcdf, other instance in api/_autosummary/starsim.distributions.rv_discrete, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py:docstring of scipy.stats._distn_infrastructure.rv_discrete.sf:1: WARNING: duplicate object description of starsim.distributions.rv_discrete.sf, other instance in api/_autosummary/starsim.distributions.rv_discrete, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py:docstring of scipy.stats._distn_infrastructure.rv_discrete.logsf:1: WARNING: duplicate object description of starsim.distributions.rv_discrete.logsf, other instance in api/_autosummary/starsim.distributions.rv_discrete, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py:docstring of scipy.stats._distn_infrastructure.rv_discrete.ppf:1: WARNING: duplicate object description of starsim.distributions.rv_discrete.ppf, other instance in api/_autosummary/starsim.distributions.rv_discrete, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py:docstring of scipy.stats._distn_infrastructure.rv_discrete.isf:1: WARNING: duplicate object description of starsim.distributions.rv_discrete.isf, other instance in api/_autosummary/starsim.distributions.rv_discrete, use :no-index: for one of them /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/latest/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py:docstring of scipy.stats._distn_infrastructure.rv_discrete.expect:1: WARNING: duplicate object description of starsim.distributions.rv_discrete.expect, other instance in api/_autosummary/starsim.distributions.rv_discrete, use :no-index: for one of them looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... done copying extra files... done done writing output... 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