Read the Docs build information Build id: 2766418 Project: institute-for-disease-modeling-starsim Version: 847 Commit: be9ea7d06e36d45d92f48892fdf2862b744a7c19 Date: 2025-01-28T22:57:22.646431Z State: finished Success: False [rtd-command-info] start-time: 2025-01-28T22:57:23.664584Z, end-time: 2025-01-28T22:57:24.221351Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/starsimhub/starsim.git . Cloning into '.'... [rtd-command-info] start-time: 2025-01-28T22:57:24.294039Z, end-time: 2025-01-28T22:57:25.612339Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/847/head:external-847 From https://github.com/starsimhub/starsim * [new ref] refs/pull/847/head -> external-847 * [new tag] v0.3.4 -> v0.3.4 * [new tag] v0.5.0 -> v0.5.0 * [new tag] v1.0.0 -> v1.0.0 * [new tag] v1.0.2 -> v1.0.2 * [new tag] v1.0.3 -> v1.0.3 * [new tag] v2.0.0 -> v2.0.0 * [new tag] v2.1.0 -> v2.1.0 * [new tag] v2.1.1 -> v2.1.1 * [new tag] v2.2.0 -> v2.2.0 [rtd-command-info] start-time: 2025-01-28T22:57:25.737525Z, end-time: 2025-01-28T22:57:25.782080Z, duration: 0, exit-code: 0 git checkout --force be9ea7d06e36d45d92f48892fdf2862b744a7c19 Note: switching to 'be9ea7d06e36d45d92f48892fdf2862b744a7c19'. 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 be9ea7d In progress [rtd-command-info] start-time: 2025-01-28T22:57:25.846081Z, end-time: 2025-01-28T22:57:25.896354Z, 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: 2025-01-28T22:57:30.432576Z, end-time: 2025-01-28T22:57:30.497609Z, duration: 0, exit-code: 0 asdf global python 3.11.10 [rtd-command-info] start-time: 2025-01-28T22:57:30.832848Z, end-time: 2025-01-28T22:57:31.679700Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.11.10.final.0-64 in 568ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847, 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: 2025-01-28T22:57:31.747426Z, end-time: 2025-01-28T22:57:41.501155Z, duration: 9, exit-code: 0 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sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl (92 kB) Downloading certifi-2024.12.14-py3-none-any.whl (164 kB) Downloading charset_normalizer-3.4.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (143 kB) Downloading idna-3.10-py3-none-any.whl (70 kB) Downloading MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB) Downloading urllib3-2.3.0-py3-none-any.whl (128 kB) Installing collected packages: snowballstemmer, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx Successfully installed Jinja2-3.1.5 MarkupSafe-3.0.2 Pygments-2.19.1 alabaster-1.0.0 babel-2.16.0 certifi-2024.12.14 charset-normalizer-3.4.1 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-24.2 requests-2.32.3 snowballstemmer-2.2.0 sphinx-8.1.3 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 urllib3-2.3.0 [rtd-command-info] start-time: 2025-01-28T22:57:47.171188Z, end-time: 2025-01-28T22:58:08.276943Z, duration: 21, 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 pypandoc-1.15-py3-none-any.whl.metadata (16 kB) Requirement already satisfied: sphinx>=7.3.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages (from -r docs/requirements.txt (line 3)) (8.1.3) Collecting sphinx-autodoc-typehints (from -r 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sha256=8b213d81c7bed74254a527fa5ade2f5632fdd555e108f11c38d7500d6d4ac66e Stored in directory: /tmp/pip-ephem-wheel-cache-oavc7fhp/wheels/4f/d7/32/c6c9b7b05e852e920fd72174487be3a0f18e633a7adcc303be Successfully built pandoc Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, ply, fastjsonschema, widgetsnbextension, 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-widgets, jupyterlab-pygments, greenlet, fonttools, executing, defusedxml, decorator, debugpy, cycler, colorlog, bleach, attrs, asttokens, accessible-pygments, stack_data, sqlalchemy, referencing, python-dateutil, pockets, plantweb, pandoc, matplotlib-inline, jupyter-core, jedi, contourpy, comm, beautifulsoup4, sphinxcontrib-napoleon, sphinx-design, sphinx-autodoc-typehints, pydata-sphinx-theme, pandas, matplotlib, jupyter-client, jsonschema-specifications, ipython, alembic, seaborn, optuna, jsonschema, ipywidgets, ipykernel, nbformat, nbclient, nbconvert, nbsphinx Successfully installed Mako-1.3.8 PyYAML-6.0.2 accessible-pygments-0.0.5 alembic-1.14.1 asttokens-3.0.0 attrs-25.1.0 beautifulsoup4-4.12.3 bleach-6.2.0 colorlog-6.9.0 comm-0.2.2 contourpy-1.3.1 cycler-0.12.1 debugpy-1.8.12 decorator-5.1.1 defusedxml-0.7.1 executing-2.2.0 fastjsonschema-2.21.1 fonttools-4.55.7 greenlet-3.1.1 ipykernel-6.29.5 ipython-8.31.0 ipywidgets-8.1.5 jedi-0.19.2 jsonschema-4.23.0 jsonschema-specifications-2024.10.1 jupyter-client-8.6.3 jupyter-core-5.7.2 jupyterlab-pygments-0.3.0 jupyterlab-widgets-3.0.13 kiwisolver-1.4.8 matplotlib-3.10.0 matplotlib-inline-0.1.7 mistune-3.1.1 nbclient-0.10.2 nbconvert-7.16.6 nbformat-5.10.4 nbsphinx-0.9.6 nest-asyncio-1.6.0 numpy-2.2.2 optuna-4.2.0 pandas-2.2.3 pandoc-2.4 pandocfilters-1.5.1 parso-0.8.4 pexpect-4.9.0 pillow-11.1.0 plantweb-1.3.0 platformdirs-4.3.6 plumbum-1.9.0 ply-3.11 pockets-0.9.1 prompt_toolkit-3.0.50 psutil-6.1.1 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.16.1 pypandoc-1.15 pyparsing-3.2.1 python-dateutil-2.9.0.post0 pytz-2024.2 pyzmq-26.2.0 readthedocs-sphinx-search-0.3.2 referencing-0.36.2 rpds-py-0.22.3 seaborn-0.13.2 six-1.17.0 soupsieve-2.6 sphinx-autodoc-typehints-3.0.1 sphinx-design-0.6.1 sphinxcontrib-napoleon-0.7 sqlalchemy-2.0.37 stack_data-0.6.3 tinycss2-1.4.0 tornado-6.4.2 tqdm-4.67.1 traitlets-5.14.3 typing-extensions-4.12.2 tzdata-2025.1 wcwidth-0.2.13 webencodings-0.5.1 widgetsnbextension-4.0.13 [rtd-command-info] start-time: 2025-01-28T22:58:08.371557Z, end-time: 2025-01-28T22:58:25.698950Z, duration: 17, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir . 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line_profiler-4.2.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (750 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 750.2/750.2 kB 748.8 MB/s eta 0:00:00 Downloading memory_profiler-0.61.0-py3-none-any.whl (31 kB) Downloading multiprocess-0.70.17-py311-none-any.whl (144 kB) Downloading openpyxl-3.1.5-py2.py3-none-any.whl (250 kB) Downloading XlsxWriter-3.2.2-py3-none-any.whl (165 kB) Downloading zstandard-0.23.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.4/5.4 MB 220.0 MB/s eta 0:00:00 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: starsim Building wheel for starsim (pyproject.toml): started Building wheel for starsim (pyproject.toml): finished with status 'done' Created wheel for starsim: filename=starsim-2.2.0-py3-none-any.whl size=155336 sha256=4034d05d9a890667786c360e78a9480c31c269dba88f695d29a093171efca3ee Stored in directory: /tmp/pip-ephem-wheel-cache-y4e4fbvx/wheels/cb/99/0f/d958ceab7a04e26e1853a33cfc76f63f7f7366c15aa5301c90 Successfully built starsim Installing collected packages: zstandard, xlsxwriter, smmap, numpy, networkx, memory-profiler, llvmlite, line-profiler, jsonpickle, jellyfish, et-xmlfile, dill, scipy, openpyxl, numba, multiprocess, gitdb, gitpython, sciris, starsim Attempting uninstall: numpy Found existing installation: numpy 2.2.2 Uninstalling numpy-2.2.2: Successfully uninstalled numpy-2.2.2 Successfully installed dill-0.3.9 et-xmlfile-2.0.0 gitdb-4.0.12 gitpython-3.1.44 jellyfish-1.1.3 jsonpickle-4.0.1 line-profiler-4.2.0 llvmlite-0.44.0 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 scipy-1.15.1 sciris-3.2.0 smmap-5.0.2 starsim-2.2.0 xlsxwriter-3.2.2 zstandard-0.23.0 [rtd-command-info] start-time: 2025-01-28T22:58:25.893060Z, end-time: 2025-01-28T22:58:25.943836Z, 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 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 nbsphinx_execute = 'always' nbsphinx_timeout = 300 # 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}", } [rtd-command-info] start-time: 2025-01-28T22:58:26.017789Z, end-time: 2025-01-28T22:58:47.555761Z, duration: 21, exit-code: 2 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v8.1.3 loading translations [en]... done 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_analyzers.ipynb, tutorials/dev_tut_diseases.ipynb, tutorials/dev_tut_nonstandard.ipynb, tutorials/dev_tut_pars.ipynb, tutorials/tut_buildsim.ipynb, tutorials/tut_calibration.ipynb, tutorials/tut_demographics.ipynb, tutorials/tut_diseases.ipynb, tutorials/tut_interventions.ipynb, tutorials/tut_intro.ipynb, tutorials/tut_transmission.ipynb, whatsnew.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.arrays.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.calibration.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.demographics.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.disease.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.distributions.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.interventions.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.loop.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.modules.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.networks.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.parameters.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.people.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.products.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.results.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.run.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.samples.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.settings.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.time.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.arrays.Arr.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.arrays.BaseArr.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.arrays.BoolArr.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.arrays.FloatArr.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.arrays.IndexArr.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.arrays.State.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.arrays.uids.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.calibration.CalibComponent.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.calibration.Calibration.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.demographics.Births.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.find_contacts.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.load.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.ndict.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.return_fig.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.save.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.set_seed.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.standardize_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.standardize_netkey.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.validate_sim_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/docs/api/_autosummary/starsim.utils.warn.rst Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/checkouts/847/_readthedocs/html/_static/nbsphinx-code-cells.css building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 18 source files that are out of date updating environment: [new config] 165 added, 0 changed, 0 removed reading sources... 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[docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/calibration.py:docstring of starsim.calibration.CalibComponent.nll_beta:12: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/calibration.py:docstring of starsim.calibration.Calibration:8: WARNING: Inline strong start-string without end-string. [docutils] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/calibration.py:docstring of starsim.calibration.Calibration:23: WARNING: Inline strong start-string without end-string. [docutils] Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/nbsphinx/__init__.py", line 634, in parse rststring, resources = exporter.from_notebook_node(nb, resources) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/nbsphinx/__init__.py", line 397, in from_notebook_node nb, resources = pp.preprocess(nb, resources) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/nbconvert/preprocessors/execute.py", line 103, in preprocess self.preprocess_cell(cell, resources, index) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/nbconvert/preprocessors/execute.py", line 124, in preprocess_cell cell = self.execute_cell(cell, index, store_history=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped return loop.run_until_complete(inner) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.asdf/installs/python/3.11.10/lib/python3.11/asyncio/base_events.py", line 654, in run_until_complete return future.result() ^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import starsim as ss import matplotlib.pyplot as plt # Store the number of edges n_edges = [] def count_edges(sim): """ Print out the number of edges in the network on each timestep """ network = sim.networks[0] # Get the first network n = len(network) n_edges.append(n) print(f'Number of edges for network {network.name} on step {sim.ti}: {n}') return # Create the sim pars = dict( diseases='sis', networks = 'mf', analyzers = count_edges, demographics = True, ) # Run the sim sim = ss.Sim(pars).run() sim.plot() # Plot the number of edges plt.figure() plt.plot(sim.timevec, n_edges) plt.title('Number of edges over time') plt.show() ------------------ --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) Cell In[1], line 24  16 pars = dict(  17 diseases='sis',  18 networks = 'mf',  19 analyzers = count_edges,  20 demographics = True,  21 )  23 # Run the sim ---> 24 sim = ss.Sim(pars).run()  25 sim.plot()  27 # Plot the number of edges File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/sim.py:296, in Sim.run(self, until, verbose)  293 """ Run the model once """  295 # Initialization steps --> 296 if not self.initialized: self.init()  297 self.verbose = sc.ifelse(verbose, self.pars.verbose)  298 self.timer.start() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/sim.py:138, in Sim.init(self, force, **kwargs)  136 # Validation and initialization -- this is "pre"  137 ss.set_seed(self.pars.rand_seed) # Reset the seed before the population is created -- shouldn't matter if only using Dist objects --> 138 self.pars.validate() # Validate parameters  139 self.init_time() # Initialize time  140 self.init_people(**kwargs) # Initialize the people File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/parameters.py:284, in SimPars.validate(self)  282 def validate(self):  283  """ Call parameter validation methods """ --> 284 self.validate_sim_pars()  285 self.validate_modules()  286 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/parameters.py:293, in SimPars.validate_sim_pars(self)  291 self.validate_agents()  292 self.validate_total_pop() --> 293 self.validate_time()  294 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/parameters.py:343, in SimPars.validate_time(self)  341 if self.unit == '':  342 self.unit = ss.time.default_unit --> 343 self.unit = ss.time.validate_unit(self.unit)  345 # Handle start  346 if self.start is None: AttributeError: module 'starsim.time' has no attribute 'validate_unit' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/sphinx/cmd/build.py", line 514, in build_main app.build(args.force_all, args.filenames) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/sphinx/application.py", line 381, in build self.builder.build_update() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 358, in build_update self.build( File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 385, in build updated_docnames = set(self.read()) ^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 502, in read self._read_serial(docnames) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 567, in _read_serial self.read_doc(docname) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 630, in read_doc publisher.publish() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/docutils/core.py", line 234, in publish self.document = self.reader.read(self.source, self.parser, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/sphinx/io.py", line 106, in read self.parse() File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/docutils/readers/__init__.py", line 76, in parse self.parser.parse(self.input, document) File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/nbsphinx/__init__.py", line 641, in parse raise NotebookError('\n'.join(lines)) nbsphinx.NotebookError: CellExecutionError in tutorials/dev_tut_analyzers.ipynb: ------------------ import starsim as ss import matplotlib.pyplot as plt # Store the number of edges n_edges = [] def count_edges(sim): """ Print out the number of edges in the network on each timestep """ network = sim.networks[0] # Get the first network n = len(network) n_edges.append(n) print(f'Number of edges for network {network.name} on step {sim.ti}: {n}') return # Create the sim pars = dict( diseases='sis', networks = 'mf', analyzers = count_edges, demographics = True, ) # Run the sim sim = ss.Sim(pars).run() sim.plot() # Plot the number of edges plt.figure() plt.plot(sim.timevec, n_edges) plt.title('Number of edges over time') plt.show() ------------------ --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) Cell In[1], line 24  16 pars = dict(  17 diseases='sis',  18 networks = 'mf',  19 analyzers = count_edges,  20 demographics = True,  21 )  23 # Run the sim ---> 24 sim = ss.Sim(pars).run()  25 sim.plot()  27 # Plot the number of edges File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/sim.py:296, in Sim.run(self, until, verbose)  293 """ Run the model once """  295 # Initialization steps --> 296 if not self.initialized: self.init()  297 self.verbose = sc.ifelse(verbose, self.pars.verbose)  298 self.timer.start() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/sim.py:138, in Sim.init(self, force, **kwargs)  136 # Validation and initialization -- this is "pre"  137 ss.set_seed(self.pars.rand_seed) # Reset the seed before the population is created -- shouldn't matter if only using Dist objects --> 138 self.pars.validate() # Validate parameters  139 self.init_time() # Initialize time  140 self.init_people(**kwargs) # Initialize the people File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/parameters.py:284, in SimPars.validate(self)  282 def validate(self):  283  """ Call parameter validation methods """ --> 284 self.validate_sim_pars()  285 self.validate_modules()  286 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/parameters.py:293, in SimPars.validate_sim_pars(self)  291 self.validate_agents()  292 self.validate_total_pop() --> 293 self.validate_time()  294 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/parameters.py:343, in SimPars.validate_time(self)  341 if self.unit == '':  342 self.unit = ss.time.default_unit --> 343 self.unit = ss.time.validate_unit(self.unit)  345 # Handle start  346 if self.start is None: AttributeError: module 'starsim.time' has no attribute 'validate_unit' You can ignore this error by setting the following in conf.py: nbsphinx_allow_errors = True Notebook error: CellExecutionError in tutorials/dev_tut_analyzers.ipynb: ------------------ import starsim as ss import matplotlib.pyplot as plt # Store the number of edges n_edges = [] def count_edges(sim): """ Print out the number of edges in the network on each timestep """ network = sim.networks[0] # Get the first network n = len(network) n_edges.append(n) print(f'Number of edges for network {network.name} on step {sim.ti}: {n}') return # Create the sim pars = dict( diseases='sis', networks = 'mf', analyzers = count_edges, demographics = True, ) # Run the sim sim = ss.Sim(pars).run() sim.plot() # Plot the number of edges plt.figure() plt.plot(sim.timevec, n_edges) plt.title('Number of edges over time') plt.show() ------------------ --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) Cell In[1], line 24  16 pars = dict(  17 diseases='sis',  18 networks = 'mf',  19 analyzers = count_edges,  20 demographics = True,  21 )  23 # Run the sim ---> 24 sim = ss.Sim(pars).run()  25 sim.plot()  27 # Plot the number of edges File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/sim.py:296, in Sim.run(self, until, verbose)  293 """ Run the model once """  295 # Initialization steps --> 296 if not self.initialized: self.init()  297 self.verbose = sc.ifelse(verbose, self.pars.verbose)  298 self.timer.start() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/sim.py:138, in Sim.init(self, force, **kwargs)  136 # Validation and initialization -- this is "pre"  137 ss.set_seed(self.pars.rand_seed) # Reset the seed before the population is created -- shouldn't matter if only using Dist objects --> 138 self.pars.validate() # Validate parameters  139 self.init_time() # Initialize time  140 self.init_people(**kwargs) # Initialize the people File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/parameters.py:284, in SimPars.validate(self)  282 def validate(self):  283  """ Call parameter validation methods """ --> 284 self.validate_sim_pars()  285 self.validate_modules()  286 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/parameters.py:293, in SimPars.validate_sim_pars(self)  291 self.validate_agents()  292 self.validate_total_pop() --> 293 self.validate_time()  294 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/parameters.py:343, in SimPars.validate_time(self)  341 if self.unit == '':  342 self.unit = ss.time.default_unit --> 343 self.unit = ss.time.validate_unit(self.unit)  345 # Handle start  346 if self.start is None: AttributeError: module 'starsim.time' has no attribute 'validate_unit' You can ignore this error by setting the following in conf.py: nbsphinx_allow_errors = True