Read the Docs build information Build id: 2878312 Project: institute-for-disease-modeling-starsim Version: 847 Commit: 09552ee88ca8ce9189e81911b14bdbb22d49a994 Date: 2025-03-13T15:12:57.838366Z State: finished Success: False [rtd-command-info] start-time: 2025-03-13T15:12:58.787576Z, end-time: 2025-03-13T15:12:59.334586Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/starsimhub/starsim.git . Cloning into '.'... [rtd-command-info] start-time: 2025-03-13T15:12:59.400181Z, end-time: 2025-03-13T15:13:00.619891Z, 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] v0.3.2 -> v0.3.2 * [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: 2025-03-13T15:13:00.733147Z, end-time: 2025-03-13T15:13:00.779487Z, duration: 0, exit-code: 0 git checkout --force 09552ee88ca8ce9189e81911b14bdbb22d49a994 Note: switching to '09552ee88ca8ce9189e81911b14bdbb22d49a994'. 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 09552ee Doc fixes [rtd-command-info] start-time: 2025-03-13T15:13:00.841391Z, end-time: 2025-03-13T15:13:00.885247Z, 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: 2025-03-13T15:13:05.043672Z, end-time: 2025-03-13T15:13:05.095675Z, duration: 0, exit-code: 0 asdf global python 3.11.10 [rtd-command-info] start-time: 2025-03-13T15:13:05.436387Z, end-time: 2025-03-13T15:13:06.294897Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.11.10.final.0-64 in 605ms 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: 2025-03-13T15:13:06.370770Z, end-time: 2025-03-13T15:13:14.990202Z, duration: 8, exit-code: 0 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installed Jinja2-3.1.6 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-3.1.0 snowballstemmer-2.2.0 sphinx-8.2.3 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.3.0 [rtd-command-info] start-time: 2025-03-13T15:13:21.304193Z, end-time: 2025-03-13T15:13:52.906405Z, duration: 31, 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) Collecting 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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, ipython-pygments-lexers, greenlet, fonttools, executing, defusedxml, decorator, debugpy, cycler, colorlog, bleach, attrs, asttokens, accessible-pygments, stack_data, sqlalchemy, sphinx, 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 Attempting uninstall: sphinx Found existing installation: Sphinx 8.2.3 Uninstalling Sphinx-8.2.3: Successfully uninstalled Sphinx-8.2.3 Successfully installed Mako-1.3.9 PyYAML-6.0.2 accessible-pygments-0.0.5 alembic-1.15.1 asttokens-3.0.0 attrs-25.3.0 beautifulsoup4-4.13.3 bleach-6.2.0 colorlog-6.9.0 comm-0.2.2 contourpy-1.3.1 cycler-0.12.1 debugpy-1.8.13 decorator-5.2.1 defusedxml-0.7.1 executing-2.2.0 fastjsonschema-2.21.1 fonttools-4.56.0 greenlet-3.1.1 ipykernel-6.29.5 ipython-9.0.2 ipython-pygments-lexers-1.1.1 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-3.10.1 matplotlib-inline-0.1.7 mistune-3.1.2 nbclient-0.10.2 nbconvert-7.16.6 nbformat-5.10.4 nbsphinx-0.9.7 nest-asyncio-1.6.0 numpy-2.2.3 optuna-4.2.1 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-7.0.0 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-2025.1 pyzmq-26.3.0 readthedocs-sphinx-search-0.3.2 referencing-0.36.2 rpds-py-0.23.1 seaborn-0.13.2 six-1.17.0 soupsieve-2.6 sphinx-8.1.3 sphinx-autodoc-typehints-3.0.1 sphinx-design-0.6.1 sphinxcontrib-napoleon-0.7 sqlalchemy-2.0.39 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: 2025-03-13T15:13:52.993398Z, end-time: 2025-03-13T15:14:08.513361Z, duration: 15, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir . 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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-2.3.1-py3-none-any.whl size=161042 sha256=574e51cfd54b6df086294b540251fe366163882c652e0b14eb52ea5e20c4a045 Stored in directory: /tmp/pip-ephem-wheel-cache-czpkn0sa/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 2.2.3 Uninstalling numpy-2.2.3: Successfully uninstalled numpy-2.2.3 Successfully installed dill-0.3.9 et-xmlfile-2.0.0 gitdb-4.0.12 gitpython-3.1.44 jellyfish-1.1.3 jsonpickle-4.0.2 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-1.15.2 sciris-3.2.0 smmap-5.0.2 starsim-2.3.1 xlsxwriter-3.2.2 zstandard-0.23.0 [rtd-command-info] start-time: 2025-03-13T15:14:08.683261Z, end-time: 2025-03-13T15:14:08.721069Z, 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}, 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: 2025-03-13T15:14:08.787179Z, end-time: 2025-03-13T15:14:53.722832Z, duration: 44, 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.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.demographics.Deaths.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] 163 added, 0 changed, 0 removed reading sources... 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[ 94%] tutorials/dev_tut_nonstandard 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: ------------------ """ Define the classic agent-based "wealth model" in Starsim """ # Imports import numpy as np import starsim as ss import matplotlib.pyplot as plt # Define the model class WealthModel(ss.Module): """ A simple wealth transfer model""" def init_post(self, bins=10): """ Define custom model attributes """ super().init_post() self.npts = len(self.sim) # Number of timepoints self.n_agents = len(sim.people) # Number of agents self.wealth = np.ones(self.n_agents) # Initial wealth of each agent self.bins = np.arange(bins+1) # Bins used for plotting self.wealth_dist = np.zeros((self.npts, len(self.bins)-1)) # Wealth distribution over time return def step(self): """ Transfer wealth between agents -- core model logic """ self.wealth_hist() # Store the wealth at this time point givers = self.wealth > 0 # People need wealth to be givers receivers = np.random.choice(self.sim.people.uid, size=givers.sum()) # Anyone can be a receiver self.wealth[givers] -= 1 # Givers are unique, so can use vectorized version for receive in receivers: # Vectorized version is: np.add.at(sim.people.wealth.raw, receivers, 1) self.wealth[receive] += 1 return def wealth_hist(self): """ Calculate the wealth histogram """ ti = self.sim.ti # Current timestep self.wealth_dist[ti,:], _ = np.histogram(self.wealth, bins=self.bins) return def plot(self): """ Plot a 2D histogram of the final wealth distribution """ plt.figure() plt.bar(self.bins[:-1], self.wealth_dist[-1,:]) plt.title('Wealth distribution at final time point') plt.xlabel('Wealth') plt.ylabel('Number of agents') plt.show() return def plot3d(self): """ Plot a 3D heatmap of the wealth distribution over time """ plt.figure() plt.pcolor(self.wealth_dist.T, cmap='turbo') plt.title('Wealth distribution over time') plt.xlabel('Time') plt.ylabel('Wealth') plt.colorbar().set_label('Number of agents', rotation=270) plt.show() return # Create sim inputs, including the wealth model wealth = WealthModel() pars = dict( n_agents = 100, # Number of agents start = 0, stop = 100, demographics = wealth, ) # Run the model sim = ss.Sim(pars, copy_inputs=False) # copy_inputs=False lets us reuse the "wealth" object from above sim.run() # Plot the results wealth.plot() wealth.plot3d() ------------------ --------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In[3], line 72  70 # Run the model  71 sim = ss.Sim(pars, copy_inputs=False) # copy_inputs=False lets us reuse the "wealth" object from above ---> 72 sim.run()  74 # Plot the results  75 wealth.plot() 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:280, in SimPars.validate(self)  278 def validate(self):  279  """ Call parameter validation methods """ --> 280 self.validate_sim_pars()  281 self.validate_modules()  282 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/parameters.py:289, in SimPars.validate_sim_pars(self)  287 self.validate_agents()  288 self.validate_total_pop() --> 289 self.validate_time()  290 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/parameters.py:349, in SimPars.validate_time(self)  347 self.start = ss.Date(self.start)  348 elif sc.isnumber(self.start) and self.stop is not None: --> 349 self.start = self.stop.__class__(self.start)  351 if sc.isnumber(self.dur):  352 self.dur = ss.Dur(self.dur) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/time.py:58, in Date.__new__(cls, *args, **kwargs)  56 year_kwarg = len(args) == 0 and len(kwargs) == 1 and 'year' in kwargs  57 if single_year_arg: ---> 58 return cls.from_year(args[0])  59 if year_kwarg:  60 return cls.from_year(kwargs['year']) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/time.py:139, in Date.from_year(cls, year)  129 """  130 Convert an int or float year to a date.  131  (...) 135  ss.Date.from_year(2024.75) # Returns <2024-10-01>  136 """  138 if isinstance(year, int): --> 139 return cls(year=year, month=1, day=1)  140 else:  141 year_start = pd.Timestamp(year=int(year),month=1,day=1).timestamp() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/time.py:63, in Date.__new__(cls, *args, **kwargs)  60 return cls.from_year(kwargs['year'])  62 # Otherwise, proceed as normal ---> 63 out = super(Date, cls).__new__(cls, *args, **kwargs)  64 out = cls._reset_class(out)  65 return out File timestamps.pyx:1844, in pandas._libs.tslibs.timestamps.Timestamp.__new__() ValueError: year 0 is out of range 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_nonstandard.ipynb: ------------------ """ Define the classic agent-based "wealth model" in Starsim """ # Imports import numpy as np import starsim as ss import matplotlib.pyplot as plt # Define the model class WealthModel(ss.Module): """ A simple wealth transfer model""" def init_post(self, bins=10): """ Define custom model attributes """ super().init_post() self.npts = len(self.sim) # Number of timepoints self.n_agents = len(sim.people) # Number of agents self.wealth = np.ones(self.n_agents) # Initial wealth of each agent self.bins = np.arange(bins+1) # Bins used for plotting self.wealth_dist = np.zeros((self.npts, len(self.bins)-1)) # Wealth distribution over time return def step(self): """ Transfer wealth between agents -- core model logic """ self.wealth_hist() # Store the wealth at this time point givers = self.wealth > 0 # People need wealth to be givers receivers = np.random.choice(self.sim.people.uid, size=givers.sum()) # Anyone can be a receiver self.wealth[givers] -= 1 # Givers are unique, so can use vectorized version for receive in receivers: # Vectorized version is: np.add.at(sim.people.wealth.raw, receivers, 1) self.wealth[receive] += 1 return def wealth_hist(self): """ Calculate the wealth histogram """ ti = self.sim.ti # Current timestep self.wealth_dist[ti,:], _ = np.histogram(self.wealth, bins=self.bins) return def plot(self): """ Plot a 2D histogram of the final wealth distribution """ plt.figure() plt.bar(self.bins[:-1], self.wealth_dist[-1,:]) plt.title('Wealth distribution at final time point') plt.xlabel('Wealth') plt.ylabel('Number of agents') plt.show() return def plot3d(self): """ Plot a 3D heatmap of the wealth distribution over time """ plt.figure() plt.pcolor(self.wealth_dist.T, cmap='turbo') plt.title('Wealth distribution over time') plt.xlabel('Time') plt.ylabel('Wealth') plt.colorbar().set_label('Number of agents', rotation=270) plt.show() return # Create sim inputs, including the wealth model wealth = WealthModel() pars = dict( n_agents = 100, # Number of agents start = 0, stop = 100, demographics = wealth, ) # Run the model sim = ss.Sim(pars, copy_inputs=False) # copy_inputs=False lets us reuse the "wealth" object from above sim.run() # Plot the results wealth.plot() wealth.plot3d() ------------------ --------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In[3], line 72  70 # Run the model  71 sim = ss.Sim(pars, copy_inputs=False) # copy_inputs=False lets us reuse the "wealth" object from above ---> 72 sim.run()  74 # Plot the results  75 wealth.plot() 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:280, in SimPars.validate(self)  278 def validate(self):  279  """ Call parameter validation methods """ --> 280 self.validate_sim_pars()  281 self.validate_modules()  282 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/parameters.py:289, in SimPars.validate_sim_pars(self)  287 self.validate_agents()  288 self.validate_total_pop() --> 289 self.validate_time()  290 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/parameters.py:349, in SimPars.validate_time(self)  347 self.start = ss.Date(self.start)  348 elif sc.isnumber(self.start) and self.stop is not None: --> 349 self.start = self.stop.__class__(self.start)  351 if sc.isnumber(self.dur):  352 self.dur = ss.Dur(self.dur) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/time.py:58, in Date.__new__(cls, *args, **kwargs)  56 year_kwarg = len(args) == 0 and len(kwargs) == 1 and 'year' in kwargs  57 if single_year_arg: ---> 58 return cls.from_year(args[0])  59 if year_kwarg:  60 return cls.from_year(kwargs['year']) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/time.py:139, in Date.from_year(cls, year)  129 """  130 Convert an int or float year to a date.  131  (...) 135  ss.Date.from_year(2024.75) # Returns <2024-10-01>  136 """  138 if isinstance(year, int): --> 139 return cls(year=year, month=1, day=1)  140 else:  141 year_start = pd.Timestamp(year=int(year),month=1,day=1).timestamp() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/time.py:63, in Date.__new__(cls, *args, **kwargs)  60 return cls.from_year(kwargs['year'])  62 # Otherwise, proceed as normal ---> 63 out = super(Date, cls).__new__(cls, *args, **kwargs)  64 out = cls._reset_class(out)  65 return out File timestamps.pyx:1844, in pandas._libs.tslibs.timestamps.Timestamp.__new__() ValueError: year 0 is out of range You can ignore this error by setting the following in conf.py: nbsphinx_allow_errors = True Notebook error: CellExecutionError in tutorials/dev_tut_nonstandard.ipynb: ------------------ """ Define the classic agent-based "wealth model" in Starsim """ # Imports import numpy as np import starsim as ss import matplotlib.pyplot as plt # Define the model class WealthModel(ss.Module): """ A simple wealth transfer model""" def init_post(self, bins=10): """ Define custom model attributes """ super().init_post() self.npts = len(self.sim) # Number of timepoints self.n_agents = len(sim.people) # Number of agents self.wealth = np.ones(self.n_agents) # Initial wealth of each agent self.bins = np.arange(bins+1) # Bins used for plotting self.wealth_dist = np.zeros((self.npts, len(self.bins)-1)) # Wealth distribution over time return def step(self): """ Transfer wealth between agents -- core model logic """ self.wealth_hist() # Store the wealth at this time point givers = self.wealth > 0 # People need wealth to be givers receivers = np.random.choice(self.sim.people.uid, size=givers.sum()) # Anyone can be a receiver self.wealth[givers] -= 1 # Givers are unique, so can use vectorized version for receive in receivers: # Vectorized version is: np.add.at(sim.people.wealth.raw, receivers, 1) self.wealth[receive] += 1 return def wealth_hist(self): """ Calculate the wealth histogram """ ti = self.sim.ti # Current timestep self.wealth_dist[ti,:], _ = np.histogram(self.wealth, bins=self.bins) return def plot(self): """ Plot a 2D histogram of the final wealth distribution """ plt.figure() plt.bar(self.bins[:-1], self.wealth_dist[-1,:]) plt.title('Wealth distribution at final time point') plt.xlabel('Wealth') plt.ylabel('Number of agents') plt.show() return def plot3d(self): """ Plot a 3D heatmap of the wealth distribution over time """ plt.figure() plt.pcolor(self.wealth_dist.T, cmap='turbo') plt.title('Wealth distribution over time') plt.xlabel('Time') plt.ylabel('Wealth') plt.colorbar().set_label('Number of agents', rotation=270) plt.show() return # Create sim inputs, including the wealth model wealth = WealthModel() pars = dict( n_agents = 100, # Number of agents start = 0, stop = 100, demographics = wealth, ) # Run the model sim = ss.Sim(pars, copy_inputs=False) # copy_inputs=False lets us reuse the "wealth" object from above sim.run() # Plot the results wealth.plot() wealth.plot3d() ------------------ --------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In[3], line 72  70 # Run the model  71 sim = ss.Sim(pars, copy_inputs=False) # copy_inputs=False lets us reuse the "wealth" object from above ---> 72 sim.run()  74 # Plot the results  75 wealth.plot() 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:280, in SimPars.validate(self)  278 def validate(self):  279  """ Call parameter validation methods """ --> 280 self.validate_sim_pars()  281 self.validate_modules()  282 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/parameters.py:289, in SimPars.validate_sim_pars(self)  287 self.validate_agents()  288 self.validate_total_pop() --> 289 self.validate_time()  290 return File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/parameters.py:349, in SimPars.validate_time(self)  347 self.start = ss.Date(self.start)  348 elif sc.isnumber(self.start) and self.stop is not None: --> 349 self.start = self.stop.__class__(self.start)  351 if sc.isnumber(self.dur):  352 self.dur = ss.Dur(self.dur) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/time.py:58, in Date.__new__(cls, *args, **kwargs)  56 year_kwarg = len(args) == 0 and len(kwargs) == 1 and 'year' in kwargs  57 if single_year_arg: ---> 58 return cls.from_year(args[0])  59 if year_kwarg:  60 return cls.from_year(kwargs['year']) File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/time.py:139, in Date.from_year(cls, year)  129 """  130 Convert an int or float year to a date.  131  (...) 135  ss.Date.from_year(2024.75) # Returns <2024-10-01>  136 """  138 if isinstance(year, int): --> 139 return cls(year=year, month=1, day=1)  140 else:  141 year_start = pd.Timestamp(year=int(year),month=1,day=1).timestamp() File ~/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/847/lib/python3.11/site-packages/starsim/time.py:63, in Date.__new__(cls, *args, **kwargs)  60 return cls.from_year(kwargs['year'])  62 # Otherwise, proceed as normal ---> 63 out = super(Date, cls).__new__(cls, *args, **kwargs)  64 out = cls._reset_class(out)  65 return out File timestamps.pyx:1844, in pandas._libs.tslibs.timestamps.Timestamp.__new__() ValueError: year 0 is out of range You can ignore this error by setting the following in conf.py: nbsphinx_allow_errors = True