Read the Docs build information
Build id: 3011058
Project: institute-for-disease-modeling-starsim
Version: 882
Commit: b846fae9420a379c05f4d62144f445bf33057fb6
Date: 2025-04-30T19:29:01.686352Z
State: finished
Success: False


[rtd-command-info] start-time: 2025-04-30T19:30:05.951401Z, end-time: 2025-04-30T19:30:06.483209Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/starsimhub/starsim.git .
Cloning into '.'...

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git fetch origin --force --prune --prune-tags --depth 50 pull/882/head:external-882
From https://github.com/starsimhub/starsim
 * [new ref]         refs/pull/882/head -> external-882
 * [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: 2025-04-30T19:30:07.705644Z, end-time: 2025-04-30T19:30:07.754291Z, duration: 0, exit-code: 0
git checkout --force b846fae9420a379c05f4d62144f445bf33057fb6
Note: switching to 'b846fae9420a379c05f4d62144f445bf33057fb6'.

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 <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at b846fae working on notebooks build

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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: 2025-04-30T19:30:11.426071Z, end-time: 2025-04-30T19:30:11.481945Z, duration: 0, exit-code: 0
asdf global python 3.11.10


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python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.11.10.final.0-64 in 470ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/882, 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

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python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/882/lib/python3.11/site-packages (23.1)
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/882/lib/python3.11/site-packages (67.6.1)
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Installing collected packages: setuptools, pip
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      Successfully uninstalled setuptools-67.6.1
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Successfully installed pip-25.1 setuptools-80.1.0

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python -m pip install --upgrade --no-cache-dir sphinx
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Installing collected packages: snowballstemmer, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, roman-numerals-py, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx

Successfully installed Jinja2-3.1.6 MarkupSafe-3.0.2 Pygments-2.19.1 alabaster-1.0.0 babel-2.17.0 certifi-2025.4.26 charset-normalizer-3.4.1 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-25.0 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 urllib3-2.4.0

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python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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Installing collected packages: webencodings, wcwidth, pure-eval, ptyprocess, fastjsonschema, zipp, widgetsnbextension, websocket-client, webcolors, watchdog, uri-template, typing-extensions, types-python-dateutil, traitlets, tornado, tinycss2, tabulate, soupsieve, sniffio, six, send2trash, rpds-py, rfc3986-validator, pyzmq, pyyaml, python-json-logger, pycparser, psutil, prompt_toolkit, prometheus-client, platformdirs, pexpect, pathspec, parso, pandocfilters, overrides, nest-asyncio, mypy-extensions, mistune, mdurl, jupyterlab_widgets, jupyterlab-pygments, jsonpointer, json5, ipython-pygments-lexers, importlib-resources, h11, greenlet, fqdn, executing, defusedxml, decorator, debugpy, colorama, click, bleach, beartype, attrs, async-lru, asttokens, annotated-types, typing-inspection, terminado, stack_data, sqlalchemy, rfc3339-validator, referencing, python-dateutil, pydantic-core, matplotlib-inline, markdown-it-py, jupyter-core, jedi, importlib-metadata, httpcore, griffe, comm, cffi, black, beautifulsoup4, anyio, rich, pydantic, jupyter-server-terminals, jupyter-client, jsonschema-specifications, ipython, httpx, arrow, argon2-cffi-bindings, plum-dispatch, jsonschema, isoduration, ipywidgets, ipykernel, argon2-cffi, sphobjinv, nbformat, jupyter-console, quartodoc, nbclient, jupyter-events, nbconvert, jupyter-cache, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab, notebook, jupyter

Successfully installed annotated-types-0.7.0 anyio-4.9.0 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-3.0.0 async-lru-2.0.5 attrs-25.3.0 beartype-0.20.2 beautifulsoup4-4.13.4 black-25.1.0 bleach-6.2.0 cffi-1.17.1 click-8.1.8 colorama-0.4.6 comm-0.2.2 debugpy-1.8.14 decorator-5.2.1 defusedxml-0.7.1 executing-2.2.0 fastjsonschema-2.21.1 fqdn-1.5.1 greenlet-3.2.1 griffe-1.7.3 h11-0.16.0 httpcore-1.0.9 httpx-0.28.1 importlib-metadata-8.7.0 importlib-resources-6.5.2 ipykernel-6.29.5 ipython-9.2.0 ipython-pygments-lexers-1.1.1 ipywidgets-8.1.6 isoduration-20.11.0 jedi-0.19.2 json5-0.12.0 jsonpointer-3.0.0 jsonschema-4.23.0 jsonschema-specifications-2025.4.1 jupyter-1.1.1 jupyter-cache-1.0.1 jupyter-client-8.6.3 jupyter-console-6.6.3 jupyter-core-5.7.2 jupyter-events-0.12.0 jupyter-lsp-2.2.5 jupyter-server-2.15.0 jupyter-server-terminals-0.5.3 jupyterlab-4.4.1 jupyterlab-pygments-0.3.0 jupyterlab-server-2.27.3 jupyterlab_widgets-3.0.14 markdown-it-py-3.0.0 matplotlib-inline-0.1.7 mdurl-0.1.2 mistune-3.1.3 mypy-extensions-1.1.0 nbclient-0.10.2 nbconvert-7.16.6 nbformat-5.10.4 nest-asyncio-1.6.0 notebook-7.4.1 notebook-shim-0.2.4 overrides-7.7.0 pandocfilters-1.5.1 parso-0.8.4 pathspec-0.12.1 pexpect-4.9.0 platformdirs-4.3.7 plum-dispatch-2.5.7 prometheus-client-0.21.1 prompt_toolkit-3.0.51 psutil-7.0.0 ptyprocess-0.7.0 pure-eval-0.2.3 pycparser-2.22 pydantic-2.11.4 pydantic-core-2.33.2 python-dateutil-2.9.0.post0 python-json-logger-3.3.0 pyyaml-6.0.2 pyzmq-26.4.0 quartodoc-0.9.1 referencing-0.36.2 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rich-14.0.0 rpds-py-0.24.0 send2trash-1.8.3 six-1.17.0 sniffio-1.3.1 soupsieve-2.7 sphobjinv-2.3.1.2 sqlalchemy-2.0.40 stack_data-0.6.3 tabulate-0.9.0 terminado-0.18.1 tinycss2-1.4.0 tornado-6.4.2 traitlets-5.14.3 types-python-dateutil-2.9.0.20241206 typing-extensions-4.13.2 typing-inspection-0.4.0 uri-template-1.3.0 watchdog-6.0.0 wcwidth-0.2.13 webcolors-24.11.1 webencodings-0.5.1 websocket-client-1.8.0 widgetsnbextension-4.0.14 zipp-3.21.0

[rtd-command-info] start-time: 2025-04-30T19:30:42.597713Z, end-time: 2025-04-30T19:31:05.220563Z, duration: 22, exit-code: 0
python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .
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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-2.3.2-py3-none-any.whl size=157731 sha256=1cacf06f5878cdb67f6fb7de8fcbabf1c9482c7f0454c1682e28901f4c08a8b2
  Stored in directory: /tmp/pip-ephem-wheel-cache-66poghke/wheels/0a/e2/cc/60cb42f61a3645607061b53e0f2c735ec68aa3861b564dd707
Successfully built starsim
Installing collected packages: pytz, zstandard, xlsxwriter, tzdata, tqdm, smmap, pyparsing, pillow, numpy, networkx, memory_profiler, Mako, llvmlite, line_profiler, kiwisolver, jsonpickle, jellyfish, fonttools, et-xmlfile, dill, cycler, colorlog, scipy, pandas, openpyxl, numba, multiprocess, gitdb, contourpy, alembic, optuna, matplotlib, gitpython, seaborn, sciris, starsim

Successfully installed Mako-1.3.10 alembic-1.15.2 colorlog-6.9.0 contourpy-1.3.2 cycler-0.12.1 dill-0.4.0 et-xmlfile-2.0.0 fonttools-4.57.0 gitdb-4.0.12 gitpython-3.1.44 jellyfish-1.2.0 jsonpickle-4.0.5 kiwisolver-1.4.8 line_profiler-4.2.0 llvmlite-0.44.0 matplotlib-3.10.1 memory_profiler-0.61.0 multiprocess-0.70.18 networkx-3.4.2 numba-0.61.2 numpy-2.2.5 openpyxl-3.1.5 optuna-4.3.0 pandas-2.2.3 pillow-11.2.1 pyparsing-3.2.3 pytz-2025.2 scipy-1.15.2 sciris-3.2.1 seaborn-0.13.2 smmap-5.0.2 starsim-2.3.2 tqdm-4.67.1 tzdata-2025.2 xlsxwriter-3.2.3 zstandard-0.23.0

[rtd-command-info] start-time: 2025-04-30T19:31:05.404251Z, end-time: 2025-04-30T19:31:05.439326Z, 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: 2025-04-30T19:31:05.500176Z, end-time: 2025-04-30T19:31:11.666925Z, duration: 6, exit-code: 2
python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v8.2.3
loading translations [en]... done

Extension error!

Versions
========

* Platform:         linux; (Linux-6.8.0-1021-aws-x86_64-with-glibc2.35)
* Python version:   3.11.10 (CPython)
* Sphinx version:   8.2.3
* Docutils version: 0.21.2
* Jinja2 version:   3.1.6
* Pygments version: 2.19.1

Last Messages
=============

None.

Loaded Extensions
=================

None.

Traceback
=========

    Traceback (most recent call last):
      File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/882/lib/python3.11/site-packages/sphinx/registry.py", line 541, in load_extension
        mod = import_module(extname)
              ^^^^^^^^^^^^^^^^^^^^^^
      File "/home/docs/.asdf/installs/python/3.11.10/lib/python3.11/importlib/__init__.py", line 126, in import_module
        return _bootstrap._gcd_import(name[level:], package, level)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "<frozen importlib._bootstrap>", line 1204, in _gcd_import
      File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
      File "<frozen importlib._bootstrap>", line 1140, in _find_and_load_unlocked
    ModuleNotFoundError: No module named 'sphinx_autodoc_typehints'
    
    The above exception was the direct cause of the following exception:
    
    Traceback (most recent call last):
      File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/882/lib/python3.11/site-packages/sphinx/cmd/build.py", line 414, in build_main
        app = Sphinx(
              ^^^^^^^
      File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/882/lib/python3.11/site-packages/sphinx/application.py", line 291, in __init__
        self.setup_extension(extension)
      File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/882/lib/python3.11/site-packages/sphinx/application.py", line 489, in setup_extension
        self.registry.load_extension(self, extname)
      File "/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-starsim/envs/882/lib/python3.11/site-packages/sphinx/registry.py", line 544, in load_extension
        raise ExtensionError(
    sphinx.errors.ExtensionError: Could not import extension sphinx_autodoc_typehints (exception: No module named 'sphinx_autodoc_typehints')


The full traceback has been saved in:
/tmp/sphinx-err-4lxrvpmy.log

To report this error to the developers, please open an issue at <https://github.com/sphinx-doc/sphinx/issues/>. Thanks!
Please also report this if it was a user error, so that a better error message can be provided next time.