Read the Docs build information Build id: 2822940 Project: institute-for-disease-modeling-synthpops-test Version: latest Commit: 6e838173b7633ca3f391bfaa038b9740782b1f5d Date: 2025-02-20T16:11:42.117786Z State: finished Success: True [rtd-command-info] start-time: 2025-02-20T16:11:43.215851Z, end-time: 2025-02-20T16:11:43.839990Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/InstituteforDiseaseModeling/synthpops.git . Cloning into '.'... [rtd-command-info] start-time: 2025-02-20T16:11:43.903464Z, end-time: 2025-02-20T16:11:45.187198Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main From https://github.com/InstituteforDiseaseModeling/synthpops * [new tag] v1.6.0 -> v1.6.0 * [new tag] v1.6.1 -> v1.6.1 * [new tag] v1.7.5 -> v1.7.5 * [new tag] v1.7.6 -> v1.7.6 * [new tag] v1.7.7 -> v1.7.7 * [new tag] v1.8.0 -> v1.8.0 * [new tag] v1.8.1 -> v1.8.1 * [new tag] v1.8.2 -> v1.8.2 * [new tag] v1.8.3 -> v1.8.3 * [new tag] v1.8.4 -> v1.8.4 * [new tag] v1.9.0 -> v1.9.0 [rtd-command-info] start-time: 2025-02-20T16:11:45.317226Z, end-time: 2025-02-20T16:11:45.403386Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: switching to 'origin/main'. You are in 'detached HEAD' state. 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[rtd-command-info] start-time: 2025-02-20T16:11:50.448394Z, end-time: 2025-02-20T16:11:50.510834Z, duration: 0, exit-code: 0 asdf global python 3.11.10 [rtd-command-info] start-time: 2025-02-20T16:11:50.838549Z, end-time: 2025-02-20T16:11:51.744793Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.11.10.final.0-64 in 652ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2025-02-20T16:11:51.817343Z, end-time: 2025-02-20T16:12:00.354517Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.11/site-packages (23.1) Collecting pip Downloading pip-25.0.1-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 10.5 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/envs/latest/lib/python3.11/site-packages (67.6.1) Collecting setuptools Downloading setuptools-75.8.0-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 21.7 MB/s eta 0:00:00 Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 67.6.1 Uninstalling setuptools-67.6.1: Successfully uninstalled setuptools-67.6.1 Attempting uninstall: pip Found existing installation: pip 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alabaster, requests, Jinja2, sphinx Successfully installed Jinja2-3.1.5 MarkupSafe-3.0.2 Pygments-2.19.1 alabaster-1.0.0 babel-2.17.0 certifi-2025.1.31 charset-normalizer-3.4.1 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-24.2 requests-2.32.3 roman-numerals-py-3.0.0 snowballstemmer-2.2.0 sphinx-8.2.0 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.3.0 [rtd-command-info] start-time: 2025-02-20T16:12:05.638490Z, end-time: 2025-02-20T16:12:07.872747Z, duration: 2, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting pytest (from -r docs/requirements.txt (line 1)) Downloading pytest-8.3.4-py3-none-any.whl.metadata (7.5 kB) Collecting sphinx-rtd-theme (from -r docs/requirements.txt (line 2)) Downloading sphinx_rtd_theme-3.0.2-py2.py3-none-any.whl.metadata (4.4 kB) Collecting sphinxcontrib-napoleon 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ply-3.11-py2.py3-none-any.whl (49 kB) Building wheels for collected packages: pandoc Building wheel for pandoc (setup.py): started Building wheel for pandoc (setup.py): finished with status 'done' Created wheel for pandoc: filename=pandoc-2.4-py3-none-any.whl size=34843 sha256=3c86ab11cfa657e6a44073ecb630f8fa7fa2f252816e01c960fcd21a369ccab3 Stored in directory: /tmp/pip-ephem-wheel-cache-pek7bc35/wheels/4f/d7/32/c6c9b7b05e852e920fd72174487be3a0f18e633a7adcc303be Successfully built pandoc Installing collected packages: ply, six, pypandoc, plumbum, pluggy, iniconfig, pytest, pockets, plantweb, pandoc, sphinxcontrib-napoleon, sphinxcontrib-jquery, sphinx-rtd-theme Successfully installed iniconfig-2.0.0 pandoc-2.4 plantweb-1.3.0 pluggy-1.5.0 plumbum-1.9.0 ply-3.11 pockets-0.9.1 pypandoc-1.15 pytest-8.3.4 six-1.17.0 sphinx-rtd-theme-3.0.2 sphinxcontrib-jquery-4.1 sphinxcontrib-napoleon-0.7 [rtd-command-info] start-time: 2025-02-20T16:12:07.942886Z, end-time: 2025-02-20T16:12:48.890007Z, 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Downloading gitdb-4.0.12-py3-none-any.whl (62 kB) Downloading et_xmlfile-2.0.0-py3-none-any.whl (18 kB) Downloading smmap-5.0.2-py3-none-any.whl (24 kB) Building wheels for collected packages: synthpops, jsonobject Building wheel for synthpops (setup.py): started Building wheel for synthpops (setup.py): finished with status 'done' Created wheel for synthpops: filename=synthpops-1.10.5-py3-none-any.whl size=1526980 sha256=ae343749e7d052979d662dd6367bee00a0056cf6c9af8252d54e345c413d9b78 Stored in directory: /tmp/pip-ephem-wheel-cache-ewbhio9q/wheels/55/96/a1/ff11c0227cb951974ca9d276ac81d2620b7907a3b2a1712829 Building wheel for jsonobject (setup.py): started Building wheel for jsonobject (setup.py): finished with status 'done' Created wheel for jsonobject: filename=jsonobject-2.2.0-cp311-cp311-linux_x86_64.whl size=1842188 sha256=b092af3efba9acfb505e0c1945a25cc689b7530f4708dd8984ccff7b34d5cebf Stored in directory: /tmp/pip-ephem-wheel-cache-ewbhio9q/wheels/a4/a1/47/6c325aee0ec8b0352ef0ff9a5bbd72a3e6ba6da43cd8646661 Successfully built synthpops jsonobject Installing collected packages: pytz, jsonobject, editorconfig, zstandard, xlsxwriter, tzdata, tqdm, smmap, pyyaml, python-dateutil, pyparsing, psutil, pillow, numpy, networkx, llvmlite, line-profiler, kiwisolver, jsonpickle, jsbeautifier, jellyfish, graphviz, fonttools, et-xmlfile, dill, cycler, scipy, pydot, pandas, openpyxl, numba, multiprocess, memory-profiler, gitdb, contourpy, colorspacious, matplotlib, gitpython, seaborn, sciris, cmocean, cmasher, synthpops Successfully installed cmasher-1.9.2 cmocean-4.0.3 colorspacious-1.1.2 contourpy-1.3.1 cycler-0.12.1 dill-0.3.9 editorconfig-0.17.0 et-xmlfile-2.0.0 fonttools-4.56.0 gitdb-4.0.12 gitpython-3.1.44 graphviz-0.20.3 jellyfish-1.1.3 jsbeautifier-1.15.3 jsonobject-2.2.0 jsonpickle-4.0.2 kiwisolver-1.4.8 line-profiler-4.2.0 llvmlite-0.44.0 matplotlib-3.10.0 memory-profiler-0.61.0 multiprocess-0.70.17 networkx-3.4.2 numba-0.61.0 numpy-2.1.3 openpyxl-3.1.5 pandas-2.2.3 pillow-11.1.0 psutil-7.0.0 pydot-3.0.4 pyparsing-3.2.1 python-dateutil-2.9.0.post0 pytz-2025.1 pyyaml-6.0.2 scipy-1.15.2 sciris-3.2.0 seaborn-0.13.2 smmap-5.0.2 synthpops-1.10.5 tqdm-4.67.1 tzdata-2025.1 xlsxwriter-3.2.2 zstandard-0.23.0 [rtd-command-info] start-time: 2025-02-20T16:12:49.076486Z, end-time: 2025-02-20T16:12:49.129782Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Configuration file for the Sphinx documentation builder. # # This file does only contain a selection of the most common options. For a # full list see the documentation: # http://www.sphinx-doc.org/en/master/config # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # import os import subprocess import sys import synthpops as sp import sphinx_rtd_theme on_rtd = os.environ.get('READTHEDOCS') == 'True' if sys.platform in ["linux", "darwin"]: subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) else: subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) # Rename "synthpops package" to "API reference" filename = 'modules.rst' # This must match the Makefile with open(filename) as f: # Read existing file lines = f.readlines() lines[0] = "API reference\n" # Blast away the existing heading and replace with this lines[1] = "=============\n" # Ensure the heading is the right length with open(filename, "w") as f: # Write new file f.writelines(lines) # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx_rtd_theme', 'sphinx.ext.mathjax', 'sphinx.ext.githubpages', 'sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'sphinx.ext.todo', 'sphinx.ext.viewcode', # Add a link to the Python source code for classes, functions etc. ] autodoc_default_options = { 'member-order': 'bysource', 'members': None } autodoc_mock_imports = [] napoleon_google_docstring = True # Configure autosummary autosummary_generate = True # Turn on sphinx.ext.autosummary autoclass_content = "both" # Add __init__ doc (ie. params) to class summaries html_show_sourcelink = False # Remove 'view source code' from top of page (for html, not python) 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'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: source_suffix = '.rst' master_doc = 'index' # General information about the project. project = 'SynthPops' copyright = f'2020 - 2021, Institute for Disease Modeling. All rights reserved.\nThese docs were built for SynthPops version {sp.__version__}.\n' author = 'Institute for Disease Modeling' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. version = sp.__version__ # The full version, including alpha/beta/rc tags. release = sp.__version__ # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = 'en' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # suppress warnings for multiple possible Python references in the namespace # suppress_warnings = ['ref.python'] pygments_style = 'sphinx' # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # RST epilog is added to the end of every topic. Useful for replace # directives to use across the docset. rst_epilog = "\n.. include:: /variables.txt" # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' html_logo = "images/IDM_white.png" html_favicon = "images/favicon.ico" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] html_context = { 'rtd_url': 'https://docs.idmod.org/projects/synthpops/en/latest', 'theme_vcs_pageview_mode': 'edit', 'css_files': [ '_static/theme_overrides.css' ] } # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the documentation. # if not on_rtd: html_extra_path = ['robots.txt'] # If not None, a 'Last updated on:' timestamp is inserted at every page # bottom, using the given strftime format. # The empty string is equivalent to '%b %d, %Y'. # html_last_updated_fmt = '%Y-%b-%d' # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. html_show_sphinx = False # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. html_use_opensearch = 'docs.idmod.org/projects/synthpops/en/latest' # Output file base name for HTML help builder. htmlhelp_basename = 'SynthPops' # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. 'preamble': '%XeLaTeX packages' '\\usepackage{xltxtra}' '\\usepackage{fontspec} %%Font package' '\\usepackage{xunicode}' '%%Select fonts' '\\setmainfont[Mapping=tex-text]{nimbusserif}' '\\setsansfont[Mapping=tex-text]{nimbussans}' '\\setmonofont{nimbusmono}', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'synthpops-docs.tex', u'SynthPops', 'Institute for Disease Modeling', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. # # latex_logo = None # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'synthpops-docs', 'SynthPops', [author], 1) ] # If true, show URL addresses after external links. # man_show_urls = True # -- Options for Texinfo output ------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'synthpops-docs', 'SynthPops', author, 'Institute for Disease Modeling', 'How to use SynthPops for creating synthetic populations.', 'Miscellaneous'), ] # Example configuration for intersphinx: refer to the Python standard library. # intersphinx_mapping = {'https://docs.python.org/': None} [rtd-command-info] start-time: 2025-02-20T16:12:49.207692Z, end-time: 2025-02-20T16:13:36.315802Z, duration: 47, exit-code: 0 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v8.2.0 Matplotlib is building the font cache; this may take a moment. loading translations [en]... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 34 source files that are out of date updating environment: [new config] 34 added, 0 changed, 0 removed reading sources... [ 3%] algorithm reading sources... [ 6%] glossary reading sources... [ 9%] households reading sources... [ 12%] index reading sources... [ 15%] input_data reading sources... [ 18%] installation reading sources... [ 21%] modules reading sources... [ 24%] overview reading sources... [ 26%] schools reading sources... [ 29%] synthpops.base reading sources... [ 32%] synthpops.config reading sources... [ 35%] synthpops.contact_networks reading sources... [ 38%] synthpops.data reading sources... [ 41%] synthpops.data_distributions reading sources... [ 44%] synthpops.defaults reading sources... [ 47%] synthpops.households reading sources... [ 50%] synthpops.ltcfs reading sources... [ 53%] synthpops.people reading sources... [ 56%] synthpops.people.country_age_data reading sources... [ 59%] synthpops.people.household_size_data reading sources... [ 62%] synthpops.people.loaders reading sources... [ 65%] synthpops.people.makepop reading sources... 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Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/_readthedocs/html/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/_readthedocs/html/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/_readthedocs/html/_static/documentation_options.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-synthpops-test/checkouts/latest/_readthedocs/html/_static/js/versions.js copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 3%] algorithm writing output... [ 6%] glossary writing output... [ 9%] households writing output... 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[ 58%] synthpops.people.loaders highlighting module code... [ 63%] synthpops.people.makepop highlighting module code... [ 68%] synthpops.people.people highlighting module code... [ 74%] synthpops.people.utils highlighting module code... [ 79%] synthpops.plotting highlighting module code... [ 84%] synthpops.pop highlighting module code... [ 89%] synthpops.sampling highlighting module code... [ 95%] synthpops.schools highlighting module code... [100%] synthpops.workplaces writing additional pages... search opensearch done dumping search index in English (code: en)... done dumping object inventory... done build succeeded. The HTML pages are in ../_readthedocs/html.