Read the Docs build information Build id: 2005175 Project: institute-for-disease-modeling-hpvsim Version: latest Commit: 300adad34dbf9e83a7a5139045e2233eb63c373e Date: 2024-02-08T22:33:37.370321Z State: cancelled Success: False [rtd-command-info] start-time: 2024-02-08T22:33:47.764175Z, end-time: 2024-02-08T22:33:48.278708Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/InstituteforDiseaseModeling/hpvsim.git . Cloning into '.'... [rtd-command-info] start-time: 2024-02-08T22:33:48.348193Z, end-time: 2024-02-08T22:33:49.789952Z, 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/hpvsim * [new tag] v0.3.7 -> v0.3.7 * [new tag] v0.4.0 -> v0.4.0 * [new tag] v0.4.16 -> v0.4.16 * [new tag] v0.4.5 -> v0.4.5 * [new tag] v1.0.0 -> v1.0.0 * [new tag] v1.1.1 -> v1.1.1 * [new tag] v1.2.0 -> v1.2.0 * [new tag] v1.2.2 -> v1.2.2 * [new tag] v1.2.3 -> v1.2.3 * [new tag] v1.2.4 -> v1.2.4 * [new tag] v1.2.5 -> v1.2.5 * [new tag] v1.2.6 -> v1.2.6 * [new tag] v1.2.7 -> v1.2.7 * [new tag] v2.0.0 -> v2.0.0 [rtd-command-info] start-time: 2024-02-08T22:33:49.920783Z, end-time: 2024-02-08T22:33:49.993849Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: switching to 'origin/main'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 300adad Merge pull request #655 from amath-idm/reconcile-docs [rtd-command-info] start-time: 2024-02-08T22:33:50.060483Z, end-time: 2024-02-08T22:33:50.120299Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2024-02-08T22:33:50.183933Z, end-time: 2024-02-08T22:33:50.242513Z, 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-20.04 tools: python: "3.9" # 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: # Optionally declare the Python requirements required to build your docs python: install: - requirements: docs/requirements.txt - method: pip path: . [rtd-command-info] start-time: 2024-02-08T22:33:55.456720Z, end-time: 2024-02-08T22:33:55.531715Z, duration: 0, exit-code: 0 asdf global python 3.9.18 [rtd-command-info] start-time: 2024-02-08T22:33:55.939879Z, end-time: 2024-02-08T22:33:57.113473Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.18.final.0-64 in 861ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2024-02-08T22:33:57.187852Z, end-time: 2024-02-08T22:34:08.864738Z, duration: 11, exit-code: 0 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(line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2b/27/77f9d5684e6bce929f5cfe18d6cfbe5133013c06cb2fbf5933670e60761d/pure_eval-0.2.2-py3-none-any.whl (11 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-2.3-py3-none-any.whl size=33262 sha256=f40795ff142334a5b8278f8db78ee67501e74a213d786818788d174159e52378 Stored in directory: /tmp/pip-ephem-wheel-cache-5tt_6dru/wheels/17/20/73/b6171d60f96c3f21affca3e77ebcc2d8be3b55e198349b1b54 Successfully built pandoc Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, ply, fastjsonschema, tzdata, typing-extensions, traitlets, tqdm, tornado, tinycss2, soupsieve, six, rpds-py, readthedocs-sphinx-search, pyzmq, PyYAML, pyparsing, pypandoc, psutil, prompt-toolkit, plumbum, platformdirs, pillow, pexpect, parso, pandocfilters, numpy, nest-asyncio, mistune, Mako, kiwisolver, jupyterlab-pygments, importlib-resources, greenlet, fonttools, executing, exceptiongroup, defusedxml, decorator, debugpy, cycler, colorlog, attrs, accessible-pygments, sqlalchemy, referencing, python-dateutil, plantweb, pandoc, matplotlib-inline, jupyter-core, jedi, contourpy, comm, bleach, beautifulsoup4, asttokens, stack-data, sphinx-design, sphinx-autodoc-typehints, pydata-sphinx-theme, pandas, matplotlib, jupyter-client, jsonschema-specifications, alembic, seaborn, optuna, jsonschema, ipython, nbformat, ipykernel, nbclient, nbconvert, nbsphinx Successfully installed Mako-1.3.2 PyYAML-6.0.1 accessible-pygments-0.0.4 alembic-1.13.1 asttokens-2.4.1 attrs-23.2.0 beautifulsoup4-4.12.3 bleach-6.1.0 colorlog-6.8.2 comm-0.2.1 contourpy-1.2.0 cycler-0.12.1 debugpy-1.8.0 decorator-5.1.1 defusedxml-0.7.1 exceptiongroup-1.2.0 executing-2.0.1 fastjsonschema-2.19.1 fonttools-4.48.1 greenlet-3.0.3 importlib-resources-6.1.1 ipykernel-6.29.2 ipython-8.18.1 jedi-0.19.1 jsonschema-4.21.1 jsonschema-specifications-2023.12.1 jupyter-client-8.6.0 jupyter-core-5.7.1 jupyterlab-pygments-0.3.0 kiwisolver-1.4.5 matplotlib-3.8.2 matplotlib-inline-0.1.6 mistune-3.0.2 nbclient-0.9.0 nbconvert-7.16.0 nbformat-5.9.2 nbsphinx-0.9.3 nest-asyncio-1.6.0 numpy-1.26.4 optuna-3.5.0 pandas-2.2.0 pandoc-2.3 pandocfilters-1.5.1 parso-0.8.3 pexpect-4.9.0 pillow-10.2.0 plantweb-1.2.1 platformdirs-4.2.0 plumbum-1.8.2 ply-3.11 prompt-toolkit-3.0.43 psutil-5.9.8 ptyprocess-0.7.0 pure-eval-0.2.2 pydata-sphinx-theme-0.15.2 pypandoc-1.12 pyparsing-3.1.1 python-dateutil-2.8.2 pytz-2024.1 pyzmq-25.1.2 readthedocs-sphinx-search-0.3.2 referencing-0.33.0 rpds-py-0.17.1 seaborn-0.13.2 six-1.16.0 soupsieve-2.5 sphinx-autodoc-typehints-2.0.0 sphinx-design-0.5.0 sqlalchemy-2.0.25 stack-data-0.6.3 tinycss2-1.2.1 tornado-6.4 tqdm-4.66.1 traitlets-5.14.1 typing-extensions-4.9.0 tzdata-2023.4 wcwidth-0.2.13 webencodings-0.5.1 [rtd-command-info] start-time: 2024-02-08T22:35:08.304710Z, end-time: 2024-02-08T22:35:24.444137Z, duration: 16, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir . 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/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hpvsim/envs/latest/lib/python3.9/site-packages (from Mako->alembic>=1.5.0->optuna->hpvsim==2.0.0) (2.1.5) Building wheels for collected packages: hpvsim Building wheel for hpvsim (setup.py): started Building wheel for hpvsim (setup.py): finished with status 'done' Created wheel for hpvsim: filename=hpvsim-2.0.0-py3-none-any.whl size=193342 sha256=4edef409672e023de4bf356cd0724f058fe8adbe9a4a453ae4263c9d0ac55424 Stored in directory: /tmp/pip-ephem-wheel-cache-cmi46_cw/wheels/51/35/6f/df976332f8d726e8d5b6219b83a0569f551e10d63ed39a50fb Successfully built hpvsim Installing collected packages: zstandard, xlsxwriter, smmap, scipy, memory-profiler, line-profiler, jsonpickle, jellyfish, et-xmlfile, dill, openpyxl, multiprocess, gitdb, gitpython, sciris, hpvsim Successfully installed dill-0.3.8 et-xmlfile-1.1.0 gitdb-4.0.11 gitpython-3.1.41 hpvsim-2.0.0 jellyfish-1.0.3 jsonpickle-3.0.2 line-profiler-4.1.2 memory-profiler-0.61.0 multiprocess-0.70.16 openpyxl-3.1.2 scipy-1.12.0 sciris-3.1.3 smmap-5.0.1 xlsxwriter-3.1.9 zstandard-0.22.0 [rtd-command-info] start-time: 2024-02-08T22:35:24.963496Z, end-time: 2024-02-08T22:35:25.025286Z, 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 hpvsim as hpv # Set environment os.environ['SPHINX_BUILD'] = 'True' # This is used so hpv.options.set('jupyter') doesn't reset the Matplotlib renderer on_rtd = os.environ.get('READTHEDOCS') == 'True' # -- Project information ----------------------------------------------------- project = 'HPVsim' copyright = f'2020 - {sc.now().year}, Bill & Melinda Gates Foundation. All rights reserved.\nThese docs were built for HPVsim version {hpv.__version__}.\n' author = 'Institute for Disease Modeling' # The short X.Y version version = hpv.__version__ # The full version, including alpha/beta/rc tags release = hpv.__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 = ["hpvsim."] # 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://hpvsim.org", "icon": "fas fa-home"}, { "name": "GitHub", "url": "https://github.com/institutefordiseasemodeling/hpvsim", "icon": "fab fa-github-square", }, ], "navbar_end": ["theme-switcher", "navbar-icon-links"], "secondary_sidebar_items": ["navbar-side"], "header_links_before_dropdown": 5, } html_sidebars = { "**": ["sidebar-nav-bs", "page-toc"], } html_logo = "images/IDM_white.png" html_favicon = "images/favicon.ico" html_static_path = ['_static'] html_baseurl = "https://docs.idmod.org/projects/hpvsim/en/latest" html_context = { 'rtd_url': 'https://docs.idmod.org/projects/hpvsim/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 = 'HPVsim' # Add customizations def setup(app): app.add_css_file("theme_overrides.css") # Modify this to not rerun the Jupyter notebook cells -- usually set by build_docs nb_ex_default = ['auto', 'never'][0] nb_ex = os.getenv('NBSPHINX_EXECUTE') if not nb_ex: nb_ex = nb_ex_default print(f'\n\nBuilding Jupyter notebooks with build option: {nb_ex}\n\n') nbsphinx_execute = nb_ex # OpenSearch options html_use_opensearch = 'docs.idmod.org/projects/hpvsim/en/latest' # -- RTD Sphinx search for searching across the entire domain, default child ------------- if os.environ.get('READTHEDOCS') == 'True': search_project_parent = "institute-for-disease-modeling-idm" search_project = os.environ["READTHEDOCS_PROJECT"] search_version = os.environ["READTHEDOCS_VERSION"] rtd_sphinx_search_default_filter = f"subprojects:{search_project}/{search_version}" rtd_sphinx_search_filters = { "Search this project": f"project:{search_project}/{search_version}", "Search all IDM docs": f"subprojects:{search_project_parent}/{search_version}", } ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Define this variable in case it's not defined by the user. # It defaults to `alabaster` which is the default from Sphinx. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme html_theme = globals().get('html_theme', 'alabaster') #Add project information to the template context. context = { 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ("v2.0.0", "/en/v2.0.0/"), ("v1.2.7", "/en/v1.2.7/"), ("v1.2.6", "/en/v1.2.6/"), ("v1.2.5", "/en/v1.2.5/"), ("v1.2.4", "/en/v1.2.4/"), ("v1.2.3", "/en/v1.2.3/"), ("v1.2.2", "/en/v1.2.2/"), ("v1.2.0", "/en/v1.2.0/"), ("v1.1.1", "/en/v1.1.1/"), ("v1.0.0", "/en/v1.0.0/"), ("v0.4.16", "/en/v0.4.16/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-hpvsim', 'name': u'hpvsim', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': '', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'hpvsim', 'github_version': 'main', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'main', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'main', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '300adad3', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): for key in context: if key not in html_context: html_context[key] = context[key] else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-hpvsim/builds/2005175/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build'])