Read the Docs build information Build id: 1357375 Project: institute-for-disease-modeling-emod-hiv Version: latest Commit: aca0a6f6b29c44bbc2ac6a3e9e4fc2ad1fc83293 Date: 2023-03-16T23:31:51.087088Z State: cancelled Success: False [rtd-command-info] start-time: 2023-03-16T23:31:52.932154Z, end-time: 2023-03-16T23:32:11.373518Z, duration: 18, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/EMOD-docs.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.112' (ECDSA) to the list of known hosts. [rtd-command-info] start-time: 2023-03-16T23:32:11.707094Z, end-time: 2023-03-16T23:32:12.175306Z, duration: 0, exit-code: 0 git checkout --force origin/malaria-ongoing Note: switching to 'origin/malaria-ongoing'. 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 aca0a6f6 Merge pull request #1621 from KElsaesser-IDM/1595-report-HIV-age-gender [rtd-command-info] start-time: 2023-03-16T23:32:12.384534Z, end-time: 2023-03-16T23:32:12.461441Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-03-16T23:32:13.609191Z, end-time: 2023-03-16T23:32:18.097467Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/bin/python Installing setuptools, pip, wheel... done. 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recommonmark Successfully installed MarkupSafe-2.1.2 Pygments-2.14.0 alabaster-0.7.13 babel-2.12.1 certifi-2022.12.7 charset-normalizer-3.1.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.0 pillow-5.4.1 pytz-2022.7.1 readthedocs-sphinx-ext-2.2.0 recommonmark-0.5.0 requests-2.28.2 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.15 [rtd-command-info] start-time: 2023-03-16T23:32:26.960674Z, end-time: 2023-03-16T23:32:30.264418Z, duration: 3, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Requirement already satisfied: sphinx-rtd-theme in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 1)) (0.4.3) Collecting sphinxcontrib-napoleon~=0.7 Downloading 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urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 3)) (1.26.15) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-websupport->sphinx->-r requirements.txt (line 3)) (1.1.5) Installing collected packages: pockets, numpy, sphinxcontrib-napoleon, plantweb, numpydoc Successfully installed numpy-1.19.5 numpydoc-1.0.0 plantweb-1.2.1 pockets-0.9.1 sphinxcontrib-napoleon-0.7 [rtd-command-info] start-time: 2023-03-16T23:32:31.928102Z, end-time: 2023-03-16T23:32:31.992385Z, duration: 0, exit-code: 0 cat emod/hiv/conf.py # -*- coding: utf-8 -*- # # Sphinx Demo documentation build configuration file, created by # sphinx-quickstart on Fri Aug 26 16:52:16 2016. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # 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. # # See all configuration options: # https://www.sphinx-doc.org/en/master/usage/configuration.html import os import sys # -- Shared Configuration ------------------------------------------------- sys.path.insert(0, os.path.abspath(f"{os.path.dirname(__file__)}/..")) from conf import * # -- Project Information -------------------------------------------------- # General information about the project. project = 'HIV Model' key = "emod-hiv" # Additional Metadata short_title = 'EMOD for HIV' long_title = 'EMOD Modeling Software for HIV' description = 'How to use the IDM EMOD software for modeling HIV.' # -- General configuration ------------------------------------------------ tags.add('hiv') # -- Options for HTML output ---------------------------------------------- # A dictionary of values to pass into the template engine’s context for all pages. # Single values can also be put in this dictionary using the -A command-line option of sphinx-build. html_context.update({ 'docset_title': short_title }) # 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 = f'{opensearch_baseurl}/{key}' # -- Options for HTML help output ----------------------------------------- # Output file base name for HTML help builder. htmlhelp_basename = short_title # -- Options for LaTeX output --------------------------------------------- # 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, f'{key}-docs.tex', long_title, author, 'manual'), ] # -- 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, f'{key}-docs', long_title, [author], 1) ] # -- 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, f'{key}-docs', long_title, author, author, description, 'Miscellaneous'), ] ########################################################################### # 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') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} # This following legacy behavior will gradually be sliced out until its deprecated and removed. # Skipped for Sphinx 6+ # Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH # Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023) if ( using_rtd_theme and version_info < (6,0) and not False ): theme = importlib.import_module('sphinx_rtd_theme') if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] # Define websupport2_base_url and websupport2_static_url if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, '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/"), ("2.21_a", "/en/2.21_a/"), ("2.20_a", "/en/2.20_a/"), ("2.18", "/en/2.18/"), ("2.14", "/en/2.14/"), ("2.13", "/en/2.13/"), ("2.10", "/en/2.10/"), ], 'downloads': [ ("html", "//docs.idmod.org/_/downloads/emod-hiv/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-emod-hiv', 'name': u'EMOD HIV', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://docs.idmod.org/projects/emod-hiv/en/2.20_a/', 'analytics_code': 'UA-87656833-3', 'single_version': False, 'conf_py_path': '/emod/hiv/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'EMOD-docs', 'github_version': 'malaria-ongoing', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'malaria-ongoing', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'malaria-ongoing', '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': 'UA-87656833-3', 'global_analytics_code': 'UA-17997319-2', 'commit': 'aca0a6f6', } # 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(): html_context.update(context) 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-emod-hiv/builds/1357375/' 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'])