Read the Docs build information Build id: 1787955 Project: institute-for-disease-modeling-emod-hiv Version: latest Commit: 59caf23d66c5742f4857d8b2a8ecd092e2470ddd Date: 2023-10-17T21:20:30.136058Z State: finished Success: True [rtd-command-info] start-time: 2023-10-17T21:20:38.286614Z, end-time: 2023-10-17T21:20:42.850463Z, duration: 4, exit-code: 0 git clone --depth 1 git@github.com:InstituteforDiseaseModeling/EMOD-docs.git . Cloning into '.'... Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. [rtd-command-info] start-time: 2023-10-17T21:20:43.427043Z, end-time: 2023-10-17T21:20:46.137228Z, duration: 2, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/malaria-ongoing:refs/remotes/origin/malaria-ongoing Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. From github.com:InstituteforDiseaseModeling/EMOD-docs * [new branch] malaria-ongoing -> origin/malaria-ongoing [rtd-command-info] start-time: 2023-10-17T21:20:46.915221Z, end-time: 2023-10-17T21:20:47.393403Z, 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 59caf23 Merge pull request #1852 from InstituteforDiseaseModeling/rtd-update-malaria [rtd-command-info] start-time: 2023-10-17T21:20:48.845119Z, end-time: 2023-10-17T21:20:48.917583Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-10-17T21:20:49.796898Z, end-time: 2023-10-17T21:20:49.862065Z, duration: 0, exit-code: 0 cat .readthedocs.yml # .readthedocs.yml # 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: fail_on_warning: true # Build documentation with MkDocs #mkdocs: # configuration: mkdocs.yml # Optionally build your docs in additional formats such as PDF formats: - htmlzip # Optionally set the version of Python and requirements required to build your docs python: install: - requirements: requirements.txt # Optionally rank topics in search results, between -10 (lower) and 10 (higher). # 0 is normal rank, not no rank search: ranking: install-overview.html: 3 model-overview.html: 3 faq.html: 2 parameter-overview.html: 2 dev*: -5 [rtd-command-info] start-time: 2023-10-17T21:20:59.394777Z, end-time: 2023-10-17T21:20:59.478095Z, duration: 0, exit-code: 0 asdf global python 3.9.18 [rtd-command-info] start-time: 2023-10-17T21:21:01.257340Z, end-time: 2023-10-17T21:21:02.328595Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.18.final.0-64 in 721ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, 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docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, readthedocs-sphinx-ext, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, sphinx Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.3 Pygments-2.16.1 alabaster-0.7.13 babel-2.13.0 certifi-2023.7.22 charset-normalizer-3.3.0 docutils-0.20.1 idna-3.4 imagesize-1.4.1 importlib-metadata-6.8.0 packaging-23.2 readthedocs-sphinx-ext-2.2.3 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.7 sphinxcontrib-devhelp-1.0.5 sphinxcontrib-htmlhelp-2.0.4 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.6 sphinxcontrib-serializinghtml-1.1.9 urllib3-2.0.7 zipp-3.17.0 [rtd-command-info] start-time: 2023-10-17T21:21:20.329866Z, end-time: 2023-10-17T21:21:42.246540Z, duration: 21, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Collecting sphinx~=6.2.1 (from -r 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-r requirements.txt (line 8)) Downloading myst_parser-2.0.0-py3-none-any.whl.metadata (5.4 kB) Collecting readthedocs-sphinx-search~=0.3.1 (from -r requirements.txt (line 9)) Downloading readthedocs_sphinx_search-0.3.1-py3-none-any.whl (21 kB) Collecting sphinx-copybutton~=0.5.2 (from -r requirements.txt (line 10)) Downloading sphinx_copybutton-0.5.2-py3-none-any.whl (13 kB) Collecting pygithub~=1.57 (from -r requirements.txt (line 11)) Downloading PyGithub-1.59.1-py3-none-any.whl.metadata (2.0 kB) Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r requirements.txt (line 1)) (1.0.7) Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.9/site-packages (from sphinx~=6.2.1->-r requirements.txt (line 1)) (1.0.5) 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stack-data, sphinxcontrib-napoleon, pynacl, mdit-py-plugins, jupyter-server-terminals, jupyter-client, jsonschema-specifications, cryptography, arrow, argon2-cffi-bindings, jsonschema, isoduration, ipython, argon2-cffi, pygithub, nbformat, ipykernel, nbclient, jupyter-events, nbconvert, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab, sphinx, sphinxcontrib-jquery, sphinxcontrib-programoutput, sphinx-rtd-theme, sphinx-copybutton, nbsphinx, myst-parser Attempting uninstall: docutils Found existing installation: docutils 0.20.1 Uninstalling docutils-0.20.1: Successfully uninstalled docutils-0.20.1 Attempting uninstall: sphinx Found existing installation: Sphinx 7.2.6 Uninstalling Sphinx-7.2.6: Successfully uninstalled Sphinx-7.2.6 Successfully installed anyio-4.0.0 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-2.4.0 async-lru-2.0.4 attrs-23.1.0 backcall-0.2.0 beautifulsoup4-4.12.2 bleach-6.1.0 cffi-1.16.0 comm-0.1.4 cryptography-41.0.4 debugpy-1.8.0 decorator-5.1.1 defusedxml-0.7.1 deprecated-1.2.14 docutils-0.18.1 exceptiongroup-1.1.3 executing-2.0.0 fastjsonschema-2.18.1 fqdn-1.5.1 ipykernel-6.25.2 ipython-8.16.1 isoduration-20.11.0 jedi-0.19.1 json5-0.9.14 jsonpointer-2.4 jsonschema-4.19.1 jsonschema-specifications-2023.7.1 jupyter-client-8.4.0 jupyter-core-5.4.0 jupyter-events-0.8.0 jupyter-lsp-2.2.0 jupyter-server-2.8.0 jupyter-server-terminals-0.4.4 jupyterlab-4.0.7 jupyterlab-pygments-0.2.2 jupyterlab-server-2.25.0 markdown-it-py-3.0.0 matplotlib-inline-0.1.6 mdit-py-plugins-0.4.0 mdurl-0.1.2 mistune-3.0.2 myst-parser-2.0.0 nbclient-0.8.0 nbconvert-7.9.2 nbformat-5.9.2 nbsphinx-0.9.3 nest-asyncio-1.5.8 notebook-shim-0.2.3 overrides-7.4.0 pandocfilters-1.5.0 parso-0.8.3 pexpect-4.8.0 pickleshare-0.7.5 plantweb-1.2.1 platformdirs-3.11.0 pockets-0.9.1 prometheus-client-0.17.1 prompt-toolkit-3.0.39 psutil-5.9.6 ptyprocess-0.7.0 pure-eval-0.2.2 pycparser-2.21 pygithub-1.59.1 pyjwt-2.8.0 pynacl-1.5.0 python-dateutil-2.8.2 python-json-logger-2.0.7 pyyaml-6.0.1 pyzmq-25.1.1 readthedocs-sphinx-search-0.3.1 referencing-0.30.2 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.10.6 send2trash-1.8.2 six-1.16.0 sniffio-1.3.0 soupsieve-2.5 sphinx-6.2.1 sphinx-copybutton-0.5.2 sphinx-rtd-theme-1.2.2 sphinxcontrib-jquery-4.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 stack-data-0.6.3 terminado-0.17.1 tinycss2-1.2.1 tomli-2.0.1 tornado-6.3.3 traitlets-5.11.2 types-python-dateutil-2.8.19.14 typing-extensions-4.8.0 uri-template-1.3.0 wcwidth-0.2.8 webcolors-1.13 webencodings-0.5.1 websocket-client-1.6.4 wrapt-1.15.0 [rtd-command-info] start-time: 2023-10-17T21:21:48.768450Z, end-time: 2023-10-17T21:21:48.842004Z, 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') # 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/"), ("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/"), ("search", "/en/search/"), ], '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': '', 'analytics_code': 'G-SVDSQH04EM', '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': 'G-SVDSQH04EM', 'global_analytics_code': 'UA-17997319-2', 'commit': '59caf23d', } # 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-emod-hiv/builds/1787955/' 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']) [rtd-command-info] start-time: 2023-10-17T21:21:49.316630Z, end-time: 2023-10-17T21:22:44.135487Z, duration: 54, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v6.2.1 making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-generic/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-generic/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-measles/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-tbhiv/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-malaria/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-generic/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-airborne/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-tuberculosis/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-sti/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-hiv/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-environmental/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-typhoid/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-vector/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'html_admonition', 'replacements', 'fieldlist', 'amsmath', 'linkify', 'deflist', 'html_image', 'colon_fence', 'attrs_inline', 'tasklist', 'strikethrough', 'dollarmath', 'substitution', 'smartquotes'}, disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) resolved configuration: {'PY3': True, 'SUFFIX': '.rst', '__file__': '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/checkouts/latest/emod/hiv/conf.py', 'author': 'Institute for Disease Modeling', 'chinese': False, 'context': {'MEDIA_URL': 'https://media.readthedocs.com/media/', 'PRODUCTION_DOMAIN': 'readthedocs.com', 'READTHEDOCS': True, 'STATIC_URL': 'https://assets.readthedocs.com/', 'ad_free': False, 'analytics_code': 'G-SVDSQH04EM', 'api_host': 'https://readthedocs.com', 'bitbucket_repo': 'None', 'bitbucket_user': 'None', 'bitbucket_version': 'malaria-ongoing', 'canonical_url': None, 'commit': '59caf23d', 'conf_py_path': '/emod/hiv/', 'current_version': 'latest', 'display_bitbucket': False, 'display_github': True, 'display_gitlab': False, 'docsearch_disabled': False, 'downloads': [('html', '//docs.idmod.org/_/downloads/emod-hiv/en/latest/htmlzip/')], 'github_repo': 'EMOD-docs', 'github_user': 'InstituteforDiseaseModeling', 'github_version': 'malaria-ongoing', 'gitlab_repo': 'None', 'gitlab_user': 'None', 'gitlab_version': 'malaria-ongoing', 'global_analytics_code': 'UA-17997319-2', 'html_theme': 'sphinx_rtd_theme', 'name': 'EMOD HIV', 'new_theme': True, 'programming_language': 'words', 'proxied_api_host': '/_', 'proxied_static_path': '/_/static/', 'rtd_language': 'en', 'single_version': False, 'slug': 'institute-for-disease-modeling-emod-hiv', 'source_suffix': '.rst', 'subprojects': [], 'user_analytics_code': 'G-SVDSQH04EM', 'using_theme': False, 'version_slug': 'latest', '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/'), ('search', '/en/search/')]}, 'copyright': '1999 - 2023, Bill & Melinda Gates Foundation. 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[rtd-command-info] start-time: 2023-10-17T21:22:44.596129Z, end-time: 2023-10-17T21:23:39.789612Z, duration: 55, exit-code: 0 python -m sphinx -T -E -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v6.2.1 making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-generic/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-generic/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-measles/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-tbhiv/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-malaria/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-generic/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-airborne/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-tuberculosis/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-sti/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-hiv/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-environmental/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-typhoid/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-vector/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'fieldlist', 'strikethrough', 'dollarmath', 'html_admonition', 'linkify', 'smartquotes', 'tasklist', 'colon_fence', 'attrs_inline', 'html_image', 'deflist', 'amsmath', 'substitution', 'replacements'}, disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) resolved configuration: {'PY3': True, 'SUFFIX': '.rst', '__file__': '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/checkouts/latest/emod/hiv/conf.py', 'author': 'Institute for Disease Modeling', 'chinese': False, 'context': {'MEDIA_URL': 'https://media.readthedocs.com/media/', 'PRODUCTION_DOMAIN': 'readthedocs.com', 'READTHEDOCS': True, 'STATIC_URL': 'https://assets.readthedocs.com/', 'ad_free': False, 'analytics_code': 'G-SVDSQH04EM', 'api_host': 'https://readthedocs.com', 'bitbucket_repo': 'None', 'bitbucket_user': 'None', 'bitbucket_version': 'malaria-ongoing', 'canonical_url': None, 'commit': '59caf23d', 'conf_py_path': '/emod/hiv/', 'current_version': 'latest', 'display_bitbucket': False, 'display_github': True, 'display_gitlab': False, 'docsearch_disabled': False, 'downloads': [('html', '//docs.idmod.org/_/downloads/emod-hiv/en/latest/htmlzip/')], 'github_repo': 'EMOD-docs', 'github_user': 'InstituteforDiseaseModeling', 'github_version': 'malaria-ongoing', 'gitlab_repo': 'None', 'gitlab_user': 'None', 'gitlab_version': 'malaria-ongoing', 'global_analytics_code': 'UA-17997319-2', 'html_theme': 'sphinx_rtd_theme', 'name': 'EMOD HIV', 'new_theme': True, 'programming_language': 'words', 'proxied_api_host': '/_', 'proxied_static_path': '/_/static/', 'rtd_language': 'en', 'single_version': False, 'slug': 'institute-for-disease-modeling-emod-hiv', 'source_suffix': '.rst', 'subprojects': [], 'user_analytics_code': 'G-SVDSQH04EM', 'using_theme': False, 'version_slug': 'latest', '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/'), ('search', '/en/search/')]}, 'copyright': '1999 - 2023, Bill & Melinda Gates Foundation. 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[100%] whats-new looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... whats-new install-overview install-windows install-linux software-overview software-inputs software-demographics software-demographics-overlay software-configuration software-configuration-overlay software-configuration-script software-parameter-sweep software-campaign software-campaign-overlay software-migration software-migration-creation software-climate software-load-balancing software-serialized software-run-simulation software-simulation-cli software-simulation-mpiexec software-simulation-python software-simulation-matlab software-simulation-performance software-serializing-pops software-serializing-create software-serializing-change-config software-serializing-change-campaign software-serializing-change-demog software-serializing-change-climate software-serializing-change-migration software-serializing-change-reports software-outputs software-custom-reporter software-error-logging software-report-binned software-report-demographic-summary software-report-inset-chart software-report-property software-report-event-counter software-report-event-recorder software-report-human-migration software-report-node-demographics software-report-spatial software-report-age-gender software-report-hivart software-report-hivinfection software-report-hivmort software-report-relationship-end software-report-relationship-census software-report-relationship-consummated software-report-relationship-migration-tracking software-report-relationship-start software-report-transmission tutorials generic-scenarios sti-scenarios hiv-scenarios troubleshooting model-overview generic-model-overview model-compartments model-sir model-seir model-si model-outbreak model-heterogeneity model-population-density model-properties model-hint model-mr-hint model-migration model-campaign model-targeted-interventions model-vaccination model-care-cascade sti-model-overview sti-model-relationships sti-model-transmission hiv-model-overview hiv-model-intrahost hiv-model-healthcare-systems hiv-disease-overview parameter-overview parameter-demographics parameter-configuration parameter-configuration-disease-progression parameter-configuration-drugs parameter-configuration-enable parameter-configuration-general-disease parameter-configuration-env parameter-configuration-immunity parameter-configuration-incubation parameter-configuration-infectivity parameter-configuration-input parameter-configuration-migration parameter-configuration-mortality parameter-configuration-output parameter-configuration-population parameter-configuration-pairs parameter-configuration-sampling parameter-configuration-scalars parameter-configuration-setup parameter-configuration-symptoms parameter-configuration-weibull parameter-campaign parameter-campaign-event-coordinators parameter-campaign-event-broadcastcoordinatorevent parameter-campaign-event-calendareventcoordinator parameter-campaign-event-campaignevent parameter-campaign-event-campaigneventbyyear parameter-campaign-event-communityhealthworkereventcoordinator parameter-campaign-event-coveragebynodeeventcoordinator parameter-campaign-event-delayeventcoordinator parameter-campaign-event-incidenceeventcoordinator parameter-campaign-event-nchoosereventcoordinator parameter-campaign-event-nchoosereventcoordinatorhiv parameter-campaign-event-nchoosereventcoordinatorsti parameter-campaign-event-referencetrackingeventcoordinator parameter-campaign-event-referencetrackingeventcoordinatorhiv parameter-campaign-event-referencetrackingeventcoordinatortrackingconfig parameter-campaign-event-standardinterventiondistributioneventcoordinator parameter-campaign-event-surveillanceeventcoordinator parameter-campaign-event-triggeredeventcoordinator parameter-campaign-node-interventions parameter-campaign-node-birthtriggerediv parameter-campaign-node-broadcastcoordinatoreventfromnode parameter-campaign-node-broadcastnodeevent parameter-campaign-node-coitalactratechanger parameter-campaign-node-condomusageprobabilitychanger parameter-campaign-node-firstnodewithnodepropertyeventcoordinator parameter-campaign-node-importpressure parameter-campaign-node-migratefamily parameter-campaign-node-multinodeinterventiondistributor parameter-campaign-node-nodelevelhealthtriggerediv parameter-campaign-node-nodelevelhealthtriggeredivscaleupswitch parameter-campaign-node-nodepropertyvaluechanger parameter-campaign-node-nlhtivnode parameter-campaign-node-outbreak parameter-campaign-node-relationshipdurationchanger parameter-campaign-node-relationshipformationratechanger parameter-campaign-individual-interventions parameter-campaign-individual-agediagnostic parameter-campaign-individual-antiretroviraltherapy parameter-campaign-individual-antiretroviraltherapyfull parameter-campaign-individual-artdropout parameter-campaign-individual-artmortalitytable parameter-campaign-individual-broadcastevent parameter-campaign-individual-broadcasteventtoothernodes parameter-campaign-individual-cd4diagnostic parameter-campaign-individual-coitalactriskfactors parameter-campaign-individual-controlledvaccine parameter-campaign-individual-delayedintervention parameter-campaign-individual-femalecontraceptive parameter-campaign-individual-hivartstagingbycd4diagnostic parameter-campaign-individual-hivartstagingcd4agnosticdiagnostic parameter-campaign-individual-hivdelayedintervention parameter-campaign-individual-hivdrawblood parameter-campaign-individual-hivmuxer parameter-campaign-individual-hivpiecewisebyyearandsexdiagnostic parameter-campaign-individual-hivrandomchoice parameter-campaign-individual-hivrapidhivdiagnostic parameter-campaign-individual-hivsigmoidbyyearandsexdiagnostic parameter-campaign-individual-hivsimplediagnostic parameter-campaign-individual-immunitybloodtest parameter-campaign-individual-individualimmunitychanger parameter-campaign-individual-individualnondiseasedeathratemodifier parameter-campaign-individual-interventionforcurrentpartners parameter-campaign-individual-ivcalendar parameter-campaign-individual-malecircumcision parameter-campaign-individual-migrateindividuals parameter-campaign-individual-modifysticoinfectionstatus parameter-campaign-individual-multieffectboostervaccine parameter-campaign-individual-multieffectvaccine parameter-campaign-individual-multiinterventiondistributor parameter-campaign-individual-outbreakindividual parameter-campaign-individual-pmtct parameter-campaign-individual-propertyvaluechanger parameter-campaign-individual-simpleboostervaccine parameter-campaign-individual-simplediagnostic parameter-campaign-individual-simplehealthseekingbehavior parameter-campaign-individual-simplevaccine parameter-campaign-individual-standarddiagnostic parameter-campaign-individual-startnewrelationship parameter-campaign-individual-stibarrier parameter-campaign-individual-sticoinfectiondiagnostic parameter-campaign-individual-stiispostdebut parameter-campaign-waningeffects parameter-campaign-targeting-config parameter-campaign-event-list parameter-schema faq glossary dev-install-overview dev-install-windows-prerequisites dev-install-centos-prerequisites dev-install-download-emod dev-install-build-emod dev-install-centos-docker dev-install-centos-docker-linux dev-install-centos-docker-win dev-architecture-overview dev-architecture-environment dev-architecture-sim-controller dev-architecture-core dev-architecture-campaigns dev-architecture-reporter dev-debugging-overview dev-logging dev-simulations dev-trouble-build dev-regression dev-regression-run dev-regression-new dev-sft done writing... done writing additional files... opensearchdone copying images... 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