Read the Docs build information Build id: 955097 Project: institute-for-disease-modeling-emod-malaria Version: 2.21_a Commit: 71a3ba58fbd7bc50b3325fb0fd85da3db2554224 Date: 2022-05-21T00:15:52.940222Z State: finished Success: True [rtd-command-info] start-time: 2022-05-21T00:26:46.475413Z, end-time: 2022-05-21T00:27:03.433460Z, duration: 16, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/EMOD-docs.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.113' (ECDSA) to the list of known hosts. [rtd-command-info] start-time: 2022-05-21T00:27:03.651100Z, end-time: 2022-05-21T00:27:04.110007Z, duration: 0, exit-code: 0 git checkout --force origin/2.21 Note: switching to 'origin/2.21'. 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 71a3ba58 removed support alias and updated requirements.txt [rtd-command-info] start-time: 2022-05-21T00:27:04.374860Z, end-time: 2022-05-21T00:27:04.443041Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-05-21T00:27:05.540168Z, end-time: 2022-05-21T00:27:10.254508Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv 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-malaria/envs/2.21_a/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-malaria/envs/2.21_a/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2022-05-21T00:27:10.468808Z, end-time: 2022-05-21T00:27:12.496634Z, duration: 2, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0 Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-malaria/envs/2.21_a/lib/python3.7/site-packages (22.1) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 kB 32.7 MB/s eta 0:00:00 Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 62.3.2 Uninstalling setuptools-62.3.2: Successfully uninstalled setuptools-62.3.2 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2022-05-21T00:27:12.741512Z, end-time: 2022-05-21T00:27:20.551000Z, duration: 7, exit-code: 0 python -m pip install --upgrade --no-cache-dir mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 jinja2<3.1.0 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 26.2 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 167.6 MB/s eta 0:00:00 Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.4/47.4 kB 188.1 MB/s eta 0:00:00 Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.6-py2.py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 203.3 MB/s 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sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.10.1-py3-none-any.whl (9.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 204.2 MB/s eta 0:00:00 Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 200.3 MB/s eta 0:00:00 Collecting packaging Downloading packaging-21.3-py3-none-any.whl (40 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 179.8 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-malaria/envs/2.21_a/lib/python3.7/site-packages (from sphinx<2) (58.2.0) Collecting Pygments>=2.0 Downloading Pygments-2.12.0-py3-none-any.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 237.1 MB/s eta 0:00:00 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status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=d3ceaf3e08db3036b203856221a4f79e398fe0021594776f8460772f0a242fc5 Stored in directory: /tmp/pip-ephem-wheel-cache-fluv7dwk/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: snowballstemmer, pytz, mock, alabaster, urllib3, sphinxcontrib-serializinghtml, six, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, certifi, babel, sphinxcontrib-websupport, requests, packaging, jinja2, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed MarkupSafe-2.1.1 Pygments-2.12.0 alabaster-0.7.12 babel-2.10.1 certifi-2022.5.18.1 charset-normalizer-2.0.12 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 jinja2-3.0.3 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.9 pytz-2022.1 readthedocs-sphinx-ext-2.1.6 recommonmark-0.5.0 requests-2.27.1 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 urllib3-1.26.9 [rtd-command-info] start-time: 2022-05-21T00:27:20.811980Z, end-time: 2022-05-21T00:27:26.689656Z, duration: 5, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Collecting sphinx-rtd-theme~=0.5.2 Downloading sphinx_rtd_theme-0.5.2-py2.py3-none-any.whl (9.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.1/9.1 MB 96.4 MB/s eta 0:00:00 Collecting sphinxcontrib-napoleon~=0.7 Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Collecting sphinx~=4.4.0 Downloading Sphinx-4.4.0-py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 198.2 MB/s eta 0:00:00 Collecting plantweb~=1.2.1 Downloading plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting numpy~=1.19.1 Downloading numpy-1.19.5-cp37-cp37m-manylinux2010_x86_64.whl (14.8 MB) 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Installing collected packages: zipp, typing-extensions, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pockets, numpy, docutils, sphinxcontrib-napoleon, plantweb, importlib-metadata, sphinx, sphinx-rtd-theme, numpydoc Attempting uninstall: docutils Found existing installation: docutils 0.17.1 Uninstalling docutils-0.17.1: Successfully uninstalled docutils-0.17.1 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed docutils-0.16 importlib-metadata-4.11.3 numpy-1.19.5 numpydoc-1.0.0 plantweb-1.2.1 pockets-0.9.1 sphinx-4.4.0 sphinx-rtd-theme-0.5.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-qthelp-1.0.3 typing-extensions-4.2.0 zipp-3.8.0 [rtd-command-info] start-time: 2022-05-21T00:27:28.267201Z, end-time: 2022-05-21T00:27:28.342678Z, duration: 0, exit-code: 0 cat emod/malaria/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 = 'Malaria Model' key = "emod-malaria" # Additional Metadata short_title = 'EMOD for Malaria' long_title = 'EMOD Modeling Software for Malaria' description = 'How to use the IDM EMOD software for modeling malaria.' # -- General configuration ------------------------------------------------ tags.add('malaria') # -- 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: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] 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': "2.21", 'version_slug': "2.21_a", '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': [ ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-emod-malaria', 'name': u'EMOD Malaria', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://docs.idmod.org/projects/emod-malaria/en/2.20_a/', 'analytics_code': 'UA-87656833-3', 'single_version': False, 'conf_py_path': '/emod/malaria/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'EMOD-docs', 'github_version': '2.21', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '2.21', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '2.21', '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': '71a3ba58', } # 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-malaria/builds/955097/' 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: 2022-05-21T00:27:28.554414Z, end-time: 2022-05-21T00:28:03.632752Z, duration: 35, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v4.4.0 loading translations [en]... done 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-covid/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... resolved configuration: {'PY3': True, 'SUFFIX': '.rst', '__file__': '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-malaria/checkouts/2.21_a/emod/malaria/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': 'UA-87656833-3', 'api_host': 'https://readthedocs.com', 'bitbucket_repo': 'None', 'bitbucket_user': 'None', 'bitbucket_version': '2.21', 'canonical_url': None, 'commit': '71a3ba58', 'conf_py_path': '/emod/malaria/', 'current_version': '2.21', 'display_bitbucket': False, 'display_github': True, 'display_gitlab': False, 'docsearch_disabled': False, 'downloads': [], 'github_repo': 'EMOD-docs', 'github_user': 'InstituteforDiseaseModeling', 'github_version': '2.21', 'gitlab_repo': 'None', 'gitlab_user': 'None', 'gitlab_version': '2.21', 'global_analytics_code': 'UA-17997319-2', 'html_theme': 'sphinx_rtd_theme', 'name': 'EMOD Malaria', '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-malaria', 'source_suffix': '.rst', 'subprojects': [], 'user_analytics_code': 'UA-87656833-3', 'using_theme': False, 'version_slug': '2.21_a', '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/')]}, 'copyright': '1999 - 2022, Bill & Melinda Gates Foundation. All rights ' 'reserved.', 'datetime': , 'description': 'How to use the IDM EMOD software for modeling malaria.', 'exclude_patterns': ['_build', 'Thumbs.db', '.DS_Store', '_build'], 'extensions': ['readthedocs_ext.readthedocs', 'sphinx.ext.mathjax', 'sphinx.ext.intersphinx'], 'html_baseurl': 'https://docs.idmod.org/projects/emod-malaria/en/2.20_a/', 'html_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': 'UA-87656833-3', 'api_host': 'https://readthedocs.com', 'bitbucket_repo': 'None', 'bitbucket_user': 'None', 'bitbucket_version': '2.21', 'canonical_url': None, 'commit': '71a3ba58', 'conf_py_path': '/emod/malaria/', 'current_version': '2.21', 'display_bitbucket': False, 'display_github': True, 'display_gitlab': False, 'docsearch_disabled': False, 'docset_title': 'EMOD for Malaria', 'downloads': [], 'github_repo': 'EMOD-docs', 'github_user': 'InstituteforDiseaseModeling', 'github_version': '2.21', 'gitlab_repo': 'None', 'gitlab_user': 'None', 'gitlab_version': '2.21', 'global_analytics_code': 'UA-17997319-2', 'html_theme': 'sphinx_rtd_theme', 'idm_docs_home': 'https://docs.idmod.org', 'name': 'EMOD Malaria', '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-malaria', 'source_suffix': '.rst', 'subprojects': [], 'user_analytics_code': 'UA-87656833-3', 'using_theme': False, 'version_slug': '2.21_a', '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/')]}, 'html_favicon': '../images/favicon.ico', 'html_logo': '../images/IDM_white.png', 'html_show_sourcelink': False, 'html_show_sphinx': False, 'html_static_path': ['../_static'], 'html_theme': 'sphinx_rtd_theme', 'html_theme_path': ['/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-malaria/envs/2.21_a/lib/python3.7/site-packages'], 'html_use_opensearch': 'docs.idmod.org/projects/emod-malaria', 'htmlhelp_basename': 'EMOD for Malaria', 'importlib': , 'intersphinx_mapping': {'emod-airborne': ('emod-airborne', ('https://docs.idmod.org/projects/emod-airborne/en/latest/', (None,))), 'emod-environmental': ('emod-environmental', ('https://docs.idmod.org/projects/emod-environmental/en/latest/', (None,))), 'emod-generic': ('emod-generic', ('https://docs.idmod.org/projects/emod-generic/en/latest/', (None,))), 'emod-hiv': ('emod-hiv', ('https://docs.idmod.org/projects/emod-hiv/en/latest/', (None,))), 'emod-malaria': ('emod-malaria', ('https://docs.idmod.org/projects/emod-malaria/en/latest/', (None,))), 'emod-sti': ('emod-sti', ('https://docs.idmod.org/projects/emod-sti/en/latest/', (None,))), 'emod-tbhiv': ('emod-tbhiv', ('https://docs.idmod.org/projects/emod-tuberculosis/en/latest/', (None,))), 'emod-typhoid': ('emod-typhoid', ('https://docs.idmod.org/projects/emod-typhoid/en/latest/', (None,))), 'emod-vector': ('emod-vector', ('https://docs.idmod.org/projects/emod-vector/en/latest/', (None,))), 'emod_api': ('emod_api', ('https://docs.idmod.org/projects/emod-api/en/latest/', (None,))), 'emodpy': ('emodpy', ('https://docs.idmod.org/projects/emodpy/en/latest/', (None,))), 'emodpy_covid': ('emodpy_covid', ('https://docs.idmod.org/projects/emodpy-covid/en/latest/', (None,))), 'emodpy_generic': ('emodpy_generic', ('https://docs.idmod.org/projects/emodpy-generic/en/latest/', (None,))), 'emodpy_malaria': ('emodpy_malaria', ('https://docs.idmod.org/projects/emodpy-generic/en/latest/', (None,))), 'emodpy_measles': ('emodpy_measles', ('https://docs.idmod.org/projects/emodpy-measles/en/latest/', (None,))), 'emodpy_tbhiv': ('emodpy_tbhiv', ('https://docs.idmod.org/projects/emodpy-tbhiv/en/latest/', (None,))), 'idmtools': ('idmtools', ('https://docs.idmod.org/projects/idmtools/en/latest/', (None,))), 'pycomps': ('pycomps', ('https://docs.idmod.org/projects/pycomps/en/latest/', (None,))), 'python': ('python', ('https://docs.python.org/3', (None,)))}, 'japanese': False, 'key': 'emod-malaria', 'language': 'en', 'language_user': None, 'latex_documents': [('index', 'emod-malaria-docs.tex', 'EMOD Modeling Software for Malaria', 'Institute for Disease Modeling', 'manual')], 'latex_elements': {}, 'latex_elements_user': {}, 'latex_engine_user': None, 'latex_use_xindy': False, 'log_config': , 'long_title': 'EMOD Modeling Software for Malaria', 'man_pages': [('index', 'emod-malaria-docs', 'EMOD Modeling Software for Malaria', ['Institute for Disease Modeling'], 1)], 'man_show_urls': True, 'master_doc': 'index', 'opensearch_baseurl': 'docs.idmod.org/projects', 'os': , 'project': 'Malaria Model', 'project_language': 'en', 'pygments_style': 'sphinx', 'rst_epilog': '\n.. include:: /../reuse/variables.txt', 'setup': , 'short_title': 'EMOD for Malaria', 'source_suffix': '.rst', 'sphinx': , 'sphinx_rtd_theme': , 'string_types': , 'sys': , 'tags': , 'templates_path': ['../_templates'], 'texinfo_documents': [('index', 'emod-malaria-docs', 'EMOD Modeling Software for Malaria', 'Institute for Disease Modeling', 'Institute for Disease Modeling', 'How to use the IDM EMOD software for modeling ' 'malaria.', 'Miscellaneous')], 'todo_include_todos': False, 'using_rtd_theme': False, 'version': '2.21', 'version_info': (4, 4, 0, 'final', 0)} building [mo]: targets for 0 po files that are out of date building [html]: targets for 206 source files that are out of date updating environment: [new config] 206 added, 0 changed, 0 removed reading sources... 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[rtd-command-info] start-time: 2022-05-21T00:28:03.969190Z, end-time: 2022-05-21T00:28:35.220544Z, duration: 31, exit-code: 0 python -m sphinx -T -E -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia Running Sphinx v4.4.0 loading translations [en]... done 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-covid/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... resolved configuration: {'PY3': True, 'SUFFIX': '.rst', '__file__': '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-malaria/checkouts/2.21_a/emod/malaria/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': 'UA-87656833-3', 'api_host': 'https://readthedocs.com', 'bitbucket_repo': 'None', 'bitbucket_user': 'None', 'bitbucket_version': '2.21', 'canonical_url': None, 'commit': '71a3ba58', 'conf_py_path': '/emod/malaria/', 'current_version': '2.21', 'display_bitbucket': False, 'display_github': True, 'display_gitlab': False, 'docsearch_disabled': False, 'downloads': [], 'github_repo': 'EMOD-docs', 'github_user': 'InstituteforDiseaseModeling', 'github_version': '2.21', 'gitlab_repo': 'None', 'gitlab_user': 'None', 'gitlab_version': '2.21', 'global_analytics_code': 'UA-17997319-2', 'html_theme': 'sphinx_rtd_theme', 'name': 'EMOD Malaria', '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-malaria', 'source_suffix': '.rst', 'subprojects': [], 'user_analytics_code': 'UA-87656833-3', 'using_theme': False, 'version_slug': '2.21_a', '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/')]}, 'copyright': '1999 - 2022, Bill & Melinda Gates Foundation. 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software-report-property software-report-spatial software-custom-reporter software-error-logging software-report-vector-species software-report-vector-habitat software-report-vector-lifecycle software-report-vector-genetics software-report-malaria-summary software-report-vector-stats software-report-malaria-stats software-report-malaria-survey software-report-malaria-immunity software-report-malaria-patient software-report-filtered-malaria software-report-malaria-transmission software-report-malaria-node-demographics software-report-malaria-spatial tutorials generic-scenarios vector-scenarios malaria-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 vector-model-overview vector-model-climate-demographics vector-model-larval-habitat vector-model-transmission malaria-model-overview malaria-model-infection-immunity malaria-model-symptoms-diagnosis malaria-model-antimalarial-drugs malaria-overview parameter-overview parameter-demographics parameter-configuration 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-larval parameter-configuration-migration parameter-configuration-mortality parameter-configuration-output parameter-configuration-parasite parameter-configuration-population parameter-configuration-sampling parameter-configuration-scalars parameter-configuration-setup parameter-configuration-symptoms parameter-configuration-vector-control parameter-configuration-vector-lifecycle parameter-campaign parameter-campaign-event-coordinators parameter-campaign-event-broadcastcoordinatorevent parameter-campaign-event-calendareventcoordinator parameter-campaign-event-campaignevent parameter-campaign-event-communityhealthworkereventcoordinator parameter-campaign-event-coveragebynodeeventcoordinator parameter-campaign-event-delayeventcoordinator parameter-campaign-event-incidenceeventcoordinator parameter-campaign-event-nchoosereventcoordinator parameter-campaign-event-standardinterventiondistributioneventcoordinator parameter-campaign-event-surveillanceeventcoordinator parameter-campaign-event-triggeredeventcoordinator parameter-campaign-node-interventions parameter-campaign-node-animalfeedkill parameter-campaign-node-artificialdiet parameter-campaign-node-birthtriggerediv parameter-campaign-node-broadcastnodeevent parameter-campaign-node-importpressure parameter-campaign-node-inputeir parameter-campaign-node-insectkillingfence parameter-campaign-node-larvicides parameter-campaign-node-malariachallenge parameter-campaign-node-migratefamily parameter-campaign-node-mosquitorelease parameter-campaign-node-multinodeinterventiondistributor parameter-campaign-node-nodelevelhealthtriggerediv parameter-campaign-node-nodelevelhealthtriggeredivscaleupswitch parameter-campaign-node-nodepropertyvaluechanger parameter-campaign-node-outbreak parameter-campaign-node-outdoorrestkill parameter-campaign-node-ovipositiontrap parameter-campaign-node-scalelarvalhabitat parameter-campaign-node-spacespraying parameter-campaign-node-spatialrepellent parameter-campaign-node-sugartrap parameter-campaign-individual-interventions parameter-campaign-individual-adherentdrug parameter-campaign-individual-antimalarialdrug parameter-campaign-individual-artificialdiethousingmodification parameter-campaign-individual-bitingrisk parameter-campaign-individual-broadcastevent parameter-campaign-individual-broadcasteventtoothernodes parameter-campaign-individual-controlledvaccine parameter-campaign-individual-delayedintervention parameter-campaign-individual-humanhostseekingtrap parameter-campaign-individual-immunitybloodtest parameter-campaign-individual-individualimmunitychanger parameter-campaign-individual-insectkillingfencehousingmodification parameter-campaign-individual-irshousingmodification parameter-campaign-individual-ivcalendar parameter-campaign-individual-ivermectin parameter-campaign-individual-malariadiagnostic parameter-campaign-individual-migrateindividuals parameter-campaign-individual-multieffectboostervaccine parameter-campaign-individual-multieffectvaccine parameter-campaign-individual-multiinterventiondistributor parameter-campaign-individual-outbreakindividual parameter-campaign-individual-outbreakindividualmalaria parameter-campaign-individual-propertyvaluechanger parameter-campaign-individual-rtssvaccine parameter-campaign-individual-screeninghousingmodification parameter-campaign-individual-simplebednet parameter-campaign-individual-simpleboostervaccine parameter-campaign-individual-simplediagnostic parameter-campaign-individual-simplehealthseekingbehavior parameter-campaign-individual-simplehousingmodification parameter-campaign-individual-simpleindividualrepellent parameter-campaign-individual-simplevaccine parameter-campaign-individual-spatialrepellenthousingmodification parameter-campaign-individual-usagedependentbednet parameter-campaign-waningeffects 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 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