Read the Docs build information Build id: 478424 Project: institute-for-disease-modeling-emod-typhoid Version: latest Commit: 63df26015b7dcfa052e13929458972ba2ff5cb49 Date: 2020-11-12T20:06:41.003966Z State: finished Success: True [rtd-command-info] start-time: 2020-11-12T20:06:43.444874Z, end-time: 2020-11-12T20:06:58.694679Z, duration: 15, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/Documentation.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.113' (RSA) to the list of known hosts. [rtd-command-info] start-time: 2020-11-12T20:06:59.505440Z, end-time: 2020-11-12T20:06:59.959962Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. 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 performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at 63df2601 Merge pull request #1169 from RCarter-IDM/param-updates [rtd-command-info] start-time: 2020-11-12T20:07:00.346720Z, end-time: 2020-11-12T20:07:00.408083Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-11-12T20:07:02.532256Z, end-time: 2020-11-12T20:07:06.625313Z, 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-typhoid/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-11-12T20:07:07.061426Z, end-time: 2020-11-12T20:07:07.794576Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (20.2.4) [rtd-command-info] start-time: 2020-11-12T20:07:08.215271Z, end-time: 2020-11-12T20:07:16.795489Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir setuptools==41.0.1 docutils==0.14 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 Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) 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) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.1-py2.py3-none-any.whl (13 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting packaging Downloading packaging-20.4-py2.py3-none-any.whl (37 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.0-py2.py3-none-any.whl (8.8 MB) Collecting requests>=2.0.0 Downloading requests-2.25.0-py2.py3-none-any.whl (61 kB) Collecting Pygments>=2.0 Downloading Pygments-2.7.2-py3-none-any.whl (948 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting pytz>=2015.7 Downloading pytz-2020.4-py2.py3-none-any.whl (509 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.1-py2.py3-none-any.whl (136 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.11.8-py2.py3-none-any.whl (155 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=7178ec8941ee6668131bdd4e9b136c1d08ef6cc3c82d19bbf8960f5db1523f22 Stored in directory: /tmp/pip-ephem-wheel-cache-5nwnhqdr/wheels/16/03/37/f0a64ab894c9102906f192db1a4071b7592292ad661563c69b Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=e75836e6b9c3bfd59a0f34ede4e228f3f840566aa85e00e5cf25453e2e19955f Stored in directory: /tmp/pip-ephem-wheel-cache-5nwnhqdr/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: setuptools, docutils, mock, pillow, alabaster, future, commonmark, MarkupSafe, Jinja2, six, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, pyparsing, packaging, imagesize, pytz, babel, urllib3, chardet, idna, certifi, requests, Pygments, snowballstemmer, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 50.3.2 Uninstalling setuptools-50.3.2: Successfully uninstalled setuptools-50.3.2 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.2 alabaster-0.7.12 babel-2.9.0 certifi-2020.11.8 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.4 readthedocs-sphinx-ext-2.1.1 recommonmark-0.5.0 requests-2.25.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.1 [rtd-command-info] start-time: 2020-11-12T20:07:16.971467Z, end-time: 2020-11-12T20:07:22.242770Z, duration: 5, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Collecting sphinx-rtd-theme~=0.5.0 Downloading sphinx_rtd_theme-0.5.0-py2.py3-none-any.whl (10.8 MB) Collecting sphinxcontrib-napoleon~=0.7 Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Collecting sphinx~=3.2.0 Downloading Sphinx-3.2.1-py3-none-any.whl (2.9 MB) Collecting plantweb~=1.2.1 Downloading plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting numpy~=1.19.1 Downloading numpy-1.19.4-cp37-cp37m-manylinux2010_x86_64.whl (14.5 MB) Collecting numpydoc~=1.0.0 Downloading numpydoc-1.0.0-py3-none-any.whl (47 kB) Collecting pockets>=0.3 Downloading pockets-0.9.1-py2.py3-none-any.whl (26 kB) Requirement already satisfied: six>=1.5.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-napoleon~=0.7->-r requirements.txt (line 2)) (1.15.0) Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (0.14) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.11.2) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.7.2) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (1.1.4) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (20.4) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (0.7.12) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (41.0.1) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (1.2.0) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.0.0) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.9.0) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.25.0) Collecting sphinxcontrib-htmlhelp Downloading sphinxcontrib_htmlhelp-1.0.3-py2.py3-none-any.whl (96 kB) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx~=3.2.0->-r requirements.txt (line 3)) (1.1.1) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from packaging->sphinx~=3.2.0->-r requirements.txt (line 3)) (2.4.7) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from babel>=1.3->sphinx~=3.2.0->-r requirements.txt (line 3)) (2020.4) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r requirements.txt (line 3)) (2020.11.8) Requirement already satisfied: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r requirements.txt (line 3)) (3.0.4) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r requirements.txt (line 3)) (1.26.1) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r requirements.txt (line 3)) (2.10) Installing collected packages: sphinxcontrib-devhelp, sphinxcontrib-qthelp, sphinxcontrib-applehelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinx, sphinx-rtd-theme, pockets, sphinxcontrib-napoleon, plantweb, numpy, numpydoc Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 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 numpy-1.19.4 numpydoc-1.0.0 plantweb-1.2.1 pockets-0.9.1 sphinx-3.2.1 sphinx-rtd-theme-0.5.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-qthelp-1.0.3 [rtd-command-info] start-time: 2020-11-12T20:07:24.176042Z, end-time: 2020-11-12T20:07:24.252429Z, duration: 0, exit-code: 0 cat emod/typhoid/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 = 'Typhoid Model' key = "emod-typhoid" # Additional Metadata short_title = 'EMOD for Typhoid' long_title = 'EMOD Modeling Software for Typhoid' description = 'How to use the IDM EMOD software for modeling typhoid.' # -- General configuration ------------------------------------------------ tags.add('typhoid') # -- 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/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types 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': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("2.21", "/en/2.21/"), ("2.20", "/en/2.20/"), ], 'downloads': [ ("html", "//docs.idmod.org/_/downloads/emod-typhoid/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-emod-typhoid', 'name': u'EMOD Typhoid', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://docs.idmod.org/projects/emod-typhoid/en/latest/', 'analytics_code': 'UA-87656833-3', 'single_version': False, 'conf_py_path': '/emod/typhoid/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'Documentation', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', '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': '63df2601', } 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") 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: 2020-11-12T20:07:24.356431Z, end-time: 2020-11-12T20:07:52.337832Z, duration: 27, exit-code: 0 python sphinx-build -T -E -W --keep-going -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v3.2.1 loading translations [en]... done making output directory... done resolved configuration: {'SUFFIX': '.rst', '__file__': '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-typhoid/checkouts/latest/emod/typhoid/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': 'master', 'canonical_url': 'https://docs.idmod.org/projects/emod-typhoid/en/latest/', 'commit': '63df2601', 'conf_py_path': '/emod/typhoid/', 'current_version': 'latest', 'display_bitbucket': False, 'display_github': True, 'display_gitlab': False, 'docsearch_disabled': False, 'downloads': [('html', '//docs.idmod.org/_/downloads/emod-typhoid/en/latest/htmlzip/')], 'github_repo': 'Documentation', 'github_user': 'InstituteforDiseaseModeling', 'github_version': 'master', 'gitlab_repo': 'None', 'gitlab_user': 'None', 'gitlab_version': 'master', 'global_analytics_code': 'UA-17997319-2', 'html_theme': 'sphinx_rtd_theme', 'name': 'EMOD Typhoid', 'new_theme': True, 'programming_language': 'words', 'proxied_api_host': '/_', 'rtd_language': 'en', 'single_version': False, 'slug': 'institute-for-disease-modeling-emod-typhoid', 'source_suffix': '.rst', 'subprojects': [], 'user_analytics_code': 'UA-87656833-3', 'using_theme': False, 'version_slug': 'latest', 'versions': [('latest', '/en/latest/'), ('2.21', '/en/2.21/'), ('2.20', '/en/2.20/')]}, 'copyright': '1999 - 2020, Bill & Melinda Gates Foundation. All rights ' 'reserved.', 'datetime': , 'description': 'How to use the IDM EMOD software for modeling typhoid.', 'exclude_patterns': ['_build', 'Thumbs.db', '.DS_Store', '_build'], 'extensions': ['readthedocs_ext.readthedocs', 'sphinx.ext.mathjax'], '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': 'master', 'canonical_url': 'https://docs.idmod.org/projects/emod-typhoid/en/latest/', 'commit': '63df2601', 'conf_py_path': '/emod/typhoid/', 'current_version': 'latest', 'display_bitbucket': False, 'display_github': True, 'display_gitlab': False, 'docsearch_disabled': False, 'docset_title': 'EMOD for Typhoid', 'downloads': [('html', '//docs.idmod.org/_/downloads/emod-typhoid/en/latest/htmlzip/')], 'github_repo': 'Documentation', 'github_user': 'InstituteforDiseaseModeling', 'github_version': 'master', 'gitlab_repo': 'None', 'gitlab_user': 'None', 'gitlab_version': 'master', 'global_analytics_code': 'UA-17997319-2', 'html_theme': 'sphinx_rtd_theme', 'idm_docs_home': 'https://docs.idmod.org', 'name': 'EMOD Typhoid', 'new_theme': True, 'programming_language': 'words', 'proxied_api_host': '/_', 'rtd_language': 'en', 'single_version': False, 'slug': 'institute-for-disease-modeling-emod-typhoid', 'source_suffix': '.rst', 'subprojects': [], 'user_analytics_code': 'UA-87656833-3', 'using_theme': False, 'version_slug': 'latest', 'versions': [('latest', '/en/latest/'), ('2.21', '/en/2.21/'), ('2.20', '/en/2.20/')]}, '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-typhoid/envs/latest/lib/python3.7/site-packages'], 'html_use_opensearch': 'docs.idmod.org/projects/emod-typhoid', 'htmlhelp_basename': 'EMOD for Typhoid', 'importlib': , 'japanese': False, 'key': 'emod-typhoid', 'language': 'en', 'language_user': None, 'latex_documents': [('index', 'emod-typhoid-docs.tex', 'EMOD Modeling Software for Typhoid', '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 Typhoid', 'man_pages': [('index', 'emod-typhoid-docs', 'EMOD Modeling Software for Typhoid', ['Institute for Disease Modeling'], 1)], 'man_show_urls': True, 'master_doc': 'index', 'opensearch_baseurl': 'docs.idmod.org/projects', 'os': , 'project': 'Typhoid Model', 'project_language': 'en', 'pygments_style': 'sphinx', 'rst_epilog': '\n.. include:: /../reuse/variables.txt', 'setup': , 'short_title': 'EMOD for Typhoid', 'source_suffix': '.rst', 'sphinx': , 'sphinx_rtd_theme': , 'string_types': (,), 'sys': , 'tags': , 'templates_path': ['../_templates'], 'texinfo_documents': [('index', 'emod-typhoid-docs', 'EMOD Modeling Software for Typhoid', 'Institute for Disease Modeling', 'Institute for Disease Modeling', 'How to use the IDM EMOD software for modeling ' 'typhoid.', 'Miscellaneous')], 'todo_include_todos': False, 'using_rtd_theme': False, 'version': '2.20', 'version_info': (3, 2, 1, 'final', 0)} building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 160 source files that are out of date updating environment: [new config] 160 added, 0 changed, 0 removed reading sources... 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software-report-spatial software-custom-reporter software-error-logging software-report-vector-species tutorials generic-scenarios environmental-scenarios typhoid-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 environmental-model-overview environmental-model-transmission environmental-model-seasonality typhoid-model-overview typhoid-model-disease-progression typhoid-model-immunity typhoid-disease-overview parameter-overview parameter-demographics parameter-configuration parameter-configuration-disease-progression 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-sampling parameter-configuration-scalars parameter-configuration-setup 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-birthtriggerediv parameter-campaign-node-broadcastnodeevent parameter-campaign-node-environmentaldiagnostic 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-outbreak parameter-campaign-node-typhoidwash parameter-campaign-individual-interventions parameter-campaign-individual-broadcastevent parameter-campaign-individual-broadcasteventtoothernodes parameter-campaign-individual-controlledvaccine parameter-campaign-individual-delayedintervention parameter-campaign-individual-immunitybloodtest parameter-campaign-individual-individualimmunitychanger parameter-campaign-individual-ivcalendar parameter-campaign-individual-migrateindividuals parameter-campaign-individual-multieffectboostervaccine parameter-campaign-individual-multieffectvaccine parameter-campaign-individual-multiinterventiondistributor parameter-campaign-individual-outbreakindividual parameter-campaign-individual-propertyvaluechanger parameter-campaign-individual-simpleboostervaccine parameter-campaign-individual-simplediagnostic parameter-campaign-individual-simplehealthseekingbehavior parameter-campaign-individual-simplevaccine parameter-campaign-individual-typhoidcarrierclear parameter-campaign-individual-typhoidcarrierdiagnostic parameter-campaign-individual-typhoidvaccine 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 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