Read the Docs build information Build id: 436549 Project: institute-for-disease-modeling-emod-generic Version: 2.14 Commit: c4324183b51d9e3659b743bd9bf2ff4d6ecc2e24 Date: 2020-09-30T02:53:04.307165Z State: finished Success: True [rtd-command-info] start-time: 2020-09-30T02:53:06.182221Z, end-time: 2020-09-30T02:53:21.477283Z, 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: 2020-09-30T02:53:22.109601Z, end-time: 2020-09-30T02:53:22.556401Z, duration: 0, exit-code: 0 git checkout --force c4324183b51d9e3659b743bd9bf2ff4d6ecc2e24 Note: checking out 'c4324183b51d9e3659b743bd9bf2ff4d6ecc2e24'. 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 c4324183 completely removed tipue search [rtd-command-info] start-time: 2020-09-30T02:53:23.069783Z, end-time: 2020-09-30T02:53:23.122208Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-09-30T02:53:24.786988Z, end-time: 2020-09-30T02:53:28.759457Z, duration: 3, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-09-30T02:53:29.119242Z, end-time: 2020-09-30T02:53:29.794822Z, 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-generic/envs/2.14/lib/python3.7/site-packages (20.2.3) [rtd-command-info] start-time: 2020-09-30T02:53:30.065907Z, end-time: 2020-09-30T02:53:38.079882Z, 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<1.1 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<1.1 Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 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 babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl 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Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 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=8f1c258ed9a2245ae41915ad109f730547623187c7651282f8322b7a013a7915 Stored in directory: /tmp/pip-ephem-wheel-cache-gdq7lj0v/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=75f49e2fecf2565fde84b2a85345774abae5ccfda390cf894322510994b41730 Stored in directory: /tmp/pip-ephem-wheel-cache-gdq7lj0v/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: setuptools, docutils, mock, pillow, alabaster, future, commonmark, MarkupSafe, Jinja2, pytz, babel, imagesize, snowballstemmer, six, pyparsing, packaging, idna, urllib3, certifi, chardet, requests, Pygments, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 50.3.0 Uninstalling setuptools-50.3.0: Successfully uninstalled setuptools-50.3.0 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 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-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 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 urllib3-1.25.10 [rtd-command-info] start-time: 2020-09-30T02:53:38.770245Z, end-time: 2020-09-30T02:53:43.723008Z, duration: 4, 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-1.19.2-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-generic/envs/2.14/lib/python3.7/site-packages (from sphinxcontrib-napoleon~=0.7->-r requirements.txt (line 2)) (1.15.0) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.7.1) Collecting sphinxcontrib-htmlhelp Downloading sphinxcontrib_htmlhelp-1.0.3-py2.py3-none-any.whl (96 kB) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/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-generic/envs/2.14/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (0.7.12) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (1.2.0) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.8.0) 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-generic/envs/2.14/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.0.0) Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (0.14) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (41.0.1) Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.24.0) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (2.11.2) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/lib/python3.7/site-packages (from sphinx~=3.2.0->-r requirements.txt (line 3)) (1.1.4) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/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-generic/envs/2.14/lib/python3.7/site-packages (from babel>=1.3->sphinx~=3.2.0->-r requirements.txt (line 3)) (2020.1) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r requirements.txt (line 3)) (2020.6.20) Requirement already satisfied: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/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!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r requirements.txt (line 3)) (1.25.10) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r requirements.txt (line 3)) (2.10) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-generic/envs/2.14/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx~=3.2.0->-r requirements.txt (line 3)) (1.1.1) Installing collected packages: sphinxcontrib-htmlhelp, sphinxcontrib-qthelp, sphinxcontrib-applehelp, sphinxcontrib-jsmath, sphinxcontrib-devhelp, 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-1.19.2 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: 2020-09-30T02:53:45.744906Z, end-time: 2020-09-30T02:53:45.817185Z, duration: 0, exit-code: 0 cat emod/generic/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. # # import os # import sys # sys.path.insert(0, os.path.abspath('.')) import sphinx_rtd_theme from datetime import datetime # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' tags.add('generic') # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.mathjax', 'sphinx.ext.githubpages', ] # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] source_suffix = '.rst' # The encoding of source files. # # source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'Generic Model' copyright = f'1999 - {datetime.today().year}, Bill and Melinda Gates Foundation. All rights reserved.' author = u'Institute for Disease Modeling' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. version = u'2.14' # The full version, including alpha/beta/rc tags. # release = u'1.0' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: # # today = '' # # Else, today_fmt is used as the format for a strftime call. # # today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # The reST default role (used for this markup: `text`) to use for all # documents. # # default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. # # add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). # # add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. # # show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. # keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # RST epilog is added to the end of every topic. Useful for replace # directives to use across the docset. rst_epilog = "\n.. include:: ../reuse/variables.txt" # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # # # html_theme_options = { # } # Add any paths that contain custom themes here, relative to this directory. html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] # The name for this set of Sphinx documents. # " v documentation" by default. # # html_title = u'Sphinx Demo v1.0' # A shorter title for the navigation bar. Default is the same as html_title. # # html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. # html_logo = "../../images/IDM_white.png" # The name of an image file (relative to this directory) to use as a favicon of # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. # html_favicon = "../../images/favicon.ico" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] html_context = { 'css_files': [ '_static/theme_overrides.css' ] } # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the documentation. # # html_extra_path = [] # If not None, a 'Last updated on:' timestamp is inserted at every page # bottom, using the given strftime format. # The empty string is equivalent to '%b %d, %Y'. # # html_last_updated_fmt = None # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. # # html_use_smartypants = True # Custom sidebar templates, maps document names to template names. # # html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. # # html_additional_pages = {} # If false, no module index is generated. # # html_domain_indices = True # If false, no index is generated. # # html_use_index = True # If true, the index is split into individual pages for each letter. # # html_split_index = False # If true, links to the reST sources are added to the pages. # html_show_sourcelink = False # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. # html_show_sphinx = False # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. # # html_show_copyright = True # 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 = 'https://institutefordiseasemodeling.github.io/EMOD/' # This is the file name suffix for HTML files (e.g. ".xhtml"). # html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh' # # html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # 'ja' uses this config value. # 'zh' user can custom change `jieba` dictionary path. # # html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. # # html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. htmlhelp_basename = 'EMOD for Generic' # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # 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, 'emod-generic-docs.tex', u'EMOD Modeling Software for Generic', u'Institute for Disease Modeling', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. # # latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. # # latex_use_parts = False # If true, show page references after internal links. # # latex_show_pagerefs = False # If true, show URL addresses after external links. # # latex_show_urls = False # Documents to append as an appendix to all manuals. # # latex_appendices = [] # It false, will not define \strong, \code, itleref, \crossref ... but only # \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added # packages. # # latex_keep_old_macro_names = True # If false, no module index is generated. # # latex_domain_indices = True # -- 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, 'emod-generic-docs', u'EMOD Modeling Software for Generic', [author], 1) ] # If true, show URL addresses after external links. # man_show_urls = True # -- 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, 'emod-generic-docs', u'EMOD Modeling Software for Generic', author, 'Institute for Disease Modeling', 'How to use the IDM EMOD software for modeling general disease.', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. # # texinfo_appendices = [] # If false, no module index is generated. # # texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. # # texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. # # texinfo_no_detailmenu = False # Example configuration for intersphinx: refer to the Python standard library. # intersphinx_mapping = {'https://docs.python.org/': None} ########################################################################### # 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': "2.14", 'version_slug': "2.14", '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/"), ("2.18", "/en/2.18/"), ("2.14", "/en/2.14/"), ("2.13", "/en/2.13/"), ("2.10", "/en/2.10/"), ], 'downloads': [ ("html", "//docs.idmod.org/_/downloads/emod-generic/en/2.14/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-emod-generic', 'name': u'EMOD Generic', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://docs.idmod.org/projects/emod-generic/en/latest/', 'analytics_code': 'UA-87656833-3', 'single_version': False, 'conf_py_path': '/emod/generic/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'Documentation', 'github_version': '2.14', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '2.14', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '2.14', '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': 'c4324183', } 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 'tag' == '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: 2020-09-30T02:53:46.063077Z, end-time: 2020-09-30T02:54:03.134120Z, duration: 17, 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 building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 121 source files that are out of date updating environment: [new config] 121 added, 0 changed, 0 removed reading sources... 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[rtd-command-info] start-time: 2020-09-30T02:54:03.453318Z, end-time: 2020-09-30T02:54:17.826125Z, duration: 14, exit-code: 0 python sphinx-build -T -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v3.2.1 loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 121 added, 0 changed, 0 removed reading sources... [ 0%] dev-architecture-campaigns reading sources... [ 1%] dev-architecture-core reading sources... [ 2%] dev-architecture-environment reading sources... [ 3%] dev-architecture-overview reading sources... [ 4%] dev-architecture-reporter reading sources... [ 4%] dev-architecture-sim-controller reading sources... [ 5%] dev-debugging-overview reading sources... [ 6%] dev-install-build-emod reading sources... 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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-centos intro-overview intro-inputs intro-configuration intro-campaign intro-run-simulation intro-outputs intro-modeling generic-simulation-tutorial-overview generic-tutorial1SIR generic-tutorial2SIR generic-tutorial3SEIR generic-tutorial4SEIR generic-tutorial5SIRS generic-tutorial6SEIRS generic-tutorial7SI generic-tutorial8SIS generic-tutorial9Density generic-tutorial-10Zoonosis hint-tutorial-overview hint-tutorial-scenario1 hint-tutorial-scenario2 hint-tutorial-scenario3 hint-tutorial-scenario4 hint-tutorial-scenario5 howto-overview howto-inputs howto-demographics-overlay howto-demographics-heterogeneity howto-hint hint-scaling howto-configuration howto-schema howto-parameter-sweep howto-config-overlay howto-campaign howto-campaign-overlay howto-targeted-interventions howto-simulations howto-simulation-cli howto-simulation-mpiexec howto-simulation-python howto-simulation-matlab howto-simulation-performance howto-outputs howto-custom-reporter parameter-overview parameter-demographics parameter-configuration parameter-campaign parameter-campaign-event-coordinators parameter-campaign-event-campaignevent parameter-campaign-event-calendareventcoordinator parameter-campaign-event-communityhealthworkereventcoordinator parameter-campaign-event-coveragebynodeeventcoordinator parameter-campaign-event-multiinterventioneventcoordinator parameter-campaign-event-nchoosereventcoordinator parameter-campaign-event-simpleinterventiondistributioneventcoordinator parameter-campaign-event-standardinterventiondistributioneventcoordinator parameter-campaign-node-interventions parameter-campaign-node-birthtriggerediv parameter-campaign-node-importpressure parameter-campaign-node-migratefamily parameter-campaign-node-nodelevelhealthtriggerediv parameter-campaign-node-nodelevelhealthtriggeredivscaleupswitch parameter-campaign-node-nodepropertyvaluechanger parameter-campaign-node-outbreak parameter-campaign-individual-interventions parameter-campaign-individual-broadcastevent parameter-campaign-individual-broadcasteventtoothernodes parameter-campaign-individual-controlledvaccine parameter-campaign-individual-delayedintervention 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-waningeffects parameter-campaign-event-list file-reference-overview file-inputs file-climate file-migration file-load-balancing file-outputs file-inset-chart file-binned file-demographic-summary file-property file-spatial file-error-logging troubleshooting glossary dev-install-overview dev-install-prerequisites dev-install-download-emod dev-install-build-emod 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 done writing... done writing additional files... opensearchdone copying images... 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