Read the Docs build information Build id: 530896 Project: institute-for-disease-modeling-idm-cms Version: latest Commit: bbe2cadf998787c4aa75fc3ba8f87a0ec7a05990 Date: 2021-01-13T23:09:33.455320Z State: finished Success: True [rtd-command-info] start-time: 2021-01-13T23:09:35.026503Z, end-time: 2021-01-13T23:09:41.477592Z, duration: 6, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/InstituteforDiseaseModeling/IDM-CMS.git . Cloning into '.'... [rtd-command-info] start-time: 2021-01-13T23:09:42.401244Z, end-time: 2021-01-13T23:09:43.007396Z, 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 bbe2cad Updated the relative link to the IDM docs in breadcrumbs [rtd-command-info] start-time: 2021-01-13T23:09:43.158426Z, end-time: 2021-01-13T23:09:43.221523Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-01-13T23:09:44.724626Z, end-time: 2021-01-13T23:09:48.751073Z, 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-idm-cms/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-01-13T23:09:48.973822Z, end-time: 2021-01-13T23:09:50.587193Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (20.3.3) [rtd-command-info] start-time: 2021-01-13T23:09:50.771608Z, end-time: 2021-01-13T23:10:00.045249Z, duration: 9, 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 six commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 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.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.2-py2.py3-none-any.whl (11 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting six Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.0-py2.py3-none-any.whl (8.8 MB) Collecting Jinja2>=2.9 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Collecting Pygments>=2.0 Downloading Pygments-2.7.4-py3-none-any.whl (950 kB) Collecting pytz>=2015.7 Downloading pytz-2020.5-py2.py3-none-any.whl (510 kB) Collecting requests Downloading requests-2.25.1-py2.py3-none-any.whl (61 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.12.5-py2.py3-none-any.whl (147 kB) Collecting chardet<5,>=3.0.2 Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.2-py2.py3-none-any.whl (136 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting packaging Downloading packaging-20.8-py2.py3-none-any.whl (39 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 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=23755 sha256=992a97060eb474af4f05a7c64c9f80f802c4cd177186b0e0cb6e34640ab01644 Stored in directory: /tmp/pip-ephem-wheel-cache-firw0wtj/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 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=d66b3f79f892c20d2e473efd183ac9cb49b28960261397f956a3f9a8209e2494 Stored in directory: /tmp/pip-ephem-wheel-cache-firw0wtj/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock Attempting uninstall: setuptools Found existing installation: setuptools 51.1.2 Uninstalling setuptools-51.1.2: Successfully uninstalled setuptools-51.1.2 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.4 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.8 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.5 readthedocs-sphinx-ext-2.1.2 recommonmark-0.5.0 requests-2.25.1 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 urllib3-1.26.2 [rtd-command-info] start-time: 2021-01-13T23:10:00.294563Z, end-time: 2021-01-13T23:10:02.816065Z, duration: 2, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting plantweb~=1.2.1 Downloading plantweb-1.2.1-py3-none-any.whl (20 kB) Requirement already satisfied: docutils in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 3)) (0.14) Requirement already satisfied: requests in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 3)) (2.25.1) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from plantweb~=1.2.1->-r docs/requirements.txt (line 3)) (1.15.0) Collecting sphinx~=3.2.0 Downloading Sphinx-3.2.1-py3-none-any.whl (2.9 MB) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 2)) (2.11.2) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 2)) (1.2.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 2)) (0.7.12) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 2)) (2.7.4) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 2)) (41.0.1) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 2)) (1.1.4) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 2)) (2.0.0) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 2)) (2.9.0) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.0->-r docs/requirements.txt (line 2)) (20.8) Collecting sphinx-rtd-theme~=0.5.0 Downloading sphinx_rtd_theme-0.5.1-py2.py3-none-any.whl (2.8 MB) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from babel>=1.3->sphinx~=3.2.0->-r docs/requirements.txt (line 2)) (2020.5) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx~=3.2.0->-r docs/requirements.txt (line 2)) (1.1.1) Requirement already satisfied: chardet<5,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from requests->plantweb~=1.2.1->-r docs/requirements.txt (line 3)) (4.0.0) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from requests->plantweb~=1.2.1->-r docs/requirements.txt (line 3)) (1.26.2) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from requests->plantweb~=1.2.1->-r docs/requirements.txt (line 3)) (2020.12.5) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from requests->plantweb~=1.2.1->-r docs/requirements.txt (line 3)) (2.10) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from packaging->sphinx~=3.2.0->-r docs/requirements.txt (line 2)) (2.4.7) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Collecting sphinxcontrib-htmlhelp Downloading sphinxcontrib_htmlhelp-1.0.3-py2.py3-none-any.whl (96 kB) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Installing collected packages: sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, sphinx, sphinx-rtd-theme, plantweb 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 plantweb-1.2.1 sphinx-3.2.1 sphinx-rtd-theme-0.5.1 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 [rtd-command-info] start-time: 2021-01-13T23:10:03.968504Z, end-time: 2021-01-13T23:10:04.043069Z, duration: 0, exit-code: 0 cat docs/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 # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # 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.imgmath', 'sphinx.ext.githubpages', 'plantweb.directive' ] plantul = 'plantweb' # 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'Compartmental Modeling Software (CMS)' copyright = u'2020, Bill & 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'0.9' # The full version, including alpha/beta/rc tags. release = u'0.9 beta' # 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:: /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 = "figures/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 = "figures/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 = '' # 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 = 'Compartmental Modeling Software (CMS)' # -- 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, 'idm-cms-docs.tex', u'Compartmental Modeling Software (CMS)', 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, 'idm-cms-docs', u'Compartmental Modeling Software(CMS)', [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, 'idm-cms-docs', u'Compartmental Modeling Software (CMS)', author, 'Institute for Disease Modeling', 'Compartmental Modeling Software (CMS) from IDM', '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': "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/"), ], 'downloads': [ ("pdf", "//docs.idmod.org/_/downloads/cms/en/latest/pdf/"), ("html", "//docs.idmod.org/_/downloads/cms/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-idm-cms', 'name': u'IDM-CMS', 'rtd_language': u'en', 'programming_language': u'csharp', 'canonical_url': 'https://docs.idmod.org/projects/cms/en/latest/', 'analytics_code': 'UA-87656833-3', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'IDM-CMS', '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': 'bbe2cadf', } # 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") 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: 2021-01-13T23:10:04.156831Z, end-time: 2021-01-13T23:10:09.230722Z, duration: 5, 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 36 source files that are out of date updating environment: [new config] 36 added, 0 changed, 0 removed reading sources... [ 2%] approximate-methods reading sources... [ 5%] bleaping reading sources... [ 8%] cms-installation reading sources... [ 11%] configuration-file reading sources... [ 13%] create-spatial-model reading sources... [ 16%] custom-propensity-function reading sources... [ 19%] dfsp reading sources... [ 22%] dwssa reading sources... [ 25%] exact-methods reading sources... [ 27%] exittimes reading sources... [ 30%] exploratory-methods reading sources... [ 33%] fractionaldiffusion reading sources... [ 36%] gibson-bruck reading sources... [ 38%] gillespie reading sources... [ 41%] gillespiefirstreaction reading sources... [ 44%] glossary reading sources... [ 47%] hybrid reading sources... [ 50%] index reading sources... [ 52%] input-files reading sources... [ 55%] introduction-modeling reading sources... [ 58%] introduction-software reading sources... [ 61%] midpoint reading sources... [ 63%] model-file reading sources... [ 66%] optimaltransportssa reading sources... 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[ 97%] tau-leaping writing output... [100%] transportssa generating indices... genindexdone writing additional pages... searchdone copying images... [ 33%] figures/SIRS_ODEvSSA.jpg copying images... [ 66%] figures/SIRS_tf_distrb_R.jpg copying images... [100%] figures/SIRS_ODEvSSA_largePop.jpg copying static files... ... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded. The HTML pages are in _build/html. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2021-01-13T23:10:09.505033Z, end-time: 2021-01-13T23:10:12.626188Z, duration: 3, 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] 36 added, 0 changed, 0 removed reading sources... [ 2%] approximate-methods reading sources... [ 5%] bleaping reading sources... [ 8%] cms-installation reading sources... [ 11%] configuration-file reading sources... [ 13%] create-spatial-model reading sources... [ 16%] custom-propensity-function reading sources... [ 19%] dfsp reading sources... [ 22%] dwssa reading sources... [ 25%] exact-methods reading sources... [ 27%] exittimes reading sources... 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[ 97%] tau-leaping reading sources... [100%] transportssa looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... introduction-modeling introduction-software cms-installation input-files run-simulations reference-overview model-file custom-propensity-function create-spatial-model configuration-file solvers exact-methods gillespie gillespiefirstreaction gibson-bruck hybrid approximate-methods bleaping rleaping tau-leaping spatial-simulation-methods dfsp fractionaldiffusion transportssa specialty-methods dwssa sdwssa exploratory-methods exittimes midpoint rleapingfast optimaltransportssa output random-number-library glossary done writing... done writing additional files... done copying images... [ 33%] figures/SIRS_ODEvSSA.jpg copying images... [ 66%] figures/SIRS_tf_distrb_R.jpg copying images... [100%] figures/SIRS_ODEvSSA_largePop.jpg copying static files... ... done copying extra files... done dumping object inventory... done build succeeded. The HTML page is in _build/localmedia. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2021-01-13T23:10:12.833521Z, end-time: 2021-01-13T23:10:14.630173Z, duration: 1, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex 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 [latex]: all documents updating environment: [new config] 36 added, 0 changed, 0 removed reading sources... [ 2%] approximate-methods reading sources... [ 5%] bleaping reading sources... [ 8%] cms-installation reading sources... [ 11%] configuration-file reading sources... [ 13%] create-spatial-model reading sources... [ 16%] custom-propensity-function reading sources... [ 19%] dfsp reading sources... [ 22%] dwssa reading sources... [ 25%] exact-methods reading sources... [ 27%] exittimes reading sources... [ 30%] exploratory-methods reading sources... [ 33%] fractionaldiffusion reading sources... [ 36%] gibson-bruck reading sources... [ 38%] gillespie reading sources... [ 41%] gillespiefirstreaction reading sources... [ 44%] glossary reading sources... [ 47%] hybrid reading sources... [ 50%] index reading sources... [ 52%] input-files reading sources... [ 55%] introduction-modeling reading sources... [ 58%] introduction-software reading sources... [ 61%] midpoint reading sources... [ 63%] model-file reading sources... [ 66%] optimaltransportssa reading sources... [ 69%] output reading sources... [ 72%] random-number-library reading sources... [ 75%] reference-overview reading sources... [ 77%] rleaping reading sources... [ 80%] rleapingfast reading sources... [ 83%] run-simulations reading sources... [ 86%] sdwssa reading sources... [ 88%] solvers reading sources... [ 91%] spatial-simulation-methods reading sources... [ 94%] specialty-methods reading sources... [ 97%] tau-leaping reading sources... [100%] transportssa looking for now-outdated files... none found pickling environment... done checking consistency... done processing idm-cms-docs.tex... index introduction-modeling introduction-software cms-installation input-files run-simulations reference-overview model-file custom-propensity-function create-spatial-model configuration-file solvers exact-methods gillespie gillespiefirstreaction gibson-bruck hybrid approximate-methods bleaping rleaping tau-leaping spatial-simulation-methods dfsp fractionaldiffusion transportssa specialty-methods dwssa sdwssa exploratory-methods exittimes midpoint rleapingfast optimaltransportssa output random-number-library glossary resolving references... done writing... done copying images... [ 33%] figures/SIRS_ODEvSSA.jpg copying images... [ 66%] figures/SIRS_tf_distrb_R.jpg copying images... [100%] figures/SIRS_ODEvSSA_largePop.jpg copying TeX support files... copying TeX support files... done build succeeded. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/checkouts/latest/docs/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2021-01-13T23:10:15.260760Z, end-time: 2021-01-13T23:10:15.319695Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2021-01-13T23:10:15.455204Z, end-time: 2021-01-13T23:10:17.243712Z, duration: 1, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-idm-cms -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-idm-cms" "idm-cms-docs.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./idm-cms-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on institute-for-disease-modeling-idm-cms.pdf (40 pages, 415143 bytes). Transcript written on institute-for-disease-modeling-idm-cms.log. Latexmk: Index file 'institute-for-disease-modeling-idm-cms.idx' was written Latexmk: Missing input file: 'institute-for-disease-modeling-idm-cms.ind' from line 'No file institute-for-disease-modeling-idm-cms.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-idm-cms.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-idm-cms.pdf' Rule 'makeindex institute-for-disease-modeling-idm-cms.idx': File changes, etc: Non-existent destination files: 'institute-for-disease-modeling-idm-cms.ind' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-idm-cms.idx' ------------ ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-idm-cms.ind" "institute-for-disease-modeling-idm-cms.idx"' ------------ Latexmk: applying rule 'makeindex institute-for-disease-modeling-idm-cms.idx'... This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file institute-for-disease-modeling-idm-cms.idx....done (18 entries accepted, 0 rejected). Sorting entries....done (67 comparisons). Generating output file institute-for-disease-modeling-idm-cms.ind....done (55 lines written, 0 warnings). Output written in institute-for-disease-modeling-idm-cms.ind. Transcript written in institute-for-disease-modeling-idm-cms.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-idm-cms.aux' 'institute-for-disease-modeling-idm-cms.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-idm-cms" "idm-cms-docs.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./idm-cms-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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[7] Underfull \hbox (badness 10000) in paragraph at lines 369--371 []\T1/pcr/m/n/10 (reaction name input-species output-species [8] [9] [10] Underfull \hbox (badness 5175) in paragraph at lines 604--607 []\T1/ptm/m/n/10 Species must be spec-i-fied with the name of the lo-cale where it be-longs in the fol-low-ing for-mat: [11] [12] [13] Overfull \hbox (3.6133pt too wide) in paragraph at lines 932--933 []|\T1/ptm/m/n/10 RejectionMethod| [14] [15] [16] [17] [18] [19] Overfull \hbox (29.71301pt too wide) in paragraph at lines 1513--1514 []|\T1/ptm/m/n/10 greenFunctionIterations| [20] Overfull \hbox (10.26335pt too wide) in paragraph at lines 1620--1621 []|\T1/ptm/m/n/10 reExpressionName| Underfull \hbox (badness 10000) in paragraph at lines 1624--1625 []|\T1/ptm/m/n/10 If un-spec-i- Underfull \hbox (badness 10000) in paragraph at lines 1624--1625 \T1/ptm/m/n/10 searches the Underfull \hbox (badness 7238) in paragraph at lines 1624--1625 [][]\T1/ptm/m/it/10 model file[][] \T1/ptm/m/n/10 for 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too wide) in paragraph at lines 1656--1657 []|\T1/ptm/m/n/10 crossEntropyThreshold| Overfull \hbox (39.61292pt too wide) in paragraph at lines 1669--1670 []|\T1/ptm/m/n/10 crossEntropyMinDataSize| Overfull \hbox (73.1928pt too wide) in paragraph at lines 1682--1683 \T1/ptm/m/n/10 name>_dwSSA_1e(), Underfull \hbox (badness 10000) in paragraph at lines 1682--1683 \T1/ptm/m/n/10 and is the Underfull \hbox (badness 10000) in paragraph at lines 1682--1683 \T1/ptm/m/n/10 name of the [21] [22] Overfull \hbox (10.26335pt too wide) in paragraph at lines 1757--1758 []|\T1/ptm/m/n/10 reExpressionName| Underfull \hbox (badness 10000) in paragraph at lines 1761--1762 []|\T1/ptm/m/n/10 If un-spec-i- Underfull \hbox (badness 10000) in paragraph at lines 1761--1762 \T1/ptm/m/n/10 searches the Underfull \hbox (badness 7238) in paragraph at lines 1761--1762 [][]\T1/ptm/m/it/10 model file[][] \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 1770--1771 []|\T1/ptm/m/n/10 If 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lines 1837--1838 \T1/ptm/m/n/10 name of the [23] [24] [25] [26] [27] Overfull \hbox (29.71301pt too wide) in paragraph at lines 2242--2243 []|\T1/ptm/m/n/10 greenFunctionIterations| Overfull \hbox (27.50319pt too wide) in paragraph at lines 2251--2252 []|\T1/ptm/m/n/10 transportSSAThreshold| Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 []|\T1/ptm/m/n/10 uMax * Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 \T1/ptm/m/n/10 graphDi-men- Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 \T1/ptm/m/n/10 sion, where Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 \T1/ptm/m/n/10 graphDi-men- Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 \T1/ptm/m/n/10 sion is the Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 \T1/ptm/m/n/10 di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 \T1/ptm/m/n/10 of the dif-fu- Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 \T1/ptm/m/n/10 sion prob-lem Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 \T1/ptm/m/n/10 (cal-cu-lated [28] Overfull \vbox (2.42427pt too high) detected at line 2311 [29] Overfull \hbox (19.00302pt too wide) in paragraph at lines 2417--2418 []|\T1/ptm/m/n/10 writerealizationindex| [30] Overfull \vbox (2.62427pt too high) detected at line 2452 [31] Overfull \vbox (2.68167pt too high) detected at line 2523 [32] Overfull \hbox (2.78377pt too wide) in paragraph at lines 2550--2551 []|\T1/ptm/m/n/10 AESCOUNTER. Underfull \hbox (badness 10000) in paragraph at lines 2550--2551 \T1/ptm/m/n/10 to PSEU-DO- [33] [34] Chapter 4. [35] (./institute-for-disease-modeling-idm-cms.ind [36] Underfull \hbox (badness 10000) in paragraph at lines 24--26 []\T1/pcr/m/n/10 Gillespie stochastic simulation [37]) (./institute-for-disease-modeling-idm-cms.aux) Package rerunfilecheck Warning: File `institute-for-disease-modeling-idm-cms.ou t' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on institute-for-disease-modeling-idm-cms.pdf (41 pages, 424239 bytes). Transcript written on institute-for-disease-modeling-idm-cms.log. Latexmk: Index file 'institute-for-disease-modeling-idm-cms.idx' was written Latexmk: References changed. 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Underfull \hbox (badness 10000) in paragraph at lines 1633--1634 []|\T1/ptm/m/n/10 If un-spec-i- Underfull \hbox (badness 10000) in paragraph at lines 1633--1634 \T1/ptm/m/n/10 searches the Underfull \hbox (badness 7238) in paragraph at lines 1633--1634 [][]\T1/ptm/m/it/10 model file[][] \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 1642--1643 \T1/ptm/m/n/10 en-tropy (CE) Underfull \hbox (badness 10000) in paragraph at lines 1642--1643 \T1/ptm/m/n/10 sim-u-la-tions Underfull \hbox (badness 10000) in paragraph at lines 1642--1643 \T1/ptm/m/n/10 are per-formed Underfull \hbox (badness 10000) in paragraph at lines 1642--1643 \T1/ptm/m/n/10 to com-pute Underfull \hbox (badness 10000) in paragraph at lines 1642--1643 \T1/ptm/m/n/10 val-ues prior Underfull \hbox (badness 10000) in paragraph at lines 1642--1643 \T1/ptm/m/n/10 to dwSSA Overfull \hbox (7.40349pt too wide) in paragraph at lines 1647--1648 []|\T1/ptm/m/n/10 crossEntropyRuns| Overfull \hbox (27.39334pt too wide) in paragraph at lines 1656--1657 []|\T1/ptm/m/n/10 crossEntropyThreshold| Overfull \hbox (39.61292pt too wide) in paragraph at lines 1669--1670 []|\T1/ptm/m/n/10 crossEntropyMinDataSize| Overfull \hbox (73.1928pt too wide) in paragraph at lines 1682--1683 \T1/ptm/m/n/10 name>_dwSSA_1e(), Underfull \hbox (badness 10000) in paragraph at lines 1682--1683 \T1/ptm/m/n/10 and is the Underfull \hbox (badness 10000) in paragraph at lines 1682--1683 \T1/ptm/m/n/10 name of the [21] [22] Overfull \hbox (10.26335pt too wide) in paragraph at lines 1757--1758 []|\T1/ptm/m/n/10 reExpressionName| Underfull \hbox (badness 10000) in paragraph at lines 1761--1762 []|\T1/ptm/m/n/10 If un-spec-i- Underfull \hbox (badness 10000) in paragraph at lines 1761--1762 \T1/ptm/m/n/10 searches the Underfull \hbox (badness 7238) in paragraph at lines 1761--1762 [][]\T1/ptm/m/it/10 model file[][] \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 1770--1771 []|\T1/ptm/m/n/10 If un-spec-i- Underfull \hbox (badness 10000) in paragraph at lines 1770--1771 \T1/ptm/m/n/10 searches the Underfull \hbox (badness 5460) in paragraph at lines 1770--1771 \T1/ptm/m/n/10 model file for Overfull \hbox (46.78256pt too wide) in paragraph at lines 1793--1794 []|\T1/ptm/m/n/10 biasingParametersFileName| Overfull \hbox (63.53258pt too wide) in paragraph at lines 1797--1798 \T1/ptm/m/n/10 Name>_biasingParameters.json.| Overfull \hbox (7.40349pt too wide) in paragraph at lines 1802--1803 []|\T1/ptm/m/n/10 crossEntropyRuns| Overfull \hbox (27.39334pt too wide) in paragraph at lines 1811--1812 []|\T1/ptm/m/n/10 crossEntropyThreshold| Overfull \hbox (39.61292pt too wide) in paragraph at lines 1824--1825 []|\T1/ptm/m/n/10 crossEntropyMinDataSize| Overfull \hbox (77.08269pt too wide) in paragraph at lines 1837--1838 \T1/ptm/m/n/10 name>_sdwSSA_1e(), Underfull \hbox (badness 10000) in paragraph at lines 1837--1838 \T1/ptm/m/n/10 and is the Underfull \hbox (badness 10000) in paragraph at lines 1837--1838 \T1/ptm/m/n/10 name of the [23] [24] [25] [26] [27] Overfull \hbox (29.71301pt too wide) in paragraph at lines 2242--2243 []|\T1/ptm/m/n/10 greenFunctionIterations| Overfull \hbox (27.50319pt too wide) in paragraph at lines 2251--2252 []|\T1/ptm/m/n/10 transportSSAThreshold| Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 []|\T1/ptm/m/n/10 uMax * Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 \T1/ptm/m/n/10 graphDi-men- Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 \T1/ptm/m/n/10 sion, where Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 \T1/ptm/m/n/10 graphDi-men- Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 \T1/ptm/m/n/10 sion is the Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 \T1/ptm/m/n/10 di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 \T1/ptm/m/n/10 of the dif-fu- Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 \T1/ptm/m/n/10 sion prob-lem Underfull \hbox (badness 10000) in paragraph at lines 2255--2256 \T1/ptm/m/n/10 (cal-cu-lated [28] Overfull \vbox (2.42427pt too high) detected at line 2311 [29] Overfull \hbox (19.00302pt too wide) in paragraph at lines 2417--2418 []|\T1/ptm/m/n/10 writerealizationindex| [30] Overfull \vbox (2.62427pt too high) detected at line 2452 [31] Overfull \vbox (2.68167pt too high) detected at line 2523 [32] Overfull \hbox (2.78377pt too wide) in paragraph at lines 2550--2551 []|\T1/ptm/m/n/10 AESCOUNTER. Underfull \hbox (badness 10000) in paragraph at lines 2550--2551 \T1/ptm/m/n/10 to PSEU-DO- [33] [34] Chapter 4. [35] (./institute-for-disease-modeling-idm-cms.ind [36] Underfull \hbox (badness 10000) in paragraph at lines 24--26 []\T1/pcr/m/n/10 Gillespie stochastic simulation [37]) (./institute-for-disease-modeling-idm-cms.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on institute-for-disease-modeling-idm-cms.pdf (41 pages, 424404 bytes). Transcript written on institute-for-disease-modeling-idm-cms.log. 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