Read the Docs build information Build id: 1564806 Project: institute-for-disease-modeling-idm-cms Version: latest Commit: 7151692febfd8ff88cc65d309cf0d840afa1ddb5 Date: 2023-06-27T19:08:44.624957Z State: finished Success: True [rtd-command-info] start-time: 2023-06-27T19:10:03.884876Z, end-time: 2023-06-27T19:10:21.946137Z, duration: 18, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/InstituteforDiseaseModeling/IDM-CMS.git . Cloning into '.'... [rtd-command-info] start-time: 2023-06-27T19:10:22.352678Z, end-time: 2023-06-27T19:10:22.435630Z, duration: 0, exit-code: 0 cat .readthedocs.yml # .readthedocs.yml # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details # Required version: 2 # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py fail_on_warning: true # Build documentation with MkDocs #mkdocs: # configuration: mkdocs.yml # Optionally build your docs in additional formats such as PDF formats: - htmlzip - pdf # Optionally set the version of Python and requirements required to build your docs python: version: 3.7 install: - requirements: docs/requirements.txt # Optionally rank topics in search results, between -10 (lower) and 10 (higher). # 0 is normal rank, not no rank search: ranking: cms-installation.html: 3 run-simulations.html: 2 configuration-file.html: 2 solvers.html: 2 [rtd-command-info] start-time: 2023-06-27T19:10:24.942665Z, end-time: 2023-06-27T19:10:29.967804Z, duration: 5, exit-code: 0 python3.7 -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH 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: 2023-06-27T19:10:30.725627Z, end-time: 2023-06-27T19:10:31.981220Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools 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 (23.1.2) 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 (68.0.0) [rtd-command-info] start-time: 2023-06-27T19:10:32.773258Z, end-time: 2023-06-27T19:10:40.083826Z, duration: 7, exit-code: 0 python -m pip install --upgrade --no-cache-dir pillow==5.4.1 mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0 Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) 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imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed MarkupSafe-2.1.3 Pygments-2.15.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.5.7 charset-normalizer-3.1.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.1 pillow-5.4.1 pytz-2023.3 readthedocs-sphinx-ext-2.2.1 recommonmark-0.5.0 requests-2.31.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-2.0.3 [rtd-command-info] start-time: 2023-06-27T19:10:40.750638Z, end-time: 2023-06-27T19:10:44.003472Z, duration: 3, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting sphinx-rtd-theme~=0.5.0 (from -r docs/requirements.txt (line 1)) Downloading sphinx_rtd_theme-0.5.2-py2.py3-none-any.whl (9.1 MB) 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/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=3.2.0->-r docs/requirements.txt (line 2)) (3.1.0) Requirement already satisfied: idna<4,>=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>=2.5.0->sphinx~=3.2.0->-r docs/requirements.txt (line 2)) (3.4) Requirement already satisfied: urllib3<3,>=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>=2.5.0->sphinx~=3.2.0->-r docs/requirements.txt (line 2)) (2.0.3) 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>=2.5.0->sphinx~=3.2.0->-r docs/requirements.txt (line 2)) (2023.5.7) Installing collected packages: sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, docutils, sphinx, plantweb, sphinx-rtd-theme Attempting uninstall: docutils Found existing installation: docutils 0.17.1 Uninstalling docutils-0.17.1: Successfully uninstalled docutils-0.17.1 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed docutils-0.16 plantweb-1.2.1 sphinx-3.2.1 sphinx-rtd-theme-0.5.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 [rtd-command-info] start-time: 2023-06-27T19:10:51.742371Z, end-time: 2023-06-27T19:10:51.813805Z, 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 from datetime import datetime # -- 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 = f'1999 - {datetime.today().year}, 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/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} # This following legacy behavior will gradually be sliced out until its deprecated and removed. # Skipped for Sphinx 6+ # Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH # Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023) if ( using_rtd_theme and version_info < (6,0) and not False ): theme = importlib.import_module('sphinx_rtd_theme') if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] # Define websupport2_base_url and websupport2_static_url 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", 'proxied_static_path': "/_/static/", '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': '', 'analytics_code': 'G-SVDSQH04EM', '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': 'G-SVDSQH04EM', 'global_analytics_code': 'UA-17997319-2', 'commit': '7151692f', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): for key in context: if key not in html_context: html_context[key] = context[key] else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-idm-cms/builds/1564806/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2023-06-27T19:10:52.261604Z, end-time: 2023-06-27T19:10:59.253390Z, duration: 6, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/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 [html]: 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... [ 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 preparing documents... done writing output... [ 2%] approximate-methods writing output... [ 5%] bleaping writing output... [ 8%] cms-installation writing output... [ 11%] configuration-file writing output... [ 13%] create-spatial-model writing output... [ 16%] custom-propensity-function writing output... [ 19%] dfsp writing output... [ 22%] dwssa writing output... [ 25%] exact-methods writing output... [ 27%] exittimes writing output... [ 30%] exploratory-methods writing output... [ 33%] fractionaldiffusion writing output... [ 36%] gibson-bruck writing output... [ 38%] gillespie writing output... [ 41%] gillespiefirstreaction writing output... [ 44%] glossary writing output... [ 47%] hybrid writing output... [ 50%] index writing output... [ 52%] input-files writing output... [ 55%] introduction-modeling writing output... [ 58%] introduction-software writing output... [ 61%] midpoint writing output... [ 63%] model-file writing output... [ 66%] optimaltransportssa writing output... [ 69%] output writing output... [ 72%] random-number-library writing output... [ 75%] reference-overview writing output... [ 77%] rleaping writing output... [ 80%] rleapingfast writing output... [ 83%] run-simulations writing output... [ 86%] sdwssa writing output... [ 88%] solvers writing output... [ 91%] spatial-simulation-methods writing output... [ 94%] specialty-methods writing output... [ 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 ../_readthedocs/html. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2023-06-27T19:10:59.693843Z, end-time: 2023-06-27T19:11:03.344198Z, duration: 3, exit-code: 0 python -m sphinx -T -E -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip 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... [ 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 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 ../_readthedocs/htmlzip. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2023-06-27T19:11:05.202382Z, end-time: 2023-06-27T19:11:07.303740Z, duration: 2, exit-code: 0 python -m sphinx -T -E -b latex -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/pdf 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... 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[ 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 ../_readthedocs/pdf. 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/_readthedocs/pdf/_static/searchtools.js [rtd-command-info] start-time: 2023-06-27T19:11:08.227556Z, end-time: 2023-06-27T19:11:08.288561Z, 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: 2023-06-27T19:11:08.930923Z, end-time: 2023-06-27T19:11:11.867382Z, duration: 2, 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. 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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, 415924 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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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, 425013 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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(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./institute-for-disease-modeling-idm-cms.out) (./institute-for-disease-modeling-idm-cms.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./institute-for-disease-modeling-idm-cms.toc) [1] [2] [1] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [3 <./SIRS_ODEvSSA.jp g>] [4 <./SIRS_tf_distrb_R.jpg> <./SIRS_ODEvSSA_largePop.jpg>] Chapter 2. [5] [6] Chapter 3. [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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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, 425178 bytes). Transcript written on institute-for-disease-modeling-idm-cms.log. Latexmk: Index file 'institute-for-disease-modeling-idm-cms.idx' was written 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' Latexmk: All targets (institute-for-disease-modeling-idm-cms.pdf) are up-to-date