Read the Docs build information Build id: 1974417 Project: institute-for-disease-modeling-idm-cms Version: latest Commit: defbb6d1b78d03fa859deb3523cb1930fdd794f9 Date: 2024-01-26T01:02:15.639987Z State: finished Success: True [rtd-command-info] start-time: 2024-01-26T01:02:17.950864Z, end-time: 2024-01-26T01:02:47.791496Z, duration: 29, exit-code: 0 git clone --depth 1 https://github.com/InstituteforDiseaseModeling/IDM-CMS.git . Cloning into '.'... [rtd-command-info] start-time: 2024-01-26T01:02:47.970735Z, end-time: 2024-01-26T01:02:48.783361Z, duration: 0, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 From https://github.com/InstituteforDiseaseModeling/IDM-CMS * [new tag] v0.82 -> v0.82 * [new tag] v0.9 -> v0.9 [rtd-command-info] start-time: 2024-01-26T01:02:48.847417Z, end-time: 2024-01-26T01:02:48.910977Z, 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 # Set the version of Python and other tools you might need build: os: ubuntu-20.04 tools: python: "3.9" # 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 # Optionally set the version of Python and requirements required to build your docs python: 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: 2024-01-26T01:02:54.569263Z, end-time: 2024-01-26T01:02:54.666839Z, duration: 0, exit-code: 0 asdf global python 3.9.18 [rtd-command-info] start-time: 2024-01-26T01:02:55.032076Z, end-time: 2024-01-26T01:02:56.242247Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.18.final.0-64 in 880ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/latest, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, 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rfc3339-validator, referencing, python-dateutil, pockets, plantweb, matplotlib-inline, markdown-it-py, jupyter-core, jedi, deprecated, comm, cffi, bleach, beautifulsoup4, async-lru, asttokens, anyio, stack-data, sphinxcontrib-programoutput, sphinxcontrib-napoleon, sphinxcontrib-jquery, sphinx-copybutton, pynacl, mdit-py-plugins, jupyter-server-terminals, jupyter-client, jsonschema-specifications, cryptography, arrow, argon2-cffi-bindings, sphinx-rtd-theme, myst-parser, jsonschema, isoduration, ipython, argon2-cffi, pygithub, nbformat, ipykernel, nbclient, jupyter-events, nbconvert, nbsphinx, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab Attempting uninstall: docutils Found existing installation: docutils 0.20.1 Uninstalling docutils-0.20.1: Successfully uninstalled docutils-0.20.1 Attempting uninstall: sphinx Found existing installation: Sphinx 7.2.6 Uninstalling Sphinx-7.2.6: Successfully uninstalled Sphinx-7.2.6 Successfully installed anyio-4.2.0 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-2.4.1 async-lru-2.0.4 attrs-23.2.0 beautifulsoup4-4.12.3 bleach-6.1.0 cffi-1.16.0 comm-0.2.1 cryptography-42.0.1 debugpy-1.8.0 decorator-5.1.1 defusedxml-0.7.1 deprecated-1.2.14 docutils-0.18.1 exceptiongroup-1.2.0 executing-2.0.1 fastjsonschema-2.19.1 fqdn-1.5.1 ipykernel-6.29.0 ipython-8.18.1 isoduration-20.11.0 jedi-0.19.1 json5-0.9.14 jsonpointer-2.4 jsonschema-4.21.1 jsonschema-specifications-2023.12.1 jupyter-client-8.6.0 jupyter-core-5.7.1 jupyter-events-0.9.0 jupyter-lsp-2.2.2 jupyter-server-2.12.5 jupyter-server-terminals-0.5.2 jupyterlab-4.0.11 jupyterlab-pygments-0.3.0 jupyterlab-server-2.25.2 markdown-it-py-3.0.0 matplotlib-inline-0.1.6 mdit-py-plugins-0.4.0 mdurl-0.1.2 mistune-3.0.2 myst-parser-2.0.0 nbclient-0.9.0 nbconvert-7.14.2 nbformat-5.9.2 nbsphinx-0.9.3 nest-asyncio-1.6.0 notebook-shim-0.2.3 overrides-7.6.0 pandocfilters-1.5.1 parso-0.8.3 pexpect-4.9.0 plantweb-1.2.1 platformdirs-4.1.0 pockets-0.9.1 prometheus-client-0.19.0 prompt-toolkit-3.0.43 psutil-5.9.8 ptyprocess-0.7.0 pure-eval-0.2.2 pycparser-2.21 pygithub-1.59.1 pyjwt-2.8.0 pynacl-1.5.0 python-dateutil-2.8.2 python-json-logger-2.0.7 pyyaml-6.0.1 pyzmq-25.1.2 readthedocs-sphinx-search-0.3.2 referencing-0.32.1 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.17.1 send2trash-1.8.2 six-1.16.0 sniffio-1.3.0 soupsieve-2.5 sphinx-6.2.1 sphinx-copybutton-0.5.2 sphinx-rtd-theme-1.2.2 sphinxcontrib-jquery-4.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 stack-data-0.6.3 terminado-0.18.0 tinycss2-1.2.1 tomli-2.0.1 tornado-6.4 traitlets-5.14.1 types-python-dateutil-2.8.19.20240106 typing-extensions-4.9.0 uri-template-1.3.0 wcwidth-0.2.13 webcolors-1.13 webencodings-0.5.1 websocket-client-1.7.0 wrapt-1.16.0 [rtd-command-info] start-time: 2024-01-26T01:03:32.457830Z, end-time: 2024-01-26T01:03:32.519196Z, 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', 'sphinx_search.extension', # search across multiple docsets in domain 'sphinx.ext.viewcode', # link to view source code 'myst_parser', # source files written in MD or RST ] myst_enable_extensions = [ "amsmath", "attrs_inline", "colon_fence", "deflist", "dollarmath", "fieldlist", "html_admonition", "html_image", "linkify", "replacements", "smartquotes", "strikethrough", "substitution", "tasklist", ] 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'] # 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 = 'en' # 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_css_files = ['theme_overrides.css'] html_js_files = ['show_block_by_os.js'] # 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)' # -- RTD Sphinx search for searching across the entire domain, default child ------------- if os.environ.get('READTHEDOCS') == 'True': search_project_parent = "institute-for-disease-modeling-idm" search_project = os.environ["READTHEDOCS_PROJECT"] search_version = os.environ["READTHEDOCS_VERSION"] rtd_sphinx_search_default_filter = f"subprojects:{search_project}/{search_version}" rtd_sphinx_search_filters = { "Search this project": f"project:{search_project}/{search_version}", "Search all IDM docs": f"subprojects:{search_project_parent}/{search_version}", } # -- 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') # Define this variable in case it's not defined by the user. # It defaults to `alabaster` which is the default from Sphinx. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme html_theme = globals().get('html_theme', 'alabaster') #Add project information to the template context. context = { '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': [ ("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': 'None', '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': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'defbb6d1', } # 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/1974417/' 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: 2024-01-26T01:03:32.583828Z, end-time: 2024-01-26T01:03:43.219205Z, duration: 10, exit-code: 0 python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v6.2.1 making output directory... done myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'colon_fence', 'html_image', 'linkify', 'fieldlist', 'strikethrough', 'deflist', 'substitution', 'dollarmath', 'amsmath', 'attrs_inline', 'smartquotes', 'html_admonition', 'tasklist', 'replacements'}, disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... 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... 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[ 97%] tau-leaping writing output... [100%] transportssa generating indices... genindex done highlighting module code... writing additional pages... search 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 search index in English (code: en)... done dumping object inventory... done Updating searchtools for Read the Docs search... build succeeded. The HTML pages are in ../_readthedocs/html. [rtd-command-info] start-time: 2024-01-26T01:03:43.296359Z, end-time: 2024-01-26T01:03:47.231666Z, 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 v6.2.1 making output directory... done myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'dollarmath', 'html_image', 'colon_fence', 'tasklist', 'smartquotes', 'attrs_inline', 'strikethrough', 'substitution', 'fieldlist', 'html_admonition', 'deflist', 'linkify', 'amsmath', 'replacements'}, disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... 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... 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[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 Updating searchtools for Read the Docs search... build succeeded. The HTML page is in ../_readthedocs/htmlzip.