Read the Docs build information
Build id: 2576227
Project: institute-for-disease-modeling-idm-cms
Version: 46
Commit: 7559a6225e5e907c708b81007a083a95eb8f53ce
Date: 2024-10-28T20:25:48.810962Z
State: finished
Success: True


[rtd-command-info] start-time: 2024-10-28T20:25:50.274756Z, end-time: 2024-10-28T20:25:53.999095Z, duration: 3, exit-code: 0
git clone --depth 1 https://github.com/InstituteforDiseaseModeling/IDM-CMS.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-10-28T20:25:54.085833Z, end-time: 2024-10-28T20:25:55.715197Z, duration: 1, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/46/head:external-46
From https://github.com/InstituteforDiseaseModeling/IDM-CMS
 * [new ref]         refs/pull/46/head -> external-46
 * [new tag]         v0.82             -> v0.82
 * [new tag]         v0.9              -> v0.9

[rtd-command-info] start-time: 2024-10-28T20:25:55.886015Z, end-time: 2024-10-28T20:25:57.018810Z, duration: 1, exit-code: 0
git checkout --force 7559a6225e5e907c708b81007a083a95eb8f53ce
Note: switching to '7559a6225e5e907c708b81007a083a95eb8f53ce'.

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 switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 7559a62 jupyter lab version fix

[rtd-command-info] start-time: 2024-10-28T20:25:57.123089Z, end-time: 2024-10-28T20:25:57.192363Z, 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: 2024-10-28T20:26:03.441841Z, end-time: 2024-10-28T20:26:03.521601Z, duration: 0, exit-code: 0
asdf global python 3.9.19


[rtd-command-info] start-time: 2024-10-28T20:26:04.009880Z, end-time: 2024-10-28T20:26:05.248273Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.9.19.final.0-64 in 895ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm-cms/envs/46, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2024-10-28T20:26:05.340663Z, end-time: 2024-10-28T20:26:17.944099Z, duration: 12, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
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Installing collected packages: setuptools, pip
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      Successfully uninstalled setuptools-67.6.1
  Attempting uninstall: pip
    Found existing installation: pip 23.1
    Uninstalling pip-23.1:
      Successfully uninstalled pip-23.1
Successfully installed pip-24.3.1 setuptools-75.2.0

[rtd-command-info] start-time: 2024-10-28T20:26:18.046753Z, end-time: 2024-10-28T20:26:25.425505Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx
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Installing collected packages: snowballstemmer, zipp, urllib3, tomli, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, sphinx
Successfully installed Jinja2-3.1.4 MarkupSafe-3.0.2 Pygments-2.18.0 alabaster-0.7.16 babel-2.16.0 certifi-2024.8.30 charset-normalizer-3.4.0 docutils-0.21.2 idna-3.10 imagesize-1.4.1 importlib-metadata-8.5.0 packaging-24.1 requests-2.32.3 snowballstemmer-2.2.0 sphinx-7.4.7 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 tomli-2.0.2 urllib3-2.2.3 zipp-3.20.2

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python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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Installing collected packages: webencodings, wcwidth, pure-eval, ptyprocess, fastjsonschema, wrapt, websocket-client, webcolors, uri-template, typing-extensions, types-python-dateutil, traitlets, tornado, tinycss2, soupsieve, sniffio, six, send2trash, rpds-py, rfc3986-validator, pyzmq, pyyaml, python-json-logger, pyjwt, pycparser, psutil, prompt-toolkit, prometheus-client, platformdirs, pexpect, parso, pandocfilters, overrides, nest-asyncio, mistune, mdurl, jupyterlab-pygments, jsonpointer, json5, h11, fqdn, executing, exceptiongroup, docutils, defusedxml, decorator, debugpy, attrs, accessible-pygments, terminado, sphinx, rfc3339-validator, referencing, python-dateutil, pockets, plantweb, matplotlib-inline, markdown-it-py, jupyter-core, jedi, httpcore, deprecated, comm, cffi, bleach, beautifulsoup4, async-lru, asttokens, anyio, stack-data, sphinxcontrib-programoutput, sphinxcontrib-napoleon, pynacl, pydata-sphinx-theme, mdit-py-plugins, jupyter-server-terminals, jupyter-client, jsonschema-specifications, httpx, cryptography, arrow, argon2-cffi-bindings, myst-parser, jsonschema, isoduration, ipython, argon2-cffi, pygithub, nbformat, ipykernel, nbclient, jupyter-events, nbconvert, nbsphinx, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab
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[rtd-command-info] start-time: 2024-10-28T20:26:45.544892Z, end-time: 2024-10-28T20:26:45.608485Z, 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.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 = 'pydata_sphinx_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 = {
    "collapse_navigation": False,
    "navigation_depth": 3,
    "show_prev_next": True,
    "icon_links": [
        {"name": "IDM docs", "url": "https://docs.idmod.org", "icon": "fas fa-home"},
        {
            "name": "GitHub",
            "url": "https://github.com/institutefordiseasemodeling/IDM-CMS",
            "icon": "fab fa-github-square",
        },
    ],
    "navbar_end": ["theme-switcher", "navbar-icon-links"],
    "secondary_sidebar_items": ["navbar-side"],
    "header_links_before_dropdown": 5,
    "footer_start": ["copyright", "footer_start"],
    "footer_end": ["theme-version", "footer_end"],
}
html_sidebars = {
    "**": ["sidebar-nav-bs", "page-toc"],
}
html_logo = "figures/idm-logo-transparent.png"
html_favicon = "figures/favicon.ico"
html_static_path = ['_static']
html_baseurl = "https://docs.idmod.org/projects/IDM-CMS/en/latest"
html_context = {
    'rtd_url': 'https://docs.idmod.org/projects/IDM-CMS/en/latest',
    "versions_dropdown": {
        "latest": "devel (latest)",
        "stable": "current (stable)",
    },
    "default_mode": "light",
}

# Add customizations
def setup(app):
    app.add_css_file("theme_overrides.css")

# 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.
# "<project> v<release> 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 <link> 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}

[rtd-command-info] start-time: 2024-10-28T20:26:45.721104Z, end-time: 2024-10-28T20:26:53.656196Z, duration: 7, exit-code: 0
python -m sphinx -T -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={'strikethrough', 'colon_fence', 'deflist', 'dollarmath', 'fieldlist', 'attrs_inline', 'html_admonition', 'linkify', 'smartquotes', 'replacements', 'substitution', 'tasklist', 'amsmath', 'html_image'}, 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... [ 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... 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
build succeeded.

The HTML pages are in ../_readthedocs/html.