Read the Docs build information
Build id: 455816
Project: institute-for-disease-modeling-idm
Version: latest
Commit: 4e1ce98c7244189127de6262edaeec0cb7ceaf40
Date: 2020-10-20T01:12:54.030026Z
State: finished
Success: True


[rtd-command-info] start-time: 2020-10-20T01:12:56.269710Z, end-time: 2020-10-20T01:12:56.888713Z, duration: 0, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/docs.idmod.org.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.113' (RSA) to the list of known hosts.

[rtd-command-info] start-time: 2020-10-20T01:12:57.546828Z, end-time: 2020-10-20T01:12:57.604742Z, duration: 0, exit-code: 0
git checkout --force origin/landing-page
Note: checking out 'origin/landing-page'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

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

  git checkout -b <new-branch-name>

HEAD is now at 4e1ce98 fix missing import

[rtd-command-info] start-time: 2020-10-20T01:12:58.097519Z, end-time: 2020-10-20T01:12:58.152719Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-10-20T01:13:05.520644Z, end-time: 2020-10-20T01:13:06.098970Z, duration: 0, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/docs.idmod.org.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.112' (RSA) to the list of known hosts.

[rtd-command-info] start-time: 2020-10-20T01:13:06.539697Z, end-time: 2020-10-20T01:13:06.593277Z, duration: 0, exit-code: 0
git checkout --force origin/landing-page
Note: checking out 'origin/landing-page'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

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

  git checkout -b <new-branch-name>

HEAD is now at 4e1ce98 fix missing import

[rtd-command-info] start-time: 2020-10-20T01:13:06.958201Z, end-time: 2020-10-20T01:13:07.030416Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-10-20T01:13:08.140315Z, end-time: 2020-10-20T01:13:12.237324Z, duration: 4, exit-code: 0
python3.8 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.8.0'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/bin/python3.8
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2020-10-20T01:13:12.625562Z, end-time: 2020-10-20T01:13:13.295150Z, duration: 0, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip
Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (20.2.4)

[rtd-command-info] start-time: 2020-10-20T01:13:13.511083Z, end-time: 2020-10-20T01:13:40.752663Z, duration: 27, exit-code: 0
python -m pip install --upgrade --no-cache-dir setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1
Collecting setuptools==41.0.1
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Collecting docutils==0.14
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Collecting mock==1.0.1
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Collecting pillow==5.4.1
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Collecting alabaster!=0.7.5,<0.8,>=0.7
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Collecting Jinja2>=2.3
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Collecting MarkupSafe>=0.23
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Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1
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Collecting pyparsing>=2.0.2
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Collecting pytz>=2015.7
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Building wheels for collected packages: mock, pillow, future
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=0ce115be4b76f9b8020c8640955613a2226239cd5dc25ced238d107d1d3abe7b
  Stored in directory: /tmp/pip-ephem-wheel-cache-k6802fsy/wheels/93/2f/a4/2f9af849a57eb554a36d31257560b5e9e207697f285eb06351
  Building wheel for pillow (setup.py): started
  Building wheel for pillow (setup.py): finished with status 'done'
  Created wheel for pillow: filename=Pillow-5.4.1-cp38-cp38-linux_x86_64.whl size=1259566 sha256=e813359ffe8644341ae7543e4dc2562f8f1d6ca32415316a1c400c5e00575dae
  Stored in directory: /tmp/pip-ephem-wheel-cache-k6802fsy/wheels/5f/a8/6b/5b7b3f764d879214eb03570f74d2b086201eb514e6ffa68d6d
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=f9d47d8a307e0f4f15f655d6e1470b92473e0a9eda4922303c856258a02cf210
  Stored in directory: /tmp/pip-ephem-wheel-cache-k6802fsy/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4
Successfully built mock pillow future
Installing collected packages: setuptools, docutils, mock, pillow, alabaster, future, commonmark, MarkupSafe, Jinja2, urllib3, chardet, certifi, idna, requests, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, pyparsing, six, packaging, pytz, babel, imagesize, snowballstemmer, Pygments, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
  Attempting uninstall: setuptools
    Found existing installation: setuptools 50.3.2
    Uninstalling setuptools-50.3.2:
      Successfully uninstalled setuptools-50.3.2
Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.25.11

[rtd-command-info] start-time: 2020-10-20T01:13:41.056229Z, end-time: 2020-10-20T01:13:41.849509Z, duration: 0, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from -r requirements.txt (line 1)) (1.8.5)
Requirement already satisfied: sphinx-rtd-theme in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from -r requirements.txt (line 2)) (0.4.3)
Collecting sphinx-notfound-page
  Downloading sphinx_notfound_page-0.5-py3-none-any.whl (13 kB)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (2.7.1)
Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (2.24.0)
Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (2.8.0)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (0.7.12)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (2.0.0)
Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (1.2.4)
Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (1.15.0)
Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (0.14)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (20.4)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (2.11.2)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (1.2.0)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (41.0.1)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (2020.6.20)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (1.25.11)
Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (2.10)
Requirement already satisfied: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (3.0.4)
Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from babel!=2.0,>=1.3->sphinx->-r requirements.txt (line 1)) (2020.1)
Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinxcontrib-websupport->sphinx->-r requirements.txt (line 1)) (1.1.4)
Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from packaging->sphinx->-r requirements.txt (line 1)) (2.4.7)
Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from Jinja2>=2.3->sphinx->-r requirements.txt (line 1)) (1.1.1)
Installing collected packages: sphinx-notfound-page
Successfully installed sphinx-notfound-page-0.5

[rtd-command-info] start-time: 2020-10-20T01:13:44.350870Z, end-time: 2020-10-20T01:13:44.424333Z, duration: 0, exit-code: 0
cat docs/conf.py
# Configuration file for the Sphinx documentation builder.
#
# Documentation: https://www.sphinx-doc.org/en/master/usage/configuration.html
import os
import sphinx_rtd_theme
from datetime import date

# -- Project information -----------------------------------------------------

project = 'idm'
copyright = f'{date.today().year}, Bill & Melinda Gates Foundation. All rights reserved.'
author = 'Institute for Disease Modeling'


# -- General configuration ---------------------------------------------------
extensions = [
    'sphinx_rtd_theme',
    'notfound.extension'
]

exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '.venv']

master_doc = 'index'

primary_domain = None

source_suffix = {
    '.rst': 'restructuredtext'
}

templates_path = ['_templates']


# -- Options for HTML output -------------------------------------------------

# Variables used in the html Jinja templates
html_add_permalinks = ""
html_additional_pages = {
    'index': 'index.html'
}
html_context = dict(
    canonical_url = "https://docs.idmod.org/",
    images = '_static/img',
    IDM_HOST = os.getenv("IDM_HOST", "idmod.org")
)
html_copy_source = False
html_favicon = "_static/favicon.ico"
html_show_sourcelink = False
html_show_sphinx = False
html_static_path = ['_static']
html_style = 'css/style.css'
html_use_index = False
html_theme = 'sphinx_rtd_theme'
html_title = "IDMOD"

notfound_no_urls_prefix = True




###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#


import importlib
import sys
import os.path
from six import string_types

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')

# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
    (
        'html_theme' in globals() and
        html_theme in ['default'] and
        # Allow people to bail with a hack of having an html_style
        'html_style' not in globals()
    ) or 'html_theme' not in globals()
)
if using_rtd_theme:
    theme = importlib.import_module('sphinx_rtd_theme')
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    websupport2_static_url = 'https://assets.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
        ("institute-for-disease-modeling-synthpops-test", "https://docs.idmod.org/projects/synthpops/en/latest/"),
        ("institute-for-disease-modeling-idmtools", "https://docs.idmod.org/projects/idmtools/en/latest/"),
        ("institute-for-disease-modeling-covasim", "https://docs.idmod.org/projects/covasim/en/latest/"),
        ("institute-for-disease-modeling-vis-tools", "https://docs.idmod.org/projects/vis-tools/en/latest/"),
        ("institute-for-disease-modeling-emodpy", "https://docs.idmod.org/projects/emodpy/en/latest/"),
        ("institute-for-disease-modeling-emod-api", "https://docs.idmod.org/projects/emod-api/en/latest/"),
        ("institute-for-disease-modeling-idm-cms", "https://docs.idmod.org/projects/cms/en/latest/"),
        ("institute-for-disease-modeling-stamp", "https://docs.idmod.org/projects/stamp/en/latest/"),
        ("institute-for-disease-modeling-emod-generic", "https://docs.idmod.org/projects/emod-generic/en/latest/"),
        ("institute-for-disease-modeling-emod-airborne", "https://docs.idmod.org/projects/emod-airborne/en/latest/"),
        ("institute-for-disease-modeling-emod-environmental", "https://docs.idmod.org/projects/emod-environmental/en/latest/"),
        ("institute-for-disease-modeling-emod-hiv", "https://docs.idmod.org/projects/emod-hiv/en/latest/"),
        ("institute-for-disease-modeling-emod-malaria", "https://docs.idmod.org/projects/emod-malaria/en/latest/"),
        ("institute-for-disease-modeling-emod-sti", "https://docs.idmod.org/projects/emod-sti/en/latest/"),
        ("institute-for-disease-modeling-emod-tuberculosis", "https://docs.idmod.org/projects/emod-tuberculosis/en/latest/"),
        ("institute-for-disease-modeling-emod-typhoid", "https://docs.idmod.org/projects/emod-typhoid/en/latest/"),
        ("institute-for-disease-modeling-emod-vector", "https://docs.idmod.org/projects/emod-vector/en/latest/"),
        ("institute-for-disease-modeling-itertool", "https://docs.idmod.org/projects/itertool/en/latest/"),
    ],
    'slug': 'institute-for-disease-modeling-idm',
    'name': u'idm',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://docs.idmod.org/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'InstituteforDiseaseModeling',
    'proxied_api_host': '/_',
    'github_repo': 'docs.idmod.org',
    'github_version': 'landing-page',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'landing-page',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'landing-page',
    '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': '4e1ce98c',
}




if 'html_context' in globals():
    
    html_context.update(context)
    
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2020-10-20T01:13:44.797379Z, end-time: 2020-10-20T01:13:45.470426Z, duration: 0, exit-code: 0
python sphinx-build -T -W --keep-going -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 2 source files that are out of date
updating environment: 2 added, 0 changed, 0 removed
reading sources... [ 50%] 404
reading sources... [100%] index

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 50%] 404
writing output... [100%] index

generating indices...
writing additional pages... index search
copying static files... done
copying readthedocs static files... done
copying searchtools... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded.

The HTML pages are in _build/html.