Read the Docs build information
Build id: 456909
Project: institute-for-disease-modeling-idm
Version: latest
Commit: 64c6f8c6a36ece9a958224d8a90bc4b52c04724c
Date: 2020-10-20T20:33:19.726776Z
State: finished
Success: True


[rtd-command-info] start-time: 2020-10-20T20:33:21.112907Z, end-time: 2020-10-20T20:33:21.726179Z, 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: 2020-10-20T20:33:22.629746Z, end-time: 2020-10-20T20:33:22.688171Z, duration: 0, exit-code: 0
git checkout --force origin/main
Note: checking out 'origin/main'.

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 64c6f8c temporary redirect until iframe is allowed

[rtd-command-info] start-time: 2020-10-20T20:33:23.368064Z, end-time: 2020-10-20T20:33:23.423925Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-10-20T20:33:26.370424Z, end-time: 2020-10-20T20:33:33.470669Z, duration: 7, exit-code: 0
python3.8 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.8.6'
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: 2020-10-20T20:33:33.801739Z, end-time: 2020-10-20T20:33:34.500049Z, 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: 2020-10-20T20:33:34.677749Z, end-time: 2020-10-20T20:34:01.479818Z, duration: 26, 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
  Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB)
Collecting docutils==0.14
  Downloading docutils-0.14-py3-none-any.whl (543 kB)
Collecting mock==1.0.1
  Downloading mock-1.0.1.tar.gz (818 kB)
Collecting pillow==5.4.1
  Downloading Pillow-5.4.1.tar.gz (16.0 MB)
Collecting alabaster!=0.7.5,<0.8,>=0.7
  Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB)
Collecting commonmark==0.8.1
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Collecting recommonmark==0.5.0
  Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB)
Collecting sphinx<2
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Collecting sphinx-rtd-theme<0.5
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Collecting readthedocs-sphinx-ext<1.1
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Collecting future
  Downloading future-0.18.2.tar.gz (829 kB)
Collecting Jinja2>=2.3
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Collecting packaging
  Downloading packaging-20.4-py2.py3-none-any.whl (37 kB)
Collecting babel!=2.0,>=1.3
  Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB)
Collecting snowballstemmer>=1.1
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Collecting imagesize
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Collecting Pygments>=2.0
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Collecting six>=1.5
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Collecting requests>=2.0.0
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Collecting sphinxcontrib-websupport
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Collecting MarkupSafe>=0.23
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Collecting pyparsing>=2.0.2
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Collecting pytz>=2015.7
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Collecting certifi>=2017.4.17
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Collecting idna<3,>=2.5
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Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1
  Downloading urllib3-1.25.11-py2.py3-none-any.whl (127 kB)
Collecting sphinxcontrib-serializinghtml
  Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB)
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=4eb4055e267b7499896f86eed0092d7faadad2c4b6d5ec38565a4e23eb102de5
  Stored in directory: /tmp/pip-ephem-wheel-cache-52k9075o/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=1259811 sha256=d56d4711ff1ced3e9d86534358225ed94172f84f911359a72cd06207d851c85d
  Stored in directory: /tmp/pip-ephem-wheel-cache-52k9075o/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=fd30163c36cb1f9a648c307fa16e513024ced9e001be83539b0ca5045fd7b521
  Stored in directory: /tmp/pip-ephem-wheel-cache-52k9075o/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4
Successfully built mock pillow future
Installing collected packages: setuptools, docutils, mock, pillow, alabaster, future, commonmark, MarkupSafe, Jinja2, pyparsing, six, packaging, pytz, babel, snowballstemmer, imagesize, Pygments, chardet, certifi, idna, urllib3, requests, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, 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: 2020-10-20T20:34:01.646539Z, end-time: 2020-10-20T20:34:02.323428Z, 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)
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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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)
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: 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: 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: 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: 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: 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: 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)

[rtd-command-info] start-time: 2020-10-20T20:34:04.380094Z, end-time: 2020-10-20T20:34:04.453744Z, duration: 0, exit-code: 0
cat conf.py
# Configuration file for the Sphinx documentation builder.
#
# Documentation: https://www.sphinx-doc.org/en/master/usage/configuration.html

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'
]

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_context = dict(
    docs_title = "Documentation | IDMOD",
    docs_home_url = "https://idmod.org/documentation"
)

html_favicon = "_static/favicon.ico"
html_show_sourcelink = False
html_show_sphinx = False
html_static_path = ['_static']
html_use_index = False
html_theme = 'sphinx_rtd_theme'



###########################################################################
#          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': '/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'InstituteforDiseaseModeling',
    'proxied_api_host': '/_',
    'github_repo': 'docs.idmod.org',
    'github_version': 'main',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'main',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'main',
    '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': '64c6f8c6',
}




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: 2020-10-20T20:34:04.568693Z, end-time: 2020-10-20T20:34:05.334211Z, 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 1 source files that are out of date
updating environment: 1 added, 0 changed, 0 removed
reading sources... [100%] index

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

generating indices...
writing additional pages... 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.