Read the Docs build information
Build id: 366321
Project: ucsd-center-for-functional-mri-cfmri-web-rtd
Version: latest
Commit: 8aacfe4aef9a8090fa7ac990b6403756993d86e0
Date: 2020-07-13T20:17:53.083370Z
State: finished
Success: True


[rtd-command-info] start-time: 2020-07-13T20:17:57.665756Z, end-time: 2020-07-13T20:18:34.296681Z, duration: 36, exit-code: 0
git clone --no-single-branch --depth 50 https://bitbucket.org/ucsdcfmri/cfmri_web_rtd.git .
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[rtd-command-info] start-time: 2020-07-13T20:18:34.577837Z, end-time: 2020-07-13T20:18:36.269975Z, duration: 1, exit-code: 0
git checkout --force origin/master
Note: checking out 'origin/master'.

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 8aacfe4 Trying to recover scrolling for large tables in CBFBIRN

[rtd-command-info] start-time: 2020-07-13T20:18:36.492189Z, end-time: 2020-07-13T20:18:36.691625Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-07-13T20:18:53.845812Z, end-time: 2020-07-13T20:19:07.205166Z, duration: 13, exit-code: 0
python3.7 -mvirtualenv  
Using base prefix '/home/docs/.pyenv/versions/3.7.3'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2020-07-13T20:19:07.354045Z, end-time: 2020-07-13T20:19:08.167742Z, 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/ucsd-center-for-functional-mri-cfmri-web-rtd/envs/latest/lib/python3.7/site-packages (20.1.1)

[rtd-command-info] start-time: 2020-07-13T20:19:08.278932Z, end-time: 2020-07-13T20:19:18.269258Z, duration: 9, exit-code: 0
python -m pip install --upgrade --no-cache-dir Pygments==2.3.1 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 Pygments==2.3.1
  Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB)
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  Downloading urllib3-1.25.9-py2.py3-none-any.whl (126 kB)
Building wheels for collected packages: mock, 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=e6e6bf11ab0933a04dc56f925b90d86441b91b570e604cfdf23769a874781ae3
  Stored in directory: /tmp/pip-ephem-wheel-cache-9_xl2txz/wheels/16/03/37/f0a64ab894c9102906f192db1a4071b7592292ad661563c69b
  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=491058 sha256=9d88d6d84c4e21ec79d9b5de43beb4f9c67883b7cbda86fb858f24914a1979c3
  Stored in directory: /tmp/pip-ephem-wheel-cache-9_xl2txz/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Successfully built mock future
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, pytz, babel, sphinxcontrib-websupport, imagesize, snowballstemmer, MarkupSafe, Jinja2, six, pyparsing, packaging, certifi, idna, chardet, urllib3, requests, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
  Attempting uninstall: setuptools
    Found existing installation: setuptools 49.2.0
    Uninstalling setuptools-49.2.0:
      Successfully uninstalled setuptools-49.2.0
Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 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-websupport-1.2.3 urllib3-1.25.9

[rtd-command-info] start-time: 2020-07-13T20:19:19.310380Z, end-time: 2020-07-13T20:19:19.526476Z, duration: 0, exit-code: 0
cat docs/source/conf.py
# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config

# -- Path setup --------------------------------------------------------------

# 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('.'))

RTD_NEW_THEME = True
master_doc = 'index'

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

project = u'UCSD Center for fMRI'
copyright = u'2019, CFMRI'
author = u'CFMRI'

# The short X.Y version
version = u''
# The full version, including alpha/beta/rc tags
#release = u'0.0.1'


# -- 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.autodoc',
]

# Add any paths that contain templates here, relative to this directory.
templates_path = ['ntemplates']

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = '.txt'

# The master toctree document.
master_doc = 'index'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = []

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = None


# -- 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 = 'alabaster'

# 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 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 = ['nstatic']

# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# The default sidebars (for documents that don't match any pattern) are
# defined by theme itself.  Builtin themes are using these templates by
# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
# 'searchbox.html']``.
#
# html_sidebars = {}
#
# Adding word wrapping into tables
# https://rackerlabs.github.io/docs-rackspace/tools/rtd-tables.html
#html_context = {
#    'css_files': [
#        '_static/theme_overrides.css',  # override wide tables in RTD theme
#        ],
#     }

# -- Options for HTMLHelp output ---------------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = 'cfmri_web_rtddoc'


# -- 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, 'cfmri_web_rtd.tex', u'cfmri\\_web\\_rtd Documentation',
     u'CFMRI', 'manual'),
]


# -- 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, 'cfmri_web_rtd', u'cfmri_web_rtd Documentation',
     [author], 1)
]


# -- 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, 'cfmri_web_rtd', u'cfmri_web_rtd Documentation',
     author, 'cfmri_web_rtd', 'One line description of project.',
     'Miscellaneous'),
]


# -- Options for Epub output -------------------------------------------------

# Bibliographic Dublin Core info.
epub_title = project

# The unique identifier of the text. This can be a ISBN number
# or the project homepage.
#
# epub_identifier = ''

# A unique identification for the text.
#
# epub_uid = ''

# A list of files that should not be packed into the epub file.
epub_exclude_files = ['search.html']


# -- Extension configuration -------------------------------------------------




###########################################################################
#          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': [ 
    ("pdf", "//ucsd-center-for-functional-mri-cfmri-web-rtd.readthedocs-hosted.com/_/downloads/en/latest/pdf/"),
    ("html", "//ucsd-center-for-functional-mri-cfmri-web-rtd.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"),
    ("epub", "//ucsd-center-for-functional-mri-cfmri-web-rtd.readthedocs-hosted.com/_/downloads/en/latest/epub/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'ucsd-center-for-functional-mri-cfmri-web-rtd',
    'name': u'cfmri_web_rtd',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://ucsd-center-for-functional-mri-cfmri-web-rtd.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/source/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'None',
    'proxied_api_host': '/_',
    'github_repo': 'None',
    'github_version': 'master',
    'display_github': False,
    'bitbucket_user': 'ucsdcfmri',
    'bitbucket_repo': 'cfmri_web_rtd',
    'bitbucket_version': 'master',
    'display_bitbucket': True,
    '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': '8aacfe4a',
}




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'

[rtd-command-info] start-time: 2020-07-13T20:19:19.679855Z, end-time: 2020-07-13T20:19:22.203510Z, duration: 2, exit-code: 0
python sphinx-build -T -E -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
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/home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/peripheral.txt:32: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/safety.txt:31: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/software.txt:3: WARNING: Duplicate explicit target name: "mac osx".
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/home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/motion_plot.txt:49: WARNING: Could not lex literal_block as "csh". Highlighting skipped.
generating indices... genindex
writing additional pages... search
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copying downloadable files... [  9%] pdf/cfmri_covid19_phone_screen-v2_20200625.pdf
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copying static files... done
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dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 5 warnings.

The HTML pages are in _build/html.

[rtd-command-info] start-time: 2020-07-13T20:19:22.445403Z, end-time: 2020-07-13T20:19:24.287883Z, duration: 1, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
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 [readthedocssinglehtmllocalmedia]: all documents
updating environment: 19 added, 0 changed, 0 removed
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reading sources... [ 31%] getstarted
reading sources... [ 36%] help
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reading sources... [ 47%] index
reading sources... [ 52%] license
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reading sources... [ 63%] motion_plot
reading sources... [ 68%] multiband_expl
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reading sources... [ 78%] protocols
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reading sources... [ 89%] software
reading sources... [ 94%] training
reading sources... [100%] troubleshooting

/home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/peripheral.txt:29: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/peripheral.txt:32: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/safety.txt:31: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/software.txt:3: WARNING: Duplicate explicit target name: "mac osx".
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
assembling single document... coronavirus getstarted training safety events protocols mb_recon_rtd troubleshooting audio_system imageanalysis motion_plot multiband_expl fmri_topup cbfbirn peripheral software license help 
writing... /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/index.txt:49: WARNING: Could not lex literal_block as "csh". Highlighting skipped.
done
writing additional files...
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copying static files... done
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dumping object inventory... done
build succeeded, 5 warnings.

The HTML page is in _build/localmedia.

[rtd-command-info] start-time: 2020-07-13T20:19:24.622131Z, end-time: 2020-07-13T20:19:26.282463Z, duration: 1, exit-code: 0
python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex
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 [latex]: all documents
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/home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/software.txt:3: WARNING: Duplicate explicit target name: "mac osx".
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processing cfmri_web_rtd.tex...index coronavirus getstarted training safety events protocols mb_recon_rtd troubleshooting audio_system imageanalysis motion_plot multiband_expl fmri_topup cbfbirn peripheral software license help 
resolving references...
writing... /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/motion_plot.txt:49: WARNING: Could not lex literal_block as "csh". Highlighting skipped.
done
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cat latexmkrc
$latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S';
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$makeindex = 'makeindex -s python.ist %O -o %D %S';
add_cus_dep( "glo", "gls", 0, "makeglo" );
sub makeglo {
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}

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Chapter 1.
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Chapter 3.
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Chapter 6.
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Chapter 11.

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Chapter 13.
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Chapter 14.
(./ucsd-center-for-functional-mri-cfmri-web-rtd.ind) [113]
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The ePub file is in _build/epub.

[rtd-command-info] start-time: 2020-07-13T20:20:36.397736Z, end-time: 2020-07-13T20:20:36.594103Z, duration: 0, exit-code: 0
mv -f /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/checkouts/latest/docs/source/_build/epub/UCSDCenterforfMRI.epub /home/docs/checkouts/readthedocs.org/user_builds/ucsd-center-for-functional-mri-cfmri-web-rtd/artifacts/latest/sphinx_epub/ucsd-center-for-functional-mri-cfmri-web-rtd.epub