Read the Docs build information
Build id: 887799
Project: ucsd-center-for-functional-mri-cfmri-web-rtd
Version: latest
Commit: 1615dd1639ea5a127ff45dc535763f9429e3c331
Date: 2022-03-17T21:27:15.534011Z
State: finished
Success: True


[rtd-command-info] start-time: 2022-03-17T21:27:17.372145Z, end-time: 2022-03-17T21:28:01.147632Z, duration: 43, 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: 2022-03-17T21:28:01.349145Z, end-time: 2022-03-17T21:28:01.783714Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to '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 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 1615dd1 updated download link format for phone screen

[rtd-command-info] start-time: 2022-03-17T21:28:01.993872Z, end-time: 2022-03-17T21:28:02.059202Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-03-17T21:28:06.771321Z, end-time: 2022-03-17T21:28:11.055064Z, duration: 4, exit-code: 0
python3.7 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
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: 2022-03-17T21:28:11.245529Z, end-time: 2022-03-17T21:28:13.033338Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
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    Found existing installation: setuptools 60.10.0
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Successfully installed setuptools-58.2.0

[rtd-command-info] start-time: 2022-03-17T21:28:13.322839Z, end-time: 2022-03-17T21:28:22.401245Z, duration: 9, exit-code: 0
python -m pip install --upgrade --no-cache-dir 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<2.2
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Building wheels for collected packages: mock, future
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Installing collected packages: snowballstemmer, pytz, mock, certifi, alabaster, urllib3, sphinxcontrib-serializinghtml, six, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, babel, sphinxcontrib-websupport, requests, packaging, Jinja2, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed Jinja2-3.0.3 MarkupSafe-2.1.1 Pygments-2.11.2 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.12 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.7 pytz-2021.3 readthedocs-sphinx-ext-2.1.5 recommonmark-0.5.0 requests-2.27.1 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.9

[rtd-command-info] start-time: 2022-03-17T21:28:24.388579Z, end-time: 2022-03-17T21:28:24.453238Z, 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.',
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]


# -- 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
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

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# Get suffix for proper linking to GitHub
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# as each page can have its own suffix
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# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
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if os.path.exists('_static'):
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# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
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        html_theme in ['default'] and
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)
if using_rtd_theme:
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    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())
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if globals().get('websupport2_base_url', False):
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    websupport2_static_url = 'https://assets.readthedocs.com/'


#Add project information to the template context.
context = {
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    ("html", "//ucsd-center-for-functional-mri-cfmri-web-rtd.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"),
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    '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,
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# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
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    context['canonical_url'] = None





if 'html_context' in globals():
    
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else:
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# Add custom RTD extension
if 'extensions' in globals():
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    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
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    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/ucsd-center-for-functional-mri-cfmri-web-rtd/builds/887799/'

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'),
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japanese = any([
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if chinese:
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elif japanese:
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# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2022-03-17T21:28:24.626706Z, end-time: 2022-03-17T21:28:27.470552Z, duration: 2, exit-code: 0
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[rtd-command-info] start-time: 2022-03-17T21:28:27.936150Z, end-time: 2022-03-17T21:28:30.069093Z, duration: 2, exit-code: 0
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[rtd-command-info] start-time: 2022-03-17T21:28:30.577889Z, end-time: 2022-03-17T21:28:31.800482Z, duration: 1, exit-code: 0
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The LaTeX files are in _build/latex.
Run 'make' in that directory to run these through (pdf)latex
(use `make latexpdf' here to do that automatically).
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cat latexmkrc
$latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S';
$makeindex = 'makeindex -s python.ist %O -o %D %S';
add_cus_dep( "glo", "gls", 0, "makeglo" );
sub makeglo {
 return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
}

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Chapter 1.
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Chapter 2.
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Chapter 3.
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Chapter 7.
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Chapter 1.
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Chapter 2.
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Chapter 3.
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Chapter 4.
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Chapter 5.
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Chapter 7.
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Chapter 8.

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Chapter 9.
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Chapter 10.

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Chapter 11.
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Chapter 12.
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Chapter 13.
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Chapter 14.

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Chapter 15.

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Chapter 16.
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Chapter 17.

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Chapter 18.
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Chapter 1.
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Chapter 2.
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Chapter 3.
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Chapter 7.
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Chapter 8.

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Chapter 10.

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Chapter 13.
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Chapter 14.

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Chapter 15.

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Chapter 16.
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Chapter 17.

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Chapter 18.
(./ucsd-center-for-functional-mri-cfmri-web-rtd.ind) [191]
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[rtd-command-info] start-time: 2022-03-17T21:29:32.076098Z, end-time: 2022-03-17T21:29:32.160632Z, duration: 0, exit-code: 0
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