Read the Docs build information
Build id: 631913
Project: cyverse-scrna-seq
Version: latest
Commit: 178df18fba0cb56893a1d86b8838471fe799a4e6
Date: 2021-05-12T17:42:50.657078Z
State: finished
Success: False


[rtd-command-info] start-time: 2021-05-12T17:42:52.065455Z, end-time: 2021-05-12T17:42:53.609198Z, duration: 1, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:CyVerse-learning-materials/scRNA-seq.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.113' (RSA) to the list of known hosts.

[rtd-command-info] start-time: 2021-05-12T17:42:53.755431Z, end-time: 2021-05-12T17:42:53.853752Z, duration: 0, 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 178df18 Update index.rst

[rtd-command-info] start-time: 2021-05-12T17:42:53.979113Z, end-time: 2021-05-12T17:42:54.054038Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-05-12T17:42:55.006026Z, end-time: 2021-05-12T17:42:59.218527Z, 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/cyverse-scrna-seq/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2021-05-12T17:42:59.329867Z, end-time: 2021-05-12T17:43:00.471502Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/lib/python3.7/site-packages (21.1.1)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/lib/python3.7/site-packages (56.2.0)

[rtd-command-info] start-time: 2021-05-12T17:43:00.596958Z, end-time: 2021-05-12T17:43:09.715339Z, 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 sphinx-rtd-theme readthedocs-sphinx-ext<2.2
Collecting mock==1.0.1
  Downloading mock-1.0.1.zip (861 kB)
Collecting pillow==5.4.1
  Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB)
Collecting alabaster!=0.7.5,<0.8,>=0.7
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Collecting sphinx
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Collecting future
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Collecting docutils>=0.11
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Collecting Pygments>=2.0
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/lib/python3.7/site-packages (from sphinx) (56.2.0)
Collecting packaging
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Collecting babel>=1.3
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Collecting requests>=2.5.0
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Collecting pytz>=2015.7
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Collecting idna<3,>=2.5
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Collecting pyparsing>=2.0.2
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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=23755 sha256=cc47cf8d47b5c3ff7a2b691c6ae6d40f1f269e60fcaa57e880aa66490f28c37b
  Stored in directory: /tmp/pip-ephem-wheel-cache-lt768jt5/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1
  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=13a24360ea93feb8979d6b8970741f6090b76aad280edba13c15fb6d2bafe96e
  Stored in directory: /tmp/pip-ephem-wheel-cache-lt768jt5/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Successfully built mock future
Installing collected packages: urllib3, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock
Successfully installed Jinja2-2.11.3 MarkupSafe-1.1.1 Pygments-2.9.0 alabaster-0.7.12 babel-2.9.1 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.16 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.9 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.25.1 snowballstemmer-2.1.0 sphinx-4.0.1 sphinx-rtd-theme-0.5.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.4 urllib3-1.26.4

[rtd-command-info] start-time: 2021-05-12T17:43:10.623606Z, end-time: 2021-05-12T17:43:10.704710Z, duration: 0, exit-code: 0
cat conf.py
#!/usr/bin/env python3
# Version 2.0, May 2020
# -*- coding: utf-8 -*-
#
# General information about the project.

import sys
import os
sys.path.insert(0, os.path.dirname(__file__))

from misc.cyverse_sphinx_conf import *  # noqa

project = 'Single-cell analysis using CyVerse'
copyright = '2020, CyVerse'
author = 'CyVerse'
version = '2.0'
release = '2.0'

epub_title = project
epub_author = author
epub_publisher = author
epub_copyright = copyright




###########################################################################
#          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 should't rely on extra depencies.

import importlib
import sys
import os.path

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

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", "//cyverse-scrna-seq.readthedocs-hosted.com/_/downloads/en/latest/pdf/"),
    ("html", "//cyverse-scrna-seq.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"),
    ("epub", "//cyverse-scrna-seq.readthedocs-hosted.com/_/downloads/en/latest/epub/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'cyverse-scrna-seq',
    'name': u'scRNA-seq',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://cyverse-scrna-seq.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'CyVerse-learning-materials',
    'proxied_api_host': '/_',
    'github_repo': 'scRNA-seq',
    'github_version': 'master',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'master',
    'display_bitbucket': False,
    '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': '178df18f',
}

# 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):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





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")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/cyverse-scrna-seq/builds/631913/'

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: 2021-05-12T17:43:10.820546Z, end-time: 2021-05-12T17:43:11.408010Z, duration: 0, exit-code: 2
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v4.0.1
loading translations [en]... done
making output directory... done

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/lib/python3.7/site-packages/sphinx/cmd/build.py", line 279, in build_main
    args.tags, args.verbosity, args.jobs, args.keep_going)
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 257, in __init__
    self.config.setup(self)
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/misc/cyverse_sphinx_conf.py", line 74, in setup
    app.add_stylesheet('cyverse.css')
AttributeError: 'Sphinx' object has no attribute 'add_stylesheet'

Exception occurred:
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-scrna-seq/checkouts/latest/misc/cyverse_sphinx_conf.py", line 74, in setup
    app.add_stylesheet('cyverse.css')
AttributeError: 'Sphinx' object has no attribute 'add_stylesheet'
The full traceback has been saved in /tmp/sphinx-err-0gbl5lx1.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!