Read the Docs build information
Build id: 763969
Project: cyverse-visual-interactive-computing-environment
Version: latest
Commit: 5762799bc22268a13bbd62cf2bd79682b54fa671
Date: 2021-11-03T21:08:38.622100Z
State: finished
Success: False


[rtd-command-info] start-time: 2021-11-03T21:10:43.458303Z, end-time: 2021-11-03T21:10:55.089399Z, duration: 11, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/Visual_Interactive_Computing_Environment.git .
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[rtd-command-info] start-time: 2021-11-03T21:10:55.237073Z, end-time: 2021-11-03T21:10:55.471206Z, 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 5762799 Update examples.rst

[rtd-command-info] start-time: 2021-11-03T21:10:55.577753Z, end-time: 2021-11-03T21:10:55.670263Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-11-03T21:10:58.217631Z, end-time: 2021-11-03T21:11:09.188736Z, duration: 10, exit-code: 0
python2.7 -mvirtualenv 
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/bin/python2.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2021-11-03T21:11:09.319899Z, end-time: 2021-11-03T21:11:11.246866Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (20.3.4)
Requirement already up-to-date: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (44.1.1)

[rtd-command-info] start-time: 2021-11-03T21:11:11.370898Z, end-time: 2021-11-03T21:11:19.834441Z, duration: 8, 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
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
Collecting mock==1.0.1
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Successfully built mock future
Installing collected packages: mock, pillow, alabaster, future, commonmark, imagesize, typing, Pygments, docutils, MarkupSafe, Jinja2, pyparsing, packaging, snowballstemmer, pytz, babel, six, certifi, urllib3, chardet, idna, requests, sphinxcontrib-websupport, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
Successfully installed Jinja2-2.11.3 MarkupSafe-1.1.1 Pygments-2.5.2 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 chardet-4.0.0 commonmark-0.8.1 docutils-0.18 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-2021.3 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.26.0 six-1.16.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 typing-3.10.0.0 urllib3-1.26.7

[rtd-command-info] start-time: 2021-11-03T21:11:19.955293Z, end-time: 2021-11-03T21:11:27.947782Z, duration: 7, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
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Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from sphinx==1.8->-r requirements.txt (line 1)) (2.26.0)
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Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx==1.8->-r requirements.txt (line 1)) (2021.3)
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  Stored in directory: /tmp/pip-ephem-wheel-cache-3ICYgK/wheels/58/2c/26/52406f7d1f19bcc47a6fbd1037a5f293492f5cf1d58c539edb
Successfully built guzzle-sphinx-theme functools32 pyrsistent scandir
Installing collected packages: sphinx, enum34, decorator, ipython-genutils, traitlets, functools32, attrs, pyrsistent, contextlib2, zipp, configparser, scandir, pathlib2, importlib-metadata, jsonschema, jupyter-core, nbformat, entrypoints, mistune, testpath, pandocfilters, defusedxml, webencodings, bleach, nbconvert, nbsphinx, sphinxcontrib-images, sphinx-bootstrap-theme, guzzle-sphinx-theme
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 1.8.5
    Uninstalling Sphinx-1.8.5:
      Successfully uninstalled Sphinx-1.8.5
ERROR: pip's legacy dependency resolver does not consider dependency conflicts when selecting packages. This behaviour is the source of the following dependency conflicts.
sphinxcontrib-images 0.9.4 requires sphinx<2.0,>=1.8.5; python_version < "3.0", but you'll have sphinx 1.8.0 which is incompatible.
Successfully installed attrs-21.2.0 bleach-3.3.1 configparser-4.0.2 contextlib2-0.6.0.post1 decorator-4.4.2 defusedxml-0.7.1 entrypoints-0.3 enum34-1.1.10 functools32-3.2.3.post2 guzzle-sphinx-theme-0.7.11 importlib-metadata-2.1.1 ipython-genutils-0.2.0 jsonschema-3.2.0 jupyter-core-4.6.3 mistune-0.8.4 nbconvert-5.6.1 nbformat-4.4.0 nbsphinx-0.5.1 pandocfilters-1.5.0 pathlib2-2.3.6 pyrsistent-0.16.1 scandir-1.10.0 sphinx-1.8.0 sphinx-bootstrap-theme-0.8.0 sphinxcontrib-images-0.9.4 testpath-0.4.4 traitlets-4.3.3 webencodings-0.5.1 zipp-1.2.0

[rtd-command-info] start-time: 2021-11-03T21:11:28.919963Z, end-time: 2021-11-03T21:11:28.988833Z, duration: 0, exit-code: 0
cat conf.py
#!/usr/bin/env python3
# -*- 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 = 'Visual Interactive Computing Environment'
copyright = '2020, CyVerse'
author = 'CyVerse'
version = '2.0'
version = '2.0'

epub_title = project
epub_author = author
epub_publisher = author
epub_copyright = copyright
exclude_patterns = ['README.md', 'License.md', 'Contributors_maintainers.md']




###########################################################################
#          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

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", "//learning.cyverse.org/_/downloads/vice/en/latest/pdf/"),
    ("html", "//learning.cyverse.org/_/downloads/vice/en/latest/htmlzip/"),
    ("epub", "//learning.cyverse.org/_/downloads/vice/en/latest/epub/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'cyverse-visual-interactive-computing-environment',
    'name': u'Visual_Interactive_Computing_Environment',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://learning.cyverse.org/projects/vice/en/latest/',
    'analytics_code': 'UA-72224033-6',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'CyVerse-learning-materials',
    'proxied_api_host': '/_',
    'github_repo': 'Visual_Interactive_Computing_Environment',
    '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': 'UA-72224033-6',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '5762799b',
}

# 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-visual-interactive-computing-environment/builds/763969/'

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: 2021-11-03T21:11:29.096099Z, end-time: 2021-11-03T21:11:30.521555Z, duration: 1, exit-code: 2
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v1.8.0
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 73 source files that are out of date
updating environment: 73 added, 0 changed, 0 removed
reading sources... [  1%] .github/ISSUE_TEMPLATE/triage-for-2-0-release
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document
  warn("Container node skipped: type={0}".format(mdnode.t))
reading sources... [  2%] buildenv/lib/python3.5/site-packages/Babel-2.5.3.dist-info/DESCRIPTION
reading sources... [  4%] buildenv/lib/python3.5/site-packages/CommonMark-0.5.4.dist-info/DESCRIPTION
reading sources... [  5%] buildenv/lib/python3.5/site-packages/Jinja2-2.10.dist-info/DESCRIPTION
reading sources... [  6%] buildenv/lib/python3.5/site-packages/MarkupSafe-1.0.dist-info/DESCRIPTION
reading sources... [  8%] buildenv/lib/python3.5/site-packages/Pygments-2.2.0.dist-info/DESCRIPTION
reading sources... [  9%] buildenv/lib/python3.5/site-packages/Sphinx-1.6.6.dist-info/DESCRIPTION
reading sources... [ 10%] buildenv/lib/python3.5/site-packages/alabaster-0.7.10.dist-info/DESCRIPTION
reading sources... [ 12%] buildenv/lib/python3.5/site-packages/certifi-2018.1.18.dist-info/DESCRIPTION
reading sources... [ 13%] buildenv/lib/python3.5/site-packages/chardet-3.0.4.dist-info/DESCRIPTION
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/checkouts/latest/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md:0: WARNING: Document or section may not begin with a transition.

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/cmd/build.py", line 304, in build_main
    app.build(args.force_all, filenames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/application.py", line 341, in build
    self.builder.build_update()
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/builders/__init__.py", line 347, in build_update
    len(to_build))
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/builders/__init__.py", line 360, in build
    updated_docnames = set(self.read())
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/builders/__init__.py", line 468, in read
    self._read_serial(docnames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/builders/__init__.py", line 490, in _read_serial
    self.read_doc(docname)
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/builders/__init__.py", line 534, in read_doc
    doctree = read_doc(self.app, self.env, self.env.doc2path(docname))
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/io.py", line 318, in read_doc
    pub.publish()
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/docutils/core.py", line 219, in publish
    self.apply_transforms()
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/docutils/core.py", line 200, in apply_transforms
    self.document.transformer.apply_transforms()
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/transforms/__init__.py", line 90, in apply_transforms
    Transformer.apply_transforms(self)
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/docutils/transforms/__init__.py", line 171, in apply_transforms
    transform.apply(**kwargs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/transforms/__init__.py", line 245, in apply
    apply_source_workaround(n)
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/util/nodes.py", line 94, in apply_source_workaround
    for classifier in reversed(node.parent.traverse(nodes.classifier)):
TypeError: argument to reversed() must be a sequence

Exception occurred:
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-visual-interactive-computing-environment/envs/latest/lib/python2.7/site-packages/sphinx/util/nodes.py", line 94, in apply_source_workaround
    for classifier in reversed(node.parent.traverse(nodes.classifier)):
TypeError: argument to reversed() must be a sequence
The full traceback has been saved in /tmp/sphinx-err-866Dmy.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!