Read the Docs build information
Build id: 560005
Project: cyverse-de2-guide
Version: latest
Commit: 0ee49b56325eb00e39c94f006b394bd5676869d3
Date: 2021-02-12T19:32:20.935309Z
State: finished
Success: False


[rtd-command-info] start-time: 2021-02-12T19:32:44.128305Z, end-time: 2021-02-12T19:32:45.704336Z, duration: 1, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/sonora_guide .
Cloning into '.'...

[rtd-command-info] start-time: 2021-02-12T19:32:45.992156Z, end-time: 2021-02-12T19:32:46.109156Z, 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 0ee49b5 Merge pull request #13 from CyVerse-learning-materials/project-ops

[rtd-command-info] start-time: 2021-02-12T19:32:46.337435Z, end-time: 2021-02-12T19:32:46.391738Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-02-12T19:32:47.629891Z, end-time: 2021-02-12T19:32:51.506716Z, duration: 3, 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-de2-guide/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de2-guide/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2021-02-12T19:32:51.751227Z, end-time: 2021-02-12T19:32:52.583022Z, duration: 0, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-de2-guide/envs/latest/lib/python3.7/site-packages (21.0.1)

[rtd-command-info] start-time: 2021-02-12T19:32:52.687013Z, end-time: 2021-02-12T19:33:02.104837Z, duration: 9, 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 six commonmark==0.8.1 recommonmark==0.5.0 sphinx sphinx-rtd-theme readthedocs-sphinx-ext<2.2
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
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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 Jinja2>=2.9
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Collecting requests
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Collecting urllib3<1.27,>=1.21.1
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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=8ac3d867010bb0131bff873ddd8962439268923b2ceb6bdd0ce02e2a6b6b6ae5
  Stored in directory: /tmp/pip-ephem-wheel-cache-0eid185h/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=90a1e66a939ee1ee9a1725859c02381b77c0370b17ab336497427cc00fd5d0b9
  Stored in directory: /tmp/pip-ephem-wheel-cache-0eid185h/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, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, six, recommonmark, readthedocs-sphinx-ext, pillow, mock
  Attempting uninstall: setuptools
    Found existing installation: setuptools 53.0.0
    Uninstalling setuptools-53.0.0:
      Successfully uninstalled setuptools-53.0.0
Successfully installed Jinja2-2.11.3 MarkupSafe-1.1.1 Pygments-2.7.4 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.14 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-2.1.3 recommonmark-0.5.0 requests-2.25.1 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.1.0 sphinx-3.4.3 sphinx-rtd-theme-0.5.1 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 urllib3-1.26.3

[rtd-command-info] start-time: 2021-02-12T19:33:02.981572Z, end-time: 2021-02-12T19:33:03.035245Z, 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 = 'Sonora Discovery Environment Guide'
copyright = '2021, CyVerse'
author = 'CyVerse Documentation Team'
version = '0.1'
release = '0.1'

epub_title = Discovery Environment 2.0 Platform Guide
epub_author = Sriram Srinivasan, Ian McEwen, Ashley Ramsey, Sarah Roberts, Paul Sandoval, John Wregglesworth, Tina Lee, and Jason Williams
epub_publisher = CyVerse
epub_copyright = 2021

# html theme configuration -- see https://sphinx-rtd-theme.readthedocs.io/en/stable/configuring.html

html_theme_options = {
# Table of Content options
    'collapse_navigation': True,
    'sticky_navigation': True,
    'navigation_depth': 4,
    'includehidden': True,
    'titles_only': False
}




###########################################################################
#          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': [
    ],
    'downloads': [ 
    ("pdf", "//cyverse-de2-guide.readthedocs-hosted.com/_/downloads/en/latest/pdf/"),
    ("html", "//cyverse-de2-guide.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"),
    ("epub", "//cyverse-de2-guide.readthedocs-hosted.com/_/downloads/en/latest/epub/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'cyverse-de2-guide',
    'name': u'DE2_guide',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://cyverse-de2-guide.readthedocs-hosted.com/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': 'sonora_guide',
    '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': '0ee49b56',
}

# 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-de2-guide/builds/560005/'

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: 2021-02-12T19:33:03.178751Z, end-time: 2021-02-12T19:33:03.692660Z, duration: 0, exit-code: 2
python -m sphinx -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v3.4.3

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-de2-guide/envs/latest/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 76, in execfile_
    code = compile(source, filepath_enc, 'exec')
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-de2-guide/checkouts/latest/conf.py", line 19
    epub_title = Discovery Environment 2.0 Platform Guide
                                     ^
SyntaxError: invalid syntax

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-de2-guide/envs/latest/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 46, in convert_with_2to3
    tree = refactoring_tool.refactor_string(source, 'conf.py')
  File "/home/docs/.pyenv/versions/3.7.9/lib/python3.7/lib2to3/refactor.py", line 361, in refactor_string
    name, err.__class__.__name__, err)
  File "/home/docs/.pyenv/versions/3.7.9/lib/python3.7/lib2to3/refactor.py", line 358, in refactor_string
    tree = self.driver.parse_string(data)
  File "/home/docs/.pyenv/versions/3.7.9/lib/python3.7/lib2to3/pgen2/driver.py", line 104, in parse_string
    return self.parse_tokens(tokens, debug)
  File "/home/docs/.pyenv/versions/3.7.9/lib/python3.7/lib2to3/pgen2/driver.py", line 72, in parse_tokens
    if p.addtoken(type, value, (prefix, start)):
  File "/home/docs/.pyenv/versions/3.7.9/lib/python3.7/lib2to3/pgen2/parse.py", line 159, in addtoken
    raise ParseError("bad input", type, value, context)
lib2to3.pgen2.parse.ParseError: bad input: type=1, value='Environment', context=(' ', (19, 23))

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-de2-guide/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 326, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-de2-guide/envs/latest/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 80, in execfile_
    source = convert_with_2to3(filepath)
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-de2-guide/envs/latest/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 52, in convert_with_2to3
    raise SyntaxError(err.msg, (filepath, lineno, offset, err.value)) from err
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-de2-guide/checkouts/latest/conf.py", line 19
    Environment
              ^
SyntaxError: bad input

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-de2-guide/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-de2-guide/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 219, in __init__
    self.config = Config.read(self.confdir, confoverrides or {}, self.tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-de2-guide/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 173, in read
    namespace = eval_config_file(filename, tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/cyverse-de2-guide/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 329, in eval_config_file
    raise ConfigError(msg % err) from err
sphinx.errors.ConfigError: There is a syntax error in your configuration file: bad input (conf.py, line 19)


Configuration error:
There is a syntax error in your configuration file: bad input (conf.py, line 19)