Read the Docs build information
Build id: 164125
Project: cyverse-learning-materials-home
Version: latest
Commit: 899bb1ba7ea1b1f42d8362023ce9a12c32fed9cd
Date: 2018-11-30T17:22:32.351603Z
State: finished
Success: False


[rtd-command-info] start-time: 2018-11-30T23:22:32.809633Z, end-time: 2018-11-30T23:22:33.095804Z, duration: 0, exit-code: 0
git clone https://github.com/CyVerse-learning-materials/learning-materials-home.git .
Cloning into '.'...

[rtd-command-info] start-time: 2018-11-30T23:22:33.164255Z, end-time: 2018-11-30T23:22:33.176414Z, 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 899bb1b Merge branch 'master' of https://github.com/CyVerse-learning-materials/learning-materials-home

[rtd-command-info] start-time: 2018-11-30T23:22:33.236165Z, end-time: 2018-11-30T23:22:33.243312Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2018-11-30T23:22:33.312364Z, end-time: 2018-11-30T23:22:33.318603Z, duration: 0, exit-code: 0
git branch -r
origin/HEAD -> origin/master
  origin/master

[rtd-command-info] start-time: 2018-11-30T23:22:33.932502Z, end-time: 2018-11-30T23:22:35.562169Z, duration: 1, exit-code: 0
python2.7 -mvirtualenv --no-site-packages --no-download 
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/bin/python2.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/bin/python
Installing setuptools, pip, wheel...done.

[rtd-command-info] start-time: 2018-11-30T23:22:35.625190Z, end-time: 2018-11-30T23:23:00.029431Z, duration: 24, exit-code: 0
python pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/.cache/pip Pygments==2.2.0 setuptools<40 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx<1.8 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6
Collecting Pygments==2.2.0
  Downloading https://files.pythonhosted.org/packages/02/ee/b6e02dc6529e82b75bb06823ff7d005b141037cb1416b10c6f00fc419dca/Pygments-2.2.0-py2.py3-none-any.whl (841kB)
Collecting setuptools<40
  Downloading https://files.pythonhosted.org/packages/7f/e1/820d941153923aac1d49d7fc37e17b6e73bfbd2904959fffbad77900cf92/setuptools-39.2.0-py2.py3-none-any.whl (567kB)
Collecting docutils==0.13.1
  Downloading https://files.pythonhosted.org/packages/5f/6d/e864b3c61b81eec57386ac62082fccfe694c7c3046d8723258a37da6d5fc/docutils-0.13.1-py2-none-any.whl (537kB)
Collecting mock==1.0.1
  Downloading https://files.pythonhosted.org/packages/a2/52/7edcd94f0afb721a2d559a5b9aae8af4f8f2c79bc63fdbe8a8a6c9b23bbe/mock-1.0.1.tar.gz (818kB)
Collecting pillow==2.6.1
  Downloading https://files.pythonhosted.org/packages/9f/53/9dafa3a48ffa25f4e22f40df880b58b99ad53648f0990caf09b1824d5db2/Pillow-2.6.1.tar.gz (7.3MB)
Collecting alabaster!=0.7.5,<0.8,>=0.7
  Downloading https://files.pythonhosted.org/packages/10/ad/00b090d23a222943eb0eda509720a404f531a439e803f6538f35136cae9e/alabaster-0.7.12-py2.py3-none-any.whl
Collecting commonmark==0.5.4
  Downloading https://files.pythonhosted.org/packages/4d/93/3808cbcebe94d205f55a9a32857df733a603339d32c46cd32669d808d964/CommonMark-0.5.4.tar.gz (120kB)
Collecting recommonmark==0.4.0
  Downloading https://files.pythonhosted.org/packages/df/a5/8ee4b84af7f997dfdba71254a88008cfc19c49df98983c9a4919e798f8ce/recommonmark-0.4.0-py2.py3-none-any.whl
Collecting sphinx<1.8
  Downloading https://files.pythonhosted.org/packages/90/f9/a0babe32c78480994e4f1b93315558f5ed756104054a7029c672a8d77b72/Sphinx-1.7.9-py2.py3-none-any.whl (1.9MB)
Collecting sphinx-rtd-theme<0.5
  Downloading https://files.pythonhosted.org/packages/ef/0c/e4a462190506bc4bff6ca8cf93da07b2d13e540466d2e8a760352d0c69b0/sphinx_rtd_theme-0.4.2-py2.py3-none-any.whl (6.4MB)
Collecting readthedocs-sphinx-ext<0.6
  Downloading https://files.pythonhosted.org/packages/2b/c5/126eb75a57918bb3d2f858ddda05f5670d6f07bfa356bc8870e2885f6aac/readthedocs_sphinx_ext-0.5.15-py2.py3-none-any.whl
Collecting sphinxcontrib-websupport (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/52/69/3c2fbdc3702358c5b34ee25e387b24838597ef099761fc9a42c166796e8f/sphinxcontrib_websupport-1.1.0-py2.py3-none-any.whl
Collecting six>=1.5 (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl
Collecting requests>=2.0.0 (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/ff/17/5cbb026005115301a8fb2f9b0e3e8d32313142fe8b617070e7baad20554f/requests-2.20.1-py2.py3-none-any.whl (57kB)
Collecting packaging (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/89/d1/92e6df2e503a69df9faab187c684585f0136662c12bb1f36901d426f3fab/packaging-18.0-py2.py3-none-any.whl
Collecting typing; python_version < "3.5" (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/cc/3e/29f92b7aeda5b078c86d14f550bf85cff809042e3429ace7af6193c3bc9f/typing-3.6.6-py2-none-any.whl
Collecting imagesize (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/fc/b6/aef66b4c52a6ad6ac18cf6ebc5731ed06d8c9ae4d3b2d9951f261150be67/imagesize-1.1.0-py2.py3-none-any.whl
Collecting babel!=2.0,>=1.3 (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/b8/ad/c6f60602d3ee3d92fbed87675b6fb6a6f9a38c223343ababdb44ba201f10/Babel-2.6.0-py2.py3-none-any.whl (8.1MB)
Collecting snowballstemmer>=1.1 (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/d4/6c/8a935e2c7b54a37714656d753e4187ee0631988184ed50c0cf6476858566/snowballstemmer-1.2.1-py2.py3-none-any.whl (64kB)
Collecting Jinja2>=2.3 (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/7f/ff/ae64bacdfc95f27a016a7bed8e8686763ba4d277a78ca76f32659220a731/Jinja2-2.10-py2.py3-none-any.whl (126kB)
Collecting idna<2.8,>=2.5 (from requests>=2.0.0->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/4b/2a/0276479a4b3caeb8a8c1af2f8e4355746a97fab05a372e4a2c6a6b876165/idna-2.7-py2.py3-none-any.whl (58kB)
Collecting urllib3<1.25,>=1.21.1 (from requests>=2.0.0->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/62/00/ee1d7de624db8ba7090d1226aebefab96a2c71cd5cfa7629d6ad3f61b79e/urllib3-1.24.1-py2.py3-none-any.whl (118kB)
Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB)
Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/9f/e0/accfc1b56b57e9750eba272e24c4dddeac86852c2bebd1236674d7887e8a/certifi-2018.11.29-py2.py3-none-any.whl (154kB)
Collecting pyparsing>=2.0.2 (from packaging->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/71/e8/6777f6624681c8b9701a8a0a5654f3eb56919a01a78e12bf3c73f5a3c714/pyparsing-2.3.0-py2.py3-none-any.whl (59kB)
Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/f8/0e/2365ddc010afb3d79147f1dd544e5ee24bf4ece58ab99b16fbb465ce6dc0/pytz-2018.7-py2.py3-none-any.whl (506kB)
Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/bc/3a/6bfd7b4b202fa33bdda8e4e3d3acc719f381fd730f9a0e7c5f34e845bd4d/MarkupSafe-1.1.0-cp27-cp27mu-manylinux1_x86_64.whl
Building wheels for collected packages: mock, pillow, commonmark
  Running setup.py bdist_wheel for mock: started
  Running setup.py bdist_wheel for mock: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/.cache/pip/wheels/7e/72/92/744b532c779242b57aab4bcba80c312b30c069bbd60025e7e6
  Running setup.py bdist_wheel for pillow: started
  Running setup.py bdist_wheel for pillow: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/.cache/pip/wheels/de/0e/6b/556798d1ac8762a076ddff5b20f65b2e6cc2ae13b0e683c263
  Running setup.py bdist_wheel for commonmark: started
  Running setup.py bdist_wheel for commonmark: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/.cache/pip/wheels/a0/f4/35/019d917f6875107ade3aad634c982f5c6b604c5631cddf20ac
Successfully built mock pillow commonmark
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, commonmark, recommonmark, sphinxcontrib-websupport, six, idna, urllib3, chardet, certifi, requests, pyparsing, packaging, typing, imagesize, pytz, babel, snowballstemmer, MarkupSafe, Jinja2, sphinx, sphinx-rtd-theme, readthedocs-sphinx-ext
  Found existing installation: setuptools 28.8.0
    Uninstalling setuptools-28.8.0:
      Successfully uninstalled setuptools-28.8.0
Successfully installed Jinja2-2.10 MarkupSafe-1.1.0 Pygments-2.2.0 alabaster-0.7.12 babel-2.6.0 certifi-2018.11.29 chardet-3.0.4 commonmark-0.5.4 docutils-0.13.1 idna-2.7 imagesize-1.1.0 mock-1.0.1 packaging-18.0 pillow-2.6.1 pyparsing-2.3.0 pytz-2018.7 readthedocs-sphinx-ext-0.5.15 recommonmark-0.4.0 requests-2.20.1 setuptools-39.2.0 six-1.11.0 snowballstemmer-1.2.1 sphinx-1.7.9 sphinx-rtd-theme-0.4.2 sphinxcontrib-websupport-1.1.0 typing-3.6.6 urllib3-1.24.1
You are using pip version 9.0.1, however version 18.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

[rtd-command-info] start-time: 2018-11-30T23:23:01.032750Z, end-time: 2018-11-30T23:23:01.093104Z, 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 = 'CyVerse Learning Center Home'
copyright = '2017, CyVerse'
author = 'CyVerse'
version = '0.1b.0'
release = '0.1b.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
#


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
    else:
        SUFFIX = source_suffix[0]
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')
html_static_path.append('/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_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://media.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://media.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ],
    'downloads': [ 
    ("htmlzip", "//readthedocs.com/projects/cyverse-learning-materials-home/downloads/htmlzip/latest/"),
    ],
    'subprojects': [ 
        ("cyverse-discovery-environment-guide", "https://learning.cyverse.org/projects/discovery-environment-guide/en/latest/"),
        ("cyverse-atmosphere-guide", "https://learning.cyverse.org/projects/atmosphere-guide/en/latest/"),
        ("cyverse-account-creation-quickstart", "https://learning.cyverse.org/projects/cyverse-account-creation-quickstart/en/latest/"),
        ("cyverse-importing-sradata-quickstart", "https://learning.cyverse.org/projects/cyverse-importing-sradata-quickstart/en/latest/"),
        ("cyverse-dnasubway-guide", "https://learning.cyverse.org/projects/dnasubway_guide/en/latest/"),
        ("cyverse-trimmomatic-quickstart", "https://learning.cyverse.org/projects/trimmomatic_quickstart/en/latest/"),
        ("cyverse-data-store-guide", "https://learning.cyverse.org/projects/data_store_guide/en/latest/"),
        ("cyverse-fastqc-quickstart", "https://learning.cyverse.org/projects/fastqc_quickstart/en/latest/"),
        ("cyverse-kallisto-tutorial", "https://learning.cyverse.org/projects/kallisto_tutorial/en/latest/"),
        ("cyverse-sra-submission-quickstart", "https://learning.cyverse.org/projects/sra_submission_quickstart/en/latest/"),
        ("cyverse-cyverse-tools-and-services-workshop", "https://learning.cyverse.org/projects/cyverse_tools_and_services_workshop/en/latest/"),
        ("cyverse-sciapps-guide", "https://learning.cyverse.org/projects/SciApps Guide/en/latest/"),
        ("cyverse-documentation-quickstart", "https://learning.cyverse.org/projects/Documentation-Quickstart/en/latest/"),
        ("cyverse-group-project-quickstart", "https://learning.cyverse.org/projects/cyverse-group-project-quickstart/en/latest/"),
        ("cyverse-visual-interactive-computing-environment", "https://learning.cyverse.org/projects/vice/en/latest/"),
        ("cyverse-doi-request-quickstart", "https://learning.cyverse.org/projects/cyverse-doi-request-quickstart/en/latest/"),
    ],
    'slug': 'cyverse-learning-materials-home',
    'name': u'learning-materials-home',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://learning.cyverse.org/en/latest/',
    'analytics_code': '',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'CyVerse-learning-materials',
    'github_repo': 'learning-materials-home',
    '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,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '899bb1ba',
}




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"]