Read the Docs build information
Build id: 265679
Project: cyverse-tools-services-and-reproducible-science-workshop
Version: latest
Commit: 1e1c754849aaeb6a2cde1493c5b4f277a6d17bc5
Date: 2019-12-04T14:14:43.041318Z
State: finished
Success: True


[rtd-command-info] start-time: 2019-12-04T14:14:43.583664Z, end-time: 2019-12-04T14:14:43.601121Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/CyVerse-learning-materials/tools-services-and-reproducible-science-workshop.git


[rtd-command-info] start-time: 2019-12-04T14:14:43.680635Z, end-time: 2019-12-04T14:14:44.142125Z, duration: 0, exit-code: 0
git fetch origin --force --tags --prune --prune-tags --depth 50
From https://github.com/CyVerse-learning-materials/tools-services-and-reproducible-science-workshop
   93f249d..1e1c754  master     -> origin/master

[rtd-command-info] start-time: 2019-12-04T14:14:44.364225Z, end-time: 2019-12-04T14:14:44.516865Z, duration: 0, exit-code: 0
git checkout --force origin/master
Previous HEAD position was 93f249d update links with Etherpad
HEAD is now at 1e1c754 Add google doc

[rtd-command-info] start-time: 2019-12-04T14:14:44.597700Z, end-time: 2019-12-04T14:14:44.616927Z, duration: 0, exit-code: 0
git clean -d -f -f
Removing _build/

[rtd-command-info] start-time: 2019-12-04T14:14:45.762040Z, end-time: 2019-12-04T14:14:50.795555Z, duration: 5, exit-code: 0
python3.7 -mvirtualenv --no-site-packages --no-download 
Using base prefix '/home/docs/.pyenv/versions/3.7.3'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/bin/python3.7
Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/bin/python3.7)
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2019-12-04T14:14:50.879504Z, end-time: 2019-12-04T14:14:51.871579Z, duration: 0, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/.cache/pip pip
Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (19.3.1)

[rtd-command-info] start-time: 2019-12-04T14:14:51.953799Z, end-time: 2019-12-04T14:14:54.083629Z, duration: 2, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/.cache/pip Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 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<1.1
Requirement already up-to-date: Pygments==2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (2.3.1)
Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (41.0.1)
Requirement already up-to-date: docutils==0.14 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (0.14)
Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (1.0.1)
Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (5.4.1)
Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (0.7.12)
Requirement already up-to-date: commonmark==0.8.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (0.8.1)
Requirement already up-to-date: recommonmark==0.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (0.5.0)
Requirement already up-to-date: sphinx<2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (1.8.5)
Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (0.4.3)
Requirement already up-to-date: readthedocs-sphinx-ext<1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (1.0.1)
Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (from commonmark==0.8.1) (0.18.2)
Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.7.0)
Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.22.0)
Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (from sphinx<2) (19.2)
Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.10.3)
Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (from sphinx<2) (2.0.0)
Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.13.0)
Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.1.2)
Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (from sphinx<2) (1.1.0)
Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.3)
Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (2.8)
Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (3.0.4)
Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (1.25.7)
Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx<2) (2019.11.28)
Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (from packaging->sphinx<2) (2.4.5)
Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1)

[rtd-command-info] start-time: 2019-12-04T14:14:54.762254Z, end-time: 2019-12-04T14:14:55.102883Z, 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 Tools, Services, and Reproducibility, Workshop'
copyright = '2019, CyVerse'
author = 'CyVerse'
version = '0.1.0'
release = '0.1.0'

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
    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://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': [ 
    ("html", "//readthedocs.com/projects/cyverse-tools-services-and-reproducible-science-workshop/downloads/htmlzip/latest/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'cyverse-tools-services-and-reproducible-science-workshop',
    'name': u'tools-services-and-reproducible-science-workshop',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://learning.cyverse.org/projects/cyverse-tools-services-and-reproducible-science-workshop/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'proxied_api_host': 'https://readthedocs.com',
    'github_user': 'CyVerse-learning-materials',
    'github_repo': 'tools-services-and-reproducible-science-workshop',
    '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': '1e1c7548',
}




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")

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'

[rtd-command-info] start-time: 2019-12-04T14:14:55.184079Z, end-time: 2019-12-04T14:14:59.079546Z, duration: 3, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 2 source files that are out of date
updating environment: 2 added, 0 changed, 0 removed
reading sources... [ 50%] index
reading sources... [100%] links

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/checkouts/latest/index.rst:182: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/checkouts/latest/index.rst:434: WARNING: Explicit markup ends without a blank line; unexpected unindent.
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 50%] index
writing output... [100%] links

generating indices... genindex
writing additional pages... search
copying images... [100%] ./img/cyverse_rgb.png

copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/checkouts/latest/_static' does not exist
done
copying readthedocs static files... done
copying searchtools... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 3 warnings.

The HTML pages are in _build/html.

[rtd-command-info] start-time: 2019-12-04T14:14:59.195369Z, end-time: 2019-12-04T14:15:01.365160Z, duration: 2, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 2 added, 0 changed, 0 removed
reading sources... [ 50%] index
reading sources... [100%] links

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/checkouts/latest/index.rst:182: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/checkouts/latest/index.rst:434: WARNING: Explicit markup ends without a blank line; unexpected unindent.
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
assembling single document... 
writing... done
writing additional files...
copying images... [100%] ./img/cyverse_rgb.png

copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/cyverse-tools-services-and-reproducible-science-workshop/checkouts/latest/_static' does not exist
done
copying readthedocs static files... done
copying extra files... done
dumping object inventory... done
build succeeded, 3 warnings.

The HTML page is in _build/localmedia.