Read the Docs build information
Build id: 242962
Project: cyverse-jupyter-qiime2
Version: latest
Commit: 5b38732cbc176a7faef7ee8c248e3ea3db3e7528
Date: 2019-09-18T19:47:38.159350Z
State: finished
Success: True


[rtd-command-info] start-time: 2019-09-18T19:47:38.624557Z, end-time: 2019-09-18T19:47:39.045961Z, duration: 0, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/jupyter_qiime2.git .
Cloning into '.'...

[rtd-command-info] start-time: 2019-09-18T19:47:39.258903Z, end-time: 2019-09-18T19:47:39.294958Z, 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 5b38732 Update index.rst

[rtd-command-info] start-time: 2019-09-18T19:47:39.383411Z, end-time: 2019-09-18T19:47:39.399981Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-09-18T19:47:40.478815Z, end-time: 2019-09-18T19:47:43.771936Z, duration: 3, exit-code: 0
python3.7 -mvirtualenv --no-site-packages --no-download 
Using base prefix '/home/docs/.pyenv/versions/3.7.1'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2019-09-18T19:47:43.863655Z, end-time: 2019-09-18T19:47:46.692997Z, duration: 2, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/.cache/pip pip
Collecting pip
  Downloading https://files.pythonhosted.org/packages/30/db/9e38760b32e3e7f40cce46dd5fb107b8c73840df38f0046d8e6514e675a1/pip-19.2.3-py2.py3-none-any.whl (1.4MB)
Installing collected packages: pip
  Found existing installation: pip 18.1
    Uninstalling pip-18.1:
      Successfully uninstalled pip-18.1
Successfully installed pip-19.2.3

[rtd-command-info] start-time: 2019-09-18T19:47:46.778427Z, end-time: 2019-09-18T19:47:58.641474Z, duration: 11, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/.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
Collecting Pygments==2.3.1
  Downloading https://files.pythonhosted.org/packages/13/e5/6d710c9cf96c31ac82657bcfb441df328b22df8564d58d0c4cd62612674c/Pygments-2.3.1-py2.py3-none-any.whl (849kB)
Collecting setuptools==41.0.1
  Downloading https://files.pythonhosted.org/packages/ec/51/f45cea425fd5cb0b0380f5b0f048ebc1da5b417e48d304838c02d6288a1e/setuptools-41.0.1-py2.py3-none-any.whl (575kB)
Collecting docutils==0.14
  Downloading https://files.pythonhosted.org/packages/36/fa/08e9e6e0e3cbd1d362c3bbee8d01d0aedb2155c4ac112b19ef3cae8eed8d/docutils-0.14-py3-none-any.whl (543kB)
Collecting mock==1.0.1
  Downloading https://files.pythonhosted.org/packages/a2/52/7edcd94f0afb721a2d559a5b9aae8af4f8f2c79bc63fdbe8a8a6c9b23bbe/mock-1.0.1.tar.gz (818kB)
Collecting pillow==5.4.1
  Downloading https://files.pythonhosted.org/packages/ae/2a/0a0ab2833e5270664fb5fae590717f867ac6319b124160c09f1d3291de28/Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0MB)
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==0.8.1
  Downloading https://files.pythonhosted.org/packages/ab/ca/439c88039583a29564a0043186875258e9a4f041fb5c422cd387b8e10175/commonmark-0.8.1-py2.py3-none-any.whl (47kB)
Collecting recommonmark==0.5.0
  Downloading https://files.pythonhosted.org/packages/9b/3d/92ea48401622510e57b4bdaa74dc9db2fb9e9e892324b48f9c02d716a93a/recommonmark-0.5.0-py2.py3-none-any.whl
Collecting sphinx<2
  Downloading https://files.pythonhosted.org/packages/7d/66/a4af242b4348b729b9d46ce5db23943ce9bca7da9bbe2ece60dc27f26420/Sphinx-1.8.5-py2.py3-none-any.whl (3.1MB)
Collecting sphinx-rtd-theme<0.5
  Downloading https://files.pythonhosted.org/packages/60/b4/4df37087a1d36755e3a3bfd2a30263f358d2dea21938240fa02313d45f51/sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4MB)
Collecting readthedocs-sphinx-ext<1.1
  Downloading https://files.pythonhosted.org/packages/51/43/a5a98d9aec325b2824bdf504fa446ae876d0909d03e28667018f9eb01bcd/readthedocs_sphinx_ext-1.0.0-py2.py3-none-any.whl
Collecting future (from commonmark==0.8.1)
  Downloading https://files.pythonhosted.org/packages/90/52/e20466b85000a181e1e144fd8305caf2cf475e2f9674e797b222f8105f5f/future-0.17.1.tar.gz (829kB)
Collecting packaging (from sphinx<2)
  Downloading https://files.pythonhosted.org/packages/ec/22/630ac83e8f8a9566c4f88038447ed9e16e6f10582767a01f31c769d9a71e/packaging-19.1-py2.py3-none-any.whl
Collecting sphinxcontrib-websupport (from sphinx<2)
  Downloading https://files.pythonhosted.org/packages/2a/59/d64bda9b7480a84a3569be4dde267c0f6675b255ba63b4c8e84469940457/sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl
Collecting babel!=2.0,>=1.3 (from sphinx<2)
  Downloading https://files.pythonhosted.org/packages/2c/60/f2af68eb046c5de5b1fe6dd4743bf42c074f7141fe7b2737d3061533b093/Babel-2.7.0-py2.py3-none-any.whl (8.4MB)
Collecting requests>=2.0.0 (from sphinx<2)
  Downloading https://files.pythonhosted.org/packages/51/bd/23c926cd341ea6b7dd0b2a00aba99ae0f828be89d72b2190f27c11d4b7fb/requests-2.22.0-py2.py3-none-any.whl (57kB)
Collecting Jinja2>=2.3 (from sphinx<2)
  Downloading https://files.pythonhosted.org/packages/1d/e7/fd8b501e7a6dfe492a433deb7b9d833d39ca74916fa8bc63dd1a4947a671/Jinja2-2.10.1-py2.py3-none-any.whl (124kB)
Collecting snowballstemmer>=1.1 (from sphinx<2)
  Downloading https://files.pythonhosted.org/packages/51/16/86a280d59b3bb439e7103ea1a275a191e3d2df8a3543cda0708f7cb4333c/snowballstemmer-1.9.1.tar.gz (82kB)
Collecting six>=1.5 (from sphinx<2)
  Downloading https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting imagesize (from sphinx<2)
  Downloading https://files.pythonhosted.org/packages/fc/b6/aef66b4c52a6ad6ac18cf6ebc5731ed06d8c9ae4d3b2d9951f261150be67/imagesize-1.1.0-py2.py3-none-any.whl
Collecting attrs (from packaging->sphinx<2)
  Downloading https://files.pythonhosted.org/packages/23/96/d828354fa2dbdf216eaa7b7de0db692f12c234f7ef888cc14980ef40d1d2/attrs-19.1.0-py2.py3-none-any.whl
Collecting pyparsing>=2.0.2 (from packaging->sphinx<2)
  Downloading https://files.pythonhosted.org/packages/11/fa/0160cd525c62d7abd076a070ff02b2b94de589f1a9789774f17d7c54058e/pyparsing-2.4.2-py2.py3-none-any.whl (65kB)
Collecting pytz>=2015.7 (from babel!=2.0,>=1.3->sphinx<2)
  Downloading https://files.pythonhosted.org/packages/87/76/46d697698a143e05f77bec5a526bf4e56a0be61d63425b68f4ba553b51f2/pytz-2019.2-py2.py3-none-any.whl (508kB)
Collecting idna<2.9,>=2.5 (from requests>=2.0.0->sphinx<2)
  Downloading https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl (58kB)
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 (from requests>=2.0.0->sphinx<2)
  Downloading https://files.pythonhosted.org/packages/e6/60/247f23a7121ae632d62811ba7f273d0e58972d75e58a94d329d51550a47d/urllib3-1.25.3-py2.py3-none-any.whl (150kB)
Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx<2)
  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<2)
  Downloading https://files.pythonhosted.org/packages/18/b0/8146a4f8dd402f60744fa380bc73ca47303cccf8b9190fd16a827281eac2/certifi-2019.9.11-py2.py3-none-any.whl (154kB)
Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx<2)
  Downloading https://files.pythonhosted.org/packages/98/7b/ff284bd8c80654e471b769062a9b43cc5d03e7a615048d96f4619df8d420/MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl
Building wheels for collected packages: mock, future, snowballstemmer
  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-cp37-none-any.whl size=23755 sha256=6a3f54ddc2c42dd1ecad896e9d6ea8a7e73c050c3f7c0381c7785f0e6eba84e9
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/.cache/pip/wheels/7e/72/92/744b532c779242b57aab4bcba80c312b30c069bbd60025e7e6
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.17.1-cp37-none-any.whl size=488730 sha256=9deaa7ab1ca6613322f1d2472153ae95dc4c583e77646cd3ef2d35827a514eff
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/.cache/pip/wheels/0c/61/d2/d6b7317325828fbb39ee6ad559dbe4664d0896da4721bf379e
  Building wheel for snowballstemmer (setup.py): started
  Building wheel for snowballstemmer (setup.py): finished with status 'done'
  Created wheel for snowballstemmer: filename=snowballstemmer-1.9.1-cp37-none-any.whl size=101576 sha256=792b925ae12857fa00b2098e0a1060755e01270b14fd135383a9dbaa5ff09cf2
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/.cache/pip/wheels/ae/9b/66/6b8f275ec6dfa2138a56faaf2b4314ca44a4746286560d5578
Successfully built mock future snowballstemmer
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, attrs, six, pyparsing, packaging, sphinxcontrib-websupport, pytz, babel, idna, urllib3, chardet, certifi, requests, MarkupSafe, Jinja2, snowballstemmer, imagesize, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
  Found existing installation: setuptools 40.6.3
    Uninstalling setuptools-40.6.3:
      Successfully uninstalled setuptools-40.6.3
Successfully installed Jinja2-2.10.1 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 attrs-19.1.0 babel-2.7.0 certifi-2019.9.11 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.17.1 idna-2.8 imagesize-1.1.0 mock-1.0.1 packaging-19.1 pillow-5.4.1 pyparsing-2.4.2 pytz-2019.2 readthedocs-sphinx-ext-1.0.0 recommonmark-0.5.0 requests-2.22.0 setuptools-41.0.1 six-1.12.0 snowballstemmer-1.9.1 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 urllib3-1.25.3

[rtd-command-info] start-time: 2019-09-18T19:47:59.231562Z, end-time: 2019-09-18T19:47:59.546773Z, 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 = 'Metagenomics in QIIME 2 Using Jupyter Notebooks in VICE'
copyright = '2019, CyVerse'
author = 'CyVerse'
version = '1.0'
release = '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': [ 
    ("pdf", "//readthedocs.com/projects/cyverse-jupyter-qiime2/downloads/pdf/latest/"),
    ("html", "//readthedocs.com/projects/cyverse-jupyter-qiime2/downloads/htmlzip/latest/"),
    ("epub", "//readthedocs.com/projects/cyverse-jupyter-qiime2/downloads/epub/latest/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'cyverse-jupyter-qiime2',
    'name': u'jupyter_qiime2',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://cyverse-jupyter-qiime2.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'CyVerse-learning-materials',
    'github_repo': 'jupyter_qiime2',
    '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': '5b38732c',
}




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: 2019-09-18T19:47:59.624689Z, end-time: 2019-09-18T19:48:01.085775Z, duration: 1, 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 3 source files that are out of date
updating environment: 3 added, 0 changed, 0 removed
reading sources... [ 33%] Contributors_maintainers
reading sources... [ 66%] License
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/envs/latest/lib/python3.7/site-packages/recommonmark/parser.py:65: UserWarning: Container node skipped: type=document
  warn("Container node skipped: type={0}".format(mdnode.t))
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/index.rst:10: WARNING: Title underline too short.

UPDATE: Newest version QIIME-2019.7
----
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/checkouts/latest/License.md: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [ 33%] Contributors_maintainers
writing output... [ 66%] License
writing output... [100%] index

generating indices... genindex
writing additional pages... search
copying images... [ 50%] ./img/cyverse_rgb.png
copying images... [100%] ./img/homeicon.png

copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/user_builds/cyverse-jupyter-qiime2/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, 4 warnings.

The HTML pages are in _build/html.

[rtd-command-info] start-time: 2019-09-18T19:48:01.203147Z, end-time: 2019-09-18T19:48:02.599534Z, duration: 1, 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: 3 added, 0 changed, 0 removed
reading sources... [ 33%] Contributors_maintainers
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[rtd-command-info] start-time: 2019-09-18T19:48:02.718988Z, end-time: 2019-09-18T19:48:03.999797Z, duration: 1, exit-code: 0
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sub makeglo {
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[rtd-command-info] start-time: 2019-09-18T19:48:05.980226Z, end-time: 2019-09-18T19:48:08.377680Z, duration: 2, exit-code: 0
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Chapter 4.
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Chapter 4.
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