Read the Docs build information
Build id: 1216033
Project: cyverse-learning-materials-home
Version: latest
Commit: a6f21ccb8c6923a7de2be24507ab166138041a61
Date: 2022-12-09T20:15:52.721971Z
State: finished
Success: True


[rtd-command-info] start-time: 2022-12-09T20:15:54.660103Z, end-time: 2022-12-09T20:15:57.768304Z, duration: 3, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/learning-materials-home.git .
Cloning into '.'...

[rtd-command-info] start-time: 2022-12-09T20:15:58.003087Z, end-time: 2022-12-09T20:15:58.519047Z, duration: 0, exit-code: 0
git checkout --force origin/main
Note: switching to 'origin/main'.

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 switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at a6f21cc Apply tyson's decorational changes

[rtd-command-info] start-time: 2022-12-09T20:15:58.725168Z, end-time: 2022-12-09T20:15:58.788669Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-12-09T20:16:00.111252Z, end-time: 2022-12-09T20:16:03.761950Z, duration: 3, exit-code: 0
python2.7 -mvirtualenv 
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: 2022-12-09T20:16:03.983689Z, end-time: 2022-12-09T20:16:05.816184Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
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 Please upgrade your Python as Python 2.7 is no longer maintained.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-learning-materials-home/envs/latest/lib/python2.7/site-packages (20.3.4)
Requirement already up-to-date: setuptools<58.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (44.1.1)

[rtd-command-info] start-time: 2022-12-09T20:16:06.063698Z, end-time: 2022-12-09T20:16:14.782317Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0
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 pillow
  Downloading Pillow-6.2.2-cp27-cp27mu-manylinux1_x86_64.whl (2.1 MB)
Collecting mock==1.0.1
  Downloading mock-1.0.1.tar.gz (818 kB)
Collecting alabaster!=0.7.5,<0.8,>=0.7
  Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB)
Collecting commonmark==0.9.1
  Downloading commonmark-0.9.1-py2.py3-none-any.whl (51 kB)
Collecting recommonmark==0.5.0
  Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB)
Collecting sphinx<2
  Downloading Sphinx-1.8.6-py2.py3-none-any.whl (3.1 MB)
Collecting sphinx-rtd-theme<0.5
  Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB)
Collecting readthedocs-sphinx-ext<2.3
  Downloading readthedocs_sphinx_ext-2.2.0-py2.py3-none-any.whl (11 kB)
Collecting jinja2<3.1.0
  Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB)
Collecting future>=0.14.0; python_version < "3"
  Downloading future-0.18.2.tar.gz (829 kB)
Collecting docutils>=0.11
  Downloading docutils-0.18.1-py2.py3-none-any.whl (570 kB)
Collecting imagesize
  Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Collecting typing; python_version < "3.5"
  Downloading typing-3.10.0.0-py2-none-any.whl (26 kB)
Collecting Pygments>=2.0
  Downloading Pygments-2.5.2-py2.py3-none-any.whl (896 kB)
Collecting packaging
  Downloading packaging-20.9-py2.py3-none-any.whl (40 kB)
Collecting snowballstemmer>=1.1
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
Requirement already satisfied, skipping upgrade: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from sphinx<2) (44.1.1)
Collecting babel!=2.0,>=1.3
  Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB)
Collecting six>=1.5
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting requests>=2.0.0
  Downloading requests-2.27.1-py2.py3-none-any.whl (63 kB)
Collecting sphinxcontrib-websupport
  Downloading sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl (39 kB)
Collecting MarkupSafe>=0.23
  Downloading MarkupSafe-1.1.1-cp27-cp27mu-manylinux1_x86_64.whl (24 kB)
Collecting pyparsing>=2.0.2
  Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
Collecting pytz>=2015.7
  Downloading pytz-2022.6-py2.py3-none-any.whl (498 kB)
Collecting certifi>=2017.4.17
  Downloading certifi-2021.10.8-py2.py3-none-any.whl (149 kB)
Collecting urllib3<1.27,>=1.21.1
  Downloading urllib3-1.26.13-py2.py3-none-any.whl (140 kB)
Collecting chardet<5,>=3.0.2; python_version < "3"
  Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB)
Collecting idna<3,>=2.5; python_version < "3"
  Downloading idna-2.10-py2.py3-none-any.whl (58 kB)
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-py2-none-any.whl size=23754 sha256=fc6758a507177b1c5ae751340baf39b4132cab2831beb5db0bb763fcc0ea580b
  Stored in directory: /tmp/pip-ephem-wheel-cache-RHd9x4/wheels/ad/62/e0/a06cc957652749e64c7904e899eca3ecb2ec47c60d52653660
  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-py2-none-any.whl size=502566 sha256=e3e899168ba6a0976c9100140efb87f25ec10052cef0729a8f3844b92c3d8843
  Stored in directory: /tmp/pip-ephem-wheel-cache-RHd9x4/wheels/5f/11/0c/aad680baf5ef4fbcbab992c9f03e1130357e0c173a4fdabfff
Successfully built mock future
Installing collected packages: pillow, mock, alabaster, future, commonmark, imagesize, typing, Pygments, MarkupSafe, jinja2, docutils, pyparsing, packaging, snowballstemmer, pytz, babel, six, certifi, urllib3, chardet, idna, requests, sphinxcontrib-websupport, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
ERROR: pip's legacy dependency resolver does not consider dependency conflicts when selecting packages. This behaviour is the source of the following dependency conflicts.
sphinx 1.8.6 requires docutils<0.18,>=0.11, but you'll have docutils 0.18.1 which is incompatible.
Successfully installed 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-0.9.1 docutils-0.18.1 future-0.18.2 idna-2.10 imagesize-1.4.1 jinja2-2.11.3 mock-1.0.1 packaging-20.9 pillow-6.2.2 pyparsing-2.4.7 pytz-2022.6 readthedocs-sphinx-ext-2.2.0 recommonmark-0.5.0 requests-2.27.1 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 typing-3.10.0.0 urllib3-1.26.13

[rtd-command-info] start-time: 2022-12-09T20:16:16.613906Z, end-time: 2022-12-09T20:16:16.712244Z, duration: 0, exit-code: 0
cat docs/conf.py
# -*- coding: utf-8 -*-

from __future__ import division, print_function, unicode_literals

from datetime import datetime

from recommonmark.parser import CommonMarkParser

extensions = []
templates_path = ['templates', '_templates', '.templates']
source_suffix = ['.rst', '.md']
source_parsers = {
            '.md': CommonMarkParser,
        }
master_doc = 'index'
project = u'learning-materials-home'
copyright = str(datetime.now().year)
version = 'latest'
release = 'latest'
exclude_patterns = ['_build']
pygments_style = 'sphinx'
htmlhelp_basename = 'cyverse-learning-materials-home'
html_theme = 'sphinx_rtd_theme'
file_insertion_enabled = False
latex_documents = [
  ('index', 'cyverse-learning-materials-home.tex', u'learning-materials-home Documentation',
   u'', 'manual'),
]




###########################################################################
#          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/main/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",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ],
    'downloads': [ 
    ("html", "//learning.cyverse.org/_/downloads/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
        ("cyverse-discovery-environment-guide", "https://learning.cyverse.org/projects/discovery-environment-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-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-creating-docker-containers-quickstart", "https://learning.cyverse.org/projects/cyverse-creating-docker-containers-quickstart/en/latest/"),
        ("cyverse-learning-center-faq", "https://learning.cyverse.org/projects/faq/en/latest/"),
        ("cyverse-cyverse-tools-and-services-workshop", "https://learning.cyverse.org/projects/cyverse-cyverse-tools-and-services-workshop/en/latest/"),
        ("cyverse-sciapps-guide", "https://learning.cyverse.org/projects/sciapps_guide/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/"),
        ("cyverse-tools-services-and-reproducible-science-workshop", "https://learning.cyverse.org/projects/cyverse-tools-services-and-reproducible-science-workshop/en/latest/"),
        ("cyverse-de2-guide", "https://learning.cyverse.org/projects/cyverse-de2-guide/en/latest/"),
        ("cyverse-glossary", "https://learning.cyverse.org/projects/glossary/en/latest/"),
        ("cyverse-data-store-manual", "https://learning.cyverse.org/projects/data-store-manual/en/latest/"),
        ("cyverse-change-password-quickstart", "https://learning.cyverse.org/projects/change_password_quickstart/en/latest/"),
        ("cyverse-sra-submission-quickstart-2", "https://learning.cyverse.org/projects/sra_submission_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': 'UA-72224033-6',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'CyVerse-learning-materials',
    'proxied_api_host': '/_',
    '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,
    'docsearch_disabled': False,
    'user_analytics_code': 'UA-72224033-6',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'a6f21ccb',
}

# 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-learning-materials-home/builds/1216033/'

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: 2022-12-09T20:16:16.904413Z, end-time: 2022-12-09T20:16:20.962997Z, duration: 4, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v1.8.6
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 42 source files that are out of date
updating environment: 42 added, 0 changed, 0 removed
reading sources... [  2%] account
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/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... [  4%] bisque/index
reading sources... [  7%] cloud/atmo
reading sources... [  9%] cloud/index
reading sources... [ 11%] de/bags
reading sources... [ 14%] de/create_apps
reading sources... [ 16%] de/index
reading sources... [ 19%] de/login
reading sources... [ 21%] de/manage_data
reading sources... [ 23%] de/managing_analyses
reading sources... [ 26%] de/using_apps
reading sources... [ 28%] dna_subway_guide
reading sources... [ 30%] ds/check_data
reading sources... [ 33%] ds/cyberduck
reading sources... [ 35%] ds/doi
reading sources... [ 38%] ds/gocommands
reading sources... [ 40%] ds/icommands
reading sources... [ 42%] ds/index
reading sources... [ 45%] ds/metadata
reading sources... [ 47%] ds/move_data/index
reading sources... [ 50%] ds/quick-data-share
reading sources... [ 52%] ds/sftp
reading sources... [ 54%] ds/share
reading sources... [ 57%] ds/webdav
reading sources... [ 59%] faq
reading sources... [ 61%] getting_help
reading sources... [ 64%] glossary
reading sources... [ 66%] index
reading sources... [ 69%] manuals
reading sources... [ 71%] mooc
reading sources... [ 73%] powered_by
reading sources... [ 76%] tutorials/index
reading sources... [ 78%] vice/about
reading sources... [ 80%] vice/extend_apps
reading sources... [ 83%] vice/quick-cloudshell
reading sources... [ 85%] vice/quick-jupyter
reading sources... [ 88%] vice/quick-rstudio
reading sources... [ 90%] vice/teaching
reading sources... [ 92%] what_is_cyverse
reading sources... [ 95%] workshops/container_camp
reading sources... [ 97%] workshops/foss
reading sources... [100%] workshops/index

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/docs/dna_subway_guide.md:0: WARNING: Document may not end with a transition.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/docs/faq.md:0: WARNING: Document may not end with a transition.
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/docs/account.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/docs/bisque/index.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/docs/cloud/atmo.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/docs/cloud/index.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/docs/de/bags.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/docs/de/create_apps.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/docs/de/index.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/docs/de/login.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/docs/de/manage_data.md: WARNING: document isn't included in any toctree
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