Read the Docs build information
Build id: 560210
Project: cyverse-glossary
Version: latest
Commit: b67ad5d3c34075618e6f7af54121900e44b0df0b
Date: 2021-02-12T22:36:46.993050Z
State: finished
Success: True


[rtd-command-info] start-time: 2021-02-12T22:36:48.597788Z, end-time: 2021-02-12T22:36:49.991799Z, duration: 1, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:CyVerse-learning-materials/glossary.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.112' (RSA) to the list of known hosts.

[rtd-command-info] start-time: 2021-02-12T22:36:50.312598Z, end-time: 2021-02-12T22:36:50.389411Z, 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 b67ad5d Update index.rst

[rtd-command-info] start-time: 2021-02-12T22:36:50.568586Z, end-time: 2021-02-12T22:36:50.622903Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-02-12T22:36:51.864567Z, end-time: 2021-02-12T22:36:55.737694Z, 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-glossary/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-glossary/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2021-02-12T22:36:55.893802Z, end-time: 2021-02-12T22:36:56.712645Z, 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-glossary/envs/latest/lib/python3.7/site-packages (21.0.1)

[rtd-command-info] start-time: 2021-02-12T22:36:56.829885Z, end-time: 2021-02-12T22:37:06.218820Z, 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
  Downloading mock-1.0.1.zip (861 kB)
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
  Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB)
Collecting six
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Collecting commonmark==0.8.1
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Collecting recommonmark==0.5.0
  Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB)
Collecting sphinx
  Downloading Sphinx-3.4.3-py3-none-any.whl (2.9 MB)
Collecting sphinx-rtd-theme
  Downloading sphinx_rtd_theme-0.5.1-py2.py3-none-any.whl (2.8 MB)
Collecting readthedocs-sphinx-ext<2.2
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Collecting future
  Downloading future-0.18.2.tar.gz (829 kB)
Collecting Jinja2>=2.9
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Collecting requests
  Downloading requests-2.25.1-py2.py3-none-any.whl (61 kB)
Collecting sphinxcontrib-htmlhelp
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Collecting Pygments>=2.0
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Collecting imagesize
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Collecting snowballstemmer>=1.1
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Collecting sphinxcontrib-applehelp
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Collecting packaging
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Collecting sphinxcontrib-jsmath
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting sphinxcontrib-serializinghtml
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Collecting sphinxcontrib-qthelp
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Collecting babel>=1.3
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Collecting pytz>=2015.7
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Collecting MarkupSafe>=0.23
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Collecting chardet<5,>=3.0.2
  Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB)
Collecting certifi>=2017.4.17
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Collecting urllib3<1.27,>=1.21.1
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Collecting idna<3,>=2.5
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Collecting pyparsing>=2.0.2
  Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 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-py3-none-any.whl size=23755 sha256=4a60a60a9c6dd62ccae22cea55299873471ffd477ccded00358b6a0beae42072
  Stored in directory: /tmp/pip-ephem-wheel-cache-5vw6il82/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=8be6d8cef786956071079a06cdf36ed3b46af3f562c5eeb2e3705afe661f5768
  Stored in directory: /tmp/pip-ephem-wheel-cache-5vw6il82/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: 2021-02-12T22:37:07.523585Z, end-time: 2021-02-12T22:37:07.603521Z, 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 = 'CyVerse Glossary and Acronyms'
copyright = '2021, CyVerse'
author = 'CyVerse Learning'
version = '2.0'
release = '2.0'

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://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': [
    ("latest", "/en/latest/"),
    ],
    'downloads': [ 
    ("html", "//learning.cyverse.org/_/downloads/glossary/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'cyverse-glossary',
    'name': u'glossary',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://learning.cyverse.org/projects/glossary/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': 'glossary',
    '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': 'b67ad5d3',
}

# 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-glossary/builds/560210/'

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: 2021-02-12T22:37:07.818505Z, end-time: 2021-02-12T22:37:09.542222Z, duration: 1, exit-code: 0
python -m sphinx -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v3.4.3
loading translations [en]... done
making output directory... done
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-glossary/checkouts/latest/misc/cyverse_sphinx_conf.py:74: RemovedInSphinx40Warning: The app.add_stylesheet() is deprecated. Please use app.add_css_file() instead.
  app.add_stylesheet('cyverse.css')
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-glossary/checkouts/latest/misc/cyverse_sphinx_conf.py:75: RemovedInSphinx40Warning: The app.add_stylesheet() is deprecated. Please use app.add_css_file() instead.
  app.add_stylesheet('detail-expand.css')
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-glossary/checkouts/latest/misc/cyverse_sphinx_conf.py:76: RemovedInSphinx40Warning: The app.add_stylesheet() is deprecated. Please use app.add_css_file() instead.
  app.add_stylesheet('question-answer.css')
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-glossary/checkouts/latest/misc/cyverse_sphinx_conf.py:78: RemovedInSphinx40Warning: The app.add_javascript() is deprecated. Please use app.add_js_file() instead.
  app.add_javascript('cyverse.js')
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-glossary/checkouts/latest/misc/cyverse_sphinx_conf.py:79: RemovedInSphinx40Warning: The app.add_javascript() is deprecated. Please use app.add_js_file() instead.
  app.add_javascript('detail-expand.js')
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-glossary/checkouts/latest/misc/cyverse_sphinx_conf.py:80: RemovedInSphinx40Warning: The app.add_javascript() is deprecated. Please use app.add_js_file() instead.
  app.add_javascript('question-answer.js')
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-glossary/checkouts/latest/misc/cyverse_sphinx_conf.py:81: RemovedInSphinx40Warning: The app.add_javascript() is deprecated. Please use app.add_js_file() instead.
  app.add_javascript('intercom-script-for-learning.js')
WARNING: html_static_path entry '_static' does not exist
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 5 source files that are out of date
updating environment: [new config] 5 added, 0 changed, 0 removed
reading sources... [ 20%] README
reading sources... [ 40%] example_directives_delete
reading sources... [ 60%] final_step
reading sources... [ 80%] index
reading sources... [100%] index0

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-glossary/checkouts/latest/README.rst:80: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-glossary/checkouts/latest/README.rst:80: WARNING: Inline emphasis start-string without end-string.
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-glossary/checkouts/latest/README.rst:394: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 5 does not contain the same number of items as row 1 (5 vs 4).

.. list-table::
    :header-rows: 1

    * - Platform
      - Interface
      - Link
      - Platform Tour
    * - Data Store
      - GUI/Command line
      - |Data Store|
      - |Data Store Guide|
    * - Discovery Environment
      - Web/Point-and-click
      - |Discovery Environment|
      - |Discovery Environment Guide|
    * - Atmosphere
      - Command line (ssh) and/or Desktop (VNC)
      - |Atmosphere|
      - |Atmosphere Guide|
    * - BisQue
      - Web/Point-and-click and/or Command-line (API)
      - |BisQue|
      - |BisQue Manual|
      - (See Manual)
    * - DNA Subway
      - Web/Point-and-click
      - |DNA Subway|
      - |DNA Subway Guide|
    * - SciApps
      - Command-line (API)
      - |SciApps|
      - |SciApps Guide|
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-glossary/checkouts/latest/README.rst:332: WARNING: Undefined substitution referenced: "Github Repo Link".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-glossary/checkouts/latest/README.rst:384: WARNING: Undefined substitution referenced: "Download Cyberduck".
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-glossary/checkouts/latest/README.rst:511: WARNING: Undefined substitution referenced: "Github Repo Link".
README.rst:80: WARNING: Inline emphasis start-string without end-string.
README.rst:80: WARNING: Inline emphasis start-string without end-string.
README.rst:394: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 5 does not contain the same number of items as row 1 (5 vs 4).

.. list-table::
    :header-rows: 1

    * - Platform
      - Interface
      - Link
      - Platform Tour
    * - Data Store
      - GUI/Command line
      - |Data Store|
      - |Data Store Guide|
    * - Discovery Environment
      - Web/Point-and-click
      - |Discovery Environment|
      - |Discovery Environment Guide|
    * - Atmosphere
      - Command line (ssh) and/or Desktop (VNC)
      - |Atmosphere|
      - |Atmosphere Guide|
    * - BisQue
      - Web/Point-and-click and/or Command-line (API)
      - |BisQue|
      - |BisQue Manual|
      - (See Manual)
    * - DNA Subway
      - Web/Point-and-click
      - |DNA Subway|
      - |DNA Subway Guide|
    * - SciApps
      - Command-line (API)
      - |SciApps|
      - |SciApps Guide|
README.rst:332: WARNING: Undefined substitution referenced: "Github Repo Link".
README.rst:384: WARNING: Undefined substitution referenced: "Download Cyberduck".
README.rst:511: WARNING: Undefined substitution referenced: "Github Repo Link".
README.rst:80: WARNING: Inline emphasis start-string without end-string.
README.rst:80: WARNING: Inline emphasis start-string without end-string.
README.rst:394: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 5 does not contain the same number of items as row 1 (5 vs 4).

.. list-table::
    :header-rows: 1

    * - Platform
      - Interface
      - Link
      - Platform Tour
    * - Data Store
      - GUI/Command line
      - |Data Store|
      - |Data Store Guide|
    * - Discovery Environment
      - Web/Point-and-click
      - |Discovery Environment|
      - |Discovery Environment Guide|
    * - Atmosphere
      - Command line (ssh) and/or Desktop (VNC)
      - |Atmosphere|
      - |Atmosphere Guide|
    * - BisQue
      - Web/Point-and-click and/or Command-line (API)
      - |BisQue|
      - |BisQue Manual|
      - (See Manual)
    * - DNA Subway
      - Web/Point-and-click
      - |DNA Subway|
      - |DNA Subway Guide|
    * - SciApps
      - Command-line (API)
      - |SciApps|
      - |SciApps Guide|
/home/docs/checkouts/readthedocs.org/user_builds/cyverse-glossary/checkouts/latest/index0.rst:3: WARNING: toctree contains reference to nonexisting document 'A'
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[rtd-command-info] start-time: 2021-02-12T22:37:09.710262Z, end-time: 2021-02-12T22:37:11.186808Z, duration: 1, exit-code: 0
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.. list-table::
    :header-rows: 1

    * - Platform
      - Interface
      - Link
      - Platform Tour
    * - Data Store
      - GUI/Command line
      - |Data Store|
      - |Data Store Guide|
    * - Discovery Environment
      - Web/Point-and-click
      - |Discovery Environment|
      - |Discovery Environment Guide|
    * - Atmosphere
      - Command line (ssh) and/or Desktop (VNC)
      - |Atmosphere|
      - |Atmosphere Guide|
    * - BisQue
      - Web/Point-and-click and/or Command-line (API)
      - |BisQue|
      - |BisQue Manual|
      - (See Manual)
    * - DNA Subway
      - Web/Point-and-click
      - |DNA Subway|
      - |DNA Subway Guide|
    * - SciApps
      - Command-line (API)
      - |SciApps|
      - |SciApps Guide|
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.. list-table::
    :header-rows: 1

    * - Platform
      - Interface
      - Link
      - Platform Tour
    * - Data Store
      - GUI/Command line
      - |Data Store|
      - |Data Store Guide|
    * - Discovery Environment
      - Web/Point-and-click
      - |Discovery Environment|
      - |Discovery Environment Guide|
    * - Atmosphere
      - Command line (ssh) and/or Desktop (VNC)
      - |Atmosphere|
      - |Atmosphere Guide|
    * - BisQue
      - Web/Point-and-click and/or Command-line (API)
      - |BisQue|
      - |BisQue Manual|
      - (See Manual)
    * - DNA Subway
      - Web/Point-and-click
      - |DNA Subway|
      - |DNA Subway Guide|
    * - SciApps
      - Command-line (API)
      - |SciApps|
      - |SciApps Guide|
README.rst:332: WARNING: Undefined substitution referenced: "Github Repo Link".
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.. list-table::
    :header-rows: 1

    * - Platform
      - Interface
      - Link
      - Platform Tour
    * - Data Store
      - GUI/Command line
      - |Data Store|
      - |Data Store Guide|
    * - Discovery Environment
      - Web/Point-and-click
      - |Discovery Environment|
      - |Discovery Environment Guide|
    * - Atmosphere
      - Command line (ssh) and/or Desktop (VNC)
      - |Atmosphere|
      - |Atmosphere Guide|
    * - BisQue
      - Web/Point-and-click and/or Command-line (API)
      - |BisQue|
      - |BisQue Manual|
      - (See Manual)
    * - DNA Subway
      - Web/Point-and-click
      - |DNA Subway|
      - |DNA Subway Guide|
    * - SciApps
      - Command-line (API)
      - |SciApps|
      - |SciApps Guide|
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