Read the Docs build information Build id: 255486 Project: cyverse-learning-materials-home Version: latest Commit: 0bd640ec6b5df7ad96c46c4fcb6b15bbb835e5cc Date: 2019-11-01T17:34:30.980269Z State: finished Success: True [rtd-command-info] start-time: 2019-11-01T17:34:31.753191Z, end-time: 2019-11-01T17:34:31.764636Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/CyVerse-learning-materials/learning-materials-home.git [rtd-command-info] start-time: 2019-11-01T17:34:31.843467Z, end-time: 2019-11-01T17:34:32.382232Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 From https://github.com/CyVerse-learning-materials/learning-materials-home 7b23df0..0bd640e master -> origin/master [rtd-command-info] start-time: 2019-11-01T17:34:32.581112Z, end-time: 2019-11-01T17:34:32.611735Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 7b23df0 Update power_users.rst HEAD is now at 0bd640e Update tools_and_apps.rst [rtd-command-info] start-time: 2019-11-01T17:34:32.690412Z, end-time: 2019-11-01T17:34:32.715764Z, duration: 0, exit-code: 0 git clean -d -f -f Removing _build/ Removing misc/__init__.pyc Removing misc/cyverse_sphinx_conf.pyc [rtd-command-info] start-time: 2019-11-01T17:34:33.716945Z, end-time: 2019-11-01T17:34:37.086382Z, duration: 3, 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: 2019-11-01T17:34:37.172337Z, end-time: 2019-11-01T17:34:39.119051Z, duration: 1, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/.cache/pip pip DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. Collecting pip Using cached https://files.pythonhosted.org/packages/00/b6/9cfa56b4081ad13874b0c6f96af8ce16cfbc1cb06bedf8e9164ce5551ec1/pip-19.3.1-py2.py3-none-any.whl Installing collected packages: pip Found existing installation: pip 19.1.1 Uninstalling pip-19.1.1: Successfully uninstalled pip-19.1.1 Successfully installed pip-19.3.1 [rtd-command-info] start-time: 2019-11-01T17:34:39.217773Z, end-time: 2019-11-01T17:34:48.818163Z, duration: 9, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/.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 DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. 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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-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-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-container-camp-workshop-2019", "https://learning.cyverse.org/projects/container_camp_workshop_2019/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-240-minute-r-tutorial", "https://learning.cyverse.org/projects/cyverse-240-minute-r-tutorial/en/latest/"), ("cyverse-git-for-mere-mortals", "https://learning.cyverse.org/projects/cyverse-git-for-mere-mortals/en/latest/"), ("cyverse-cyverse-tools-and-services-workshop", "https://learning.cyverse.org/projects/cyverse-cyverse-tools-and-services-workshop/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-foundational-open-science-skills-2020", "https://learning.cyverse.org/projects/foss-2020/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': '0bd640ec', } 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: 2019-11-01T17:34:51.394136Z, end-time: 2019-11-01T17:34:53.690240Z, duration: 2, 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 9 source files that are out of date updating environment: 9 added, 0 changed, 0 removed reading sources... 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[ 11%] README writing output... [ 22%] contributing writing output... [ 33%] index writing output... [ 44%] platform_guides writing output... [ 55%] power_users writing output... [ 66%] quick_starts writing output... [ 77%] tools_and_apps writing output... [ 88%] tutorials writing output... [100%] workshops generating indices... genindex writing additional pages... search copying images... [ 50%] ./img/homeicon.png copying images... [100%] ./img/cyverse_cmyk.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/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, 28 warnings. The HTML pages are in _build/html. [rtd-command-info] start-time: 2019-11-01T17:34:53.902664Z, end-time: 2019-11-01T17:34:55.961740Z, 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: 9 added, 0 changed, 0 removed reading sources... [ 11%] README reading sources... [ 22%] contributing reading sources... [ 33%] index reading sources... [ 44%] platform_guides reading sources... [ 55%] power_users reading sources... [ 66%] quick_starts reading sources... [ 77%] tools_and_apps reading sources... [ 88%] tutorials reading sources... 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README platform_guides tools_and_apps quick_starts tutorials workshops contributing power_users writing... done writing additional files... copying images... [ 50%] ./img/homeicon.png copying images... [100%] ./img/cyverse_cmyk.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/_static' does not exist done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded, 28 warnings. The HTML page is in _build/localmedia.