Read the Docs build information Build id: 293652 Project: cyverse-dnasubway-guide Version: latest Commit: cb748f1762b6af2c77c8a2b453dcc9e7d66d168a Date: 2020-02-25T22:45:49.976174Z State: finished Success: True [rtd-command-info] start-time: 2020-02-25T22:45:52.127765Z, end-time: 2020-02-25T22:45:55.417957Z, duration: 3, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/dnasubway_guide.git . Cloning into '.'... [rtd-command-info] start-time: 2020-02-25T22:45:55.682525Z, end-time: 2020-02-25T22:45:56.216753Z, 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 HEAD is now at cb748f1 add rarefaction depth recommendation for test data [rtd-command-info] start-time: 2020-02-25T22:45:56.525920Z, end-time: 2020-02-25T22:45:56.757951Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-02-25T22:45:58.146515Z, end-time: 2020-02-25T22:46:02.925960Z, duration: 4, exit-code: 0 python2.7 -mvirtualenv --no-site-packages New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/bin/python2.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-02-25T22:46:02.994139Z, end-time: 2020-02-25T22:46:03.925617Z, duration: 0, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.cache/pip pip 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 Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/envs/latest/lib/python2.7/site-packages (20.0.2) [rtd-command-info] start-time: 2020-02-25T22:46:04.163674Z, end-time: 2020-02-25T22:46:18.375065Z, duration: 14, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.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 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) 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-py2-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp27-cp27mu-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 commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-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<1.1 Downloading readthedocs_sphinx_ext-1.0.1-py2.py3-none-any.whl (14 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting typing; python_version < "3.5" Downloading typing-3.7.4.1-py2-none-any.whl (26 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.1-py2.py3-none-any.whl (126 kB) Collecting requests>=2.0.0 Downloading requests-2.23.0-py2.py3-none-any.whl (58 kB) Collecting packaging Downloading packaging-20.1-py2.py3-none-any.whl (36 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting six>=1.5 Downloading six-1.14.0-py2.py3-none-any.whl (10 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl (39 kB) Collecting pytz>=2015.7 Downloading pytz-2019.3-py2.py3-none-any.whl (509 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp27-cp27mu-manylinux1_x86_64.whl (24 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.8-py2.py3-none-any.whl (125 kB) Collecting certifi>=2017.4.17 Downloading certifi-2019.11.28-py2.py3-none-any.whl (156 kB) Collecting idna<3,>=2.5 Downloading idna-2.9-py2.py3-none-any.whl (58 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.6-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-py2-none-any.whl size=23755 sha256=bbaf92269ba07fbd94ecab302f43be314a84e6a22dd1eaa4a346f707a45a6db5 Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.cache/pip/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=642fb764da5695616b772c0b66fb8111150ccad4e90a4141a313dd0c1ff55eb1 Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/.cache/pip/wheels/5f/11/0c/aad680baf5ef4fbcbab992c9f03e1130357e0c173a4fdabfff Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, pytz, babel, imagesize, typing, MarkupSafe, Jinja2, urllib3, certifi, idna, chardet, requests, six, pyparsing, packaging, snowballstemmer, sphinxcontrib-websupport, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 44.0.0 Uninstalling setuptools-44.0.0: Successfully uninstalled setuptools-44.0.0 Successfully installed Jinja2-2.11.1 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2019.11.28 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.9 imagesize-1.2.0 mock-1.0.1 packaging-20.1 pillow-5.4.1 pyparsing-2.4.6 pytz-2019.3 readthedocs-sphinx-ext-1.0.1 recommonmark-0.5.0 requests-2.23.0 setuptools-41.0.1 six-1.14.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 typing-3.7.4.1 urllib3-1.25.8 [rtd-command-info] start-time: 2020-02-25T22:46:19.152404Z, end-time: 2020-02-25T22:46:19.391031Z, 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 = 'DNA Subway Guide' copyright = '2016, 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': [ ("html", "//learning.cyverse.org/_/downloads/dnasubway_guide/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'cyverse-dnasubway-guide', 'name': u'dnasubway_guide', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://learning.cyverse.org/projects/dnasubway_guide/en/latest/', 'analytics_code': '', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'proxied_api_host': '/_', 'github_user': 'CyVerse-learning-materials', 'github_repo': 'dnasubway_guide', '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': 'cb748f17', } 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: 2020-02-25T22:46:19.452303Z, end-time: 2020-02-25T22:46:22.298806Z, 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 11 source files that are out of date updating environment: 11 added, 0 changed, 0 removed reading sources... 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[100%] step8 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:194: WARNING: Enumerated list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst:196: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:488: WARNING: Duplicate substitution definition name: "CyVerse logo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step7.rst:492: WARNING: Duplicate substitution definition name: "Home_Icon". looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/Contributors_maintainers.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/License.md: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-dnasubway-guide/checkouts/latest/step6.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... 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