Read the Docs build information Build id: 272391 Project: icb-scanpy-tutorials Version: latest Commit: e082d21f9c4efb54b4310d9b38731ccb0a91467c Date: 2019-12-28T13:56:49.251192Z State: finished Success: True [rtd-command-info] start-time: 2019-12-28T13:56:49.783262Z, end-time: 2019-12-28T13:56:49.796405Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/theislab/scanpy-tutorials.git [rtd-command-info] start-time: 2019-12-28T13:56:49.883215Z, end-time: 2019-12-28T13:56:50.929292Z, duration: 1, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 From https://github.com/theislab/scanpy-tutorials 6318785..e082d21 master -> origin/master [rtd-command-info] start-time: 2019-12-28T13:56:51.143271Z, end-time: 2019-12-28T13:56:51.621824Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 6318785 fix period behind author HEAD is now at e082d21 updated ingest tutorial [rtd-command-info] start-time: 2019-12-28T13:56:51.698916Z, end-time: 2019-12-28T13:56:51.711020Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-12-28T13:56:52.588616Z, end-time: 2019-12-28T13:56:56.692594Z, duration: 4, exit-code: 0 python3.6 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.6.8' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/bin/python3.6 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/bin/python Installing setuptools, pip, wheel... done. 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Installing collected packages: tornado, decorator, ipython-genutils, traitlets, ptyprocess, pexpect, backcall, parso, jedi, wcwidth, prompt-toolkit, pickleshare, ipython, python-dateutil, pyzmq, jupyter-core, jupyter-client, ipykernel, more-itertools, zipp, importlib-metadata, pyrsistent, attrs, jsonschema, nbformat, testpath, pandocfilters, defusedxml, webencodings, bleach, entrypoints, mistune, nbconvert, nbsphinx, tqdm, terminado, prometheus-client, Send2Trash, notebook, qtconsole, jupyter-console, widgetsnbextension, ipywidgets, jupyter, Mako, python-editor, sqlalchemy, alembic, fuzzywuzzy, nbgrader, numpy, kiwisolver, cycler, matplotlib, nbclean Successfully installed Mako-1.1.0 Send2Trash-1.5.0 alembic-1.3.2 attrs-19.3.0 backcall-0.1.0 bleach-3.1.0 cycler-0.10.0 decorator-4.4.1 defusedxml-0.6.0 entrypoints-0.3 fuzzywuzzy-0.17.0 importlib-metadata-1.3.0 ipykernel-5.1.3 ipython-7.11.0 ipython-genutils-0.2.0 ipywidgets-7.5.1 jedi-0.15.2 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-5.3.4 jupyter-console-6.0.0 jupyter-core-4.6.1 kiwisolver-1.1.0 matplotlib-3.1.2 mistune-0.8.4 more-itertools-8.0.2 nbclean-0.3.2 nbconvert-5.6.1 nbformat-4.4.0 nbgrader-0.6.1 nbsphinx-0.5.0 notebook-6.0.2 numpy-1.18.0 pandocfilters-1.4.2 parso-0.5.2 pexpect-4.7.0 pickleshare-0.7.5 prometheus-client-0.7.1 prompt-toolkit-3.0.2 ptyprocess-0.6.0 pyrsistent-0.15.6 python-dateutil-2.8.1 python-editor-1.0.4 pyzmq-18.1.1 qtconsole-4.6.0 sqlalchemy-1.3.12 terminado-0.8.3 testpath-0.4.4 tornado-6.0.3 tqdm-4.41.0 traitlets-4.3.3 wcwidth-0.1.7 webencodings-0.5.1 widgetsnbextension-3.5.1 zipp-0.6.0 [rtd-command-info] start-time: 2019-12-28T13:57:28.225664Z, end-time: 2019-12-28T13:57:28.450281Z, duration: 0, exit-code: 0 cat conf.py from datetime import datetime project = 'Scanpy' author = 'Alex Wolf, Fidel Ramirez, Sergei Rybakov' copyright = f'{datetime.now():%Y}, {author}' version = '' release = version extensions = [ 'nbsphinx', ] templates_path = ['_templates'] source_suffix = '.rst' master_doc = 'index' language = None exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints'] pygments_style = 'sphinx' # -- Options for HTML output ---------------------------------------------- html_theme = 'sphinx_rtd_theme' html_theme_options = dict( navigation_depth=2, logo_only=True # Only show the logo ) html_context = dict( display_github=True, # Integrate GitHub github_user='theislab', # Username github_repo='scanpy-tutorials', # Repo name github_version='master', # Version conf_py_path='/', # Path in the checkout to the docs root ) html_static_path = ['_static'] html_show_sphinx = False html_logo = '_static/img/Scanpy_Logo_BrightFG.svg' def setup(app): app.add_stylesheet('css/custom.css') # -- Strip output ---------------------------------------------- import nbclean, glob for filename in glob.glob('**/*.ipynb', recursive=True): ntbk = nbclean.NotebookCleaner(filename) ntbk.clear('stderr') ntbk.save(filename) ########################################################################### # 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", "//readthedocs.com/projects/icb-scanpy-tutorials/downloads/htmlzip/latest/"), ], 'subprojects': [ ], 'slug': 'icb-scanpy-tutorials', 'name': u'scanpy-tutorials', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://icb-scanpy-tutorials.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'proxied_api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'github_repo': 'scanpy-tutorials', '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': 'e082d21f', } 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: 2019-12-28T13:57:28.532770Z, end-time: 2019-12-28T13:57:38.424936Z, duration: 9, 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 6 source files that are out of date updating environment: 6 added, 0 changed, 0 removed reading sources... 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[rtd-command-info] start-time: 2019-12-28T13:57:38.592108Z, end-time: 2019-12-28T13:57:48.097479Z, duration: 9, 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... loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [] 1 added, 4 changed, 1 removed reading sources... [ 20%] index reading sources... [ 40%] integrating-data-using-ingest reading sources... [ 60%] paga-paul15 reading sources... [ 80%] pbmc3k reading sources... 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