Read the Docs build information Build id: 272432 Project: icb-scanpy-tutorials Version: latest Commit: 348b905ebb9f0f9f0c77e049b96517551da46cc8 Date: 2019-12-30T00:19:19.051330Z State: finished Success: True [rtd-command-info] start-time: 2019-12-30T00:19:19.481629Z, end-time: 2019-12-30T00:19:19.491192Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/theislab/scanpy-tutorials.git [rtd-command-info] start-time: 2019-12-30T00:19:19.574242Z, end-time: 2019-12-30T00:19:20.848438Z, duration: 1, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 From https://github.com/theislab/scanpy-tutorials 985c930..348b905 master -> origin/master [rtd-command-info] start-time: 2019-12-30T00:19:21.063009Z, end-time: 2019-12-30T00:19:21.201224Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 985c930 updated data integration and titles HEAD is now at 348b905 further improve header [rtd-command-info] start-time: 2019-12-30T00:19:21.276446Z, end-time: 2019-12-30T00:19:21.285953Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-12-30T00:19:22.150315Z, end-time: 2019-12-30T00:19:26.590310Z, 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 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/bin/python3.6) Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2019-12-30T00:19:26.681542Z, end-time: 2019-12-30T00:19:27.882698Z, duration: 1, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (19.3.1) [rtd-command-info] start-time: 2019-12-30T00:19:27.957404Z, end-time: 2019-12-30T00:19:30.365215Z, duration: 2, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.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 Requirement already up-to-date: Pygments==2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (2.3.1) Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (41.0.1) Requirement already up-to-date: docutils==0.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (0.14) Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (1.0.1) Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (5.4.1) Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (0.7.12) Requirement already up-to-date: commonmark==0.8.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (0.8.1) Requirement already up-to-date: recommonmark==0.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (0.5.0) Requirement already up-to-date: sphinx<2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (1.8.5) Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (0.4.3) Requirement already up-to-date: readthedocs-sphinx-ext<1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (1.0.1) Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from commonmark==0.8.1) (0.18.2) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.10.3) Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.22.0) Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.2.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.1.2) Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.13.0) Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx<2) (19.2) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.0.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.7.0) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (2019.11.28) Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (3.0.4) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (2.8) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (1.25.7) Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from packaging->sphinx<2) (2.4.6) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.3) [rtd-command-info] start-time: 2019-12-30T00:19:30.448220Z, end-time: 2019-12-30T00:19:31.704755Z, duration: 1, exit-code: 0 python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip -r requirements.txt Requirement already satisfied: sphinx>=1.4 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from -r requirements.txt (line 1)) (1.8.5) Requirement already satisfied: ipykernel in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from 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in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from zipp>=0.5->importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat->nbsphinx>=0.4->-r requirements.txt (line 3)) (8.0.2) [rtd-command-info] start-time: 2019-12-30T00:19:32.439600Z, end-time: 2019-12-30T00:19:32.654245Z, 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=4, 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': '348b905e', } 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: 2019-12-30T00:19:32.741476Z, end-time: 2019-12-30T00:19:42.891057Z, duration: 10, 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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