Read the Docs build information Build id: 283870 Project: icb-scanpy-tutorials Version: latest Commit: 5592e554fb6545a22a22fa2290a946874d86cfa4 Date: 2020-02-03T21:22:42.729637Z State: finished Success: True [rtd-command-info] start-time: 2020-02-03T21:22:45.440520Z, end-time: 2020-02-03T21:22:48.738876Z, duration: 3, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy-tutorials.git . Cloning into '.'... [rtd-command-info] start-time: 2020-02-03T21:22:49.365779Z, end-time: 2020-02-03T21:22:49.855418Z, 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 5592e55 spatial tutorial (#7) [rtd-command-info] start-time: 2020-02-03T21:22:49.914535Z, end-time: 2020-02-03T21:22:50.238546Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-02-03T21:22:51.782564Z, end-time: 2020-02-03T21:22:57.548791Z, duration: 5, exit-code: 0 python3.6 -mvirtualenv --no-site-packages 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. [rtd-command-info] start-time: 2020-02-03T21:22:57.614218Z, end-time: 2020-02-03T21:22:58.704935Z, 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 (20.0.2) [rtd-command-info] start-time: 2020-02-03T21:22:58.764980Z, end-time: 2020-02-03T21:23:12.146197Z, duration: 13, 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 Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading 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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, six, MarkupSafe, Jinja2, pyparsing, packaging, urllib3, chardet, certifi, idna, requests, sphinxcontrib-websupport, imagesize, snowballstemmer, pytz, babel, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 45.1.0 Uninstalling setuptools-45.1.0: Successfully uninstalled setuptools-45.1.0 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-2.8 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-2.22.0 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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/43/9a/e4/7f687f2bb934e9a26a6e1158778ed7c5436b9ea15db48c888a Building wheel for prometheus-client (setup.py): started Building wheel for prometheus-client (setup.py): finished with status 'done' Created wheel for prometheus-client: filename=prometheus_client-0.7.1-py3-none-any.whl size=41404 sha256=e1f380f9e06279af286a835bd7451b086925de5a117671cc37ac499367dd22b1 Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/1d/4a/79/a3ad3f74b3495b4555359375ca33ad7b64e77f8b7a53c8894f Building wheel for Mako (setup.py): started Building wheel for Mako (setup.py): finished with status 'done' Created wheel for Mako: filename=Mako-1.1.1-py3-none-any.whl size=75409 sha256=eb8a32f32552395db9ef02b4d372122387a97b6576f4f2333b68e17a8942db5c Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/43/b1/7c/f14ef20f4683e5087ae684c6447194e09695315f20b9c45575 Successfully built tornado nbgrader backcall pandocfilters sqlalchemy alembic pyrsistent prometheus-client Mako Installing collected packages: parso, jedi, wcwidth, prompt-toolkit, ipython-genutils, decorator, traitlets, ptyprocess, pexpect, backcall, pickleshare, ipython, tornado, pyzmq, python-dateutil, jupyter-core, jupyter-client, ipykernel, attrs, zipp, importlib-metadata, pyrsistent, jsonschema, nbformat, defusedxml, pandocfilters, testpath, mistune, webencodings, bleach, entrypoints, nbconvert, nbsphinx, tqdm, numpy, kiwisolver, cycler, matplotlib, sqlalchemy, prometheus-client, Send2Trash, terminado, notebook, widgetsnbextension, ipywidgets, qtconsole, jupyter-console, jupyter, Mako, python-editor, alembic, fuzzywuzzy, nbgrader, nbclean Successfully installed Mako-1.1.1 Send2Trash-1.5.0 alembic-1.3.3 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-1.5.0 ipykernel-5.1.4 ipython-7.12.0 ipython-genutils-0.2.0 ipywidgets-7.5.1 jedi-0.16.0 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-5.3.4 jupyter-console-6.1.0 jupyter-core-4.6.1 kiwisolver-1.1.0 matplotlib-3.1.3 mistune-0.8.4 nbclean-0.3.2 nbconvert-5.6.1 nbformat-5.0.4 nbgrader-0.6.1 nbsphinx-0.5.1 notebook-6.0.3 numpy-1.18.1 pandocfilters-1.4.2 parso-0.6.1 pexpect-4.8.0 pickleshare-0.7.5 prometheus-client-0.7.1 prompt-toolkit-3.0.3 ptyprocess-0.6.0 pyrsistent-0.15.7 python-dateutil-2.8.1 python-editor-1.0.4 pyzmq-18.1.1 qtconsole-4.6.0 sqlalchemy-1.3.13 terminado-0.8.3 testpath-0.4.4 tornado-6.0.3 tqdm-4.42.1 traitlets-4.3.3 wcwidth-0.1.8 webencodings-0.5.1 widgetsnbextension-3.5.1 zipp-2.1.0 [rtd-command-info] start-time: 2020-02-03T21:23:48.182463Z, end-time: 2020-02-03T21:23:48.669501Z, 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", "//icb-scanpy-tutorials.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ], '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': '5592e554', } 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: 2020-02-03T21:23:48.735950Z, end-time: 2020-02-03T21:24:08.227820Z, duration: 19, 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 7 source files that are out of date updating environment: 7 added, 0 changed, 0 removed reading sources... 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