Read the Docs build information Build id: 367371 Project: icb-scanpy-tutorials Version: latest Commit: 52574dd763e1057c372729f05a74dfc7d884d6e9 Date: 2020-07-14T19:16:08.559570Z State: finished Success: True [rtd-command-info] start-time: 2020-07-14T19:16:11.226932Z, end-time: 2020-07-14T19:16:15.906027Z, duration: 4, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy-tutorials.git . Cloning into '.'... [rtd-command-info] start-time: 2020-07-14T19:16:16.368232Z, end-time: 2020-07-14T19:16:16.844515Z, 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 52574dd Updates visualization tutorial (#27) [rtd-command-info] start-time: 2020-07-14T19:16:16.945646Z, end-time: 2020-07-14T19:16:17.143995Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-07-14T19:16:19.188342Z, end-time: 2020-07-14T19:16:30.835950Z, duration: 11, exit-code: 0 python3.6 -mvirtualenv 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: 2020-07-14T19:16:31.058332Z, end-time: 2020-07-14T19:16:31.944304Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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 (20.1.1) [rtd-command-info] start-time: 2020-07-14T19:16:32.260664Z, end-time: 2020-07-14T19:16:42.823653Z, duration: 10, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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 setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-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-cp36-cp36m-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-1.0.4-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting 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MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (27 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-py3-none-any.whl size=23754 sha256=0f61c6780da18dc9021db32ede24e41d07c08810068675fe08298e6738b54016 Stored in directory: /tmp/pip-ephem-wheel-cache-u5kxu__1/wheels/15/fd/39/f238f155700d6d5e6231e82ae3ccf3aa7490a1b17d2073251b 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-py3-none-any.whl size=491058 sha256=2a8ab2a0820eb51dacf42b175fff7089fd529e20eb3405709e00fe768a7c7241 Stored in directory: /tmp/pip-ephem-wheel-cache-u5kxu__1/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, imagesize, six, snowballstemmer, pyparsing, packaging, sphinxcontrib-websupport, pytz, babel, idna, certifi, urllib3, chardet, requests, MarkupSafe, Jinja2, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 49.2.0 Uninstalling setuptools-49.2.0: Successfully uninstalled setuptools-49.2.0 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.2.3 urllib3-1.25.9 [rtd-command-info] start-time: 2020-07-14T19:16:42.933691Z, end-time: 2020-07-14T19:17:07.645502Z, duration: 24, exit-code: 0 python -m pip install 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bleach-3.1.5-py2.py3-none-any.whl (151 kB) Collecting pandocfilters>=1.4.1 Downloading pandocfilters-1.4.2.tar.gz (14 kB) Collecting defusedxml Downloading defusedxml-0.6.0-py2.py3-none-any.whl (23 kB) Collecting sqlalchemy Downloading SQLAlchemy-1.3.18-cp36-cp36m-manylinux2010_x86_64.whl (1.2 MB) Collecting jupyter Downloading jupyter-1.0.0-py2.py3-none-any.whl (2.7 kB) Collecting notebook>=4.2 Downloading notebook-6.0.3-py3-none-any.whl (9.7 MB) Collecting alembic Downloading alembic-1.4.2.tar.gz (1.1 MB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing wheel metadata: started Preparing wheel metadata: finished with status 'done' Collecting fuzzywuzzy Downloading fuzzywuzzy-0.18.0-py2.py3-none-any.whl (18 kB) Collecting cycler>=0.10 Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB) Collecting kiwisolver>=1.0.1 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Collecting terminado>=0.8.1 Downloading terminado-0.8.3-py2.py3-none-any.whl (33 kB) Collecting prometheus-client Downloading prometheus_client-0.8.0-py2.py3-none-any.whl (53 kB) Collecting Mako Downloading Mako-1.1.3-py2.py3-none-any.whl (75 kB) Collecting python-editor>=0.3 Downloading python_editor-1.0.4-py3-none-any.whl (4.9 kB) Collecting zipp>=0.5 Downloading zipp-3.1.0-py3-none-any.whl (4.9 kB) Collecting widgetsnbextension~=3.5.0 Downloading widgetsnbextension-3.5.1-py2.py3-none-any.whl (2.2 MB) Collecting qtpy Downloading QtPy-1.9.0-py2.py3-none-any.whl (54 kB) Building wheels for collected packages: tornado, nbgrader, pandocfilters, alembic, pyrsistent Building wheel for tornado (setup.py): started Building wheel for tornado (setup.py): finished with status 'done' Created wheel for tornado: filename=tornado-6.0.4-cp36-cp36m-linux_x86_64.whl size=427643 sha256=c9e36a7be0a11881be73facf9bae812e76f864fe742dda9d06e942b4b851a902 Stored in directory: 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finished with status 'done' Created wheel for alembic: filename=alembic-1.4.2-py2.py3-none-any.whl size=159543 sha256=dc07b186b0a8e7f1060efa12a8e64678dbd26d1bcbc3389fbb557fa486809762 Stored in directory: /tmp/pip-ephem-wheel-cache-0hda3hvg/wheels/f2/50/61/5cc491b0ca39be60dfb4dce940b389ff91b847d62e0eb2d680 Building wheel for pyrsistent (setup.py): started Building wheel for pyrsistent (setup.py): finished with status 'done' Created wheel for pyrsistent: filename=pyrsistent-0.16.0-cp36-cp36m-linux_x86_64.whl size=115066 sha256=d481783aa90df29d1ba10d146f3525f76aee85c51116223ba763ff8c501b2b01 Stored in directory: /tmp/pip-ephem-wheel-cache-0hda3hvg/wheels/d1/8a/1c/32ab9017418a2c64e4fbaf503c08648bed2f8eb311b869a464 Successfully built tornado nbgrader pandocfilters alembic pyrsistent Installing collected packages: decorator, ipython-genutils, traitlets, jupyter-core, pyzmq, tornado, python-dateutil, jupyter-client, backcall, pickleshare, parso, jedi, wcwidth, prompt-toolkit, ptyprocess, pexpect, ipython, ipykernel, pyrsistent, zipp, importlib-metadata, attrs, jsonschema, nbformat, mistune, testpath, entrypoints, webencodings, bleach, pandocfilters, defusedxml, nbconvert, nbsphinx, tqdm, sqlalchemy, Send2Trash, terminado, prometheus-client, notebook, widgetsnbextension, ipywidgets, qtpy, qtconsole, jupyter-console, jupyter, Mako, python-editor, alembic, fuzzywuzzy, nbgrader, numpy, cycler, kiwisolver, matplotlib, nbclean Successfully installed Mako-1.1.3 Send2Trash-1.5.0 alembic-1.4.2 attrs-19.3.0 backcall-0.2.0 bleach-3.1.5 cycler-0.10.0 decorator-4.4.2 defusedxml-0.6.0 entrypoints-0.3 fuzzywuzzy-0.18.0 importlib-metadata-1.7.0 ipykernel-5.3.2 ipython-7.16.1 ipython-genutils-0.2.0 ipywidgets-7.5.1 jedi-0.17.1 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-6.1.6 jupyter-console-6.1.0 jupyter-core-4.6.3 kiwisolver-1.2.0 matplotlib-3.2.2 mistune-0.8.4 nbclean-0.3.2 nbconvert-5.6.1 nbformat-5.0.7 nbgrader-0.6.1 nbsphinx-0.7.1 notebook-6.0.3 numpy-1.19.0 pandocfilters-1.4.2 parso-0.7.0 pexpect-4.8.0 pickleshare-0.7.5 prometheus-client-0.8.0 prompt-toolkit-3.0.5 ptyprocess-0.6.0 pyrsistent-0.16.0 python-dateutil-2.8.1 python-editor-1.0.4 pyzmq-19.0.1 qtconsole-4.7.5 qtpy-1.9.0 sqlalchemy-1.3.18 terminado-0.8.3 testpath-0.4.4 tornado-6.0.4 tqdm-4.47.0 traitlets-4.3.3 wcwidth-0.2.5 webencodings-0.5.1 widgetsnbextension-3.5.1 zipp-3.1.0 [rtd-command-info] start-time: 2020-07-14T19:17:09.232262Z, end-time: 2020-07-14T19:17:09.460552Z, 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://assets.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://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("multiomics", "/en/multiomics/"), ], 'downloads': [ ("html", "//scanpy-tutorials.readthedocs.io/_/downloads/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'icb-scanpy-tutorials', 'name': u'scanpy-tutorials', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://scanpy-tutorials.readthedocs.io/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'proxied_api_host': '/_', '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, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '52574dd7', } 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: 2020-07-14T19:17:09.562050Z, end-time: 2020-07-14T19:17:33.097999Z, duration: 23, 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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