Read the Docs build information Build id: 328827 Project: icb-scanpy-tutorials Version: latest Commit: af6c377761b6532b4de7d8275ed1df6d1a8cc03c Date: 2020-05-10T16:17:33.745620Z State: finished Success: True [rtd-command-info] start-time: 2020-05-10T16:17:36.043077Z, end-time: 2020-05-10T16:17:39.212706Z, 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: 2020-05-10T16:17:39.550804Z, end-time: 2020-05-10T16:17:39.926877Z, 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 af6c377 renamed spatial tutorials [rtd-command-info] start-time: 2020-05-10T16:17:40.123226Z, end-time: 2020-05-10T16:17:40.321845Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-05-10T16:17:41.690447Z, end-time: 2020-05-10T16:17:45.481577Z, duration: 3, 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: 2020-05-10T16:17:45.635849Z, end-time: 2020-05-10T16:17:46.471066Z, 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) [rtd-command-info] start-time: 2020-05-10T16:17:46.645692Z, end-time: 2020-05-10T16:17:55.995244Z, duration: 9, 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-1.0.3-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting six>=1.5 Downloading six-1.14.0-py2.py3-none-any.whl (10 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.2-py2.py3-none-any.whl (39 kB) Collecting requests>=2.0.0 Downloading requests-2.23.0-py2.py3-none-any.whl (58 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting packaging Downloading packaging-20.3-py2.py3-none-any.whl (37 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.4.5.1-py2.py3-none-any.whl (157 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.9-py2.py3-none-any.whl (126 kB) Collecting idna<3,>=2.5 Downloading idna-2.9-py2.py3-none-any.whl (58 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting MarkupSafe>=0.23 Downloading 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=d44114152a452d5705a8e4d223d5a877fa2cefe8ae568201ebe11a55481f4ad6 Stored in directory: /tmp/pip-ephem-wheel-cache-b7mwstsa/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=9fd4579dea28213b42e0229528a5c266d45d219d05642283c7401f2b693a64ab Stored in directory: /tmp/pip-ephem-wheel-cache-b7mwstsa/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, six, pytz, babel, sphinxcontrib-websupport, chardet, certifi, urllib3, idna, requests, snowballstemmer, pyparsing, packaging, imagesize, MarkupSafe, Jinja2, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 46.1.3 Uninstalling setuptools-46.1.3: Successfully uninstalled setuptools-46.1.3 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.4.5.1 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-20.3 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.3 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-1.2.2 urllib3-1.25.9 [rtd-command-info] start-time: 2020-05-10T16:17:56.162888Z, end-time: 2020-05-10T16:18:19.968085Z, duration: 23, exit-code: 0 python -m pip install 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Downloading Send2Trash-1.5.0-py3-none-any.whl (12 kB) Collecting python-editor>=0.3 Downloading python_editor-1.0.4-py3-none-any.whl (4.9 kB) Collecting Mako Downloading Mako-1.1.2-py2.py3-none-any.whl (75 kB) Collecting zipp>=0.5 Downloading zipp-3.1.0-py3-none-any.whl (4.9 kB) Collecting qtpy Downloading QtPy-1.9.0-py2.py3-none-any.whl (54 kB) Collecting widgetsnbextension~=3.5.0 Downloading widgetsnbextension-3.5.1-py2.py3-none-any.whl (2.2 MB) Building wheels for collected packages: tornado, nbgrader, backcall, pandocfilters, alembic, pyrsistent, prometheus-client 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=427642 sha256=e62f4cd323403b2ed83944301d20a761bf6808a908e190716f2b0f7c2b543d6c Stored in directory: /tmp/pip-ephem-wheel-cache-imr44glh/wheels/37/a7/db/2d592e44029ef817f3ef63ea991db34191cebaef087a96f505 Building wheel for 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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=4a1cd58902e8475ebc992990006fdb874be98b88ac685e7fa4019d35066232cb Stored in directory: /tmp/pip-ephem-wheel-cache-imr44glh/wheels/1d/4a/79/a3ad3f74b3495b4555359375ca33ad7b64e77f8b7a53c8894f Successfully built tornado nbgrader backcall pandocfilters alembic pyrsistent prometheus-client Installing collected packages: tornado, python-dateutil, pyzmq, ipython-genutils, decorator, traitlets, jupyter-core, jupyter-client, pickleshare, parso, jedi, ptyprocess, pexpect, backcall, wcwidth, prompt-toolkit, ipython, ipykernel, zipp, importlib-metadata, pyrsistent, attrs, jsonschema, nbformat, mistune, pandocfilters, webencodings, bleach, defusedxml, testpath, entrypoints, nbconvert, nbsphinx, sqlalchemy, jupyter-console, qtpy, qtconsole, terminado, prometheus-client, Send2Trash, notebook, widgetsnbextension, ipywidgets, jupyter, python-editor, Mako, alembic, fuzzywuzzy, nbgrader, kiwisolver, cycler, numpy, matplotlib, tqdm, nbclean Successfully installed Mako-1.1.2 Send2Trash-1.5.0 alembic-1.4.2 attrs-19.3.0 backcall-0.1.0 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-1.6.0 ipykernel-5.2.1 ipython-7.14.0 ipython-genutils-0.2.0 ipywidgets-7.5.1 jedi-0.17.0 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-6.1.3 jupyter-console-6.1.0 jupyter-core-4.6.3 kiwisolver-1.2.0 matplotlib-3.2.1 mistune-0.8.4 nbclean-0.3.2 nbconvert-5.6.1 nbformat-5.0.6 nbgrader-0.6.1 nbsphinx-0.7.0 notebook-6.0.3 numpy-1.18.4 pandocfilters-1.4.2 parso-0.7.0 pexpect-4.8.0 pickleshare-0.7.5 prometheus-client-0.7.1 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-4.7.3 qtpy-1.9.0 sqlalchemy-1.3.16 terminado-0.8.3 testpath-0.4.4 tornado-6.0.4 tqdm-4.46.0 traitlets-4.3.3 wcwidth-0.1.9 webencodings-0.5.1 widgetsnbextension-3.5.1 zipp-3.1.0 [rtd-command-info] start-time: 2020-05-10T16:18:21.228191Z, end-time: 2020-05-10T16:18:21.456543Z, 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', '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': 'af6c3777', } 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: 2020-05-10T16:18:21.565139Z, end-time: 2020-05-10T16:18:35.021005Z, duration: 13, 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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[rtd-command-info] start-time: 2020-05-10T16:18:35.334682Z, end-time: 2020-05-10T16:18:51.160311Z, duration: 15, 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... building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 11 added, 0 changed, 0 removed reading sources... [ 9%] README reading sources... [ 18%] cite-seq/index reading sources... [ 27%] cite-seq/pbmc5k reading sources... [ 36%] cite-seq/pbmc5k_alex reading sources... [ 45%] index reading sources... [ 54%] integrating-data-using-ingest reading sources... [ 63%] paga-paul15 reading sources... [ 72%] pbmc3k reading sources... [ 81%] spatial/basic-visualization reading sources... [ 90%] spatial/integration-scanoroma reading sources... 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