Read the Docs build information Build id: 332768 Project: icb-scanpy-tutorials Version: latest Commit: a07d115a87b9f33a2cd7cb61431c3116bccc3545 Date: 2020-05-18T21:10:13.901757Z State: finished Success: True [rtd-command-info] start-time: 2020-05-18T21:10:16.229804Z, end-time: 2020-05-18T21:10:23.061264Z, duration: 6, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy-tutorials.git . Cloning into '.'... [rtd-command-info] start-time: 2020-05-18T21:10:23.494727Z, end-time: 2020-05-18T21:10:23.750447Z, 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 a07d115 final polish basic analysis [rtd-command-info] start-time: 2020-05-18T21:10:24.054505Z, end-time: 2020-05-18T21:10:24.254439Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-05-18T21:10:26.825527Z, end-time: 2020-05-18T21:10:30.827350Z, duration: 4, 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: 2020-05-18T21:10:30.957478Z, end-time: 2020-05-18T21:10:31.785537Z, 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: 2020-05-18T21:10:31.995535Z, end-time: 2020-05-18T21:10:41.979707Z, 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 packaging Downloading packaging-20.3-py2.py3-none-any.whl (37 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting requests>=2.0.0 Downloading requests-2.23.0-py2.py3-none-any.whl (58 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.2-py2.py3-none-any.whl (39 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting six>=1.5 Downloading six-1.14.0-py2.py3-none-any.whl (10 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 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 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=cb08bf875bd56bb0743180c6ef02faff94f3b05444c8ad40cf98708dae32df6f Stored in directory: /tmp/pip-ephem-wheel-cache-lx0381pw/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=b822bad7a51af5acb7a70de53844b1f2ac46862292fd9de9176dbcca69ab2032 Stored in directory: /tmp/pip-ephem-wheel-cache-lx0381pw/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, pyparsing, six, packaging, snowballstemmer, imagesize, pytz, babel, chardet, certifi, urllib3, idna, requests, sphinxcontrib-websupport, MarkupSafe, Jinja2, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 46.4.0 Uninstalling setuptools-46.4.0: Successfully uninstalled setuptools-46.4.0 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.4.5.1 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: 2020-05-18T21:10:42.188374Z, end-time: 2020-05-18T21:11:07.215681Z, duration: 25, exit-code: 0 python -m pip install 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Collecting parso>=0.7.0 Downloading parso-0.7.0-py2.py3-none-any.whl (100 kB) Collecting ptyprocess>=0.5 Downloading ptyprocess-0.6.0-py2.py3-none-any.whl (39 kB) Collecting wcwidth Downloading wcwidth-0.1.9-py2.py3-none-any.whl (19 kB) Collecting pyrsistent>=0.14.0 Downloading pyrsistent-0.16.0.tar.gz (108 kB) Collecting importlib-metadata; python_version < "3.8" Downloading importlib_metadata-1.6.0-py2.py3-none-any.whl (30 kB) Collecting attrs>=17.4.0 Downloading attrs-19.3.0-py2.py3-none-any.whl (39 kB) Collecting webencodings Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Collecting jupyter-console Downloading jupyter_console-6.1.0-py2.py3-none-any.whl (21 kB) Collecting qtconsole Downloading qtconsole-4.7.4-py2.py3-none-any.whl (118 kB) Collecting ipywidgets Downloading ipywidgets-7.5.1-py2.py3-none-any.whl (121 kB) Collecting terminado>=0.8.1 Downloading terminado-0.8.3-py2.py3-none-any.whl (33 kB) Collecting Send2Trash Downloading Send2Trash-1.5.0-py3-none-any.whl (12 kB) Collecting prometheus-client Downloading prometheus_client-0.7.1.tar.gz (38 kB) Collecting Mako Downloading Mako-1.1.2-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 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=427643 sha256=21ac4d4e734912d4714a0ca0099d9871a8cc4f853cc2437cea5b67bbeb113ea9 Stored in directory: 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with status 'done' Created wheel for pandocfilters: filename=pandocfilters-1.4.2-py3-none-any.whl size=7856 sha256=2a845c794cf32179afe55a218cd086c42d96dddecc28d049168fb52ee1905fc4 Stored in directory: /tmp/pip-ephem-wheel-cache-xq06v2gl/wheels/46/c4/40/718c6fd14c2129ccaee10e0cf03ef6c4d01d98cad5dbbfda38 Building wheel for alembic (PEP 517): started Building wheel for alembic (PEP 517): finished with status 'done' Created wheel for alembic: filename=alembic-1.4.2-py2.py3-none-any.whl size=159543 sha256=41a4c76386995cc987b050068172454ffbe37b78a6d4c42af39f005fd730255c Stored in directory: /tmp/pip-ephem-wheel-cache-xq06v2gl/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=115059 sha256=b7be24ca31ecc63a440c9a0b3f836e5d61763506292122dcdaeabcba9920a360 Stored in directory: /tmp/pip-ephem-wheel-cache-xq06v2gl/wheels/d1/8a/1c/32ab9017418a2c64e4fbaf503c08648bed2f8eb311b869a464 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=02eb22154aa8843e5fe0ed49f9666c943e48a4cce7abe51d6e9717de5a2c0868 Stored in directory: /tmp/pip-ephem-wheel-cache-xq06v2gl/wheels/1d/4a/79/a3ad3f74b3495b4555359375ca33ad7b64e77f8b7a53c8894f Successfully built tornado nbgrader backcall pandocfilters alembic pyrsistent prometheus-client Installing collected packages: python-dateutil, decorator, ipython-genutils, traitlets, tornado, pyzmq, jupyter-core, jupyter-client, parso, jedi, ptyprocess, pexpect, backcall, wcwidth, prompt-toolkit, pickleshare, ipython, ipykernel, pyrsistent, zipp, importlib-metadata, attrs, jsonschema, nbformat, entrypoints, pandocfilters, webencodings, bleach, testpath, defusedxml, mistune, nbconvert, nbsphinx, tqdm, cycler, numpy, kiwisolver, matplotlib, sqlalchemy, jupyter-console, qtpy, qtconsole, terminado, Send2Trash, prometheus-client, notebook, widgetsnbextension, ipywidgets, jupyter, Mako, python-editor, alembic, fuzzywuzzy, nbgrader, 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-4.7.4 qtpy-1.9.0 sqlalchemy-1.3.17 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: 2020-05-18T21:11:08.428512Z, end-time: 2020-05-18T21:11:08.644540Z, 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': 'a07d115a', } 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: 2020-05-18T21:11:08.896009Z, end-time: 2020-05-18T21:11:26.488734Z, duration: 17, 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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