Read the Docs build information Build id: 397154 Project: icb-scanpy-tutorials Version: latest Commit: 5ba5d5d103c1530022d6f948a8ac490a07d88821 Date: 2020-08-17T11:38:00.493629Z State: finished Success: True [rtd-command-info] start-time: 2020-08-17T11:38:02.007060Z, end-time: 2020-08-17T11:38:08.821037Z, 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: 2020-08-17T11:38:09.487485Z, end-time: 2020-08-17T11:38:09.814156Z, 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 5ba5d5d updated for 1.6.0 [rtd-command-info] start-time: 2020-08-17T11:38:09.915605Z, end-time: 2020-08-17T11:38:09.967769Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-08-17T11:38:12.189202Z, end-time: 2020-08-17T11:38:16.325577Z, 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: 2020-08-17T11:38:16.469815Z, end-time: 2020-08-17T11:38:17.200074Z, 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 (20.2.2) [rtd-command-info] start-time: 2020-08-17T11:38:17.477520Z, end-time: 2020-08-17T11:38:25.625042Z, duration: 8, 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 packaging Downloading packaging-20.4-py2.py3-none-any.whl (37 kB) Collecting snowballstemmer>=1.1 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sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 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=f5b2cd2ec0da4eced64e67fe5cd1aed0548958fba337bebdd315865bddf4901c Stored in directory: /tmp/pip-ephem-wheel-cache-wpjbt5pz/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=491059 sha256=70cdaf794c6a86b005e4be394f84711ef9aa23695274c3a449741c6304f564d2 Stored in directory: /tmp/pip-ephem-wheel-cache-wpjbt5pz/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, imagesize, six, pyparsing, packaging, snowballstemmer, chardet, idna, certifi, urllib3, requests, pytz, babel, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, MarkupSafe, Jinja2, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 49.6.0 Uninstalling setuptools-49.6.0: Successfully uninstalled setuptools-49.6.0 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-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.25.10 [rtd-command-info] start-time: 2020-08-17T11:38:25.766035Z, end-time: 2020-08-17T11:38:47.197040Z, duration: 21, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -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) Collecting ipykernel Downloading ipykernel-5.3.4-py3-none-any.whl (120 kB) Collecting nbsphinx>=0.4 Downloading nbsphinx-0.7.1-py3-none-any.whl (24 kB) Collecting nbclean Downloading nbclean-0.3.2-py2.py3-none-any.whl (21 kB) Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (2.24.0) Requirement already satisfied: imagesize in 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nbgrader-0.6.1.tar.gz (13.3 MB) Collecting numpy Downloading numpy-1.19.1-cp36-cp36m-manylinux2010_x86_64.whl (14.5 MB) Collecting tqdm Downloading tqdm-4.48.2-py2.py3-none-any.whl (68 kB) Requirement already satisfied: 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>=1.4->-r requirements.txt (line 1)) (2020.6.20) Requirement already satisfied: chardet<4,>=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>=1.4->-r requirements.txt (line 1)) (3.0.4) Requirement already satisfied: idna<3,>=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>=1.4->-r requirements.txt (line 1)) (2.10) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in 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attrs>=17.4.0 Downloading attrs-19.3.0-py2.py3-none-any.whl (39 kB) Collecting importlib-metadata; python_version < "3.8" Downloading importlib_metadata-1.7.0-py2.py3-none-any.whl (31 kB) Collecting pyrsistent>=0.14.0 Downloading pyrsistent-0.16.0.tar.gz (108 kB) Collecting ipywidgets Downloading ipywidgets-7.5.1-py2.py3-none-any.whl (121 kB) Collecting qtconsole Downloading qtconsole-4.7.5-py2.py3-none-any.whl (118 kB) Collecting jupyter-console Downloading jupyter_console-6.1.0-py2.py3-none-any.whl (21 kB) Collecting prometheus-client Downloading prometheus_client-0.8.0-py2.py3-none-any.whl (53 kB) Collecting argon2-cffi Downloading argon2_cffi-20.1.0-cp35-abi3-manylinux1_x86_64.whl (97 kB) Collecting Send2Trash Downloading Send2Trash-1.5.0-py3-none-any.whl (12 kB) Collecting terminado>=0.8.3 Downloading terminado-0.8.3-py2.py3-none-any.whl (33 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) Collecting cffi>=1.0.0 Downloading cffi-1.14.2-cp36-cp36m-manylinux1_x86_64.whl (400 kB) Collecting pycparser Downloading pycparser-2.20-py2.py3-none-any.whl (112 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=34222d5aaabe66fa67a170b7a49032cb2670bbb4ceebbc1fe35a77930e9449c2 Stored in directory: /tmp/pip-ephem-wheel-cache-6da7ku_l/wheels/37/a7/db/2d592e44029ef817f3ef63ea991db34191cebaef087a96f505 Building wheel for nbgrader (setup.py): started Building wheel for nbgrader (setup.py): finished with status 'done' Created wheel for nbgrader: filename=nbgrader-0.6.1-py3-none-any.whl size=13507856 sha256=18d0592042be3e5c9c792b7adc417b8af73e715721c160c6f0cb026c8b109482 Stored in directory: /tmp/pip-ephem-wheel-cache-6da7ku_l/wheels/13/3a/de/ac4f96b6bc643b13fb358e0b05f463e8843fef478e2086ebe0 Building wheel for pandocfilters (setup.py): started Building wheel for pandocfilters (setup.py): finished with status 'done' Created wheel for pandocfilters: filename=pandocfilters-1.4.2-py3-none-any.whl size=7855 sha256=9c008f51556c4d7f0eaeba199398faf37d10154998d7016a3bfdbc3bd7cf3994 Stored in directory: /tmp/pip-ephem-wheel-cache-6da7ku_l/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=159540 sha256=760c02759c691ae90a5d2747bfb068ae6c0831b157a69b0312610966d7cb8934 Stored in directory: /tmp/pip-ephem-wheel-cache-6da7ku_l/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=115064 sha256=30b63038304e9fca331d9a7b9998bf54a31694bff250ad3a2c33a92c260fbd0f Stored in directory: /tmp/pip-ephem-wheel-cache-6da7ku_l/wheels/d1/8a/1c/32ab9017418a2c64e4fbaf503c08648bed2f8eb311b869a464 Successfully built tornado nbgrader pandocfilters alembic pyrsistent Installing collected packages: tornado, decorator, ipython-genutils, traitlets, backcall, wcwidth, prompt-toolkit, parso, jedi, ptyprocess, pexpect, pickleshare, ipython, python-dateutil, pyzmq, jupyter-core, jupyter-client, ipykernel, mistune, attrs, zipp, importlib-metadata, pyrsistent, jsonschema, nbformat, entrypoints, pandocfilters, webencodings, bleach, testpath, defusedxml, nbconvert, nbsphinx, cycler, pillow, numpy, kiwisolver, matplotlib, sqlalchemy, prometheus-client, pycparser, cffi, argon2-cffi, Send2Trash, terminado, notebook, widgetsnbextension, ipywidgets, qtpy, qtconsole, jupyter-console, jupyter, Mako, python-editor, alembic, fuzzywuzzy, nbgrader, tqdm, nbclean Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Successfully installed Mako-1.1.3 Send2Trash-1.5.0 alembic-1.4.2 argon2-cffi-20.1.0 attrs-19.3.0 backcall-0.2.0 bleach-3.1.5 cffi-1.14.2 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-5.3.4 ipython-7.16.1 ipython-genutils-0.2.0 ipywidgets-7.5.1 jedi-0.17.2 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-3.3.1 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-6.1.3 numpy-1.19.1 pandocfilters-1.4.2 parso-0.7.1 pexpect-4.8.0 pickleshare-0.7.5 pillow-7.2.0 prometheus-client-0.8.0 prompt-toolkit-3.0.6 ptyprocess-0.6.0 pycparser-2.20 pyrsistent-0.16.0 python-dateutil-2.8.1 python-editor-1.0.4 pyzmq-19.0.2 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-4.48.2 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: 2020-08-17T11:38:48.835292Z, end-time: 2020-08-17T11:38:48.906897Z, 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': '5ba5d5d1', } 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' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2020-08-17T11:38:49.083069Z, end-time: 2020-08-17T11:39:11.894554Z, duration: 22, 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 12 source files that are out of date updating environment: 12 added, 0 changed, 0 removed reading sources... 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