Read the Docs build information Build id: 303028 Project: icb-scanpy-tutorials Version: multiomics Commit: e1460952c74a4375ada2f0af1f3002b7b6a8511a Date: 2020-03-17T10:17:10.792695Z State: finished Success: True [rtd-command-info] start-time: 2020-03-17T10:17:13.570412Z, end-time: 2020-03-17T10:17:16.883927Z, 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: 2020-03-17T10:17:17.653355Z, end-time: 2020-03-17T10:17:18.321578Z, duration: 0, exit-code: 0 git checkout --force origin/multiomics Note: checking out 'origin/multiomics'. 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 e146095 initial multiomics [rtd-command-info] start-time: 2020-03-17T10:17:18.510764Z, end-time: 2020-03-17T10:17:18.830596Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-03-17T10:17:20.310862Z, end-time: 2020-03-17T10:17:25.577779Z, duration: 5, 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/multiomics/bin/python3.6 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/multiomics/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-03-17T10:17:25.752887Z, end-time: 2020-03-17T10:17:26.855054Z, duration: 1, 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/multiomics/lib/python3.6/site-packages (20.0.2) [rtd-command-info] start-time: 2020-03-17T10:17:27.012035Z, end-time: 2020-03-17T10:17:39.654546Z, duration: 12, 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-1.0.1-py2.py3-none-any.whl (14 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 sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.0-py2.py3-none-any.whl (39 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.1-py2.py3-none-any.whl (126 kB) 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pyparsing-2.4.6-py2.py3-none-any.whl (67 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=92c7b7dc2463102eda523895c3fb07603a668ca95133140499a64334de81e614 Stored in directory: /tmp/pip-ephem-wheel-cache-qx9obbwe/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=d11b1864194ffd0d56744b0aae7b9fcbec1eb7b4b854e1bc2101627f50247e78 Stored in directory: /tmp/pip-ephem-wheel-cache-qx9obbwe/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, imagesize, sphinxcontrib-websupport, MarkupSafe, Jinja2, certifi, urllib3, chardet, idna, requests, pytz, babel, snowballstemmer, six, pyparsing, packaging, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 46.0.0 Uninstalling setuptools-46.0.0: Successfully uninstalled setuptools-46.0.0 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-2.9 imagesize-1.2.0 mock-1.0.1 packaging-20.3 pillow-5.4.1 pyparsing-2.4.6 pytz-2019.3 readthedocs-sphinx-ext-1.0.1 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-1.2.0 urllib3-1.25.8 [rtd-command-info] start-time: 2020-03-17T10:17:39.821540Z, end-time: 2020-03-17T10:18:16.819912Z, duration: 36, exit-code: 0 python -m pip install 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terminado>=0.8.1 Downloading terminado-0.8.3-py2.py3-none-any.whl (33 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, sqlalchemy, 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=427645 sha256=ea6aeb3ddd10e7fafcdc2396bf33da047366b02af9a3371afc71320956eafdf8 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=0e9016ce2f34ec4003dbdca4493235f465b3a0b55597dafb80491f86bb7b5f7a Stored in directory: /tmp/pip-ephem-wheel-cache-_o0ufrv4/wheels/46/c4/40/718c6fd14c2129ccaee10e0cf03ef6c4d01d98cad5dbbfda38 Building wheel for sqlalchemy (PEP 517): started Building wheel for sqlalchemy (PEP 517): finished with status 'done' Created wheel for sqlalchemy: filename=SQLAlchemy-1.3.15-cp36-cp36m-linux_x86_64.whl size=1230221 sha256=23f4fdf36e5f4aeb786f6a6da61531fb41510bd3bf82a7a33d78bfc637587caf Stored in directory: /tmp/pip-ephem-wheel-cache-_o0ufrv4/wheels/4a/1b/3a/c73044d7be48baeb47cbee343334f7803726ca1e9ba7b29095 Building wheel for alembic (setup.py): started Building wheel for alembic (setup.py): finished with status 'done' Created wheel for alembic: filename=alembic-1.4.1-py2.py3-none-any.whl size=158154 sha256=79aa5f0e74dabfd53bda2c866bcd7092b561ade2706f14010b76ec379475a797 Stored in 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pandocfilters sqlalchemy alembic pyrsistent prometheus-client Installing collected packages: decorator, ipython-genutils, traitlets, pickleshare, backcall, ptyprocess, pexpect, parso, jedi, wcwidth, prompt-toolkit, ipython, python-dateutil, jupyter-core, pyzmq, tornado, jupyter-client, ipykernel, zipp, importlib-metadata, attrs, pyrsistent, jsonschema, nbformat, pandocfilters, entrypoints, testpath, defusedxml, webencodings, bleach, mistune, nbconvert, nbsphinx, cycler, kiwisolver, numpy, matplotlib, sqlalchemy, Send2Trash, prometheus-client, terminado, notebook, qtpy, qtconsole, jupyter-console, widgetsnbextension, ipywidgets, jupyter, Mako, python-editor, alembic, fuzzywuzzy, nbgrader, tqdm, nbclean Successfully installed Mako-1.1.2 Send2Trash-1.5.0 alembic-1.4.1 attrs-19.3.0 backcall-0.1.0 bleach-3.1.1 cycler-0.10.0 decorator-4.4.2 defusedxml-0.6.0 entrypoints-0.3 fuzzywuzzy-0.18.0 importlib-metadata-1.5.0 ipykernel-5.1.4 ipython-7.13.0 ipython-genutils-0.2.0 ipywidgets-7.5.1 jedi-0.16.0 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-6.0.0 jupyter-console-6.1.0 jupyter-core-4.6.3 kiwisolver-1.1.0 matplotlib-3.2.0 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-0.6.2 pexpect-4.8.0 pickleshare-0.7.5 prometheus-client-0.7.1 prompt-toolkit-3.0.4 ptyprocess-0.6.0 pyrsistent-0.15.7 python-dateutil-2.8.1 python-editor-1.0.4 pyzmq-19.0.0 qtconsole-4.7.1 qtpy-1.9.0 sqlalchemy-1.3.15 terminado-0.8.3 testpath-0.4.4 tornado-6.0.4 tqdm-4.43.0 traitlets-4.3.3 wcwidth-0.1.8 webencodings-0.5.1 widgetsnbextension-3.5.1 zipp-3.1.0 [rtd-command-info] start-time: 2020-03-17T10:18:18.001187Z, end-time: 2020-03-17T10:18:18.344983Z, 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': "multiomics", 'version_slug': "multiomics", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("multiomics", "/en/multiomics/"), ], 'downloads': [ ], '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': '/_', 'github_user': 'theislab', 'github_repo': 'scanpy-tutorials', 'github_version': 'multiomics', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'multiomics', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'multiomics', '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': 'e1460952', } 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: 2020-03-17T10:18:18.483903Z, end-time: 2020-03-17T10:18:42.509755Z, duration: 24, exit-code: 0 python sphinx-build -T -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 8 source files that are out of date updating environment: 8 added, 0 changed, 0 removed reading sources... 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