Read the Docs build information Build id: 195015 Project: icb-scanpy Version: latest Commit: c78de5b9664ab8399319b4d87a19db1265cea884 Date: 2019-03-26T11:11:32.159419Z State: finished Success: True [rtd-command-info] start-time: 2019-03-26T11:11:34.298519Z, end-time: 2019-03-26T11:11:34.310660Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/theislab/scanpy.git [rtd-command-info] start-time: 2019-03-26T11:11:34.370065Z, end-time: 2019-03-26T11:11:34.949168Z, duration: 0, exit-code: 0 git fetch --tags --prune --prune-tags --depth 50 From https://github.com/theislab/scanpy - [deleted] (none) -> origin/stylefix 6306262..c78de5b master -> origin/master [rtd-command-info] start-time: 2019-03-26T11:11:35.438317Z, end-time: 2019-03-26T11:11:35.448314Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 6306262 embedding_density style fixes (#556) HEAD is now at c78de5b only show the logo [rtd-command-info] start-time: 2019-03-26T11:11:35.603076Z, end-time: 2019-03-26T11:11:35.613268Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-03-26T11:11:36.267086Z, end-time: 2019-03-26T11:11:40.249106Z, duration: 3, exit-code: 0 python3.6 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.6.4' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python3.6 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python3.6) Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2019-03-26T11:11:40.311238Z, end-time: 2019-03-26T11:11:41.314544Z, duration: 1, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (19.0.3) [rtd-command-info] start-time: 2019-03-26T11:11:41.371507Z, end-time: 2019-03-26T11:11:49.306776Z, duration: 7, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip Pygments==2.2.0 setuptools<40 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx<1.8 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6 Requirement already up-to-date: Pygments==2.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (2.2.0) Collecting setuptools<40 Using cached https://files.pythonhosted.org/packages/7f/e1/820d941153923aac1d49d7fc37e17b6e73bfbd2904959fffbad77900cf92/setuptools-39.2.0-py2.py3-none-any.whl Requirement already up-to-date: docutils==0.13.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.13.1) Collecting mock==1.0.1 Requirement already up-to-date: pillow==2.6.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (2.6.1) Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.7.12) Requirement already up-to-date: commonmark==0.5.4 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.5.4) Requirement already up-to-date: recommonmark==0.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.4.0) Collecting sphinx<1.8 Using cached https://files.pythonhosted.org/packages/90/f9/a0babe32c78480994e4f1b93315558f5ed756104054a7029c672a8d77b72/Sphinx-1.7.9-py2.py3-none-any.whl Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.4.3) Requirement already up-to-date: readthedocs-sphinx-ext<0.6 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.5.17) Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<1.8) (1.12.0) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<1.8) (2.10) Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<1.8) (1.1.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<1.8) (1.1.0) Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<1.8) (19.0) Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<1.8) (2.21.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<1.8) (2.6.0) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<1.8) (1.2.1) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx<1.8) (1.1.1) Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from packaging->sphinx<1.8) (2.3.1) Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<1.8) (3.0.4) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<1.8) (2019.3.9) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<1.8) (2.8) Requirement already satisfied, skipping upgrade: urllib3<1.25,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<1.8) (1.24.1) Requirement already satisfied, skipping upgrade: pytz>=0a in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from babel!=2.0,>=1.3->sphinx<1.8) (2018.9) tables 3.5.1 has requirement mock>=2.0, but you'll have mock 1.0.1 which is incompatible. scanpydoc 0.3.3 has requirement sphinx>=1.8, but you'll have sphinx 1.7.9 which is incompatible. Installing collected packages: setuptools, mock, sphinx Found existing installation: setuptools 40.6.3 Uninstalling setuptools-40.6.3: Successfully uninstalled setuptools-40.6.3 Found existing installation: mock 2.0.0 Uninstalling mock-2.0.0: Successfully uninstalled mock-2.0.0 Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Successfully installed mock-1.0.1 setuptools-39.2.0 sphinx-1.7.9 [rtd-command-info] start-time: 2019-03-26T11:11:49.364492Z, end-time: 2019-03-26T11:11:52.208595Z, duration: 2, exit-code: 0 python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip -r docs/requirements.txt Requirement already satisfied: sphinx_rtd_theme>=0.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 2)) (0.4.3) Collecting sphinx>=1.8 (from -r docs/requirements.txt (line 4)) Using cached https://files.pythonhosted.org/packages/7d/66/a4af242b4348b729b9d46ce5db23943ce9bca7da9bbe2ece60dc27f26420/Sphinx-1.8.5-py2.py3-none-any.whl Requirement already satisfied: sphinx-autodoc-typehints in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 5)) (1.6.0) Requirement already satisfied: scanpydoc>=0.3.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 6)) (0.3.3) Requirement already satisfied: anndata>=0.6.18 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 8)) (0.6.19) Requirement already satisfied: matplotlib>=2.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 9)) (3.0.3) Requirement already satisfied: pandas>=0.21 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 10)) (0.24.2) Requirement already satisfied: scipy in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 11)) (1.2.1) Requirement already satisfied: seaborn in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 12)) (0.9.0) Requirement already satisfied: h5py in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 13)) (2.9.0) Requirement already satisfied: tables in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 14)) (3.5.1) Requirement already satisfied: scikit-learn>=0.19.1 in 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(line 4)) (39.2.0) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requirements.txt (line 4)) (1.2.1) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requirements.txt (line 4)) (2.6.0) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requirements.txt (line 4)) (2.2.0) Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requirements.txt (line 4)) (0.13.1) Requirement already satisfied: packaging in 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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from matplotlib>=2.2->-r docs/requirements.txt (line 9)) (2.3.1) Requirement already satisfied: pytz>=2011k in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from pandas>=0.21->-r docs/requirements.txt (line 10)) (2018.9) Requirement already satisfied: numexpr>=2.6.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from tables->-r docs/requirements.txt (line 14)) (2.6.9) Collecting mock>=2.0 (from tables->-r docs/requirements.txt (line 14)) Using cached https://files.pythonhosted.org/packages/e6/35/f187bdf23be87092bd0f1200d43d23076cee4d0dec109f195173fd3ebc79/mock-2.0.0-py2.py3-none-any.whl Requirement already satisfied: decorator>=4.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from networkx->-r docs/requirements.txt 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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.8->-r docs/requirements.txt (line 4)) (2.8) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx>=1.8->-r docs/requirements.txt (line 4)) (1.1.1) Requirement already satisfied: pbr>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from mock>=2.0->tables->-r docs/requirements.txt (line 14)) (5.1.3) Installing collected packages: sphinx, mock Found existing installation: Sphinx 1.7.9 Uninstalling Sphinx-1.7.9: Successfully uninstalled Sphinx-1.7.9 Found existing installation: mock 1.0.1 Uninstalling mock-1.0.1: Successfully uninstalled mock-1.0.1 Successfully installed mock-2.0.0 sphinx-1.8.5 [rtd-command-info] start-time: 2019-03-26T11:11:52.701688Z, end-time: 2019-03-26T11:11:52.763011Z, duration: 0, exit-code: 0 cat docs/conf.py import sys import logging from pathlib import Path from datetime import datetime from jinja2.defaults import DEFAULT_FILTERS import matplotlib # noqa # Don’t use tkinter agg when importing scanpy → … → matplotlib matplotlib.use('agg') HERE = Path(__file__).parent sys.path.insert(0, str(HERE.parent)) import scanpy # noqa logger = logging.getLogger(__name__) # -- General configuration ------------------------------------------------ needs_sphinx = '1.7' # autosummary bugfix # General information project = 'Scanpy' author = scanpy.__author__ copyright = f'{datetime.now():%Y}, {author}.' version = scanpy.__version__.replace('.dirty', '') release = version # default settings templates_path = ['_templates'] source_suffix = '.rst' master_doc = 'index' default_role = 'literal' exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] pygments_style = 'sphinx' extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.doctest', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.autosummary', # 'plot_generator', # 'plot_directive', 'sphinx_autodoc_typehints', # needs to be after napoleon # 'ipython_directive', # 'ipython_console_highlighting', 'scanpydoc', ] # Generate the API documentation when building autosummary_generate = True autodoc_member_order = 'bysource' # autodoc_default_flags = ['members'] napoleon_google_docstring = False napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_use_rtype = True # having a separate entry generally helps readability napoleon_use_param = True napoleon_custom_sections = [('Params', 'Parameters')] todo_include_todos = False intersphinx_mapping = dict( anndata=('https://anndata.readthedocs.io/en/latest/', None), bbknn=('https://bbknn.readthedocs.io/en/latest/', None), leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None), louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None), matplotlib=('https://matplotlib.org/', None), networkx=('https://networkx.github.io/documentation/networkx-1.10/', None), numpy=('https://docs.scipy.org/doc/numpy/', None), pandas=('http://pandas.pydata.org/pandas-docs/stable/', None), python=('https://docs.python.org/3', None), scipy=('https://docs.scipy.org/doc/scipy/reference/', None), sklearn=('https://scikit-learn.org/stable/', None), ) # -- 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', # Repo name github_version='master', # Version conf_py_path='/docs/', # Path in the checkout to the docs root ) html_static_path = ['_static'] html_logo = '_static/img/Scanpy_Logo_RGB.png' def setup(app): app.add_stylesheet('css/custom.css') # -- Options for other output formats ------------------------------------------ htmlhelp_basename = f'{project}doc' doc_title = f'{project} Documentation' latex_documents = [ (master_doc, f'{project}.tex', doc_title, author, 'manual'), ] man_pages = [ (master_doc, project, doc_title, [author], 1) ] texinfo_documents = [ (master_doc, project, doc_title, author, project, 'One line description of project.', 'Miscellaneous'), ] # -- Images for plot functions ------------------------------------------------- def api_image(qualname: str) -> str: # I’d like to make this a contextfilter, but the jinja context doesn’t contain the path, # so no chance to not hardcode “api/” here. path = Path(__file__).parent / 'api' / f'{qualname}.png' print(path, path.is_file()) return f'.. image:: {path.name}\n :width: 200\n :align: right' if path.is_file() else '' # html_context doesn’t apply to autosummary templates ☹ # and there’s no way to insert filters into those templates # so we have to modify the default filters DEFAULT_FILTERS['api_image'] = api_image ########################################################################### # 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 mulitple 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': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ], 'downloads': [ ("htmlzip", "//readthedocs.com/projects/icb-scanpy/downloads/htmlzip/latest/"), ], 'subprojects': [ ], 'slug': 'icb-scanpy', 'name': u'scanpy', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://icb-scanpy.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'github_repo': 'scanpy', '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': 'c78de5b9', } 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"] [rtd-command-info] start-time: 2019-03-26T11:11:52.875145Z, end-time: 2019-03-26T11:12:46.027580Z, duration: 53, 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... loading intersphinx inventory from https://anndata.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://leidenalg.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://louvain-igraph.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://matplotlib.org/objects.inv... loading intersphinx inventory from https://networkx.github.io/documentation/networkx-1.10/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/numpy/objects.inv... loading intersphinx inventory from http://pandas.pydata.org/pandas-docs/stable/objects.inv... loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv... loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv... [autosummary] generating autosummary for: api/index.rst, api/plotting.rst, api/scanpy.Neighbors.compute_eigen.rst, api/scanpy.Neighbors.compute_neighbors.rst, api/scanpy.Neighbors.compute_transitions.rst, api/scanpy.Neighbors.connectivities.rst, api/scanpy.Neighbors.distances.rst, api/scanpy.Neighbors.distances_dpt.rst, api/scanpy.Neighbors.eigen_basis.rst, api/scanpy.Neighbors.eigen_values.rst, ..., api/scanpy.tl.sim.rst, api/scanpy.tl.tsne.rst, api/scanpy.tl.umap.rst, basic_usage.rst, examples.rst, index.rst, installation.rst, references.rst, release_notes.rst, tutorials.rst WARNING: [autosummary] failed to import 'scanpy.api.tl.dendrogram': no module named scanpy.api.tl.dendrogram WARNING: [autosummary] failed to import 'scanpy.api.tl.filter_rank_genes_groups': no module named scanpy.api.tl.filter_rank_genes_groups building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 195 source files that are out of date updating environment: 195 added, 0 changed, 0 removed reading sources... 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[100%] tutorials /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:103: WARNING: failed to import tl.dendrogram /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:103: WARNING: toctree references unknown document 'api/tl.dendrogram' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:115: WARNING: failed to import tl.filter_rank_genes_groups /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:115: WARNING: toctree references unknown document 'api/tl.filter_rank_genes_groups' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:212: WARNING: duplicate label settings, other instance in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/index.rst /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/_tools/_palantir.py:docstring of scanpy.external.tl.palantir:103: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:docstring of scanpy.pl.embedding_density:10: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:docstring of scanpy.pl.embedding_density:33: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:docstring of scanpy.pl.embedding_density:40: WARNING: Unexpected section title. Examples -------- /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/__init__.py:docstring of scanpy.plotting:101: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_normalization.py:docstring of scanpy.pp.normalize_quantile:25: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_normalization.py:docstring of scanpy.pp.normalize_total:24: WARNING: Bullet list ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.pl.embedding_density.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:32: WARNING: Citation [Ester96] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:45: WARNING: Citation [Fruchterman91] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:49: WARNING: Citation [Hagberg08] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:53: WARNING: Citation [Hastie09] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:70: WARNING: Citation [Huber15] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:90: WARNING: Citation [Krumsiek10] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:138: WARNING: Citation [Murphy12] is not referenced. done preparing documents... done writing output... 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toctree contains reference to nonexisting document 'api/tl.filter_rank_genes_groups' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.dotplot:32: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.heatmap:26: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.matrixplot:22: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.stacked_violin:25: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header) generating indices... genindex py-modindex writing additional pages... search copying images... [ 11%] api/scanpy.pl.dotplot.png copying images... [ 22%] api/scanpy.pl.heatmap.png copying images... [ 33%] api/scanpy.pl.matrixplot.png copying images... [ 44%] api/scanpy.pl.rank_genes_groups_dotplot.png copying images... [ 55%] api/scanpy.pl.rank_genes_groups_heatmap.png copying images... [ 66%] api/scanpy.pl.rank_genes_groups_matrixplot.png copying images... [ 77%] api/scanpy.pl.rank_genes_groups_stacked_violin.png copying images... [ 88%] api/scanpy.pl.stacked_violin.png copying images... [100%] api/scanpy.pl.violin.png copying static files... done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 178 warnings. The HTML pages are in _build/html. [rtd-command-info] start-time: 2019-03-26T11:12:46.200692Z, end-time: 2019-03-26T11:13:07.816267Z, duration: 21, 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... loading pickled environment... done [autosummary] generating autosummary for: api/index.rst, api/plotting.rst, api/scanpy.Neighbors.compute_eigen.rst, api/scanpy.Neighbors.compute_neighbors.rst, api/scanpy.Neighbors.compute_transitions.rst, api/scanpy.Neighbors.connectivities.rst, api/scanpy.Neighbors.distances.rst, api/scanpy.Neighbors.distances_dpt.rst, api/scanpy.Neighbors.eigen_basis.rst, api/scanpy.Neighbors.eigen_values.rst, ..., api/scanpy.tl.sim.rst, api/scanpy.tl.tsne.rst, api/scanpy.tl.umap.rst, basic_usage.rst, examples.rst, index.rst, installation.rst, references.rst, release_notes.rst, tutorials.rst WARNING: [autosummary] failed to import 'scanpy.api.tl.dendrogram': no module named scanpy.api.tl.dendrogram WARNING: [autosummary] failed to import 'scanpy.api.tl.filter_rank_genes_groups': no module named scanpy.api.tl.filter_rank_genes_groups building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 195 added, 0 changed, 0 removed reading sources... 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[100%] tutorials /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/index.rst:204: WARNING: duplicate label settings, other instance in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.api.rst /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:103: WARNING: failed to import tl.dendrogram /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:103: WARNING: toctree references unknown document 'api/tl.dendrogram' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:115: WARNING: failed to import tl.filter_rank_genes_groups /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:115: WARNING: toctree references unknown document 'api/tl.filter_rank_genes_groups' /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:212: WARNING: duplicate label settings, other instance in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/index.rst /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/_tools/_palantir.py:docstring of scanpy.external.tl.palantir:103: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:docstring of scanpy.pl.embedding_density:10: WARNING: Unexpected section title. Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:docstring of scanpy.pl.embedding_density:33: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:docstring of scanpy.pl.embedding_density:40: WARNING: Unexpected section title. Examples -------- /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/__init__.py:docstring of scanpy.plotting:101: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_normalization.py:docstring of scanpy.pp.normalize_quantile:25: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_normalization.py:docstring of scanpy.pp.normalize_total:24: WARNING: Bullet list ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.pl.embedding_density.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:32: WARNING: Citation [Ester96] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:45: WARNING: Citation [Fruchterman91] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:49: WARNING: Citation [Hagberg08] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:53: WARNING: Citation [Hastie09] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:70: WARNING: Citation [Huber15] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:90: WARNING: Citation [Krumsiek10] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/references.rst:138: WARNING: Citation [Murphy12] is not referenced. done preparing documents... done assembling single document... tutorials basic_usage installation api/index api/scanpy.pp.calculate_qc_metrics api/scanpy.pp.filter_cells api/scanpy.pp.filter_genes api/scanpy.pp.highly_variable_genes api/scanpy.pp.log1p api/scanpy.pp.pca api/scanpy.pp.normalize_total api/scanpy.pp.normalize_quantile api/scanpy.pp.regress_out api/scanpy.pp.scale api/scanpy.pp.subsample api/scanpy.pp.downsample_counts api/scanpy.pp.recipe_zheng17 api/scanpy.pp.recipe_weinreb17 api/scanpy.pp.recipe_seurat api/scanpy.pp.combat api/scanpy.pp.neighbors api/scanpy.tl.pca api/scanpy.tl.tsne api/scanpy.tl.umap api/scanpy.tl.draw_graph api/scanpy.tl.diffmap api/scanpy.tl.leiden api/scanpy.tl.louvain api/scanpy.tl.dpt api/scanpy.tl.paga api/scanpy.tl.rank_genes_groups api/scanpy.tl.score_genes api/scanpy.tl.score_genes_cell_cycle api/scanpy.tl.sim api/plotting api/scanpy.read api/scanpy.read_10x_h5 api/scanpy.read_10x_mtx api/scanpy.read_h5ad api/scanpy.read_csv api/scanpy.read_excel api/scanpy.read_hdf api/scanpy.read_loom api/scanpy.read_mtx api/scanpy.read_text api/scanpy.read_umi_tools api/scanpy.queries.mitochondrial_genes api/scanpy.Neighbors api/scanpy.Neighbors.connectivities api/scanpy.Neighbors.distances api/scanpy.Neighbors.distances_dpt api/scanpy.Neighbors.eigen_basis api/scanpy.Neighbors.eigen_values api/scanpy.Neighbors.getdoc api/scanpy.Neighbors.laplacian api/scanpy.Neighbors.transitions api/scanpy.Neighbors.transitions_sym api/scanpy.Neighbors.compute_eigen api/scanpy.Neighbors.compute_neighbors api/scanpy.Neighbors.compute_transitions api/scanpy.Neighbors.to_igraph api/scanpy.set_figure_params api/scanpy.logging.print_versions api/scanpy.datasets.blobs api/scanpy.datasets.krumsiek11 api/scanpy.datasets.moignard15 api/scanpy.datasets.pbmc3k api/scanpy.datasets.pbmc68k_reduced api/scanpy.datasets.paul15 api/scanpy.datasets.toggleswitch api/scanpy.external api/scanpy.external.pp.bbknn api/scanpy.external.pp.mnn_correct api/scanpy.external.pp.dca api/scanpy.external.pp.magic api/scanpy.external.tl.phate api/scanpy.external.tl.palantir api/scanpy.external.tl.phenograph api/scanpy.external.tl.sandbag api/scanpy.external.tl.cyclone api/scanpy.external.pl.phate api/scanpy.external.exporting.spring_project api/scanpy.external.exporting.cellbrowser api/scanpy.api api/scanpy.api.pp.calculate_qc_metrics api/scanpy.api.pp.filter_cells api/scanpy.api.pp.filter_genes api/scanpy.api.pp.highly_variable_genes api/scanpy.api.pp.filter_genes_dispersion api/scanpy.api.pp.log1p api/scanpy.api.pp.pca api/scanpy.api.pp.normalize_per_cell api/scanpy.api.pp.regress_out api/scanpy.api.pp.scale api/scanpy.api.pp.subsample api/scanpy.api.pp.downsample_counts api/scanpy.api.pp.recipe_zheng17 api/scanpy.api.pp.recipe_weinreb17 api/scanpy.api.pp.recipe_seurat api/scanpy.api.pp.bbknn api/scanpy.api.pp.mnn_correct api/scanpy.api.pp.dca api/scanpy.api.pp.magic api/scanpy.api.pp.neighbors api/scanpy.api.tl.pca api/scanpy.api.tl.tsne api/scanpy.api.tl.umap api/scanpy.api.tl.draw_graph api/scanpy.api.tl.diffmap api/scanpy.api.tl.phate api/scanpy.api.tl.leiden api/scanpy.api.tl.louvain api/scanpy.api.tl.dpt api/scanpy.api.tl.paga api/tl.dendrogram /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.api.rst: WARNING: toctree contains ref to nonexisting file 'api/tl.dendrogram' api/scanpy.api.tl.rank_genes_groups api/tl.filter_rank_genes_groups /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.api.rst: WARNING: toctree contains ref to nonexisting file 'api/tl.filter_rank_genes_groups' api/scanpy.api.tl.score_genes api/scanpy.api.tl.score_genes_cell_cycle api/scanpy.api.tl.sandbag api/scanpy.api.tl.cyclone api/scanpy.api.tl.sim api/scanpy.api.read api/scanpy.api.read_10x_h5 api/scanpy.api.read_10x_mtx api/scanpy.api.read_h5ad api/scanpy.api.read_csv api/scanpy.api.read_excel api/scanpy.api.read_hdf api/scanpy.api.read_loom api/scanpy.api.read_mtx api/scanpy.api.read_text api/scanpy.api.read_umi_tools api/scanpy.api.queries.mitochondrial_genes api/scanpy.api.Neighbors api/scanpy.api.Neighbors.connectivities api/scanpy.api.Neighbors.distances api/scanpy.api.Neighbors.distances_dpt api/scanpy.api.Neighbors.eigen_basis api/scanpy.api.Neighbors.eigen_values api/scanpy.api.Neighbors.getdoc api/scanpy.api.Neighbors.laplacian api/scanpy.api.Neighbors.transitions api/scanpy.api.Neighbors.transitions_sym api/scanpy.api.Neighbors.compute_eigen api/scanpy.api.Neighbors.compute_neighbors api/scanpy.api.Neighbors.compute_transitions api/scanpy.api.Neighbors.to_igraph api/scanpy.api.set_figure_params api/scanpy.api.logging.print_versions api/scanpy.api.datasets.blobs api/scanpy.api.datasets.krumsiek11 api/scanpy.api.datasets.moignard15 api/scanpy.api.datasets.pbmc3k api/scanpy.api.datasets.pbmc68k_reduced api/scanpy.api.datasets.paul15 api/scanpy.api.datasets.toggleswitch api/scanpy.api.export_to.spring_project api/scanpy.plotting api/scanpy.pl.scatter api/scanpy.pl.heatmap api/scanpy.pl.dotplot api/scanpy.pl.violin api/scanpy.pl.stacked_violin api/scanpy.pl.matrixplot api/scanpy.pl.clustermap api/scanpy.pl.ranking api/scanpy.pl.highest_expr_genes api/scanpy.pl.filter_genes_dispersion api/scanpy.pl.highly_variable_genes api/scanpy.pl.pca api/scanpy.pl.pca_loadings api/scanpy.pl.pca_variance_ratio api/scanpy.pl.pca_overview api/scanpy.pl.tsne api/scanpy.pl.umap api/scanpy.pl.diffmap api/scanpy.pl.draw_graph api/scanpy.pl.dpt_groups_pseudotime api/scanpy.pl.dpt_timeseries api/scanpy.pl.paga api/scanpy.pl.paga_path api/scanpy.pl.paga_compare api/scanpy.pl.rank_genes_groups api/scanpy.pl.rank_genes_groups_violin api/scanpy.pl.rank_genes_groups_stacked_violin api/scanpy.pl.rank_genes_groups_heatmap api/scanpy.pl.rank_genes_groups_dotplot api/scanpy.pl.rank_genes_groups_matrixplot api/scanpy.pl.sim api/scanpy.pp.filter_genes_dispersion api/scanpy.pp.normalize_per_cell references /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/index.rst:145: WARNING: undefined label: pandas:/io.rst#io-tools-text-csv-hdf5 (if the link has no caption the label must precede a section header) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/api/__init__.py:docstring of scanpy.api:152: WARNING: undefined label: pandas:/io.rst#io-tools-text-csv-hdf5 (if the link has no caption the label must precede a section header) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.heatmap:26: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.dotplot:32: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.stacked_violin:25: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:docstring of scanpy.pl.matrixplot:22: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header) writing... 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