Read the Docs build information
Build id: 866733
Project: icb-scanpy
Version: latest
Commit: 43733482d4d9dc3a04d7e3dc9f62a8a9fbc5394f
Date: 2022-02-28T14:39:58.946648Z
State: finished
Success: False


[rtd-command-info] start-time: 2022-02-28T14:45:56.523121Z, end-time: 2022-02-28T14:45:59.847076Z, duration: 3, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2022-02-28T14:46:00.059930Z, end-time: 2022-02-28T14:46:00.273931Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to '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 switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 43733482 Remove pytables dependency (#2064)

[rtd-command-info] start-time: 2022-02-28T14:46:00.452662Z, end-time: 2022-02-28T14:46:00.524449Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-02-28T14:46:01.777695Z, end-time: 2022-02-28T14:46:06.329321Z, duration: 4, exit-code: 0
python3.8 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.8.6'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python3.8
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2022-02-28T14:46:06.504049Z, end-time: 2022-02-28T14:46:08.254201Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (22.0.3)
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Installing collected packages: setuptools
  Attempting uninstall: setuptools
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    Uninstalling setuptools-60.9.3:
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[rtd-command-info] start-time: 2022-02-28T14:46:08.438026Z, end-time: 2022-02-28T14:46:34.268525Z, duration: 25, exit-code: 0
python -m pip install --upgrade --no-cache-dir 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<2.2
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Building wheels for collected packages: mock, pillow, future
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Installing collected packages: snowballstemmer, pytz, mock, certifi, alabaster, urllib3, sphinxcontrib-serializinghtml, six, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, babel, sphinxcontrib-websupport, requests, packaging, Jinja2, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed Jinja2-3.0.3 MarkupSafe-2.1.0 Pygments-2.11.2 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.12 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.7 pytz-2021.3 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.27.1 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.8

[rtd-command-info] start-time: 2022-02-28T14:46:34.508943Z, end-time: 2022-02-28T14:47:44.258395Z, duration: 69, exit-code: 0
python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[doc]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest
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[rtd-command-info] start-time: 2022-02-28T14:47:45.618977Z, end-time: 2022-02-28T14:47:45.685771Z, duration: 0, exit-code: 0
cat docs/conf.py
import os
import sys
from pathlib import Path
from datetime import datetime

import matplotlib  # noqa

# Don’t use tkinter agg when importing scanpy → … → matplotlib
matplotlib.use('agg')

HERE = Path(__file__).parent
sys.path[:0] = [str(HERE.parent), str(HERE / 'extensions')]
import scanpy  # noqa

on_rtd = os.environ.get('READTHEDOCS') == 'True'

# -- General configuration ------------------------------------------------


nitpicky = True  # Warn about broken links. This is here for a reason: Do not change.
needs_sphinx = '2.0'  # Nicer param docs
suppress_warnings = ['ref.citation']

# General information
project = 'Scanpy'
author = 'Scanpy development team'
copyright = f'{datetime.now():%Y}, the Scanpy development team.'
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',
    'matplotlib.sphinxext.plot_directive',
    'sphinx_autodoc_typehints',  # needs to be after napoleon
    # 'ipython_directive',
    # 'ipython_console_highlighting',
    'scanpydoc',
    *[p.stem for p in (HERE / 'extensions').glob('*.py')],
]

# 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
api_dir = HERE / 'api'  # function_images

scanpy_tutorials_url = 'https://scanpy-tutorials.readthedocs.io/en/latest/'

intersphinx_mapping = dict(
    anndata=('https://anndata.readthedocs.io/en/stable/', None),
    bbknn=('https://bbknn.readthedocs.io/en/latest/', None),
    cycler=('https://matplotlib.org/cycler/', None),
    h5py=('http://docs.h5py.org/en/stable/', None),
    ipython=('https://ipython.readthedocs.io/en/stable/', 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=('https://pandas.pydata.org/pandas-docs/stable/', None),
    pytest=('https://docs.pytest.org/en/latest/', None),
    python=('https://docs.python.org/3', None),
    scipy=('https://docs.scipy.org/doc/scipy/reference/', None),
    seaborn=('https://seaborn.pydata.org/', None),
    sklearn=('https://scikit-learn.org/stable/', None),
    scanpy_tutorials=(scanpy_tutorials_url, None),
)


# -- Options for HTML output ----------------------------------------------


html_theme = 'scanpydoc'
html_theme_options = dict(
    navigation_depth=4,
    logo_only=True,
    docsearch_index='scanpy',
    docsearch_key='fa4304eb95d2134997e3729553a674b2',
)
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_show_sphinx = False
html_logo = '_static/img/Scanpy_Logo_BrightFG.svg'


def setup(app):
    app.warningiserror = on_rtd


# -- 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',
    )
]


# -- Suppress link warnings ----------------------------------------------------

qualname_overrides = {
    "sklearn.neighbors._dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric",
    # If the docs are built with an old version of numpy, this will make it work:
    "numpy.random.RandomState": "numpy.random.mtrand.RandomState",
    "scanpy.plotting._matrixplot.MatrixPlot": "scanpy.pl.MatrixPlot",
    "scanpy.plotting._dotplot.DotPlot": "scanpy.pl.DotPlot",
    "scanpy.plotting._stacked_violin.StackedViolin": "scanpy.pl.StackedViolin",
    "pandas.core.series.Series": "pandas.Series",
}

nitpick_ignore = [
    # Will probably be documented
    ('py:class', 'scanpy._settings.Verbosity'),
    # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810
    ('py:class', 'seaborn.ClusterGrid'),
    # Won’t be documented
    ('py:class', 'scanpy.plotting._utils._AxesSubplot'),
    ('py:class', 'scanpy._utils.Empty'),
    ('py:class', 'numpy.random.mtrand.RandomState'),
    # Will work once scipy 1.8 is released
    ('py:class', 'scipy.sparse.base.spmatrix'),
    ('py:class', 'scipy.sparse.csr.csr_matrix'),
]

# Options for plot examples

plot_include_source = True
plot_formats = [("png", 90)]
plot_html_show_formats = False
plot_html_show_source_link = False
plot_working_directory = HERE.parent  # Project root




###########################################################################
#          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
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

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/"),
    ("stable", "/en/stable/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-scanpy',
    'name': u'scanpy',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://scanpy.readthedocs.io/en/stable/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'theislab',
    'proxied_api_host': '/_',
    '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,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '43733482',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





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")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/866733/'

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: 2022-02-28T14:47:45.882518Z, end-time: 2022-02-28T14:48:21.321483Z, duration: 35, exit-code: 2
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v4.1.2
Matplotlib is building the font cache; this may take a moment.
loading translations [en]... done
making output directory... done
loading intersphinx inventory from https://anndata.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://matplotlib.org/cycler/objects.inv...
loading intersphinx inventory from http://docs.h5py.org/en/stable/objects.inv...
loading intersphinx inventory from https://ipython.readthedocs.io/en/stable/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 https://pandas.pydata.org/pandas-docs/stable/objects.inv...
loading intersphinx inventory from https://docs.pytest.org/en/latest/objects.inv...
intersphinx inventory has moved: https://networkx.github.io/documentation/networkx-1.10/objects.inv -> https://networkx.org/documentation/networkx-1.10/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://seaborn.pydata.org/objects.inv...
intersphinx inventory has moved: http://docs.h5py.org/en/stable/objects.inv -> https://docs.h5py.org/en/stable/objects.inv
loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv...
loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv...
intersphinx inventory has moved: https://docs.scipy.org/doc/scipy/reference/objects.inv -> https://docs.scipy.org/doc/scipy/objects.inv
intersphinx inventory has moved: https://docs.scipy.org/doc/numpy/objects.inv -> https://numpy.org/doc/stable/objects.inv

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/sphinx/cmd/build.py", line 276, in build_main
    app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/sphinx/application.py", line 270, in __init__
    self._init_builder()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/sphinx/application.py", line 328, in _init_builder
    self.events.emit('builder-inited')
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/sphinx/events.py", line 101, in emit
    results.append(listener.handler(self.app, *args))
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/sphinx/ext/intersphinx.py", line 239, in load_mappings
    updated = [f.result() for f in concurrent.futures.as_completed(futures)]
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/sphinx/ext/intersphinx.py", line 239, in <listcomp>
    updated = [f.result() for f in concurrent.futures.as_completed(futures)]
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/concurrent/futures/_base.py", line 432, in result
    return self.__get_result()
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/concurrent/futures/_base.py", line 388, in __get_result
    raise self._exception
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/concurrent/futures/thread.py", line 57, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/sphinx/ext/intersphinx.py", line 224, in fetch_inventory_group
    logger.warning(__("failed to reach any of the inventories "
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/logging/__init__.py", line 1800, in warning
    self.log(WARNING, msg, *args, **kwargs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/sphinx/util/logging.py", line 123, in log
    super().log(level, msg, *args, **kwargs)
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/logging/__init__.py", line 1832, in log
    self.logger.log(level, msg, *args, **kwargs)
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/logging/__init__.py", line 1500, in log
    self._log(level, msg, args, **kwargs)
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/logging/__init__.py", line 1577, in _log
    self.handle(record)
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/logging/__init__.py", line 1587, in handle
    self.callHandlers(record)
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/logging/__init__.py", line 1649, in callHandlers
    hdlr.handle(record)
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/logging/__init__.py", line 946, in handle
    rv = self.filter(record)
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/logging/__init__.py", line 807, in filter
    result = f.filter(record)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/sphinx/util/logging.py", line 423, in filter
    raise exc
sphinx.errors.SphinxWarning: failed to reach any of the inventories with the following issues:
intersphinx inventory 'https://matplotlib.org/cycler/objects.inv' not fetchable due to <class 'requests.exceptions.HTTPError'>: 404 Client Error: Not Found for url: https://matplotlib.org/cycler/objects.inv

Warning, treated as error:
failed to reach any of the inventories with the following issues:
intersphinx inventory 'https://matplotlib.org/cycler/objects.inv' not fetchable due to <class 'requests.exceptions.HTTPError'>: 404 Client Error: Not Found for url: https://matplotlib.org/cycler/objects.inv