Read the Docs build information
Build id: 239464
Project: icb-scanpy
Version: latest
Commit: 1a5defbe624d437fe9d4ca40f3a50642139b902e
Date: 2019-09-06T15:01:22.355656Z
State: finished
Success: False


[rtd-command-info] start-time: 2019-09-06T15:01:22.920000Z, end-time: 2019-09-06T15:01:22.927810Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/theislab/scanpy.git


[rtd-command-info] start-time: 2019-09-06T15:01:23.027148Z, end-time: 2019-09-06T15:01:23.371065Z, duration: 0, exit-code: 0
git fetch origin --tags --prune --prune-tags --depth 50
From https://github.com/theislab/scanpy
   26fd770..1a5defb  master     -> origin/master

[rtd-command-info] start-time: 2019-09-06T15:01:23.639156Z, end-time: 2019-09-06T15:01:23.649419Z, duration: 0, exit-code: 0
git checkout --force origin/master
Previous HEAD position was 26fd770 Renamed all used utils to _*
HEAD is now at 1a5defb Adopt changes from PR (Fixes #656)

[rtd-command-info] start-time: 2019-09-06T15:01:23.742035Z, end-time: 2019-09-06T15:01:23.764258Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-09-06T15:01:24.872062Z, end-time: 2019-09-06T15:01:30.144222Z, duration: 5, exit-code: 0
python3.6 -mvirtualenv --no-site-packages --no-download 
Using base prefix '/home/docs/.pyenv/versions/3.6.8'
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: 2019-09-06T15:01:30.238482Z, end-time: 2019-09-06T15:01:31.584867Z, 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 (19.2.3)

[rtd-command-info] start-time: 2019-09-06T15:01:31.677947Z, end-time: 2019-09-06T15:01:35.862454Z, duration: 4, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip 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
Requirement already up-to-date: Pygments==2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (2.3.1)
Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (41.0.1)
Requirement already up-to-date: docutils==0.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.14)
Collecting mock==1.0.1
Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (5.4.1)
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==0.8.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.8.1)
Requirement already up-to-date: recommonmark==0.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.5.0)
Collecting sphinx<2
  Using cached https://files.pythonhosted.org/packages/7d/66/a4af242b4348b729b9d46ce5db23943ce9bca7da9bbe2ece60dc27f26420/Sphinx-1.8.5-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<1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (1.0.0)
Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from commonmark==0.8.1) (0.17.1)
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<2) (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<2) (1.1.2)
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<2) (1.9.1)
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<2) (2.7.0)
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<2) (1.12.0)
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<2) (19.1)
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<2) (2.10.1)
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<2) (2.22.0)
Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.2)
Requirement already satisfied, skipping upgrade: attrs in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from packaging->sphinx<2) (19.1.0)
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<2) (2.4.2)
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<2) (1.1.1)
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<2) (2.8)
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<2) (2019.6.16)
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<2) (3.0.4)
Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=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<2) (1.25.3)
Installing collected packages: mock, sphinx
  Found existing installation: mock 3.0.5
ERROR: tables 3.5.2 has requirement mock>=2.0, but you'll have mock 1.0.1 which is incompatible.
ERROR: sphinx-autodoc-typehints 1.7.0 has requirement Sphinx>=2.1, but you'll have sphinx 1.8.5 which is incompatible.
    Uninstalling mock-3.0.5:
      Successfully uninstalled mock-3.0.5
  Found existing installation: Sphinx 2.2.0
    Uninstalling Sphinx-2.2.0:
      Successfully uninstalled Sphinx-2.2.0
Successfully installed mock-1.0.1 sphinx-1.8.5

[rtd-command-info] start-time: 2019-09-06T15:01:35.953715Z, end-time: 2019-09-06T15:01:38.988505Z, duration: 3, 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>=2.0.1 (from -r docs/requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/8e/4c/95a21788db2e1653e931420f561015a0bbc9bd4660c4520467ab9e733eb2/Sphinx-2.2.0-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 6)) (1.7.0)
Requirement already satisfied: scanpydoc>=0.4 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 7)) (0.4)
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 9)) (0.6.22.post1)
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 10)) (3.1.1)
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 11)) (0.25.1)
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Collecting mock>=2.0 (from tables->-r docs/requirements.txt (line 15))
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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>=2.0.1->-r docs/requirements.txt (line 5)) (1.1.1)
Requirement already satisfied: future-fstrings in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from get_version->scanpydoc>=0.4->-r docs/requirements.txt (line 7)) (1.2.0)
Requirement already satisfied: more-itertools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from zipp>=0.5->importlib_metadata->-r docs/requirements.txt (line 23)) (7.2.0)
Installing collected packages: sphinx, mock
  Found existing installation: Sphinx 1.8.5
    Uninstalling Sphinx-1.8.5:
      Successfully uninstalled Sphinx-1.8.5
  Found existing installation: mock 1.0.1
    Uninstalling mock-1.0.1:
      Successfully uninstalled mock-1.0.1
Successfully installed mock-3.0.5 sphinx-2.2.0

[rtd-command-info] start-time: 2019-09-06T15:01:39.710956Z, end-time: 2019-09-06T15:01:40.056278Z, duration: 0, exit-code: 0
cat docs/conf.py
import os
import sys
import warnings
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.insert(0, str(HERE.parent))
import scanpy  # noqa
with warnings.catch_warnings():
    warnings.filterwarnings('ignore', category=FutureWarning)
    import scanpy.api

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

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


nitpicky = True       # Warn about broken links
needs_sphinx = '1.7'  # autosummary bugfix
suppress_warnings = ['ref.citation']

# 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),
    cycler=('https://matplotlib.org/cycler/', 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),
    python=('https://docs.python.org/3', None),
    scipy=('https://docs.scipy.org/doc/scipy/reference/', None),
    scvelo=('https://scvelo.readthedocs.io/en/stable/', None),
    seaborn=('https://seaborn.pydata.org/', None),
    sklearn=('https://scikit-learn.org/stable/', None),
    scanpy_tutorials=('https://scanpy-tutorials.readthedocs.io/en/latest', 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_show_sphinx = False
html_logo = '_static/img/Scanpy_Logo_RGB.png'
gh_url = 'https://github.com/{github_user}/{github_repo}'.format_map(html_context)


def setup(app):
    app.warningiserror = on_rtd
    app.add_stylesheet('css/custom.css')
    app.connect('autodoc-process-docstring', insert_function_images)
    app.connect('build-finished', show_param_warnings)
    app.add_role('pr', autolink(f'{gh_url}/pull/{{}}', 'PR {}'))

# -- 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 insert_function_images(app, what, name, obj, options, lines):
    path = Path(__file__).parent / 'api' / f'{name}.png'
    if what != 'function' or not path.is_file(): return
    lines[0:0] = [f'.. image:: {path.name}', '   :width: 200', '   :align: right', '']


# -- GitHub links --------------------------------------------------------------


def autolink(url_template, title_template='{}'):
    from docutils import nodes
    def role(name, rawtext, text, lineno, inliner, options={}, content=[]):
        url = url_template.format(text)
        title = title_template.format(text)
        node = nodes.reference(rawtext, title, refuri=url, **options)
        return [node], []
    return role


# -- Test for new scanpydoc functionality --------------------------------------


import re
from sphinx.ext.napoleon import NumpyDocstring


def process_return(lines):
    for line in lines:
        m = re.fullmatch(r'(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)', line)
        if m:
            # Once this is in scanpydoc, we can use the fancy hover stuff
            yield f'**{m["param"]}** : :class:`~{m["type"]}`'
        else:
            yield line


def scanpy_parse_returns_section(self, section):
    lines_raw = list(process_return(self._dedent(self._consume_to_next_section())))
    lines = self._format_block(':returns: ', lines_raw)
    if lines and lines[-1]:
        lines.append('')
    return lines


NumpyDocstring._parse_returns_section = scanpy_parse_returns_section


# -- Warn for non-annotated params ---------------------------------------------


_format_docutils_params_orig = NumpyDocstring._format_docutils_params
param_warnings = {}


def scanpy_log_param_types(self, fields, field_role='param', type_role='type'):
    for _name, _type, _desc in fields:
        if not _type: continue
        set_item = r"`'[a-z0-9_.-]+'`"
        if re.fullmatch(rf"{{{set_item}(, {set_item})*}}", _type): continue
        param_warnings.setdefault((self._name, self._obj), []).append((_name, _type))
    return _format_docutils_params_orig(self, fields, field_role, type_role)


def show_param_warnings(app, exception):
    import inspect
    for (fname, fun), params in param_warnings.items():
        _, line = inspect.getsourcelines(fun)
        file_name = inspect.getsourcefile(fun)
        params_str = '\n'.join(f'\t{n}: {t}' for n, t in params)
        warnings.warn_explicit(
            f'\nParameters in `{fname}` not set-like: {{`elm-1`, `s_el.2`}}.\n'
            'Convert to this format or replace with type annotations:\n'
            + params_str,
            UserWarning, file_name, line,
        )


NumpyDocstring._format_docutils_params = scanpy_log_param_types


# -- Debug code ----------------------------------------------------------------


# Just do the following to see the rst of a function:
# rm -f _build/doctrees/api/scanpy.<what_you_want>.doctree; DEBUG=1 make html
import os
if os.environ.get('DEBUG') is not None:
    import sphinx.ext.napoleon
    pd = sphinx.ext.napoleon._process_docstring
    def pd_new(app, what, name, obj, options, lines):
        pd(app, what, name, obj, options, lines)
        print(*lines, sep='\n')
    sphinx.ext.napoleon._process_docstring = pd_new


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

qualname_overrides = {
    "sklearn.neighbors.dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric",
}

nitpick_ignore = [
    # Will probably be documented
    ('py:class', 'scanpy._settings.Verbosity'),
    # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810
    ('py:class', 'seaborn.ClusterGrid'),
    # Bug: https://github.com/agronholm/sphinx-autodoc-typehints/issues/96
    ('py:class', 'typing.Textio'),
]

for mod_name in [
    'pp', 'tl', 'pl',
    'queries', 'logging', 'datasets', 'export_to',
    None,
]:
    if mod_name is None:
        mod = scanpy.api
        mod_name = 'scanpy.api'
    else:
        mod = getattr(scanpy.api, mod_name)
        mod_name = f'scanpy.api.{mod_name}'
    for name, item in vars(mod).items():
        if not callable(item):
            continue
        for kind in ['func', 'obj']:
            nitpick_ignore.append((f'py:{kind}', f'{mod_name}.{name}'))




###########################################################################
#          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': "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/"),
    ("contributors", "/en/contributors/"),
    ],
    'downloads': [ 
    ("html", "//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/stable/',
    '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': '1a5defbe',
}




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: 2019-09-06T15:01:40.641169Z, end-time: 2019-09-06T15:01:58.302122Z, duration: 17, exit-code: 2
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v2.2.0
loading translations [en]... done
making output directory... done
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://matplotlib.org/cycler/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.python.org/3/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv...
loading intersphinx inventory from https://scvelo.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://seaborn.pydata.org/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...
[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, ..., external/scanpy.external.tl.cyclone.rst, external/scanpy.external.tl.palantir.rst, external/scanpy.external.tl.phate.rst, external/scanpy.external.tl.phenograph.rst, external/scanpy.external.tl.sandbag.rst, index.rst, installation.rst, references.rst, release_notes.rst, tutorials.rst
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest" is shallow and may cause errors
  warnings.warn('"%s" is shallow and may cause errors' % (wd.path,))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name: <function annotate_doc_types at 0x7f310e2a2bf8>
  warnings.warn(f"Found an util with public name: {obj}")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name: <function matrix at 0x7f3104aff950>
  warnings.warn(f"Found an util with public name: {obj}")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name: <function timeseries at 0x7f3104aff9d8>
  warnings.warn(f"Found an util with public name: {obj}")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name: <function timeseries_subplot at 0x7f3104affbf8>
  warnings.warn(f"Found an util with public name: {obj}")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name: <function timeseries_as_heatmap at 0x7f3104affc80>
  warnings.warn(f"Found an util with public name: {obj}")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name: <function matrix at 0x7f3104aff950>
  warnings.warn(f"Found an util with public name: {obj}")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name: <function timeseries at 0x7f3104aff9d8>
  warnings.warn(f"Found an util with public name: {obj}")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name: <function timeseries_subplot at 0x7f3104affbf8>
  warnings.warn(f"Found an util with public name: {obj}")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name: <function timeseries_as_heatmap at 0x7f3104affc80>
  warnings.warn(f"Found an util with public name: {obj}")

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/ext/autosummary/generate.py", line 247, in generate_autosummary_docs
    name, obj, parent, mod_name = import_by_name(name)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/ext/autosummary/__init__.py", line 599, in import_by_name
    raise ImportError('no module named %s' % ' or '.join(tried))
ImportError: no module named scanpy._settings.ScanpyConfig.getdoc

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/cmd/build.py", line 275, in build_main
    args.tags, args.verbosity, args.jobs, args.keep_going)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 269, in __init__
    self._init_builder()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 330, in _init_builder
    self.events.emit('builder-inited')
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/events.py", line 103, in emit
    results.append(callback(self.app, *args))
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/ext/autosummary/__init__.py", line 748, in process_generate_options
    app=app, imported_members=imported_members)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/ext/autosummary/generate.py", line 249, in generate_autosummary_docs
    _warn('[autosummary] failed to import %r: %s' % (name, e))
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1642, in warning
    self.log(WARNING, msg, *args, **kwargs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 124, in log
    super().log(level, msg, *args, **kwargs)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1674, in log
    self.logger.log(level, msg, *args, **kwargs)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1374, in log
    self._log(level, msg, args, **kwargs)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1444, in _log
    self.handle(record)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1454, in handle
    self.callHandlers(record)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1516, in callHandlers
    hdlr.handle(record)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 861, in handle
    rv = self.filter(record)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 720, in filter
    result = f.filter(record)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 406, in filter
    raise SphinxWarning(message)
sphinx.errors.SphinxWarning: [autosummary] failed to import 'scanpy._settings.ScanpyConfig.getdoc': no module named scanpy._settings.ScanpyConfig.getdoc

Warning, treated as error:
[autosummary] failed to import 'scanpy._settings.ScanpyConfig.getdoc': no module named scanpy._settings.ScanpyConfig.getdoc