Read the Docs build information
Build id: 274181
Project: icb-scanpy
Version: stable
Commit: 16ccdaf7df328aaaeac46b8f6ac7cc7496479ce6
Date: 2020-01-08T10:25:04.820128Z
State: finished
Success: True


[rtd-command-info] start-time: 2020-01-08T10:25:05.315757Z, end-time: 2020-01-08T10:25:07.300060Z, duration: 1, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2020-01-08T10:25:07.696366Z, end-time: 2020-01-08T10:25:07.801536Z, duration: 0, exit-code: 0
git checkout --force fd4bc99b167856b43245da5cbbd60020c43c49aa
Note: checking out 'fd4bc99b167856b43245da5cbbd60020c43c49aa'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

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

  git checkout -b <new-branch-name>

HEAD is now at fd4bc99 fixed link to image; version 1.4.5

[rtd-command-info] start-time: 2020-01-08T10:25:07.878939Z, end-time: 2020-01-08T10:25:07.891937Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-01-08T10:32:09.452835Z, end-time: 2020-01-08T10:32:09.596793Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/theislab/scanpy.git


[rtd-command-info] start-time: 2020-01-08T10:32:09.678934Z, end-time: 2020-01-08T10:32:10.955548Z, duration: 1, exit-code: 0
git fetch origin --force --tags --prune --prune-tags --depth 50


[rtd-command-info] start-time: 2020-01-08T10:32:11.238562Z, end-time: 2020-01-08T10:32:11.252764Z, duration: 0, exit-code: 0
git checkout --force 16ccdaf7df328aaaeac46b8f6ac7cc7496479ce6
HEAD is now at 16ccdaf potential 1.4.5.post1, fix requirements

[rtd-command-info] start-time: 2020-01-08T10:32:11.360904Z, end-time: 2020-01-08T10:32:11.374733Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-01-08T10:32:12.352957Z, end-time: 2020-01-08T10:32:17.316616Z, duration: 4, 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/stable/bin/python3.6
Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/bin/python3.6)
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2020-01-08T10:32:17.401248Z, end-time: 2020-01-08T10:32:18.529177Z, 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/stable/lib/python3.6/site-packages (19.3.1)

[rtd-command-info] start-time: 2020-01-08T10:32:18.613689Z, end-time: 2020-01-08T10:32:22.187313Z, duration: 3, 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/stable/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/stable/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/stable/lib/python3.6/site-packages (0.14)
Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (1.0.1)
Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/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/stable/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/stable/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/stable/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/stable/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/stable/lib/python3.6/site-packages (1.0.1)
Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from commonmark==0.8.1) (0.18.2)
Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx<2) (2.10.3)
Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx<2) (20.0)
Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx<2) (2.8.0)
Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx<2) (2.22.0)
Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx<2) (1.13.0)
Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/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/stable/lib/python3.6/site-packages (from sphinx<2) (2.0.0)
Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx<2) (1.2.0)
Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1)
Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from packaging->sphinx<2) (2.4.6)
Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.3)
Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (3.0.4)
Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (2019.11.28)
Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (2.8)
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/stable/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (1.25.7)
ERROR: sphinx-autodoc-typehints 1.10.3 has requirement Sphinx>=2.1, but you'll have sphinx 1.8.5 which is incompatible.
Installing collected packages: sphinx
  Found existing installation: Sphinx 2.3.1
    Uninstalling Sphinx-2.3.1:
      Successfully uninstalled Sphinx-2.3.1
Successfully installed sphinx-1.8.5

[rtd-command-info] start-time: 2020-01-08T10:32:22.264417Z, end-time: 2020-01-08T10:32:24.746622Z, 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: anndata>=0.6.22.post1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 1)) (0.6.22.post1)
Requirement already satisfied: matplotlib==3.0.* in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 3)) (3.0.3)
Requirement already satisfied: pandas>=0.21 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 4)) (0.25.3)
Requirement already satisfied: scipy>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 5)) (1.4.1)
Requirement already satisfied: seaborn in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 6)) (0.9.0)
Requirement already satisfied: h5py!=2.10.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 7)) (2.9.0)
Requirement already satisfied: tables in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 8)) (3.6.1)
Requirement already satisfied: tqdm in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 9)) (4.41.1)
Requirement already satisfied: importlib_metadata>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 10)) (1.3.0)
Requirement already satisfied: scikit-learn>=0.21.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 11)) (0.22.1)
Requirement already satisfied: statsmodels>=0.10.0rc2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 12)) (0.11.0rc1)
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Requirement already satisfied: networkx in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 14)) (2.4)
Requirement already satisfied: natsort in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 15)) (6.2.0)
Requirement already satisfied: joblib in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 16)) (0.14.1)
Requirement already satisfied: numba>=0.41.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 17)) (0.47.0)
Requirement already satisfied: umap-learn>=0.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 18)) (0.3.10)
Requirement already satisfied: legacy-api-wrap in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 19)) (1.2)
Requirement already satisfied: setuptools_scm in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/../requirements.txt (line 20)) (3.3.3)
Requirement already satisfied: sphinx_rtd_theme>=0.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/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 3))
  Using cached https://files.pythonhosted.org/packages/c4/bb/64c45dd915150952feda858a112a13dc43fb24df2f397d82cdbd4db274b6/Sphinx-2.3.1-py3-none-any.whl
Requirement already satisfied: sphinx-autodoc-typehints in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/requirements.txt (line 4)) (1.10.3)
Requirement already satisfied: scanpydoc>=0.4.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/requirements.txt (line 5)) (0.4.4)
Requirement already satisfied: typing_extensions in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/requirements.txt (line 6)) (3.7.4.1)
Requirement already satisfied: numpy~=1.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from anndata>=0.6.22.post1->-r docs/../requirements.txt (line 1)) (1.18.1)
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Requirement already satisfied: numexpr>=2.6.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from tables->-r docs/../requirements.txt (line 8)) (2.7.1)
Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from importlib_metadata>=0.7->-r docs/../requirements.txt (line 10)) (0.6.0)
Requirement already satisfied: decorator>=4.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from networkx->-r docs/../requirements.txt (line 14)) (4.4.1)
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Installing collected packages: sphinx
  Found existing installation: Sphinx 1.8.5
    Uninstalling Sphinx-1.8.5:
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Successfully installed sphinx-2.3.1

[rtd-command-info] start-time: 2020-01-08T10:32:25.528709Z, end-time: 2020-01-08T10:32:25.744893Z, 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[:0] = [str(HERE.parent), str(HERE / 'extensions')]
import scanpy  # noqa

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

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


nitpicky = False  # 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.__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',
    *[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),
    python=('https://docs.python.org/3', None),
    scipy=('https://docs.scipy.org/doc/scipy/reference/', None),
    scvelo=('https://scvelo.readthedocs.io/', 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 = '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_BrightFG.svg'


def setup(app):
    app.warningiserror = on_rtd
    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',
    )
]


# -- 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'),
    # Won’t be documented
    ('py:class', 'scanpy.readwrite.Empty'),
]




###########################################################################
#          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': "stable",
    'version_slug': "stable",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://media.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ("1.4.4.post1", "/en/1.4.4.post1/"),
    ("1.1", "/en/1.1/"),
    ],
    'downloads': [ 
    ("html", "//readthedocs.com/projects/icb-scanpy/downloads/htmlzip/stable/"),
    ],
    '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',
    'proxied_api_host': 'https://readthedocs.com',
    'github_user': 'theislab',
    'github_repo': 'scanpy',
    'github_version': '16ccdaf7df328aaaeac46b8f6ac7cc7496479ce6',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '16ccdaf7df328aaaeac46b8f6ac7cc7496479ce6',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '16ccdaf7df328aaaeac46b8f6ac7cc7496479ce6',
    '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': '16ccdaf7',
}




if 'html_context' in globals():
    
    html_context.update(context)
    
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

[rtd-command-info] start-time: 2020-01-08T10:32:26.860237Z, end-time: 2020-01-08T10:33:03.647223Z, duration: 36, exit-code: 0
python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v2.3.1
loading translations [en]... done
making output directory... done
loading pickled environment... done
[autosummary] generating autosummary for: _key_contributors.rst, _links.rst, 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, ..., external/scanpy.external.tl.phenograph.rst, external/scanpy.external.tl.sandbag.rst, external/scanpy.external.tl.trimap.rst, index.rst, installation.rst, references.rst, release-latest.rst, release-notes.rst, tutorials.rst, usage-principles.rst
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 163 source files that are out of date
updating environment: 0 added, 0 changed, 0 removed
looking for now-outdated files... none found
preparing documents... done
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writing output... [  1%] api/index
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writing output... [ 11%] api/scanpy._settings.ScanpyConfig
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writing output... [ 17%] api/scanpy._settings.ScanpyConfig.logfile
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writing output... [ 30%] api/scanpy.get.var_df
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writing output... [ 85%] basic_usage
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writing output... [ 98%] release-notes
writing output... [ 99%] tutorials
writing output... [100%] usage-principles

generating indices...  genindex py-modindexdone
writing additional pages...  searchdone
copying images... [ 11%] api/scanpy.pl.dotplot.png
copying images... [ 22%] api/scanpy.pl.heatmap.png
copying images... [ 33%] api/scanpy.pl.matrixplot.png
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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.

The HTML pages are in _build/html.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable" 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/envs/stable/lib/python3.6/site-packages/sphinx_rtd_theme/search.html:20: RemovedInSphinx30Warning: To modify script_files in the theme is deprecated. Please insert a <script> tag directly in your theme instead.
  {{ super() }}

[rtd-command-info] start-time: 2020-01-08T10:33:03.846148Z, end-time: 2020-01-08T10:33:13.345668Z, duration: 9, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
Running Sphinx v2.3.1
loading translations [en]... done
making output directory... done
loading pickled environment... done
[autosummary] generating autosummary for: _key_contributors.rst, _links.rst, 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, ..., external/scanpy.external.tl.phenograph.rst, external/scanpy.external.tl.sandbag.rst, external/scanpy.external.tl.trimap.rst, index.rst, installation.rst, references.rst, release-latest.rst, release-notes.rst, tutorials.rst, usage-principles.rst
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 0 added, 0 changed, 0 removed
looking for now-outdated files... none found
preparing documents... done
assembling single document... tutorials usage-principles 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.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.embedding_density api/scanpy.tl.leiden api/scanpy.tl.louvain api/scanpy.tl.dendrogram api/scanpy.tl.dpt api/scanpy.tl.paga api/scanpy.tl.ingest api/scanpy.tl.rank_genes_groups api/scanpy.tl.filter_rank_genes_groups api/scanpy.tl.marker_gene_overlap api/scanpy.tl.score_genes api/scanpy.tl.score_genes_cell_cycle api/scanpy.tl.sim api/scanpy.plotting api/scanpy.pl.scatter api/scanpy.pl.heatmap api/scanpy.pl.dotplot api/scanpy.pl.tracksplot api/scanpy.pl.violin api/scanpy.pl.stacked_violin api/scanpy.pl.matrixplot api/scanpy.pl.clustermap api/scanpy.pl.ranking api/scanpy.pl.dendrogram 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.embedding api/scanpy.pl.embedding_density 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.rank_genes_groups_tracksplot api/scanpy.pl.sim 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.get.obs_df api/scanpy.get.var_df api/scanpy.get.rank_genes_groups_df api/scanpy.queries.biomart_annotations api/scanpy.queries.gene_coordinates api/scanpy.queries.mitochondrial_genes api/scanpy.queries.enrich 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.rp_forest 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._settings.ScanpyConfig api/scanpy._settings.ScanpyConfig.autosave api/scanpy._settings.ScanpyConfig.autoshow api/scanpy._settings.ScanpyConfig.cache_compression api/scanpy._settings.ScanpyConfig.cachedir api/scanpy._settings.ScanpyConfig.categories_to_ignore api/scanpy._settings.ScanpyConfig.datasetdir api/scanpy._settings.ScanpyConfig.figdir api/scanpy._settings.ScanpyConfig.file_format_data api/scanpy._settings.ScanpyConfig.file_format_figs api/scanpy._settings.ScanpyConfig.logfile api/scanpy._settings.ScanpyConfig.logpath api/scanpy._settings.ScanpyConfig.max_memory api/scanpy._settings.ScanpyConfig.n_jobs api/scanpy._settings.ScanpyConfig.plot_suffix api/scanpy._settings.ScanpyConfig.verbosity api/scanpy._settings.ScanpyConfig.writedir api/scanpy._settings.ScanpyConfig.set_figure_params api/scanpy.logging.print_versions api/scanpy.datasets.blobs api/scanpy.datasets.ebi_expression_atlas api/scanpy.datasets.krumsiek11 api/scanpy.datasets.moignard15 api/scanpy.datasets.pbmc3k api/scanpy.datasets.pbmc3k_processed api/scanpy.datasets.pbmc68k_reduced api/scanpy.datasets.paul15 api/scanpy.datasets.toggleswitch api/scanpy.pp.filter_genes_dispersion api/scanpy.pp.normalize_per_cell external/index external/scanpy.external.pp.bbknn external/scanpy.external.pp.mnn_correct external/scanpy.external.pp.dca external/scanpy.external.pp.magic external/scanpy.external.tl.phate external/scanpy.external.tl.palantir external/scanpy.external.tl.trimap external/scanpy.external.tl.phenograph external/scanpy.external.tl.sandbag external/scanpy.external.tl.cyclone external/scanpy.external.pl.phate external/scanpy.external.pl.trimap external/scanpy.external.exporting.spring_project external/scanpy.external.exporting.cellbrowser ecosystem release-notes references done
writing... done
writing additional files... done
copying images... [ 11%] api/scanpy.pl.heatmap.png
copying images... [ 22%] api/scanpy.pl.dotplot.png
copying images... [ 33%] api/scanpy.pl.violin.png
copying images... [ 44%] api/scanpy.pl.stacked_violin.png
copying images... [ 55%] api/scanpy.pl.matrixplot.png
copying images... [ 66%] api/scanpy.pl.rank_genes_groups_stacked_violin.png
copying images... [ 77%] api/scanpy.pl.rank_genes_groups_heatmap.png
copying images... [ 88%] api/scanpy.pl.rank_genes_groups_dotplot.png
copying images... [100%] api/scanpy.pl.rank_genes_groups_matrixplot.png

copying static files... ... done
copying readthedocs static files... done
copying extra files... done
dumping object inventory... done
build succeeded.

The HTML page is in _build/localmedia.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable" is shallow and may cause errors
  warnings.warn('"%s" is shallow and may cause errors' % (wd.path,))