Read the Docs build information
Build id: 484057
Project: icb-scanpy
Version: 1501
Commit: 7006fec955c17bb3083cc0d53c61e2620d1c0b62
Date: 2020-11-19T08:02:05.553329Z
State: finished
Success: False


[rtd-command-info] start-time: 2020-11-19T08:02:06.795171Z, end-time: 2020-11-19T08:02:09.282741Z, duration: 2, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2020-11-19T08:02:09.442331Z, end-time: 2020-11-19T08:02:10.013043Z, duration: 0, exit-code: 0
git fetch origin --force --tags --prune --prune-tags --depth 50 pull/1501/head:external-1501
From https://github.com/theislab/scanpy
 * [new ref]         refs/pull/1501/head -> external-1501

[rtd-command-info] start-time: 2020-11-19T08:02:10.388773Z, end-time: 2020-11-19T08:02:10.555801Z, duration: 0, exit-code: 0
git checkout --force 7006fec955c17bb3083cc0d53c61e2620d1c0b62
Note: checking out '7006fec955c17bb3083cc0d53c61e2620d1c0b62'.

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 7006fec Adjust Combat for control cells

[rtd-command-info] start-time: 2020-11-19T08:02:10.688188Z, end-time: 2020-11-19T08:02:10.740732Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-11-19T08:02:11.836135Z, end-time: 2020-11-19T08:02:31.413596Z, duration: 19, 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/1501/bin/python3.8
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1501/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2020-11-19T08:02:31.584698Z, end-time: 2020-11-19T08:02:32.254082Z, duration: 0, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip
Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1501/lib/python3.8/site-packages (20.2.4)

[rtd-command-info] start-time: 2020-11-19T08:02:32.410572Z, end-time: 2020-11-19T08:03:01.669218Z, duration: 29, exit-code: 0
python -m pip install --upgrade --no-cache-dir 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<2.2
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Collecting MarkupSafe>=0.23
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Building wheels for collected packages: mock, pillow, future
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=8ff0dddebb1687312a0fe599c7f25f8da6c8f185963f4b4c6f2d10cb29523139
  Stored in directory: /tmp/pip-ephem-wheel-cache-ezrq4ah6/wheels/93/2f/a4/2f9af849a57eb554a36d31257560b5e9e207697f285eb06351
  Building wheel for pillow (setup.py): started
  Building wheel for pillow (setup.py): finished with status 'done'
  Created wheel for pillow: filename=Pillow-5.4.1-cp38-cp38-linux_x86_64.whl size=1259829 sha256=15aaff9a78f15a8aba223a6273c5a997011c0a77c331ef949e583b005db4deee
  Stored in directory: /tmp/pip-ephem-wheel-cache-ezrq4ah6/wheels/5f/a8/6b/5b7b3f764d879214eb03570f74d2b086201eb514e6ffa68d6d
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=a46479d707b99dbad7934c78e80c55040e7c98891b160deff127aae92dbd7060
  Stored in directory: /tmp/pip-ephem-wheel-cache-ezrq4ah6/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4
Successfully built mock pillow future
Installing collected packages: setuptools, docutils, mock, pillow, alabaster, future, commonmark, pytz, babel, snowballstemmer, chardet, idna, urllib3, certifi, requests, six, pyparsing, packaging, imagesize, Pygments, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, MarkupSafe, Jinja2, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
  Attempting uninstall: setuptools
    Found existing installation: setuptools 50.3.2
    Uninstalling setuptools-50.3.2:
      Successfully uninstalled setuptools-50.3.2
Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.2 alabaster-0.7.12 babel-2.9.0 certifi-2020.11.8 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.4 readthedocs-sphinx-ext-2.1.1 recommonmark-0.5.0 requests-2.25.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.2

[rtd-command-info] start-time: 2020-11-19T08:03:02.190537Z, end-time: 2020-11-19T08:03:34.506989Z, duration: 32, 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/1501
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
    Preparing wheel metadata: started
    Preparing wheel metadata: finished with status 'done'
Collecting joblib
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Collecting tqdm
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Collecting pandas>=0.21
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Requirement already up-to-date: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1501/lib/python3.8/site-packages (from scanpy==0.1.dev50+g7006fec) (20.4)
Collecting matplotlib>=3.1.2
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Collecting sphinx<3.1,>3; extra == "doc"
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Collecting scanpydoc>=0.5; extra == "doc"
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Requirement already up-to-date: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1501/lib/python3.8/site-packages (from patsy->scanpy==0.1.dev50+g7006fec) (1.15.0)
Requirement already up-to-date: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1501/lib/python3.8/site-packages (from packaging->scanpy==0.1.dev50+g7006fec) (2.4.7)
Collecting pillow>=6.2.0
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Requirement already up-to-date: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1501/lib/python3.8/site-packages (from sphinx<3.1,>3; extra == "doc"->scanpy==0.1.dev50+g7006fec) (1.1.4)
Requirement already up-to-date: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1501/lib/python3.8/site-packages (from sphinx<3.1,>3; extra == "doc"->scanpy==0.1.dev50+g7006fec) (2.0.0)
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Requirement already up-to-date: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1501/lib/python3.8/site-packages (from Jinja2>=2.3->sphinx<3.1,>3; extra == "doc"->scanpy==0.1.dev50+g7006fec) (1.1.1)
Building wheels for collected packages: scanpy, umap-learn, sinfo
  Building wheel for scanpy (PEP 517): started
  Building wheel for scanpy (PEP 517): finished with status 'done'
  Created wheel for scanpy: filename=scanpy-0.1.dev50+g7006fec-py3-none-any.whl size=10146081 sha256=5081903ffd57cc98a9334b5194de5b6519c83acabcb12319a441018515c2bdf0
  Stored in directory: /tmp/pip-ephem-wheel-cache-4tknymj5/wheels/5c/80/d5/86347dd3eb9d9bb4a7916be9fb47a6e62b176b47398dd6faba
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Successfully built scanpy umap-learn sinfo
Installing collected packages: joblib, tqdm, natsort, numpy, python-dateutil, pandas, h5py, scipy, anndata, pillow, kiwisolver, cycler, matplotlib, seaborn, decorator, networkx, setuptools, get-version, legacy-api-wrap, threadpoolctl, scikit-learn, patsy, statsmodels, numexpr, tables, llvmlite, numba, umap-learn, stdlib-list, sinfo, sphinxcontrib-qthelp, docutils, sphinxcontrib-applehelp, sphinxcontrib-devhelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinx, scanpydoc, sphinx-rtd-theme, sphinx-autodoc-typehints, scanpy
  Attempting uninstall: pillow
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  Attempting uninstall: setuptools
    Found existing installation: setuptools 41.0.1
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    Found existing installation: sphinx-rtd-theme 0.4.3
    Uninstalling sphinx-rtd-theme-0.4.3:
      Successfully uninstalled sphinx-rtd-theme-0.4.3
Successfully installed anndata-0.7.5 cycler-0.10.0 decorator-4.4.2 docutils-0.16 get-version-2.1 h5py-3.1.0 joblib-0.17.0 kiwisolver-1.3.1 legacy-api-wrap-1.2 llvmlite-0.34.0 matplotlib-3.3.3 natsort-7.0.1 networkx-2.5 numba-0.51.2 numexpr-2.7.1 numpy-1.19.4 pandas-1.1.4 patsy-0.5.1 pillow-8.0.1 python-dateutil-2.8.1 scanpy-0.1.dev50+g7006fec scanpydoc-0.5.5 scikit-learn-0.23.2 scipy-1.5.4 seaborn-0.11.0 setuptools-50.3.2 sinfo-0.3.1 sphinx-3.0.4 sphinx-autodoc-typehints-1.11.1 sphinx-rtd-theme-0.5.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 statsmodels-0.12.1 stdlib-list-0.7.0 tables-3.6.1 threadpoolctl-2.1.0 tqdm-4.52.0 umap-learn-0.4.6

[rtd-command-info] start-time: 2020-11-19T08:03:36.256646Z, end-time: 2020-11-19T08:03:36.337166Z, 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 = 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.__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 = 'scanpydoc'
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


# -- 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",
}

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'),
]




###########################################################################
#          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://assets.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "1501",
    'version_slug': "1501",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.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': [ 
    ],
    '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': '7006fec955c17bb3083cc0d53c61e2620d1c0b62',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '7006fec955c17bb3083cc0d53c61e2620d1c0b62',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '7006fec955c17bb3083cc0d53c61e2620d1c0b62',
    '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': '7006fec9',
}




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 'external' == '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'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2020-11-19T08:03:36.499560Z, end-time: 2020-11-19T08:05:21.875592Z, duration: 105, exit-code: 2
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v3.0.4
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.python.org/3/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv...
intersphinx inventory has moved: https://docs.scipy.org/doc/numpy/objects.inv -> https://numpy.org/doc/stable/objects.inv
loading intersphinx inventory from https://scvelo.readthedocs.io/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://seaborn.pydata.org/objects.inv...
loading intersphinx inventory from https://scikit-learn.org/stable/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://scanpy-tutorials.readthedocs.io/en/latest/objects.inv...
[autosummary] generating autosummary for: _key_contributors.rst, _links.rst, api/index.rst, api/plotting.rst, api/scanpy.external.rst, api/scanpy.plotting.rst, basic_usage.rst, ecosystem.rst, external/index.rst, index.rst, installation.rst, news.rst, references.rst, release-latest.rst, release-notes.rst, tutorials.rst, usage-principles.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy._settings.ScanpyConfig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.datasets.moignard15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.datasets.paul15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.datasets.pbmc3k.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.datasets.pbmc3k_processed.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.datasets.pbmc68k_reduced.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/external/scanpy.external.tl.cyclone.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/external/scanpy.external.tl.harmony_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/external/scanpy.external.tl.palantir.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/external/scanpy.external.tl.palantir_results.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/external/scanpy.external.tl.phate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/external/scanpy.external.tl.phenograph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/external/scanpy.external.tl.sam.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/external/scanpy.external.tl.sandbag.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/external/scanpy.external.tl.trimap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/external/scanpy.external.tl.wishbone.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.Neighbors.compute_eigen.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.Neighbors.compute_neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.Neighbors.compute_transitions.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.Neighbors.connectivities.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.Neighbors.distances.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.Neighbors.distances_dpt.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.Neighbors.eigen_basis.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.Neighbors.eigen_values.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.Neighbors.getdoc.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.Neighbors.rp_forest.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.pl.StackedViolin.add_dendrogram.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.pl.StackedViolin.add_totals.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.pl.StackedViolin.get_axes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.pl.StackedViolin.getdoc.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.pl.StackedViolin.legend.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.pl.StackedViolin.make_figure.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.pl.StackedViolin.savefig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.pl.StackedViolin.show.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.pl.StackedViolin.style.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/docs/api/scanpy.pl.StackedViolin.swap_axes.rst
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 17 source files that are out of date
updating environment: [new config] 258 added, 0 changed, 0 removed
reading sources... [  0%] _key_contributors
reading sources... [  0%] _links
reading sources... [  1%] api/index
reading sources... [  1%] api/plotting
reading sources... [  1%] api/scanpy.Neighbors
reading sources... [  2%] api/scanpy.Neighbors.compute_eigen
reading sources... [  2%] api/scanpy.Neighbors.compute_neighbors
reading sources... [  3%] api/scanpy.Neighbors.compute_transitions
reading sources... [  3%] api/scanpy.Neighbors.connectivities
reading sources... [  3%] api/scanpy.Neighbors.distances
reading sources... [  4%] api/scanpy.Neighbors.distances_dpt
reading sources... [  4%] api/scanpy.Neighbors.eigen_basis
reading sources... [  5%] api/scanpy.Neighbors.eigen_values
reading sources... [  5%] api/scanpy.Neighbors.getdoc
reading sources... [  5%] api/scanpy.Neighbors.rp_forest
reading sources... [  6%] api/scanpy.Neighbors.to_igraph
reading sources... [  6%] api/scanpy.Neighbors.transitions
reading sources... [  6%] api/scanpy.Neighbors.transitions_sym
reading sources... [  7%] api/scanpy._settings.ScanpyConfig
reading sources... [  7%] api/scanpy._settings.ScanpyConfig.autosave
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reading sources... [  9%] api/scanpy._settings.ScanpyConfig.categories_to_ignore
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reading sources... [ 11%] api/scanpy._settings.ScanpyConfig.logfile
reading sources... [ 11%] api/scanpy._settings.ScanpyConfig.logpath
reading sources... [ 12%] api/scanpy._settings.ScanpyConfig.max_memory
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reading sources... [ 12%] api/scanpy._settings.ScanpyConfig.plot_suffix
reading sources... [ 13%] api/scanpy._settings.ScanpyConfig.set_figure_params
reading sources... [ 13%] api/scanpy._settings.ScanpyConfig.verbosity
reading sources... [ 13%] api/scanpy._settings.ScanpyConfig.writedir
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Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1501/lib/python3.8/site-packages/sphinx/cmd/build.py", line 280, in build_main
    app.build(args.force_all, filenames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1501/lib/python3.8/site-packages/sphinx/application.py", line 348, in build
    self.builder.build_update()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1501/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 297, in build_update
    self.build(to_build,
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1501/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 311, in build
    updated_docnames = set(self.read())
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/contextlib.py", line 120, in __exit__
    next(self.gen)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1501/lib/python3.8/site-packages/sphinx/util/logging.py", line 213, in pending_warnings
    memhandler.flushTo(logger)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1501/lib/python3.8/site-packages/sphinx/util/logging.py", line 178, in flushTo
    logger.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/1501/lib/python3.8/site-packages/sphinx/util/logging.py", line 415, in filter
    raise SphinxWarning(location + ":" + str(message))
sphinx.errors.SphinxWarning: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/scanpy/preprocessing/_combat.py:docstring of scanpy.pp.combat:12:Unexpected indentation.

Warning, treated as error:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1501/scanpy/preprocessing/_combat.py:docstring of scanpy.pp.combat:12:Unexpected indentation.