Read the Docs build information
Build id: 403860
Project: icb-scanpy
Version: 1390
Commit: 4d42a40761c3d9d3f95e14135c641cd89d19e89c
Date: 2020-08-25T03:18:26.385815Z
State: finished
Success: False


[rtd-command-info] start-time: 2020-08-25T03:18:27.949646Z, end-time: 2020-08-25T03:18:30.082044Z, 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: 2020-08-25T03:18:30.318634Z, end-time: 2020-08-25T03:18:30.938213Z, duration: 0, exit-code: 0
git fetch origin --force --tags --prune --prune-tags --depth 50 pull/1390/head:external-1390
From https://github.com/theislab/scanpy
 * [new ref]         refs/pull/1390/head -> external-1390

[rtd-command-info] start-time: 2020-08-25T03:18:31.304258Z, end-time: 2020-08-25T03:18:31.430040Z, duration: 0, exit-code: 0
git checkout --force 4d42a40761c3d9d3f95e14135c641cd89d19e89c
Note: checking out '4d42a40761c3d9d3f95e14135c641cd89d19e89c'.

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 4d42a40 Fix black

[rtd-command-info] start-time: 2020-08-25T03:18:31.898442Z, end-time: 2020-08-25T03:18:31.954587Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-08-25T03:18:33.081393Z, end-time: 2020-08-25T03:18:37.044596Z, duration: 3, exit-code: 0
python3.6 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.6.8'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/bin/python3.6
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2020-08-25T03:18:37.179313Z, end-time: 2020-08-25T03:18:37.899516Z, 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/1390/lib/python3.6/site-packages (20.2.2)

[rtd-command-info] start-time: 2020-08-25T03:18:38.150403Z, end-time: 2020-08-25T03:18:46.816941Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir 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
Collecting Pygments==2.3.1
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Building wheels for collected packages: mock, 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=56c18f2df79cd05699ba26bb32b63757a2e3d01b3c567950d7091b01d83d48c2
  Stored in directory: /tmp/pip-ephem-wheel-cache-og05dad8/wheels/15/fd/39/f238f155700d6d5e6231e82ae3ccf3aa7490a1b17d2073251b
  Building wheel for future (setup.py): started
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  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=5b450113bbbea63dea245e32b116853cf5d7a27e4f86f2f60e1c57f7d2a8dd73
  Stored in directory: /tmp/pip-ephem-wheel-cache-og05dad8/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94
Successfully built mock future
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, imagesize, snowballstemmer, pytz, babel, urllib3, chardet, idna, certifi, requests, pyparsing, six, packaging, MarkupSafe, Jinja2, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
  Attempting uninstall: setuptools
    Found existing installation: setuptools 49.6.0
    Uninstalling setuptools-49.6.0:
      Successfully uninstalled setuptools-49.6.0
Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 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-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 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 urllib3-1.25.10

[rtd-command-info] start-time: 2020-08-25T03:18:46.996825Z, end-time: 2020-08-25T03:19:23.170767Z, duration: 36, 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/1390
  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 scikit-learn>=0.21.2
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Collecting scanpydoc>=0.5; extra == "doc"
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Requirement already up-to-date: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages (from matplotlib>=3.1.2->scanpy==1.6.1.dev19+g4d42a40) (2.4.7)
Collecting kiwisolver>=1.0.1
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Requirement already up-to-date: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages (from patsy->scanpy==1.6.1.dev19+g4d42a40) (1.15.0)
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Requirement already up-to-date: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages (from sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev19+g4d42a40) (2.8.0)
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Requirement already up-to-date: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages (from sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev19+g4d42a40) (2.24.0)
Requirement already up-to-date: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages (from sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev19+g4d42a40) (2.11.2)
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Requirement already up-to-date: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages (from requests>=2.5.0->sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev19+g4d42a40) (2.10)
Requirement already up-to-date: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev19+g4d42a40) (1.1.1)
Building wheels for collected packages: scanpy, sinfo, umap-learn
  Building wheel for scanpy (PEP 517): started
  Building wheel for scanpy (PEP 517): finished with status 'done'
  Created wheel for scanpy: filename=scanpy-1.6.1.dev19+g4d42a40-py3-none-any.whl size=7683404 sha256=955d24c1ef8dd2bf2327ab2262c6f5b688f132a9b499aba87631b7c884f1e0d2
  Stored in directory: /tmp/pip-ephem-wheel-cache-8m0prt65/wheels/18/93/7c/b0f058cbc2cf8d9bec6e28d5cd2b31a5f0c2565437de5ea96d
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  Created wheel for sinfo: filename=sinfo-0.3.1-py3-none-any.whl size=7016 sha256=cbfcd285f337b3614dc584fae43373b8579db2780938007f9cd14ecdf78d280f
  Stored in directory: /tmp/pip-ephem-wheel-cache-8m0prt65/wheels/f3/57/7c/26afb068dd34e984706ae3b99ef4145c76afcdb8070b4f1244
  Building wheel for umap-learn (setup.py): started
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  Created wheel for umap-learn: filename=umap_learn-0.4.6-py3-none-any.whl size=67950 sha256=220709e3f0db27c4c286bb56e1171e38cbd1897c960b53db83ecbe68f58f1741
  Stored in directory: /tmp/pip-ephem-wheel-cache-8m0prt65/wheels/22/ce/3d/75f6600b4d93c851021aceeec51b7b330c0ad4d9692e69be6a
Successfully built scanpy sinfo umap-learn
Installing collected packages: threadpoolctl, joblib, numpy, scipy, scikit-learn, llvmlite, setuptools, numba, stdlib-list, sinfo, zipp, importlib-metadata, python-dateutil, pandas, natsort, h5py, anndata, tqdm, cycler, kiwisolver, pillow, matplotlib, get-version, legacy-api-wrap, seaborn, numexpr, tables, umap-learn, patsy, statsmodels, decorator, networkx, sphinxcontrib-devhelp, Pygments, sphinxcontrib-qthelp, sphinxcontrib-htmlhelp, docutils, sphinxcontrib-jsmath, sphinxcontrib-applehelp, sphinx, sphinx-autodoc-typehints, scanpydoc, typing-extensions, sphinx-rtd-theme, scanpy
  Attempting uninstall: setuptools
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    Uninstalling sphinx-rtd-theme-0.4.3:
      Successfully uninstalled sphinx-rtd-theme-0.4.3
Successfully installed Pygments-2.6.1 anndata-0.7.4 cycler-0.10.0 decorator-4.4.2 docutils-0.16 get-version-2.1 h5py-2.10.0 importlib-metadata-1.7.0 joblib-0.16.0 kiwisolver-1.2.0 legacy-api-wrap-1.2 llvmlite-0.34.0 matplotlib-3.3.1 natsort-7.0.1 networkx-2.5 numba-0.51.0 numexpr-2.7.1 numpy-1.19.1 pandas-1.1.1 patsy-0.5.1 pillow-7.2.0 python-dateutil-2.8.1 scanpy-1.6.1.dev19+g4d42a40 scanpydoc-0.5 scikit-learn-0.23.2 scipy-1.5.2 seaborn-0.10.1 setuptools-49.6.0 sinfo-0.3.1 sphinx-3.0.4 sphinx-autodoc-typehints-1.11.0 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-0.12.0rc0 stdlib-list-0.7.0 tables-3.6.1 threadpoolctl-2.1.0 tqdm-4.48.2 typing-extensions-3.7.4.3 umap-learn-0.4.6 zipp-3.1.0

[rtd-command-info] start-time: 2020-08-25T03:19:24.950012Z, end-time: 2020-08-25T03:19:25.033951Z, 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': "1390",
    'version_slug': "1390",
    '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': '4d42a40761c3d9d3f95e14135c641cd89d19e89c',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '4d42a40761c3d9d3f95e14135c641cd89d19e89c',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '4d42a40761c3d9d3f95e14135c641cd89d19e89c',
    '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': '4d42a407',
}




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: 2020-08-25T03:19:25.460916Z, end-time: 2020-08-25T03:19:27.142293Z, duration: 1, exit-code: 2
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v3.0.4

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages/sphinx/config.py", line 319, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 81, in execfile_
    exec(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/docs/conf.py", line 14, in <module>
    import scanpy  # noqa
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/scanpy/__init__.py", line 11, in <module>
    from . import tools as tl
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/scanpy/tools/__init__.py", line 1, in <module>
    from ..preprocessing import pca
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/scanpy/preprocessing/__init__.py", line 2, in <module>
    from ._simple import filter_cells, filter_genes
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/scanpy/preprocessing/_simple.py", line 22, in <module>
    from ..get import _get_obs_rep, _set_obs_rep
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/scanpy/get.py", line 2, in <module>
    from typing import Optional, Iterable, Tuple, Mapping, Union, Sequence, Literal
ImportError: cannot import name 'Literal'

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/1390/lib/python3.6/site-packages/sphinx/cmd/build.py", line 279, in build_main
    args.tags, args.verbosity, args.jobs, args.keep_going)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages/sphinx/application.py", line 218, in __init__
    self.config = Config.read(self.confdir, confoverrides or {}, self.tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages/sphinx/config.py", line 174, in read
    namespace = eval_config_file(filename, tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages/sphinx/config.py", line 332, in eval_config_file
    raise ConfigError(msg % traceback.format_exc())
sphinx.errors.ConfigError: There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages/sphinx/config.py", line 319, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 81, in execfile_
    exec(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/docs/conf.py", line 14, in <module>
    import scanpy  # noqa
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/scanpy/__init__.py", line 11, in <module>
    from . import tools as tl
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/scanpy/tools/__init__.py", line 1, in <module>
    from ..preprocessing import pca
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/scanpy/preprocessing/__init__.py", line 2, in <module>
    from ._simple import filter_cells, filter_genes
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/scanpy/preprocessing/_simple.py", line 22, in <module>
    from ..get import _get_obs_rep, _set_obs_rep
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/scanpy/get.py", line 2, in <module>
    from typing import Optional, Iterable, Tuple, Mapping, Union, Sequence, Literal
ImportError: cannot import name 'Literal'


Configuration error:
There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages/sphinx/config.py", line 319, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 81, in execfile_
    exec(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/docs/conf.py", line 14, in <module>
    import scanpy  # noqa
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/scanpy/__init__.py", line 11, in <module>
    from . import tools as tl
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/scanpy/tools/__init__.py", line 1, in <module>
    from ..preprocessing import pca
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/scanpy/preprocessing/__init__.py", line 2, in <module>
    from ._simple import filter_cells, filter_genes
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/scanpy/preprocessing/_simple.py", line 22, in <module>
    from ..get import _get_obs_rep, _set_obs_rep
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1390/scanpy/get.py", line 2, in <module>
    from typing import Optional, Iterable, Tuple, Mapping, Union, Sequence, Literal
ImportError: cannot import name 'Literal'