Read the Docs build information
Build id: 403861
Project: icb-scanpy
Version: 1390
Commit: 7932bb14ec13cf5335a7045779095aa854f7ac6c
Date: 2020-08-25T03:19:42.939606Z
State: finished
Success: False


[rtd-command-info] start-time: 2020-08-25T03:19:44.848072Z, end-time: 2020-08-25T03:19:46.893363Z, 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: 2020-08-25T03:19:47.122348Z, end-time: 2020-08-25T03:19:47.705035Z, 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: 2020-08-25T03:19:48.242702Z, end-time: 2020-08-25T03:19:48.390989Z, duration: 0, exit-code: 0
git checkout --force 7932bb14ec13cf5335a7045779095aa854f7ac6c
Note: checking out '7932bb14ec13cf5335a7045779095aa854f7ac6c'.

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 7932bb1 Fix Literal

[rtd-command-info] start-time: 2020-08-25T03:19:48.522870Z, end-time: 2020-08-25T03:19:48.579564Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-08-25T03:19:50.166980Z, end-time: 2020-08-25T03:19:54.216813Z, duration: 4, 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: 2020-08-25T03:19:54.369358Z, end-time: 2020-08-25T03:19:55.117866Z, 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: 2020-08-25T03:19:55.349034Z, end-time: 2020-08-25T03:20:03.968792Z, 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
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Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
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  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=0e6a4c7c6f263bbb03bcb7c585740b12363cde947754828e9338145fd8e8187b
  Stored in directory: /tmp/pip-ephem-wheel-cache-v9ctqyq8/wheels/15/fd/39/f238f155700d6d5e6231e82ae3ccf3aa7490a1b17d2073251b
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  Stored in directory: /tmp/pip-ephem-wheel-cache-v9ctqyq8/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94
Successfully built mock future
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, six, pyparsing, packaging, certifi, idna, urllib3, chardet, requests, snowballstemmer, pytz, babel, imagesize, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, 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: 2020-08-25T03:20:04.152689Z, end-time: 2020-08-25T03:20:37.604070Z, duration: 33, 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 importlib-metadata>=0.7; python_version < "3.8"
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Requirement already up-to-date: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1390/lib/python3.6/site-packages (from scanpy==1.6.1.dev20+g7932bb1) (20.4)
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Collecting kiwisolver>=1.0.1
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Requirement already up-to-date: alabaster<0.8,>=0.7 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.dev20+g7932bb1) (0.7.12)
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.dev20+g7932bb1) (2.24.0)
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Requirement already up-to-date: chardet<4,>=3.0.2 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.dev20+g7932bb1) (3.0.4)
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-1.6.1.dev20+g7932bb1-py3-none-any.whl size=7683437 sha256=499badc490fe4d71687fe5d17aed3ba28c4e7320404d488072c53a9c7a7330f1
  Stored in directory: /tmp/pip-ephem-wheel-cache-_mt98240/wheels/18/93/7c/b0f058cbc2cf8d9bec6e28d5cd2b31a5f0c2565437de5ea96d
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Successfully built scanpy umap-learn sinfo
Installing collected packages: zipp, importlib-metadata, numpy, scipy, patsy, threadpoolctl, joblib, scikit-learn, llvmlite, setuptools, numba, umap-learn, numexpr, tables, get-version, legacy-api-wrap, python-dateutil, pandas, h5py, natsort, anndata, decorator, networkx, stdlib-list, sinfo, cycler, kiwisolver, pillow, matplotlib, statsmodels, tqdm, seaborn, sphinxcontrib-qthelp, sphinxcontrib-htmlhelp, Pygments, sphinxcontrib-devhelp, sphinxcontrib-applehelp, docutils, sphinxcontrib-jsmath, sphinx, sphinx-rtd-theme, typing-extensions, sphinx-autodoc-typehints, scanpydoc, 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.dev20+g7932bb1 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: 2020-08-25T03:20:38.674906Z, end-time: 2020-08-25T03:20:38.753641Z, 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': '7932bb14ec13cf5335a7045779095aa854f7ac6c',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '7932bb14ec13cf5335a7045779095aa854f7ac6c',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '7932bb14ec13cf5335a7045779095aa854f7ac6c',
    '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': '7932bb14',
}




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: 2020-08-25T03:20:38.942827Z, end-time: 2020-08-25T03:20:40.644776Z, 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 11
    import numpy as np
                     ^
IndentationError: expected an indented block

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 322, in eval_config_file
    raise ConfigError(msg % err)
sphinx.errors.ConfigError: There is a syntax error in your configuration file: expected an indented block (get.py, line 11)


Configuration error:
There is a syntax error in your configuration file: expected an indented block (get.py, line 11)