Read the Docs build information
Build id: 239460
Project: icb-scanpy
Version: latest
Commit: 26fd7707d4b2881cb07ce507733cc458977238c1
Date: 2019-09-06T14:54:47.553607Z
State: finished
Success: False
[rtd-command-info] start-time: 2019-09-06T14:54:48.149049Z, end-time: 2019-09-06T14:54:48.174612Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/theislab/scanpy.git
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git fetch origin --tags --prune --prune-tags --depth 50
From https://github.com/theislab/scanpy
525c96a..26fd770 master -> origin/master
[rtd-command-info] start-time: 2019-09-06T14:54:49.276831Z, end-time: 2019-09-06T14:54:49.330578Z, duration: 0, exit-code: 0
git checkout --force origin/master
Previous HEAD position was 525c96a Add obs_key support to PAGA plots and fix the cax parameter.
HEAD is now at 26fd770 Renamed all used utils to _*
[rtd-command-info] start-time: 2019-09-06T14:54:49.423168Z, end-time: 2019-09-06T14:54:49.447977Z, duration: 0, exit-code: 0
git clean -d -f -f
[rtd-command-info] start-time: 2019-09-06T14:54:50.738915Z, end-time: 2019-09-06T14:54:56.269255Z, duration: 5, exit-code: 0
python3.6 -mvirtualenv --no-site-packages --no-download
Using base prefix '/home/docs/.pyenv/versions/3.6.8'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python3.6
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.
[rtd-command-info] start-time: 2019-09-06T14:54:56.368293Z, end-time: 2019-09-06T14:54:59.246972Z, duration: 2, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip pip
Collecting pip
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Installing collected packages: pip
Found existing installation: pip 19.1.1
Uninstalling pip-19.1.1:
Successfully uninstalled pip-19.1.1
Successfully installed pip-19.2.3
[rtd-command-info] start-time: 2019-09-06T14:54:59.335186Z, end-time: 2019-09-06T14:55:11.098730Z, duration: 11, exit-code: 0
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Installing collected packages: sphinxcontrib-applehelp, sphinxcontrib-qthelp, sphinxcontrib-serializinghtml, sphinxcontrib-devhelp, sphinxcontrib-htmlhelp, sphinxcontrib-jsmath, sphinx, sphinx-autodoc-typehints, future-fstrings, get-version, scanpydoc, numpy, h5py, natsort, python-dateutil, pandas, scipy, anndata, cycler, kiwisolver, matplotlib, seaborn, numexpr, mock, tables, joblib, scikit-learn, decorator, networkx, llvmlite, numba, tqdm, more-itertools, zipp, importlib-metadata, setuptools-scm, umap-learn
Found existing installation: Sphinx 1.8.5
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[rtd-command-info] start-time: 2019-09-06T14:55:48.316613Z, end-time: 2019-09-06T14:55:48.645159Z, duration: 0, exit-code: 0
cat docs/conf.py
import os
import sys
import warnings
from pathlib import Path
from datetime import datetime
import matplotlib # noqa
# Don’t use tkinter agg when importing scanpy → … → matplotlib
matplotlib.use('agg')
HERE = Path(__file__).parent
sys.path.insert(0, str(HERE.parent))
import scanpy # noqa
with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=FutureWarning)
import scanpy.api
on_rtd = os.environ.get('READTHEDOCS') == 'True'
# -- General configuration ------------------------------------------------
nitpicky = True # Warn about broken links
needs_sphinx = '1.7' # autosummary bugfix
suppress_warnings = ['ref.citation']
# General information
project = 'Scanpy'
author = scanpy.__author__
copyright = f'{datetime.now():%Y}, {author}.'
version = scanpy.__version__.replace('.dirty', '')
release = version
# default settings
templates_path = ['_templates']
source_suffix = '.rst'
master_doc = 'index'
default_role = 'literal'
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
pygments_style = 'sphinx'
extensions = [
'sphinx.ext.autodoc',
'sphinx.ext.intersphinx',
'sphinx.ext.doctest',
'sphinx.ext.coverage',
'sphinx.ext.mathjax',
'sphinx.ext.napoleon',
'sphinx.ext.autosummary',
# 'plot_generator',
# 'plot_directive',
'sphinx_autodoc_typehints', # needs to be after napoleon
# 'ipython_directive',
# 'ipython_console_highlighting',
'scanpydoc',
]
# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = 'bysource'
# autodoc_default_flags = ['members']
napoleon_google_docstring = False
napoleon_numpy_docstring = True
napoleon_include_init_with_doc = False
napoleon_use_rtype = True # having a separate entry generally helps readability
napoleon_use_param = True
napoleon_custom_sections = [('Params', 'Parameters')]
todo_include_todos = False
intersphinx_mapping = dict(
anndata=('https://anndata.readthedocs.io/en/latest/', None),
bbknn=('https://bbknn.readthedocs.io/en/latest/', None),
cycler=('https://matplotlib.org/cycler/', None),
ipython=('https://ipython.readthedocs.io/en/stable/', None),
leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None),
louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None),
matplotlib=('https://matplotlib.org/', None),
networkx=('https://networkx.github.io/documentation/networkx-1.10/', None),
numpy=('https://docs.scipy.org/doc/numpy/', None),
pandas=('https://pandas.pydata.org/pandas-docs/stable/', None),
python=('https://docs.python.org/3', None),
scipy=('https://docs.scipy.org/doc/scipy/reference/', None),
scvelo=('https://scvelo.readthedocs.io/en/stable/', None),
seaborn=('https://seaborn.pydata.org/', None),
sklearn=('https://scikit-learn.org/stable/', None),
scanpy_tutorials=('https://scanpy-tutorials.readthedocs.io/en/latest', None),
)
# -- Options for HTML output ----------------------------------------------
html_theme = 'sphinx_rtd_theme'
html_theme_options = dict(
navigation_depth=4,
logo_only=True, # Only show the logo
)
html_context = dict(
display_github=True, # Integrate GitHub
github_user='theislab', # Username
github_repo='scanpy', # Repo name
github_version='master', # Version
conf_py_path='/docs/', # Path in the checkout to the docs root
)
html_static_path = ['_static']
html_show_sphinx = False
html_logo = '_static/img/Scanpy_Logo_RGB.png'
gh_url = 'https://github.com/{github_user}/{github_repo}'.format_map(html_context)
def setup(app):
app.warningiserror = on_rtd
app.add_stylesheet('css/custom.css')
app.connect('autodoc-process-docstring', insert_function_images)
app.connect('build-finished', show_param_warnings)
app.add_role('pr', autolink(f'{gh_url}/pull/{{}}', 'PR {}'))
# -- Options for other output formats ------------------------------------------
htmlhelp_basename = f'{project}doc'
doc_title = f'{project} Documentation'
latex_documents = [
(master_doc, f'{project}.tex', doc_title, author, 'manual'),
]
man_pages = [
(master_doc, project, doc_title, [author], 1)
]
texinfo_documents = [
(master_doc, project, doc_title, author, project, 'One line description of project.', 'Miscellaneous'),
]
# -- Images for plot functions -------------------------------------------------
def insert_function_images(app, what, name, obj, options, lines):
path = Path(__file__).parent / 'api' / f'{name}.png'
if what != 'function' or not path.is_file(): return
lines[0:0] = [f'.. image:: {path.name}', ' :width: 200', ' :align: right', '']
# -- GitHub links --------------------------------------------------------------
def autolink(url_template, title_template='{}'):
from docutils import nodes
def role(name, rawtext, text, lineno, inliner, options={}, content=[]):
url = url_template.format(text)
title = title_template.format(text)
node = nodes.reference(rawtext, title, refuri=url, **options)
return [node], []
return role
# -- Test for new scanpydoc functionality --------------------------------------
import re
from sphinx.ext.napoleon import NumpyDocstring
def process_return(lines):
for line in lines:
m = re.fullmatch(r'(?P\w+)\s+:\s+(?P[\w.]+)', line)
if m:
# Once this is in scanpydoc, we can use the fancy hover stuff
yield f'**{m["param"]}** : :class:`~{m["type"]}`'
else:
yield line
def scanpy_parse_returns_section(self, section):
lines_raw = list(process_return(self._dedent(self._consume_to_next_section())))
lines = self._format_block(':returns: ', lines_raw)
if lines and lines[-1]:
lines.append('')
return lines
NumpyDocstring._parse_returns_section = scanpy_parse_returns_section
# -- Warn for non-annotated params ---------------------------------------------
_format_docutils_params_orig = NumpyDocstring._format_docutils_params
param_warnings = {}
def scanpy_log_param_types(self, fields, field_role='param', type_role='type'):
for _name, _type, _desc in fields:
if not _type: continue
set_item = r"`'[a-z0-9_.-]+'`"
if re.fullmatch(rf"{{{set_item}(, {set_item})*}}", _type): continue
param_warnings.setdefault((self._name, self._obj), []).append((_name, _type))
return _format_docutils_params_orig(self, fields, field_role, type_role)
def show_param_warnings(app, exception):
import inspect
for (fname, fun), params in param_warnings.items():
_, line = inspect.getsourcelines(fun)
file_name = inspect.getsourcefile(fun)
params_str = '\n'.join(f'\t{n}: {t}' for n, t in params)
warnings.warn_explicit(
f'\nParameters in `{fname}` not set-like: {{`elm-1`, `s_el.2`}}.\n'
'Convert to this format or replace with type annotations:\n'
+ params_str,
UserWarning, file_name, line,
)
NumpyDocstring._format_docutils_params = scanpy_log_param_types
# -- Debug code ----------------------------------------------------------------
# Just do the following to see the rst of a function:
# rm -f _build/doctrees/api/scanpy..doctree; DEBUG=1 make html
import os
if os.environ.get('DEBUG') is not None:
import sphinx.ext.napoleon
pd = sphinx.ext.napoleon._process_docstring
def pd_new(app, what, name, obj, options, lines):
pd(app, what, name, obj, options, lines)
print(*lines, sep='\n')
sphinx.ext.napoleon._process_docstring = pd_new
# -- Suppress link warnings ----------------------------------------------------
qualname_overrides = {
"sklearn.neighbors.dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric",
}
nitpick_ignore = [
# Will probably be documented
('py:class', 'scanpy._settings.Verbosity'),
# Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810
('py:class', 'seaborn.ClusterGrid'),
# Bug: https://github.com/agronholm/sphinx-autodoc-typehints/issues/96
('py:class', 'typing.Textio'),
]
for mod_name in [
'pp', 'tl', 'pl',
'queries', 'logging', 'datasets', 'export_to',
None,
]:
if mod_name is None:
mod = scanpy.api
mod_name = 'scanpy.api'
else:
mod = getattr(scanpy.api, mod_name)
mod_name = f'scanpy.api.{mod_name}'
for name, item in vars(mod).items():
if not callable(item):
continue
for kind in ['func', 'obj']:
nitpick_ignore.append((f'py:{kind}', f'{mod_name}.{name}'))
###########################################################################
# auto-created readthedocs.org specific configuration #
###########################################################################
#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
import importlib
import sys
import os.path
from six import string_types
from sphinx import version_info
# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
if isinstance(source_suffix, string_types):
SUFFIX = source_suffix
elif isinstance(source_suffix, (list, tuple)):
# Sphinx >= 1.3 supports list/tuple to define multiple suffixes
SUFFIX = source_suffix[0]
elif isinstance(source_suffix, dict):
# Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility
else:
# default to .rst
SUFFIX = '.rst'
else:
SUFFIX = '.rst'
# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
html_static_path = []
if os.path.exists('_static'):
html_static_path.append('_static')
# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
(
'html_theme' in globals() and
html_theme in ['default'] and
# Allow people to bail with a hack of having an html_style
'html_style' not in globals()
) or 'html_theme' not in globals()
)
if using_rtd_theme:
theme = importlib.import_module('sphinx_rtd_theme')
html_theme = 'sphinx_rtd_theme'
html_style = None
html_theme_options = {}
if 'html_theme_path' in globals():
html_theme_path.append(theme.get_html_theme_path())
else:
html_theme_path = [theme.get_html_theme_path()]
if globals().get('websupport2_base_url', False):
websupport2_base_url = 'https://readthedocs.com/websupport'
websupport2_static_url = 'https://media.readthedocs.com/'
#Add project information to the template context.
context = {
'using_theme': using_rtd_theme,
'html_theme': html_theme,
'current_version': "latest",
'version_slug': "latest",
'MEDIA_URL': "https://media.readthedocs.com/media/",
'STATIC_URL': "https://media.readthedocs.com/",
'PRODUCTION_DOMAIN': "readthedocs.com",
'versions': [
("latest", "/en/latest/"),
("stable", "/en/stable/"),
("contributors", "/en/contributors/"),
],
'downloads': [
("html", "//readthedocs.com/projects/icb-scanpy/downloads/htmlzip/latest/"),
],
'subprojects': [
],
'slug': 'icb-scanpy',
'name': u'scanpy',
'rtd_language': u'en',
'programming_language': u'py',
'canonical_url': 'https://icb-scanpy.readthedocs-hosted.com/en/stable/',
'analytics_code': 'None',
'single_version': False,
'conf_py_path': '/docs/',
'api_host': 'https://readthedocs.com',
'github_user': 'theislab',
'github_repo': 'scanpy',
'github_version': 'master',
'display_github': True,
'bitbucket_user': 'None',
'bitbucket_repo': 'None',
'bitbucket_version': 'master',
'display_bitbucket': False,
'gitlab_user': 'None',
'gitlab_repo': 'None',
'gitlab_version': 'master',
'display_gitlab': False,
'READTHEDOCS': True,
'using_theme': (html_theme == "default"),
'new_theme': (html_theme == "sphinx_rtd_theme"),
'source_suffix': SUFFIX,
'ad_free': False,
'user_analytics_code': '',
'global_analytics_code': 'UA-17997319-2',
'commit': '26fd7707',
}
if 'html_context' in globals():
html_context.update(context)
else:
html_context = context
# Add custom RTD extension
if 'extensions' in globals():
# Insert at the beginning because it can interfere
# with other extensions.
# See https://github.com/rtfd/readthedocs.org/pull/4054
extensions.insert(0, "readthedocs_ext.readthedocs")
else:
extensions = ["readthedocs_ext.readthedocs"]
# Add External version warning banner to the external version documentation
if 'branch' == 'external':
extensions.insert(1, "readthedocs_ext.external_version_warning")
project_language = 'en'
# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)
# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False
chinese = any([
language_user in ('zh_CN', 'zh_TW'),
project_language in ('zh_CN', 'zh_TW'),
])
japanese = any([
language_user == 'ja',
project_language == 'ja',
])
if chinese:
latex_engine = latex_engine_user or 'xelatex'
latex_elements_rtd = {
'preamble': '\\usepackage[UTF8]{ctex}\n',
}
latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
latex_engine = latex_engine_user or 'platex'
[rtd-command-info] start-time: 2019-09-06T14:55:48.738855Z, end-time: 2019-09-06T14:56:04.758829Z, duration: 16, exit-code: 2
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v2.2.0
loading translations [en]... done
making output directory... done
loading intersphinx inventory from https://anndata.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://matplotlib.org/cycler/objects.inv...
loading intersphinx inventory from https://ipython.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://leidenalg.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://louvain-igraph.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://matplotlib.org/objects.inv...
loading intersphinx inventory from https://networkx.github.io/documentation/networkx-1.10/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/numpy/objects.inv...
loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv...
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv...
loading intersphinx inventory from https://scvelo.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://seaborn.pydata.org/objects.inv...
loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv...
loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv...
[autosummary] generating autosummary for: api/index.rst, api/plotting.rst, api/scanpy.Neighbors.compute_eigen.rst, api/scanpy.Neighbors.compute_neighbors.rst, api/scanpy.Neighbors.compute_transitions.rst, api/scanpy.Neighbors.connectivities.rst, api/scanpy.Neighbors.distances.rst, api/scanpy.Neighbors.distances_dpt.rst, api/scanpy.Neighbors.eigen_basis.rst, api/scanpy.Neighbors.eigen_values.rst, ..., external/scanpy.external.tl.cyclone.rst, external/scanpy.external.tl.palantir.rst, external/scanpy.external.tl.phate.rst, external/scanpy.external.tl.phenograph.rst, external/scanpy.external.tl.sandbag.rst, index.rst, installation.rst, references.rst, release_notes.rst, tutorials.rst
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest" is shallow and may cause errors
warnings.warn('"%s" is shallow and may cause errors' % (wd.path,))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name:
warnings.warn(f"Found an util with public name: {obj}")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name:
warnings.warn(f"Found an util with public name: {obj}")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name:
warnings.warn(f"Found an util with public name: {obj}")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name:
warnings.warn(f"Found an util with public name: {obj}")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name:
warnings.warn(f"Found an util with public name: {obj}")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name:
warnings.warn(f"Found an util with public name: {obj}")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name:
warnings.warn(f"Found an util with public name: {obj}")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name:
warnings.warn(f"Found an util with public name: {obj}")
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_utils.py:132: UserWarning: Found an util with public name:
warnings.warn(f"Found an util with public name: {obj}")
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/ext/autosummary/generate.py", line 247, in generate_autosummary_docs
name, obj, parent, mod_name = import_by_name(name)
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/ext/autosummary/__init__.py", line 599, in import_by_name
raise ImportError('no module named %s' % ' or '.join(tried))
ImportError: no module named scanpy._settings.ScanpyConfig.getdoc
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/cmd/build.py", line 275, in build_main
args.tags, args.verbosity, args.jobs, args.keep_going)
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 269, in __init__
self._init_builder()
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 330, in _init_builder
self.events.emit('builder-inited')
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/events.py", line 103, in emit
results.append(callback(self.app, *args))
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/ext/autosummary/__init__.py", line 748, in process_generate_options
app=app, imported_members=imported_members)
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/ext/autosummary/generate.py", line 249, in generate_autosummary_docs
_warn('[autosummary] failed to import %r: %s' % (name, e))
File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1642, in warning
self.log(WARNING, msg, *args, **kwargs)
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 124, in log
super().log(level, msg, *args, **kwargs)
File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1674, in log
self.logger.log(level, msg, *args, **kwargs)
File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1374, in log
self._log(level, msg, args, **kwargs)
File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1444, in _log
self.handle(record)
File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1454, in handle
self.callHandlers(record)
File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1516, in callHandlers
hdlr.handle(record)
File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 861, in handle
rv = self.filter(record)
File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 720, in filter
result = f.filter(record)
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 406, in filter
raise SphinxWarning(message)
sphinx.errors.SphinxWarning: [autosummary] failed to import 'scanpy._settings.ScanpyConfig.getdoc': no module named scanpy._settings.ScanpyConfig.getdoc
Warning, treated as error:
[autosummary] failed to import 'scanpy._settings.ScanpyConfig.getdoc': no module named scanpy._settings.ScanpyConfig.getdoc