Read the Docs build information
Build id: 204408
Project: icb-scanpy
Version: stable
Commit: e36102af57694042831b0760e8b5aa45287da09d
Date: 2019-04-28T13:14:09.127459Z
State: finished
Success: True
[rtd-command-info] start-time: 2019-04-28T13:14:19.233513Z, end-time: 2019-04-28T13:14:19.238940Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/theislab/scanpy.git
[rtd-command-info] start-time: 2019-04-28T13:14:19.303945Z, end-time: 2019-04-28T13:14:20.121943Z, duration: 0, exit-code: 0
git fetch --tags --prune --prune-tags --depth 50
From https://github.com/theislab/scanpy
- [deleted] (none) -> origin/stable
[rtd-command-info] start-time: 2019-04-28T13:14:20.349377Z, end-time: 2019-04-28T13:14:20.358125Z, duration: 0, exit-code: 0
git checkout --force e36102af57694042831b0760e8b5aa45287da09d
HEAD is now at e36102a version 1.4.1 amended release notes
[rtd-command-info] start-time: 2019-04-28T13:14:20.428734Z, end-time: 2019-04-28T13:14:20.436706Z, duration: 0, exit-code: 0
git clean -d -f -f
[rtd-command-info] start-time: 2019-04-28T13:14:21.295318Z, end-time: 2019-04-28T13:14:24.423884Z, duration: 3, exit-code: 0
python3.6 -mvirtualenv --no-site-packages --no-download
Using base prefix '/home/docs/.pyenv/versions/3.6.4'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/bin/python3.6
Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/bin/python3.6)
Installing setuptools, pip, wheel...
done.
[rtd-command-info] start-time: 2019-04-28T13:14:24.487404Z, end-time: 2019-04-28T13:14:25.379638Z, duration: 0, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip pip
Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (19.1)
[rtd-command-info] start-time: 2019-04-28T13:14:25.453095Z, end-time: 2019-04-28T13:14:28.879694Z, duration: 3, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip Pygments==2.3.1 setuptools<41 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<0.6
Requirement already up-to-date: Pygments==2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (2.3.1)
Requirement already up-to-date: setuptools<41 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (40.9.0)
Requirement already up-to-date: docutils==0.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (0.14)
Collecting mock==1.0.1
Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (5.4.1)
Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (0.7.12)
Requirement already up-to-date: commonmark==0.8.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (0.8.1)
Requirement already up-to-date: recommonmark==0.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (0.5.0)
Collecting sphinx<2
Using cached https://files.pythonhosted.org/packages/7d/66/a4af242b4348b729b9d46ce5db23943ce9bca7da9bbe2ece60dc27f26420/Sphinx-1.8.5-py2.py3-none-any.whl
Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (0.4.3)
Requirement already up-to-date: readthedocs-sphinx-ext<0.6 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (0.5.17)
Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from commonmark==0.8.1) (0.17.1)
Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx<2) (2.10.1)
Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx<2) (2.6.0)
Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx<2) (2.21.0)
Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx<2) (1.1.0)
Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx<2) (1.2.1)
Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx<2) (1.12.0)
Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx<2) (1.1.0)
Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from sphinx<2) (19.0)
Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1)
Requirement already satisfied, skipping upgrade: pytz>=0a in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.1)
Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (2.8)
Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (2019.3.9)
Requirement already satisfied, skipping upgrade: urllib3<1.25,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (1.24.2)
Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (3.0.4)
Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from packaging->sphinx<2) (2.4.0)
tables 3.5.1 has requirement mock>=2.0, but you'll have mock 1.0.1 which is incompatible.
Installing collected packages: mock, sphinx
Found existing installation: mock 2.0.0
Uninstalling mock-2.0.0:
Successfully uninstalled mock-2.0.0
Found existing installation: Sphinx 2.0.1
Uninstalling Sphinx-2.0.1:
Successfully uninstalled Sphinx-2.0.1
Successfully installed mock-1.0.1 sphinx-1.8.5
[rtd-command-info] start-time: 2019-04-28T13:14:28.940063Z, end-time: 2019-04-28T13:14:31.542615Z, duration: 2, exit-code: 0
python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip -r docs/requirements.txt
Requirement already satisfied: sphinx_rtd_theme>=0.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/requirements.txt (line 2)) (0.4.3)
Collecting sphinx>=2.0.1 (from -r docs/requirements.txt (line 5))
Using cached https://files.pythonhosted.org/packages/9a/b0/a8cf1d35237aebefd63f05543ed49ea24d302239828ca89409b0c1a35b27/Sphinx-2.0.1-py2.py3-none-any.whl
Requirement already satisfied: sphinx-autodoc-typehints in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/requirements.txt (line 6)) (1.6.0)
Requirement already satisfied: scanpydoc>=0.3.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/requirements.txt (line 7)) (0.3.3)
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Requirement already satisfied: matplotlib>=2.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/requirements.txt (line 10)) (3.0.3)
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Collecting mock>=2.0 (from tables->-r docs/requirements.txt (line 15))
Using cached https://files.pythonhosted.org/packages/e6/35/f187bdf23be87092bd0f1200d43d23076cee4d0dec109f195173fd3ebc79/mock-2.0.0-py2.py3-none-any.whl
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Installing collected packages: sphinx, mock
Found existing installation: Sphinx 1.8.5
Uninstalling Sphinx-1.8.5:
Successfully uninstalled Sphinx-1.8.5
Found existing installation: mock 1.0.1
Uninstalling mock-1.0.1:
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Successfully installed mock-2.0.0 sphinx-2.0.1
[rtd-command-info] start-time: 2019-04-28T13:14:32.202712Z, end-time: 2019-04-28T13:14:32.255287Z, duration: 0, exit-code: 0
cat docs/conf.py
import sys
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
# -- General configuration ------------------------------------------------
needs_sphinx = '1.7' # autosummary bugfix
# 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),
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=('http://pandas.pydata.org/pandas-docs/stable/', None),
python=('https://docs.python.org/3', None),
scipy=('https://docs.scipy.org/doc/scipy/reference/', None),
sklearn=('https://scikit-learn.org/stable/', 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_logo = '_static/img/Scanpy_Logo_RGB.png'
def setup(app):
app.add_stylesheet('css/custom.css')
app.connect('autodoc-process-docstring', insert_function_images)
# -- 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', '']
# -- 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
# -- 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
###########################################################################
# 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 mulitple suffixes
SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility
else:
# default to .rst
SUFFIX = '.rst'
else:
SUFFIX = '.rst'
# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
html_static_path = []
if os.path.exists('_static'):
html_static_path.append('_static')
# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
(
'html_theme' in globals() and
html_theme in ['default'] and
# Allow people to bail with a hack of having an html_style
'html_style' not in globals()
) or 'html_theme' not in globals()
)
if using_rtd_theme:
theme = importlib.import_module('sphinx_rtd_theme')
html_theme = 'sphinx_rtd_theme'
html_style = None
html_theme_options = {}
if 'html_theme_path' in globals():
html_theme_path.append(theme.get_html_theme_path())
else:
html_theme_path = [theme.get_html_theme_path()]
if globals().get('websupport2_base_url', False):
websupport2_base_url = 'https://readthedocs.com/websupport'
websupport2_static_url = 'https://media.readthedocs.com/'
#Add project information to the template context.
context = {
'using_theme': using_rtd_theme,
'html_theme': html_theme,
'current_version': "stable",
'version_slug': "stable",
'MEDIA_URL': "https://media.readthedocs.com/media/",
'STATIC_URL': "https://media.readthedocs.com/",
'PRODUCTION_DOMAIN': "readthedocs.com",
'versions': [
("latest", "/en/latest/"),
("stable", "/en/stable/"),
],
'downloads': [
("html", "//readthedocs.com/projects/icb-scanpy/downloads/htmlzip/stable/"),
],
'subprojects': [
],
'slug': 'icb-scanpy',
'name': u'scanpy',
'rtd_language': u'en',
'programming_language': u'py',
'canonical_url': 'https://icb-scanpy.readthedocs-hosted.com/en/stable/',
'analytics_code': 'None',
'single_version': False,
'conf_py_path': '/docs/',
'api_host': 'https://readthedocs.com',
'github_user': 'theislab',
'github_repo': 'scanpy',
'github_version': 'e36102af57694042831b0760e8b5aa45287da09d',
'display_github': True,
'bitbucket_user': 'None',
'bitbucket_repo': 'None',
'bitbucket_version': 'e36102af57694042831b0760e8b5aa45287da09d',
'display_bitbucket': False,
'gitlab_user': 'None',
'gitlab_repo': 'None',
'gitlab_version': 'e36102af57694042831b0760e8b5aa45287da09d',
'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': 'e36102af',
}
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"]
[rtd-command-info] start-time: 2019-04-28T13:14:32.330967Z, end-time: 2019-04-28T13:14:54.036640Z, duration: 21, exit-code: 0
python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v2.0.1
loading translations [en]... done
making output directory... done
loading pickled environment... done
[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, ..., api/scanpy.tl.sim.rst, api/scanpy.tl.tsne.rst, api/scanpy.tl.umap.rst, basic_usage.rst, examples.rst, index.rst, installation.rst, references.rst, release_notes.rst, tutorials.rst
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 215 source files that are out of date
updating environment: 0 added, 0 changed, 0 removed
looking for now-outdated files... none found
preparing documents... done
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/index.rst:148: WARNING: undefined label: pandas:/io.rst#io-tools-text-csv-hdf5 (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/api/__init__.py:docstring of scanpy.api:150: WARNING: undefined label: pandas:/io.rst#io-tools-text-csv-hdf5 (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/plotting/_anndata.py:docstring of scanpy.pl.dotplot:36: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/plotting/_anndata.py:docstring of scanpy.pl.heatmap:30: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/plotting/_anndata.py:docstring of scanpy.pl.matrixplot:26: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/plotting/_anndata.py:docstring of scanpy.pl.stacked_violin:29: WARNING: undefined label: scanpy.tl.dendrogram (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/tools/_rank_genes_groups.py:docstring of scanpy.tl.filter_rank_genes_groups:22: WARNING: undefined label: scanpy.tl.rank_genes_groups (if the link has no caption the label must precede a section header)
generating indices... genindex py-modindex
writing additional pages... search
copying images... [ 11%] api/scanpy.pl.dotplot.png
copying images... [ 22%] api/scanpy.pl.heatmap.png
copying images... [ 33%] api/scanpy.pl.matrixplot.png
copying images... [ 44%] api/scanpy.pl.rank_genes_groups_dotplot.png
copying images... [ 55%] api/scanpy.pl.rank_genes_groups_heatmap.png
copying images... [ 66%] api/scanpy.pl.rank_genes_groups_matrixplot.png
copying images... [ 77%] api/scanpy.pl.rank_genes_groups_stacked_violin.png
copying images... [ 88%] api/scanpy.pl.stacked_violin.png
copying images... [100%] api/scanpy.pl.violin.png
copying static files... done
copying readthedocs static files... done
copying searchtools... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 7 warnings.
The HTML pages are in _build/html.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx_rtd_theme/search.html:20: RemovedInSphinx30Warning: To modify script_files in the theme is deprecated. Please insert a