Read the Docs build information
Build id: 251509
Project: icb-scanpy
Version: latest
Commit: dd892fa280c1d528056f471a6c0b493f254d90ca
Date: 2019-10-19T18:59:44.019297Z
State: finished
Success: False
[rtd-command-info] start-time: 2019-10-19T18:59:44.477063Z, end-time: 2019-10-19T18:59:44.484214Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/theislab/scanpy.git
[rtd-command-info] start-time: 2019-10-19T18:59:44.565182Z, end-time: 2019-10-19T18:59:45.240268Z, duration: 0, exit-code: 0
git fetch origin --force --tags --prune --prune-tags --depth 50
From https://github.com/theislab/scanpy
* [new branch] doc-tl -> origin/doc-tl
f112719..dd892fa master -> origin/master
[rtd-command-info] start-time: 2019-10-19T18:59:45.654391Z, end-time: 2019-10-19T18:59:45.667177Z, duration: 0, exit-code: 0
git checkout --force origin/master
Previous HEAD position was f112719 Add and use bright logo
HEAD is now at dd892fa tl doc fixes (#880)
[rtd-command-info] start-time: 2019-10-19T18:59:45.763260Z, end-time: 2019-10-19T18:59:45.771779Z, duration: 0, exit-code: 0
git clean -d -f -f
[rtd-command-info] start-time: 2019-10-19T18:59:46.727703Z, end-time: 2019-10-19T18:59:51.085135Z, duration: 4, 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
Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python3.6)
Installing setuptools, pip, wheel...
done.
[rtd-command-info] start-time: 2019-10-19T18:59:51.174402Z, end-time: 2019-10-19T18:59:52.296857Z, duration: 1, 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/latest/lib/python3.6/site-packages (19.3.1)
[rtd-command-info] start-time: 2019-10-19T18:59:52.380619Z, end-time: 2019-10-19T18:59:55.844145Z, 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==41.0.1 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
Requirement already up-to-date: Pygments==2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (2.3.1)
Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (41.0.1)
Requirement already up-to-date: docutils==0.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.14)
Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (1.0.1)
Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/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/latest/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/latest/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/latest/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/latest/lib/python3.6/site-packages (0.4.3)
Requirement already up-to-date: readthedocs-sphinx-ext<1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (1.0.0)
Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from commonmark==0.8.1) (0.18.1)
Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.7.0)
Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.22.0)
Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.1.2)
Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.0.0)
Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/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/latest/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/latest/lib/python3.6/site-packages (from sphinx<2) (19.2)
Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.10.3)
Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.3)
Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (2019.9.11)
Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (3.0.4)
Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (2.8)
Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (1.25.6)
Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from packaging->sphinx<2) (2.4.2)
Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1)
ERROR: sphinx-autodoc-typehints 1.8.0 has requirement Sphinx>=2.1, but you'll have sphinx 1.8.5 which is incompatible.
Installing collected packages: sphinx
Found existing installation: Sphinx 2.2.0
Uninstalling Sphinx-2.2.0:
Successfully uninstalled Sphinx-2.2.0
Successfully installed sphinx-1.8.5
[rtd-command-info] start-time: 2019-10-19T18:59:55.921076Z, end-time: 2019-10-19T18:59:58.442448Z, 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/latest/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/8e/4c/95a21788db2e1653e931420f561015a0bbc9bd4660c4520467ab9e733eb2/Sphinx-2.2.0-py3-none-any.whl
Requirement already satisfied: sphinx-autodoc-typehints in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 6)) (1.8.0)
Requirement already satisfied: scanpydoc>=0.4.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 7)) (0.4.2)
Requirement already satisfied: anndata>=0.6.18 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 9)) (0.6.22.post1)
Requirement already satisfied: matplotlib>=2.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 10)) (3.1.1)
Requirement already satisfied: pandas>=0.21 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 11)) (0.25.1)
Requirement already satisfied: scipy in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 12)) (1.3.1)
Requirement already satisfied: seaborn in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 13)) (0.9.0)
Requirement already satisfied: h5py in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 14)) (2.10.0)
Requirement already satisfied: tables in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 15)) (3.6.0)
Requirement already satisfied: scikit-learn>=0.19.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 16)) (0.21.3)
Requirement already satisfied: networkx in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 18)) (2.4)
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Requirement already satisfied: setuptools_scm in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 25)) (3.3.3)
Requirement already satisfied: umap-learn in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 26)) (0.3.10)
Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (0.14)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2.0.0)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (19.2)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (0.7.12)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (41.0.1)
Requirement already satisfied: sphinxcontrib-htmlhelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.0.2)
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Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.1.3)
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Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2.10.3)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.1.0)
Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.0.1)
Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.0.1)
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Requirement already satisfied: get_version in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from scanpydoc>=0.4.2->-r docs/requirements.txt (line 7)) (2.1)
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Installing collected packages: sphinx
Found existing installation: Sphinx 1.8.5
Uninstalling Sphinx-1.8.5:
Successfully uninstalled Sphinx-1.8.5
Successfully installed sphinx-2.2.0
[rtd-command-info] start-time: 2019-10-19T18:59:59.178217Z, end-time: 2019-10-19T18:59:59.488660Z, 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 = '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',
]
# 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/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=(
'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_BrightFG.svg'
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
w_list = param_warnings.setdefault((self._name, self._obj), [])
if (_name, _type) not in w_list:
w_list.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}` have types in docstring.\n'
f'Replace them 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'),
# Won’t be documented
('py:class', 'scanpy.readwrite.Empty'),
]
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': 'dd892fa2',
}
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: 2019-10-19T18:59:59.580738Z, end-time: 2019-10-19T19:01:39.727463Z, duration: 100, 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/stable/objects.inv...
loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://matplotlib.org/cycler/objects.inv...
loading intersphinx inventory from http://docs.h5py.org/en/stable/objects.inv...
loading intersphinx inventory from https://ipython.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://leidenalg.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://louvain-igraph.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://matplotlib.org/objects.inv...
loading intersphinx inventory from https://networkx.github.io/documentation/networkx-1.10/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/numpy/objects.inv...
loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv...
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv...
loading intersphinx inventory from https://scvelo.readthedocs.io/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
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 154 source files that are out of date
updating environment: [new config] 154 added, 0 changed, 0 removed
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/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/envs/latest/lib/python3.6/site-packages/anndata/readwrite/read.py:416: UserWarning:
Parameters in `scanpy.read_h5ad` have types in docstring.
Replace them with type annotations.
backed: {``None``, ``'r'``, ``'r+'``}
def read_h5ad(filename, backed: Optional[str] = None, chunk_size: int = 6000):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/neighbors/__init__.py:812: UserWarning:
Parameters in `scanpy.Neighbors.compute_eigen` have types in docstring.
Replace them with type annotations.
n_comps: `int`
sym: `bool`
matrix: sparse matrix, np.ndarray, optional (default: `.connectivities`)
def compute_eigen(self, n_comps=15, sym=None, sort='decrease'):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/neighbors/__init__.py:774: UserWarning:
Parameters in `scanpy.Neighbors.compute_transitions` have types in docstring.
Replace them with type annotations.
density_normalize: `bool`
def compute_transitions(self, density_normalize=True):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/pp/_dca.py:6: UserWarning:
Parameters in `scanpy.api.pp.dca` have types in docstring.
Replace them with type annotations.
mode: `str`, optional. `denoise`(default), or `latent`.
ae_type: `str`, optional. `zinb-conddisp`(default), `zinb`, `nb-conddisp` or `nb`.
normalize_per_cell: `bool`, optional. Default: `True`.
scale: `bool`, optional. Default: `True`.
log1p: `bool`, optional. Default: `True`.
hidden_size: `tuple` or `list`, optional. Default: (64, 32, 64).
hidden_dropout: `float`, `tuple` or `list`, optional. Default: 0.0.
batchnorm: `bool`, optional. Default: `True`.
activation: `str`, optional. Default: `relu`.
init: `str`, optional. Default: `glorot_uniform`.
network_kwds: `dict`, optional.
epochs: `int`, optional. Default: 300.
reduce_lr: `int`, optional. Default: 10.
early_stop: `int`, optional. Default: 15.
batch_size: `int`, optional. Default: 32.
optimizer: `str`, optional. Default: "rmsprop".
random_state: `int`, optional. Default: 0.
threads: `int` or None, optional. Default: None
learning_rate: `float`, optional. Default: None.
verbose: `bool`, optional. Default: `False`.
training_kwds: `dict`, optional.
return_model: `bool`, optional. Default: `False`.
return_info: `bool`, optional. Default: `False`.
copy: `bool`, optional. Default: `False`.
def dca(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/anndata/readwrite/read.py:416: UserWarning:
Parameters in `scanpy.api.read_h5ad` have types in docstring.
Replace them with type annotations.
backed: {``None``, ``'r'``, ``'r+'``}
def read_h5ad(filename, backed: Optional[str] = None, chunk_size: int = 6000):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:1364: UserWarning:
Parameters in `scanpy.pl.dotplot` have types in docstring.
Replace them with type annotations.
adata: :class:`~anndata.AnnData`
var_names: `str`, list of `str`, dict or OrderedDict
groupby: `str` or `None`, optional (default: `None`)
log: `bool`, optional (default: `False`)
use_raw: `bool`, optional (default: `None`)
num_categories: `int`, optional (default: `7`)
figsize: (`float`, `float`), optional (default: `None`)
dendrogram: `bool` or `str`, optional (default, `False`)
gene_symbols: string, optional (default: `None`)
var_group_positions: list of `tuples`.
var_group_labels: list of `str`
var_group_rotation: `float` (default: `None`)
layer: `str`, (default `None`)
expression_cutoff: `float` (default: `0.`)
mean_only_expressed: `bool` (default: `False`)
color_map: `str`, optional (default: `Reds`)
dot_max: `float` optional (default: `None`)
dot_min: `float` optional (default: `None`)
smallest_dot: `float` optional (default: 0.)
@_doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:26: UserWarning:
Parameters in `scanpy.pl.draw_graph` have types in docstring.
Replace them with type annotations.
edges_color: matplotlib color(s), optional (default: `'grey'`)
@_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:26: UserWarning:
Parameters in `scanpy.pl.embedding` have types in docstring.
Replace them with type annotations.
edges_color: matplotlib color(s), optional (default: `'grey'`)
@_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_preprocessing.py:69: UserWarning:
Parameters in `scanpy.pl.filter_genes_dispersion` have types in docstring.
Replace them with type annotations.
show: bool, optional (default: `None`)
save: `bool` or `str`, optional (default: `None`)
def filter_genes_dispersion(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:1075: UserWarning:
Parameters in `scanpy.pl.heatmap` have types in docstring.
Replace them with type annotations.
adata: :class:`~anndata.AnnData`
var_names: `str`, list of `str`, dict or OrderedDict
groupby: `str` or `None`, optional (default: `None`)
log: `bool`, optional (default: `False`)
use_raw: `bool`, optional (default: `None`)
num_categories: `int`, optional (default: `7`)
figsize: (`float`, `float`), optional (default: `None`)
dendrogram: `bool` or `str`, optional (default, `False`)
gene_symbols: string, optional (default: `None`)
var_group_positions: list of `tuples`.
var_group_labels: list of `str`
var_group_rotation: `float` (default: `None`)
layer: `str`, (default `None`)
@_doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_preprocessing.py:14: UserWarning:
Parameters in `scanpy.pl.highly_variable_genes` have types in docstring.
Replace them with type annotations.
adata: :class:`~anndata.AnnData`, `np.recarray`
log: `bool`
show: bool, optional (default: `None`)
save: `bool` or `str`, optional (default: `None`)
def highly_variable_genes(adata_or_result, log=False, show=None, save=None, highly_variable_genes=True):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:1696: UserWarning:
Parameters in `scanpy.pl.matrixplot` have types in docstring.
Replace them with type annotations.
adata: :class:`~anndata.AnnData`
var_names: `str`, list of `str`, dict or OrderedDict
groupby: `str` or `None`, optional (default: `None`)
log: `bool`, optional (default: `False`)
use_raw: `bool`, optional (default: `None`)
num_categories: `int`, optional (default: `7`)
figsize: (`float`, `float`), optional (default: `None`)
dendrogram: `bool` or `str`, optional (default, `False`)
gene_symbols: string, optional (default: `None`)
var_group_positions: list of `tuples`.
var_group_labels: list of `str`
var_group_rotation: `float` (default: `None`)
layer: `str`, (default `None`)
@_doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/paga.py:243: UserWarning:
Parameters in `scanpy.pl.paga` have types in docstring.
Replace them with type annotations.
normalize_to_color: `bool`, optional (default: `False`)
def paga(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/paga.py:23: UserWarning:
Parameters in `scanpy.pl.paga_compare` have types in docstring.
Replace them with type annotations.
adata: :class:`~anndata.AnnData`
kwds_scatter: `dict`
kwds_paga: `dict`
def paga_compare(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:26: UserWarning:
Parameters in `scanpy.pl.pca_overview` have types in docstring.
Replace them with type annotations.
color: string or list of strings, optional (default: `None`)
use_raw: `bool`, optional (default: `True`)
show: bool, optional (default: `None`)
save: `bool` or `str`, optional (default: `None`)
@_doc_params(scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:104: UserWarning:
Parameters in `scanpy.pl.pca_variance_ratio` have types in docstring.
Replace them with type annotations.
n_pcs: `int`, optional (default: `30`)
log: `bool`, optional (default: `False`)
show: `bool`, optional (default: `None`)
save: `bool` or `str`, optional (default: `None`)
def pca_variance_ratio(adata, n_pcs=30, log=False, show=None, save=None):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:395: UserWarning:
Parameters in `scanpy.pl.rank_genes_groups_heatmap` have types in docstring.
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adata: :class:`~anndata.AnnData`
groups: `str` or `list` of `str`
@_doc_params(show_save_ax=doc_show_save_ax)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:512: UserWarning:
Parameters in `scanpy.pl.rank_genes_groups_stacked_violin` have types in docstring.
Replace them with type annotations.
groups: `str` or `list` of `str`
n_genes: `int`, optional (default: 10)
groupby: `str` or `None`, optional (default: `None`)
@_doc_params(show_save_ax=doc_show_save_ax)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:590: UserWarning:
Parameters in `scanpy.pl.rank_genes_groups_violin` have types in docstring.
Replace them with type annotations.
use_raw: `bool`, optional (default: `None`)
@_doc_params(show_save_ax=doc_show_save_ax)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:733: UserWarning:
Parameters in `scanpy.pl.stacked_violin` have types in docstring.
Replace them with type annotations.
adata: :class:`~anndata.AnnData`
var_names: `str`, list of `str`, dict or OrderedDict
groupby: `str` or `None`, optional (default: `None`)
log: `bool`, optional (default: `False`)
use_raw: `bool`, optional (default: `None`)
num_categories: `int`, optional (default: `7`)
figsize: (`float`, `float`), optional (default: `None`)
dendrogram: `bool` or `str`, optional (default, `False`)
gene_symbols: string, optional (default: `None`)
var_group_positions: list of `tuples`.
var_group_labels: list of `str`
var_group_rotation: `float` (default: `None`)
layer: `str`, (default `None`)
@_doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:1922: UserWarning:
Parameters in `scanpy.pl.tracksplot` have types in docstring.
Replace them with type annotations.
adata: :class:`~anndata.AnnData`
var_names: `str`, list of `str`, dict or OrderedDict
groupby: `str` or `None`, optional (default: `None`)
log: `bool`, optional (default: `False`)
use_raw: `bool`, optional (default: `None`)
num_categories: `int`, optional (default: `7`)
figsize: (`float`, `float`), optional (default: `None`)
dendrogram: `bool` or `str`, optional (default, `False`)
gene_symbols: string, optional (default: `None`)
var_group_positions: list of `tuples`.
var_group_labels: list of `str`
var_group_rotation: `float` (default: `None`)
layer: `str`, (default `None`)
@_doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:26: UserWarning:
Parameters in `scanpy.pl.tsne` have types in docstring.
Replace them with type annotations.
edges_color: matplotlib color(s), optional (default: `'grey'`)
@_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:26: UserWarning:
Parameters in `scanpy.pl.umap` have types in docstring.
Replace them with type annotations.
edges_color: matplotlib color(s), optional (default: `'grey'`)
@_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/pp/_dca.py:6: UserWarning:
Parameters in `scanpy.external.pp.dca` have types in docstring.
Replace them with type annotations.
mode: `str`, optional. `denoise`(default), or `latent`.
ae_type: `str`, optional. `zinb-conddisp`(default), `zinb`, `nb-conddisp` or `nb`.
normalize_per_cell: `bool`, optional. Default: `True`.
scale: `bool`, optional. Default: `True`.
log1p: `bool`, optional. Default: `True`.
hidden_size: `tuple` or `list`, optional. Default: (64, 32, 64).
hidden_dropout: `float`, `tuple` or `list`, optional. Default: 0.0.
batchnorm: `bool`, optional. Default: `True`.
activation: `str`, optional. Default: `relu`.
init: `str`, optional. Default: `glorot_uniform`.
network_kwds: `dict`, optional.
epochs: `int`, optional. Default: 300.
reduce_lr: `int`, optional. Default: 10.
early_stop: `int`, optional. Default: 15.
batch_size: `int`, optional. Default: 32.
optimizer: `str`, optional. Default: "rmsprop".
random_state: `int`, optional. Default: 0.
threads: `int` or None, optional. Default: None
learning_rate: `float`, optional. Default: None.
verbose: `bool`, optional. Default: `False`.
training_kwds: `dict`, optional.
return_model: `bool`, optional. Default: `False`.
return_info: `bool`, optional. Default: `False`.
copy: `bool`, optional. Default: `False`.
def dca(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:26: UserWarning:
Parameters in `scanpy.external.pl.phate` have types in docstring.
Replace them with type annotations.
edges_color: matplotlib color(s), optional (default: `'grey'`)
@_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax)
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 276, in build_main
app.build(args.force_all, filenames)
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 346, in build
self.builder.build_update()
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 299, in build_update
len(to_build))
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 361, in build
self.write(docnames, list(updated_docnames), method)
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 535, in write
self._write_serial(sorted(docnames))
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 545, in _write_serial
self.write_doc(docname, doctree)
File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/contextlib.py", line 88, in __exit__
next(self.gen)
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 219, in pending_warnings
memhandler.flushTo(logger)
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 184, in flushTo
logger.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 404, in filter
raise SphinxWarning(location + ":" + message)
sphinx.errors.SphinxWarning: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_dendrogram.py:docstring of scanpy.tl.dendrogram:11:py:func reference target not found: scanpy.pl.dendrogram
Warning, treated as error:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_dendrogram.py:docstring of scanpy.tl.dendrogram:11:py:func reference target not found: scanpy.pl.dendrogram