Read the Docs build information
Build id: 241968
Project: icb-scanpy
Version: latest
Commit: 1875df186516d737a746c314315aa87fd7178755
Date: 2019-09-16T12:28:51.980458Z
State: finished
Success: False


[rtd-command-info] start-time: 2019-09-16T12:28:52.629343Z, end-time: 2019-09-16T12:28:52.638444Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/theislab/scanpy.git


[rtd-command-info] start-time: 2019-09-16T12:28:52.717194Z, end-time: 2019-09-16T12:28:53.208210Z, duration: 0, exit-code: 0
git fetch origin --tags --prune --prune-tags --depth 50
From https://github.com/theislab/scanpy
 - [deleted]         (none)     -> origin/black
 - [deleted]         (none)     -> origin/isinstance-fix
 - [deleted]         (none)     -> origin/limit-n-top-genes
   bb62b33..1875df1  master     -> origin/master

[rtd-command-info] start-time: 2019-09-16T12:28:53.467142Z, end-time: 2019-09-16T12:28:53.507150Z, duration: 0, exit-code: 0
git checkout --force origin/master
Previous HEAD position was bb62b33 Unify all isinstance calls (#839)
HEAD is now at 1875df1 added cache_compression kwarg to read() (#831)

[rtd-command-info] start-time: 2019-09-16T12:28:53.590409Z, end-time: 2019-09-16T12:28:53.602662Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-09-16T12:28:54.675141Z, end-time: 2019-09-16T12:28:58.915754Z, 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
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: 2019-09-16T12:28:59.005512Z, end-time: 2019-09-16T12:29:01.359777Z, 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:
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Successfully installed pip-19.2.3

[rtd-command-info] start-time: 2019-09-16T12:29:01.452789Z, end-time: 2019-09-16T12:29:11.642783Z, duration: 10, exit-code: 0
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[rtd-command-info] start-time: 2019-09-16T12:29:11.751298Z, end-time: 2019-09-16T12:29:45.518540Z, duration: 33, exit-code: 0
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Installing collected packages: sphinxcontrib-jsmath, sphinxcontrib-applehelp, sphinxcontrib-htmlhelp, sphinxcontrib-qthelp, sphinxcontrib-serializinghtml, sphinxcontrib-devhelp, sphinx, sphinx-autodoc-typehints, get-version, scanpydoc, natsort, python-dateutil, numpy, pandas, h5py, scipy, anndata, kiwisolver, cycler, matplotlib, seaborn, mock, numexpr, tables, joblib, scikit-learn, decorator, networkx, llvmlite, numba, tqdm, more-itertools, zipp, importlib-metadata, setuptools-scm, umap-learn
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[rtd-command-info] start-time: 2019-09-16T12:29:46.249481Z, end-time: 2019-09-16T12:29:46.577965Z, 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),
    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<param>\w+)\s+:\s+(?P<type>[\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.<what_you_want>.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'),
]

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': '1875df18',
}




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: 2019-09-16T12:29:46.686084Z, end-time: 2019-09-16T12:31:33.478006Z, duration: 106, 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 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...
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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/checkouts/latest/scanpy/preprocessing/_highly_variable_genes.py:167: UserWarning: 
Parameters in `scanpy.pp.highly_variable_genes` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	min_mean: `float`, optional (default: 0.0125)
	max_mean: `float`, optional (default: 3)
	min_disp: `float`, optional (default: 0.5)
	max_disp: `float`, optional (default: `None`)
	n_top_genes: `int` or `None`, optional (default: `None`)
	n_bins: `int`, optional (default: 20)
	subset: `bool`, optional (default: `False`)
	inplace: `bool`, optional (default: `True`)
	batch_key: `str`, optional (default: `None`)
	min_mean: `float`, optional (default: 0.0125)
	max_mean: `float`, optional (default: 3)
	min_disp: `float`, optional (default: 0.5)
	max_disp: `float`, optional (default: `None`)
	n_top_genes: `int` or `None`, optional (default: `None`)
	n_bins: `int`, optional (default: 20)
	subset: `bool`, optional (default: `False`)
	inplace: `bool`, optional (default: `True`)
	batch_key: `str`, optional (default: `None`)
  def highly_variable_genes(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:714: UserWarning: 
Parameters in `scanpy.pp.regress_out` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	adata: :class:`~anndata.AnnData`
	keys: `str` or list of `str`
	n_jobs: `int` or `None`, optional. If None is given, then the n_jobs seting is used (default: `None`)
	copy: `bool`, optional (default: `False`)
	adata: :class:`~anndata.AnnData`
	keys: `str` or list of `str`
	n_jobs: `int` or `None`, optional. If None is given, then the n_jobs seting is used (default: `None`)
	copy: `bool`, optional (default: `False`)
  def regress_out(adata, keys, n_jobs=None, copy=False) -> Optional[AnnData]:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:842: UserWarning: 
Parameters in `scanpy.pp.scale` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse`
	zero_center: `bool`, optional (default: `True`)
	max_value: `float` or `None`, optional (default: `None`)
	copy: `bool`, optional (default: `False`)
	data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse`
	zero_center: `bool`, optional (default: `True`)
	max_value: `float` or `None`, optional (default: `None`)
	copy: `bool`, optional (default: `False`)
  def scale(data, zero_center=True, max_value=None, copy=False) -> Optional[AnnData]:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:898: UserWarning: 
Parameters in `scanpy.pp.subsample` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse`
	fraction: `float` in [0, 1] or `None`, optional (default: `None`)
	n_obs: `int` or `None`, optional (default: `None`)
	random_state: `int` or `None`, optional (default: 0)
	copy: `bool`, optional (default: `False`)
	data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse`
	fraction: `float` in [0, 1] or `None`, optional (default: `None`)
	n_obs: `int` or `None`, optional (default: `None`)
	random_state: `int` or `None`, optional (default: 0)
	copy: `bool`, optional (default: `False`)
  def subsample(data, fraction=None, n_obs=None, random_state=0, copy=False) -> Optional[AnnData]:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_recipes.py:74: UserWarning: 
Parameters in `scanpy.pp.recipe_zheng17` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	adata: :class:`~anndata.AnnData`
	n_top_genes: `int`, optional (default: 1000)
	log: `bool`, optional (default: `True`)
	plot: `bool`, optional (default: `True`)
	copy: `bool`, optional (default: `False`)
	adata: :class:`~anndata.AnnData`
	n_top_genes: `int`, optional (default: 1000)
	log: `bool`, optional (default: `True`)
	plot: `bool`, optional (default: `True`)
	copy: `bool`, optional (default: `False`)
  def recipe_zheng17(adata, n_top_genes=1000, log=True, plot=False, copy=False):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_combat.py:135: UserWarning: 
Parameters in `scanpy.pp.combat` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	adata: :class:`~anndata.AnnData`
	key: `str`, optional (default: `"batch"`)
	inplace: bool, optional (default: `True`)
	adata: :class:`~anndata.AnnData`
	key: `str`, optional (default: `"batch"`)
	inplace: bool, optional (default: `True`)
  def combat(adata: AnnData, key: str = 'batch', covariates: Optional[Collection[str]] = None, inplace: bool = True):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/neighbors/__init__.py:22: UserWarning: 
Parameters in `scanpy.pp.neighbors` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	n_pcs: `int` or `None`, optional (default: `None`)
	use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`)
	method: {`'umap'`, `'gauss'`, `None`}  (default: `'umap'`)
	n_pcs: `int` or `None`, optional (default: `None`)
	use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`)
	method: {`'umap'`, `'gauss'`, `None`}  (default: `'umap'`)
  @_doc_params(n_pcs=doc_n_pcs, use_rep=doc_use_rep)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_tsne.py:7: UserWarning: 
Parameters in `scanpy.tl.tsne` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	adata: :class:`~anndata.AnnData`
	n_pcs: `int` or `None`, optional (default: `None`)
	use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`)
	perplexity: `float`, optional (default: 30)
	early_exaggeration: `float`, optional (default: 12.0)
	learning_rate: `float`, optional (default: 1000)
	random_state: `int` or `None`, optional (default: 0)
	use_fast_tsne: `bool`, optional (default: `True`)
	n_jobs: `int` or `None` (default: `sc.settings.n_jobs`)
	copy: `bool` (default: `False`)
	adata: :class:`~anndata.AnnData`
	n_pcs: `int` or `None`, optional (default: `None`)
	use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`)
	perplexity: `float`, optional (default: 30)
	early_exaggeration: `float`, optional (default: 12.0)
	learning_rate: `float`, optional (default: 1000)
	random_state: `int` or `None`, optional (default: 0)
	use_fast_tsne: `bool`, optional (default: `True`)
	n_jobs: `int` or `None` (default: `sc.settings.n_jobs`)
	copy: `bool` (default: `False`)
  @_doc_params(doc_n_pcs=doc_n_pcs, use_rep=doc_use_rep)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_umap.py:10: UserWarning: 
Parameters in `scanpy.tl.umap` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	adata: :class:`~anndata.AnnData`
	min_dist: `float`, optional (default: 0.5)
	spread: `float` (optional, default 1.0)
	n_components: `int`, optional (default: 2)
	maxiter: `int`, optional (default: `None`)
	alpha: `float`, optional (default: 1.0)
	gamma: `float` (optional, default 1.0)
	negative_sample_rate: `int` (optional, default 5)
	init_pos: `string` or `np.array`, optional (default: 'spectral')
	random_state: `int`, `RandomState` or `None`, optional (default: 0)
	a: `float` (optional, default `None`)
	b: `float` (optional, default `None`)
	copy: `bool` (default: `False`)
	adata: :class:`~anndata.AnnData`
	min_dist: `float`, optional (default: 0.5)
	spread: `float` (optional, default 1.0)
	n_components: `int`, optional (default: 2)
	maxiter: `int`, optional (default: `None`)
	alpha: `float`, optional (default: 1.0)
	gamma: `float` (optional, default 1.0)
	negative_sample_rate: `int` (optional, default 5)
	init_pos: `string` or `np.array`, optional (default: 'spectral')
	random_state: `int`, `RandomState` or `None`, optional (default: 0)
	a: `float` (optional, default `None`)
	b: `float` (optional, default `None`)
	copy: `bool` (default: `False`)
  def umap(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_diffmap.py:4: UserWarning: 
Parameters in `scanpy.tl.diffmap` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	adata: :class:`~anndata.AnnData`
	n_comps: `int`, optional (default: 15)
	copy: `bool` (default: `False`)
	adata: :class:`~anndata.AnnData`
	n_comps: `int`, optional (default: 15)
	copy: `bool` (default: `False`)
  def diffmap(adata, n_comps=15, copy=False):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_louvain.py:22: UserWarning: 
Parameters in `scanpy.tl.louvain` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	flavor: {``'vtraag'``, ``'igraph'``}
	flavor: {``'vtraag'``, ``'igraph'``}
  def louvain(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_dendrogram.py:16: UserWarning: 
Parameters in `scanpy.tl.dendrogram` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	n_pcs: `int` or `None`, optional (default: `None`)
	use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`)
	n_pcs: `int` or `None`, optional (default: `None`)
	use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`)
  @_doc_params(n_pcs=doc_n_pcs, use_rep=doc_use_rep)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_dpt.py:30: UserWarning: 
Parameters in `scanpy.tl.dpt` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	adata: :class:`~anndata.AnnData`
	n_dcs: `int`, optional (default: 10)
	n_branchings: `int`, optional (default: 0)
	min_group_size: [0, 1] or `float`, optional (default: 0.01)
	allow_kendall_tau_shift: `bool`, optional (default: `True`)
	copy: `bool`, optional (default: `False`)
	adata: :class:`~anndata.AnnData`
	n_dcs: `int`, optional (default: 10)
	n_branchings: `int`, optional (default: 0)
	min_group_size: [0, 1] or `float`, optional (default: 0.01)
	allow_kendall_tau_shift: `bool`, optional (default: `True`)
	copy: `bool`, optional (default: `False`)
  def dpt(adata, n_dcs=10, n_branchings=0, min_group_size=0.01,
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_rank_genes_groups.py:17: UserWarning: 
Parameters in `scanpy.tl.rank_genes_groups` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	method: {`'logreg'`, `'t-test'`, `'wilcoxon'`, `'t-test_overestim_var'`}`
	method: {`'logreg'`, `'t-test'`, `'wilcoxon'`, `'t-test_overestim_var'`}`
  def rank_genes_groups(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_marker_gene_overlap.py:72: UserWarning: 
Parameters in `scanpy.tl.marker_gene_overlap` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	method: `{'overlap_count', 'overlap_coef', 'jaccard'}`, optional
	normalize: `{'reference', 'data', 'None'}`, optional (default: `None`)
	method: `{'overlap_count', 'overlap_coef', 'jaccard'}`, optional
	normalize: `{'reference', 'data', 'None'}`, optional (default: `None`)
  def marker_gene_overlap(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/readwrite.py:38: UserWarning: 
Parameters in `scanpy.read` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	backed: {``None``, ``'r'``, ``'r+'``}
	cache_compression: {`'gzip'`, `'lzf'`, `None`}
	backed: {``None``, ``'r'``, ``'r+'``}
	cache_compression: {`'gzip'`, `'lzf'`, `None`}
  def read(
/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` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	backed: {``None``, ``'r'``, ``'r+'``}
	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/_settings.py:361: UserWarning: 
Parameters in `scanpy.set_figure_params` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	format: {`'png'`, `'pdf'`, `'svg'`, etc.}, optional (default: `'pdf'`)
	format: {`'png'`, `'pdf'`, `'svg'`, etc.}, optional (default: `'pdf'`)
  def set_figure_params(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:544: UserWarning: 
Parameters in `scanpy.pp.normalize_per_cell` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse`
	counts_per_cell_after: `float` or `None`, optional (default: `None`)
	counts_per_cell: `np.array`, optional (default: `None`)
	key_n_counts: `str`, optional (default: `'n_counts'`)
	copy: `bool`, optional (default: `False`)
	min_counts: `int`, optional (default: 1)
	data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse`
	counts_per_cell_after: `float` or `None`, optional (default: `None`)
	counts_per_cell: `np.array`, optional (default: `None`)
	key_n_counts: `str`, optional (default: `'n_counts'`)
	copy: `bool`, optional (default: `False`)
	min_counts: `int`, optional (default: 1)
  def normalize_per_cell(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/neighbors/__init__.py:768: UserWarning: 
Parameters in `scanpy.Neighbors.compute_eigen` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	n_comps: `int`
	sym: `bool`
	matrix: sparse matrix, np.ndarray, optional (default: `.connectivities`)
	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:576: UserWarning: 
Parameters in `scanpy.Neighbors.compute_neighbors` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	n_pcs: `int` or `None`, optional (default: `None`)
	use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`)
	n_pcs: `int` or `None`, optional (default: `None`)
	use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`)
  @_doc_params(n_pcs=doc_n_pcs, use_rep=doc_use_rep)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/neighbors/__init__.py:730: UserWarning: 
Parameters in `scanpy.Neighbors.compute_transitions` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	density_normalize: `bool`
	density_normalize: `bool`
  def compute_transitions(self, density_normalize=True):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_settings.py:361: UserWarning: 
Parameters in `scanpy._settings.ScanpyConfig.set_figure_params` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	format: {`'png'`, `'pdf'`, `'svg'`, etc.}, optional (default: `'pdf'`)
	format: {`'png'`, `'pdf'`, `'svg'`, etc.}, optional (default: `'pdf'`)
  def set_figure_params(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_highly_variable_genes.py:167: UserWarning: 
Parameters in `scanpy.api.pp.highly_variable_genes` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	min_mean: `float`, optional (default: 0.0125)
	max_mean: `float`, optional (default: 3)
	min_disp: `float`, optional (default: 0.5)
	max_disp: `float`, optional (default: `None`)
	n_top_genes: `int` or `None`, optional (default: `None`)
	n_bins: `int`, optional (default: 20)
	subset: `bool`, optional (default: `False`)
	inplace: `bool`, optional (default: `True`)
	batch_key: `str`, optional (default: `None`)
  def highly_variable_genes(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:544: UserWarning: 
Parameters in `scanpy.api.pp.normalize_per_cell` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse`
	counts_per_cell_after: `float` or `None`, optional (default: `None`)
	counts_per_cell: `np.array`, optional (default: `None`)
	key_n_counts: `str`, optional (default: `'n_counts'`)
	copy: `bool`, optional (default: `False`)
	min_counts: `int`, optional (default: 1)
  def normalize_per_cell(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:714: UserWarning: 
Parameters in `scanpy.api.pp.regress_out` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	adata: :class:`~anndata.AnnData`
	keys: `str` or list of `str`
	n_jobs: `int` or `None`, optional. If None is given, then the n_jobs seting is used (default: `None`)
	copy: `bool`, optional (default: `False`)
  def regress_out(adata, keys, n_jobs=None, copy=False) -> Optional[AnnData]:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:842: UserWarning: 
Parameters in `scanpy.api.pp.scale` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse`
	zero_center: `bool`, optional (default: `True`)
	max_value: `float` or `None`, optional (default: `None`)
	copy: `bool`, optional (default: `False`)
  def scale(data, zero_center=True, max_value=None, copy=False) -> Optional[AnnData]:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:898: UserWarning: 
Parameters in `scanpy.api.pp.subsample` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse`
	fraction: `float` in [0, 1] or `None`, optional (default: `None`)
	n_obs: `int` or `None`, optional (default: `None`)
	random_state: `int` or `None`, optional (default: 0)
	copy: `bool`, optional (default: `False`)
  def subsample(data, fraction=None, n_obs=None, random_state=0, copy=False) -> Optional[AnnData]:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_recipes.py:74: UserWarning: 
Parameters in `scanpy.api.pp.recipe_zheng17` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	adata: :class:`~anndata.AnnData`
	n_top_genes: `int`, optional (default: 1000)
	log: `bool`, optional (default: `True`)
	plot: `bool`, optional (default: `True`)
	copy: `bool`, optional (default: `False`)
  def recipe_zheng17(adata, n_top_genes=1000, log=True, plot=False, copy=False):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/pp/_dca.py:6: UserWarning: 
Parameters in `scanpy.api.pp.dca` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace 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/neighbors/__init__.py:22: UserWarning: 
Parameters in `scanpy.api.pp.neighbors` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	n_pcs: `int` or `None`, optional (default: `None`)
	use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`)
	method: {`'umap'`, `'gauss'`, `None`}  (default: `'umap'`)
  @_doc_params(n_pcs=doc_n_pcs, use_rep=doc_use_rep)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_tsne.py:7: UserWarning: 
Parameters in `scanpy.api.tl.tsne` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	adata: :class:`~anndata.AnnData`
	n_pcs: `int` or `None`, optional (default: `None`)
	use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`)
	perplexity: `float`, optional (default: 30)
	early_exaggeration: `float`, optional (default: 12.0)
	learning_rate: `float`, optional (default: 1000)
	random_state: `int` or `None`, optional (default: 0)
	use_fast_tsne: `bool`, optional (default: `True`)
	n_jobs: `int` or `None` (default: `sc.settings.n_jobs`)
	copy: `bool` (default: `False`)
  @_doc_params(doc_n_pcs=doc_n_pcs, use_rep=doc_use_rep)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_umap.py:10: UserWarning: 
Parameters in `scanpy.api.tl.umap` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	adata: :class:`~anndata.AnnData`
	min_dist: `float`, optional (default: 0.5)
	spread: `float` (optional, default 1.0)
	n_components: `int`, optional (default: 2)
	maxiter: `int`, optional (default: `None`)
	alpha: `float`, optional (default: 1.0)
	gamma: `float` (optional, default 1.0)
	negative_sample_rate: `int` (optional, default 5)
	init_pos: `string` or `np.array`, optional (default: 'spectral')
	random_state: `int`, `RandomState` or `None`, optional (default: 0)
	a: `float` (optional, default `None`)
	b: `float` (optional, default `None`)
	copy: `bool` (default: `False`)
  def umap(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_diffmap.py:4: UserWarning: 
Parameters in `scanpy.api.tl.diffmap` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	adata: :class:`~anndata.AnnData`
	n_comps: `int`, optional (default: 15)
	copy: `bool` (default: `False`)
  def diffmap(adata, n_comps=15, copy=False):
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_louvain.py:22: UserWarning: 
Parameters in `scanpy.api.tl.louvain` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	flavor: {``'vtraag'``, ``'igraph'``}
  def louvain(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_dpt.py:30: UserWarning: 
Parameters in `scanpy.api.tl.dpt` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	adata: :class:`~anndata.AnnData`
	n_dcs: `int`, optional (default: 10)
	n_branchings: `int`, optional (default: 0)
	min_group_size: [0, 1] or `float`, optional (default: 0.01)
	allow_kendall_tau_shift: `bool`, optional (default: `True`)
	copy: `bool`, optional (default: `False`)
  def dpt(adata, n_dcs=10, n_branchings=0, min_group_size=0.01,
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_rank_genes_groups.py:17: UserWarning: 
Parameters in `scanpy.api.tl.rank_genes_groups` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	method: {`'logreg'`, `'t-test'`, `'wilcoxon'`, `'t-test_overestim_var'`}`
  def rank_genes_groups(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/readwrite.py:38: UserWarning: 
Parameters in `scanpy.api.read` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	backed: {``None``, ``'r'``, ``'r+'``}
	cache_compression: {`'gzip'`, `'lzf'`, `None`}
  def read(
/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` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace 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/_settings.py:361: UserWarning: 
Parameters in `scanpy.api.set_figure_params` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	format: {`'png'`, `'pdf'`, `'svg'`, etc.}, optional (default: `'pdf'`)
  def set_figure_params(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:24: UserWarning: 
Parameters in `scanpy.pl.diffmap` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	legend_fontweight: {`'normal'`, `'bold'`, ...}
	legend_fontweight: {`'normal'`, `'bold'`, ...}
  @_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/_anndata.py:1353: UserWarning: 
Parameters in `scanpy.pl.dotplot` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace 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`)
	standard_scale: {`'var'`, `'group'`}, optional (default: `None`)
	smallest_dot: `float` optional (default: 0.)
	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`)
	standard_scale: {`'var'`, `'group'`}, 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:24: UserWarning: 
Parameters in `scanpy.pl.draw_graph` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	layout: {`'fa'`, `'fr'`, `'drl'`, ...}, optional (default: last computed)
	edges_color: matplotlib color(s), optional (default: `'grey'`)
	legend_fontweight: {`'normal'`, `'bold'`, ...}
	layout: {`'fa'`, `'fr'`, `'drl'`, ...}, optional (default: last computed)
	edges_color: matplotlib color(s), optional (default: `'grey'`)
	legend_fontweight: {`'normal'`, `'bold'`, ...}
  @_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:24: UserWarning: 
Parameters in `scanpy.pl.embedding` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	edges_color: matplotlib color(s), optional (default: `'grey'`)
	legend_fontweight: {`'normal'`, `'bold'`, ...}
	edges_color: matplotlib color(s), optional (default: `'grey'`)
	legend_fontweight: {`'normal'`, `'bold'`, ...}
  @_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` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	show: bool, optional (default: `None`)
	save: `bool` or `str`, optional (default: `None`)
	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:1064: UserWarning: 
Parameters in `scanpy.pl.heatmap` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace 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`)
	standard_scale: {`'var'`, `'obs'`}, optional (default: `None`)
	swap_axes: `bool`, optional (default: `False`)
	show_gene_labels: `bool`, optional (default: `None`).
	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`)
	standard_scale: {`'var'`, `'obs'`}, optional (default: `None`)
	swap_axes: `bool`, optional (default: `False`)
	show_gene_labels: `bool`, optional (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` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	adata: :class:`~anndata.AnnData`, `np.recarray`
	log: `bool`
	show: bool, optional (default: `None`)
	save: `bool` or `str`, optional (default: `None`)
	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:1685: UserWarning: 
Parameters in `scanpy.pl.matrixplot` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace 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`)
	standard_scale: {`'var'`, `'group'`}, optional (default: `None`)
	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`)
	standard_scale: {`'var'`, `'group'`}, optional (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:242: UserWarning: 
Parameters in `scanpy.pl.paga` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	layout: {`'fa'`, `'fr'`, `'rt'`, `'rt_circular'`, `'eq_tree'`, ...}, optional (default: `'fr'`)
	normalize_to_color: `bool`, optional (default: `False`)
	layout: {`'fa'`, `'fr'`, `'rt'`, `'rt_circular'`, `'eq_tree'`, ...}, optional (default: `'fr'`)
	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:22: UserWarning: 
Parameters in `scanpy.pl.paga_compare` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	adata: :class:`~anndata.AnnData`
	kwds_scatter: `dict`
	kwds_paga: `dict`
	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/scatterplots.py:24: UserWarning: 
Parameters in `scanpy.pl.pca` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	legend_fontweight: {`'normal'`, `'bold'`, ...}
	legend_fontweight: {`'normal'`, `'bold'`, ...}
  @_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/__init__.py:26: UserWarning: 
Parameters in `scanpy.pl.pca_overview` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	color: string or list of strings, optional (default: `None`)
	use_raw: `bool`, optional (default: `True`)
	legend_fontweight: {`'normal'`, `'bold'`, ...}
	show: bool, optional (default: `None`)
	save: `bool` or `str`, optional (default: `None`)
	color: string or list of strings, optional (default: `None`)
	use_raw: `bool`, optional (default: `True`)
	legend_fontweight: {`'normal'`, `'bold'`, ...}
	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` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace 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`)
	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` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	adata: :class:`~anndata.AnnData`
	groups: `str` or `list` of `str`
	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` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	groups: `str` or `list` of `str`
	n_genes: `int`, optional (default: 10)
	groupby: `str` or `None`, optional (default: `None`)
	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` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	use_raw: `bool`, optional (default: `None`)
	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:38: UserWarning: 
Parameters in `scanpy.pl.scatter` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	basis: {`'pca'`, `'tsne'`, `'umap'`, `'diffmap'`, `'draw_graph_fr'`, etc.}
	legend_fontweight: {`'normal'`, `'bold'`, ...}
	basis: {`'pca'`, `'tsne'`, `'umap'`, `'diffmap'`, `'draw_graph_fr'`, etc.}
	legend_fontweight: {`'normal'`, `'bold'`, ...}
  @_doc_params(scatter_temp=doc_scatter_basic, show_save_ax=doc_show_save_ax)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:722: UserWarning: 
Parameters in `scanpy.pl.stacked_violin` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace 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`)
	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:1911: UserWarning: 
Parameters in `scanpy.pl.tracksplot` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace 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`)
	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:24: UserWarning: 
Parameters in `scanpy.pl.tsne` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	edges_color: matplotlib color(s), optional (default: `'grey'`)
	legend_fontweight: {`'normal'`, `'bold'`, ...}
	edges_color: matplotlib color(s), optional (default: `'grey'`)
	legend_fontweight: {`'normal'`, `'bold'`, ...}
  @_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:24: UserWarning: 
Parameters in `scanpy.pl.umap` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	edges_color: matplotlib color(s), optional (default: `'grey'`)
	legend_fontweight: {`'normal'`, `'bold'`, ...}
	edges_color: matplotlib color(s), optional (default: `'grey'`)
	legend_fontweight: {`'normal'`, `'bold'`, ...}
  @_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` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace 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`.
	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:24: UserWarning: 
Parameters in `scanpy.external.pl.phate` not set-like: {`elm-1`, `s_el.2`}.
Convert to this format or replace with type annotations:
	edges_color: matplotlib color(s), optional (default: `'grey'`)
	legend_fontweight: {`'normal'`, `'bold'`, ...}
	edges_color: matplotlib color(s), optional (default: `'grey'`)
	legend_fontweight: {`'normal'`, `'bold'`, ...}
  @_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/readwrite.py:docstring of scanpy.read:34:undefined label: dataset_compression (if the link has no caption the label must precede a section header)

Warning, treated as error:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/readwrite.py:docstring of scanpy.read:34:undefined label: dataset_compression (if the link has no caption the label must precede a section header)