Read the Docs build information
Build id: 1972424
Project: icb-scanpy
Version: 1.9.x
Commit: 07c6e90b52f8e937119bc5da1721ab6a1961db25
Date: 2024-01-25T11:25:25.690011Z
State: finished
Success: True


[rtd-command-info] start-time: 2024-01-25T11:25:26.855899Z, end-time: 2024-01-25T11:25:27.824857Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy.git .
Cloning into '.'...

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git fetch origin --force --prune --prune-tags --depth 50 refs/heads/1.9.x:refs/remotes/origin/1.9.x
From https://github.com/scverse/scanpy
 * [new branch]      1.9.x      -> origin/1.9.x
 * [new tag]         1.9.4      -> 1.9.4
 * [new tag]         1.9.5      -> 1.9.5
 * [new tag]         1.9.6      -> 1.9.6

[rtd-command-info] start-time: 2024-01-25T11:25:29.391728Z, end-time: 2024-01-25T11:25:29.600498Z, duration: 0, exit-code: 0
git checkout --force origin/1.9.x
Note: switching to 'origin/1.9.x'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 07c6e90 Backport PR #2826 on branch 1.9.x (Prepare 1.9.7 release) (#2827)

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git clean -d -f -f


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cat .readthedocs.yml
version: 2
build:
  os: ubuntu-20.04
  tools:
    python: '3.9'
sphinx:
  configuration: docs/conf.py
python:
  install:
  - method: pip
    path: .
    extra_requirements:
    - doc

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asdf global python 3.9.18


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python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.9.18.final.0-64 in 855ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.9.x, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2024-01-25T11:25:40.547168Z, end-time: 2024-01-25T11:25:49.969030Z, duration: 9, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.9.x/lib/python3.9/site-packages (23.1)
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.9.x/lib/python3.9/site-packages (67.6.1)
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Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 67.6.1
    Uninstalling setuptools-67.6.1:
      Successfully uninstalled setuptools-67.6.1
  Attempting uninstall: pip
    Found existing installation: pip 23.1
    Uninstalling pip-23.1:
      Successfully uninstalled pip-23.1
Successfully installed pip-23.3.2 setuptools-69.0.3

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python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext
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Installing collected packages: snowballstemmer, zipp, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext
Successfully installed Jinja2-3.1.3 MarkupSafe-2.1.4 Pygments-2.17.2 alabaster-0.7.16 babel-2.14.0 certifi-2023.11.17 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.6 imagesize-1.4.1 importlib-metadata-7.0.1 packaging-23.2 readthedocs-sphinx-ext-2.2.5 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.8 sphinxcontrib-devhelp-1.0.6 sphinxcontrib-htmlhelp-2.0.5 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.7 sphinxcontrib-serializinghtml-1.1.10 urllib3-2.1.0 zipp-3.17.0

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python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
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Building wheels for collected packages: scanpy, umap-learn, session-info
  Building wheel for scanpy (pyproject.toml): started
  Building wheel for scanpy (pyproject.toml): finished with status 'done'
  Created wheel for scanpy: filename=scanpy-1.9.7.dev10+g07c6e90-py3-none-any.whl size=2034261 sha256=967c8ab2761a3d12faec371646963f639ec6a8eab8ae2ef6bbd9c55629fc18b5
  Stored in directory: /tmp/pip-ephem-wheel-cache-jkcey7cp/wheels/6a/38/46/29c747133e331f5aadf58ef1079a12176bb985d3018161ab34
  Building wheel for umap-learn (setup.py): started
  Building wheel for umap-learn (setup.py): finished with status 'done'
  Created wheel for umap-learn: filename=umap_learn-0.5.5-py3-none-any.whl size=86836 sha256=970d02c835f142332fc1d33279211c2a9d68345eb6f6d9025ec1772601528c9b
  Stored in directory: /tmp/pip-ephem-wheel-cache-jkcey7cp/wheels/0f/01/17/26951217a11fb724b7027c6dd5b620b6d368104f7e6d4171fc
  Building wheel for session-info (setup.py): started
  Building wheel for session-info (setup.py): finished with status 'done'
  Created wheel for session-info: filename=session_info-1.0.0-py3-none-any.whl size=8024 sha256=11c34e37eb1580a353a0afd35405ca56383a8b75789d1a14db0d7c87b46285d6
  Stored in directory: /tmp/pip-ephem-wheel-cache-jkcey7cp/wheels/d4/fc/2e/00ca60bac7954b84907efd41baa9b4853500eaeec4228410c6
Successfully built scanpy umap-learn session-info
Installing collected packages: texttable, pytz, tzdata, tqdm, threadpoolctl, stdlib_list, six, pyyaml, pyparsing, pillow, numpy, networkx, natsort, mdurl, llvmlite, kiwisolver, joblib, importlib-resources, igraph, get-annotations, fonttools, exceptiongroup, cycler, array-api-compat, session-info, scipy, python-dateutil, patsy, numba, markdown-it-py, h5py, contourpy, sphinxcontrib-jquery, sphinx-autodoc-typehints, scikit-learn, scanpydoc, pandas, mdit-py-plugins, matplotlib, statsmodels, sphinx-rtd-theme, seaborn, pynndescent, myst-parser, anndata, umap-learn, scanpy
Successfully installed anndata-0.10.4 array-api-compat-1.4.1 contourpy-1.2.0 cycler-0.12.1 exceptiongroup-1.2.0 fonttools-4.47.2 get-annotations-0.1.2 h5py-3.10.0 igraph-0.11.3 importlib-resources-6.1.1 joblib-1.3.2 kiwisolver-1.4.5 llvmlite-0.41.1 markdown-it-py-3.0.0 matplotlib-3.8.2 mdit-py-plugins-0.4.0 mdurl-0.1.2 myst-parser-2.0.0 natsort-8.4.0 networkx-3.2.1 numba-0.58.1 numpy-1.26.3 pandas-2.2.0 patsy-0.5.6 pillow-10.2.0 pynndescent-0.5.11 pyparsing-3.1.1 python-dateutil-2.8.2 pytz-2023.3.post1 pyyaml-6.0.1 scanpy-1.9.7.dev10+g07c6e90 scanpydoc-0.7.11 scikit-learn-1.4.0 scipy-1.12.0 seaborn-0.13.1 session-info-1.0.0 six-1.16.0 sphinx-autodoc-typehints-1.25.2 sphinx-rtd-theme-2.0.0 sphinxcontrib-jquery-4.1 statsmodels-0.14.1 stdlib_list-0.10.0 texttable-1.7.0 threadpoolctl-3.2.0 tqdm-4.66.1 tzdata-2023.4 umap-learn-0.5.5

[rtd-command-info] start-time: 2024-01-25T11:26:35.478113Z, end-time: 2024-01-25T11:26:35.538912Z, duration: 0, exit-code: 0
cat docs/conf.py
import os
import sys
from pathlib import Path
from datetime import datetime

import matplotlib  # noqa
from packaging.version import parse as parse_version

# Don’t use tkinter agg when importing scanpy → … → matplotlib
matplotlib.use('agg')

HERE = Path(__file__).parent
sys.path[:0] = [str(HERE.parent), str(HERE / 'extensions')]
import scanpy  # noqa

on_rtd = os.environ.get('READTHEDOCS') == 'True'

# -- General configuration ------------------------------------------------


nitpicky = True  # Warn about broken links. This is here for a reason: Do not change.
needs_sphinx = '2.0'  # Nicer param docs
suppress_warnings = [
    'ref.citation',
    'myst.header',  # https://github.com/executablebooks/MyST-Parser/issues/262
]

# General information
project = 'Scanpy'
author = 'Scanpy development team'
copyright = f'{datetime.now():%Y}, the Scanpy development team.'
version = scanpy.__version__.replace('.dirty', '')

# Bumping the version updates all docs, so don't do that
if parse_version(version).is_devrelease:
    parsed = parse_version(version)
    version = f"{parsed.major}.{parsed.minor}.{parsed.micro}.dev"

release = version

# default settings
templates_path = ['_templates']
master_doc = 'index'
default_role = 'literal'
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
pygments_style = 'sphinx'

extensions = [
    'myst_parser',
    'sphinx.ext.autodoc',
    'sphinx.ext.intersphinx',
    'sphinx.ext.doctest',
    'sphinx.ext.coverage',
    'sphinx.ext.mathjax',
    'sphinx.ext.napoleon',
    'sphinx.ext.autosummary',
    # 'plot_generator',
    'matplotlib.sphinxext.plot_directive',
    'sphinx_autodoc_typehints',  # needs to be after napoleon
    # 'ipython_directive',
    # 'ipython_console_highlighting',
    # 'scanpydoc',  # scanpydoc.elegant_typehints causes full doc rebuilds
    'scanpydoc.rtd_github_links',
    'scanpydoc.theme',
    'scanpydoc.definition_list_typed_field',
    'scanpydoc.autosummary_generate_imported',
    *[p.stem for p in (HERE / 'extensions').glob('*.py')],
]

# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = 'bysource'
# autodoc_default_flags = ['members']
napoleon_google_docstring = False
napoleon_numpy_docstring = True
napoleon_include_init_with_doc = False
napoleon_use_rtype = True  # having a separate entry generally helps readability
napoleon_use_param = True
napoleon_custom_sections = [('Params', 'Parameters')]
todo_include_todos = False
api_dir = HERE / 'api'  # function_images

typehints_defaults = 'braces'

scanpy_tutorials_url = 'https://scanpy-tutorials.readthedocs.io/en/latest/'

intersphinx_mapping = dict(
    anndata=('https://anndata.readthedocs.io/en/stable/', None),
    bbknn=('https://bbknn.readthedocs.io/en/latest/', None),
    cycler=('https://matplotlib.org/cycler/', None),
    h5py=('https://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/stable/', None),
    networkx=('https://networkx.org/documentation/stable/', None),
    numpy=('https://numpy.org/doc/stable/', None),
    pandas=('https://pandas.pydata.org/pandas-docs/stable/', None),
    pytest=('https://docs.pytest.org/en/latest/', None),
    python=('https://docs.python.org/3', None),
    scipy=('https://docs.scipy.org/doc/scipy/', None),
    seaborn=('https://seaborn.pydata.org/', None),
    sklearn=('https://scikit-learn.org/stable/', None),
    scanpy_tutorials=(scanpy_tutorials_url, None),
)


# -- Options for HTML output ----------------------------------------------


html_theme = 'scanpydoc'
html_theme_options = dict(
    navigation_depth=4,
    logo_only=True,
    docsearch_index='scanpy',
    docsearch_key='fa4304eb95d2134997e3729553a674b2',
)
html_context = dict(
    display_github=True,  # Integrate GitHub
    github_user='theislab',  # Username
    github_repo='scanpy',  # Repo name
    github_version='master',  # Version
    conf_py_path='/docs/',  # Path in the checkout to the docs root
)
html_static_path = ['_static']
html_show_sphinx = False
html_logo = '_static/img/Scanpy_Logo_BrightFG.svg'


def setup(app):
    app.warningiserror = (
        False  # Temporarily disable warnings as errors to get 1.9.2 out
    )


# -- Options for other output formats ------------------------------------------

htmlhelp_basename = f'{project}doc'
doc_title = f'{project} Documentation'
latex_documents = [(master_doc, f'{project}.tex', doc_title, author, 'manual')]
man_pages = [(master_doc, project, doc_title, [author], 1)]
texinfo_documents = [
    (
        master_doc,
        project,
        doc_title,
        author,
        project,
        'One line description of project.',
        'Miscellaneous',
    )
]


# -- Suppress link warnings ----------------------------------------------------

qualname_overrides = {
    "sklearn.neighbors._dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric",
    # If the docs are built with an old version of numpy, this will make it work:
    "numpy.random.RandomState": "numpy.random.mtrand.RandomState",
    "scanpy.plotting._matrixplot.MatrixPlot": "scanpy.pl.MatrixPlot",
    "scanpy.plotting._dotplot.DotPlot": "scanpy.pl.DotPlot",
    "scanpy.plotting._stacked_violin.StackedViolin": "scanpy.pl.StackedViolin",
    "pandas.core.series.Series": "pandas.Series",
}

nitpick_ignore = [
    # Will probably be documented
    ('py:class', 'scanpy._settings.Verbosity'),
    # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810
    ('py:class', 'seaborn.ClusterGrid'),
    # Won’t be documented
    ('py:class', 'scanpy.plotting._utils._AxesSubplot'),
    ('py:class', 'scanpy._utils.Empty'),
    ('py:class', 'numpy.random.mtrand.RandomState'),
    # Will work once scipy 1.8 is released
    ('py:class', 'scipy.sparse.base.spmatrix'),
    ('py:class', 'scipy.sparse.csr.csr_matrix'),
]

# Options for plot examples

plot_include_source = True
plot_formats = [("png", 90)]
plot_html_show_formats = False
plot_html_show_source_link = False
plot_working_directory = HERE.parent  # Project root




###########################################################################
#          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/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

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')

# Define this variable in case it's not defined by the user.
# It defaults to `alabaster` which is the default from Sphinx.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme
html_theme = globals().get('html_theme', 'alabaster')

#Add project information to the template context.
context = {
    'html_theme': html_theme,
    'current_version': "1.9.x",
    'version_slug': "1.9.x",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ("1.9.x", "/en/1.9.x/"),
    ("1.8.x", "/en/1.8.x/"),
    ("1.7.x", "/en/1.7.x/"),
    ("1.6.x", "/en/1.6.x/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-scanpy',
    'name': u'scanpy',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': '',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'scverse',
    'proxied_api_host': '/_',
    'github_repo': 'scanpy',
    'github_version': '1.9.x',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '1.9.x',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '1.9.x',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '07c6e90b',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





if 'html_context' in globals():
    for key in context:
        if key not in html_context:
            html_context[key] = context[key]
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")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/1972424/'

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2024-01-25T11:26:35.607574Z, end-time: 2024-01-25T11:29:20.028562Z, duration: 164, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v7.2.6
Matplotlib is building the font cache; this may take a moment.
making output directory... done
myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=set(), disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
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://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/stable/objects.inv...
loading intersphinx inventory from https://networkx.org/documentation/stable/objects.inv...
loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv...
loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv...
loading intersphinx inventory from https://docs.pytest.org/en/latest/objects.inv...
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/scipy/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: _key_contributors.rst, api.md, basic_usage.md, community.md, contributors.md, dev/ci.md, dev/code.md, dev/documentation.md, dev/external-tools.md, dev/getting-set-up.md, ..., release-notes/1.9.2.md, release-notes/1.9.3.md, release-notes/1.9.4.md, release-notes/1.9.5.md, release-notes/1.9.6.md, release-notes/1.9.7.md, release-notes/index.md, release-notes/release-latest.md, tutorials.md, usage-principles.md
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.datasets.moignard15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.datasets.paul15.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.pca.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.umap.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.writedir.rst
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_matrixplot.py:143: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  values_df = self.obs_tidy.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_matrixplot.py:143: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  values_df = self.obs_tidy.groupby(level=0).mean()
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_matrixplot.py:143: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  values_df = self.obs_tidy.groupby(level=0).mean()
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  mean_df = rep_df.groupby(level=0).mean()
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:1234: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:168: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  obs_bool.groupby(level=0).sum() / obs_bool.groupby(level=0).count()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:178: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  dot_color_df = self.obs_tidy.groupby(level=0).mean()
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_dendrogram.py:135: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  mean_df = rep_df.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:168: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  obs_bool.groupby(level=0).sum() / obs_bool.groupby(level=0).count()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:178: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  dot_color_df = self.obs_tidy.groupby(level=0).mean()
WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:168: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  obs_bool.groupby(level=0).sum() / obs_bool.groupby(level=0).count()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:178: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  dot_color_df = self.obs_tidy.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
reading sources... [ 58%] generated/scanpy.pl.dpt_groups_pseudotime
reading sources... [ 58%] generated/scanpy.pl.dpt_timeseries
reading sources... [ 58%] generated/scanpy.pl.draw_graph
WARNING: Package 'fa2' is not installed, falling back to layout 'fr'.To use the faster and better ForceAtlas2 layout, install package 'fa2' (`pip install fa2`).
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:1234: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:1234: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 59%] generated/scanpy.pl.embedding
reading sources... [ 59%] generated/scanpy.pl.embedding_density
:65: (ERROR/3) no path specified
:75: (ERROR/3) no path specified
:82: (ERROR/3) no path specified
reading sources... [ 59%] generated/scanpy.pl.filter_genes_dispersion
reading sources... [ 60%] generated/scanpy.pl.heatmap
reading sources... [ 60%] generated/scanpy.pl.highest_expr_genes
reading sources... [ 60%] generated/scanpy.pl.highly_variable_genes
reading sources... [ 61%] generated/scanpy.pl.matrixplot
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_matrixplot.py:143: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  values_df = self.obs_tidy.groupby(level=0).mean()
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_dendrogram.py:135: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  mean_df = rep_df.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_matrixplot.py:143: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  values_df = self.obs_tidy.groupby(level=0).mean()
WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_matrixplot.py:143: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  values_df = self.obs_tidy.groupby(level=0).mean()
reading sources... [ 61%] generated/scanpy.pl.paga

  0%|          | 0.00/23.5M [00:00<?, ?B/s]
 67%|██████▋   | 15.7M/23.5M [00:00<00:00, 164MB/s]
100%|██████████| 23.5M/23.5M [00:00<00:00, 181MB/s]
reading sources... [ 61%] generated/scanpy.pl.paga_compare
reading sources... [ 61%] generated/scanpy.pl.paga_path
reading sources... [ 62%] generated/scanpy.pl.pca
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  cax = scatter(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:1234: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 62%] generated/scanpy.pl.pca_loadings
reading sources... [ 62%] generated/scanpy.pl.pca_overview
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:1234: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 63%] generated/scanpy.pl.pca_variance_ratio
reading sources... [ 63%] generated/scanpy.pl.rank_genes_groups
reading sources... [ 63%] generated/scanpy.pl.rank_genes_groups_dotplot
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:168: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  obs_bool.groupby(level=0).sum() / obs_bool.groupby(level=0).count()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:178: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  dot_color_df = self.obs_tidy.groupby(level=0).mean()
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_dendrogram.py:135: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  mean_df = rep_df.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:168: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  obs_bool.groupby(level=0).sum() / obs_bool.groupby(level=0).count()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:178: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  dot_color_df = self.obs_tidy.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:168: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  obs_bool.groupby(level=0).sum() / obs_bool.groupby(level=0).count()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:168: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  obs_bool.groupby(level=0).sum() / obs_bool.groupby(level=0).count()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:168: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  obs_bool.groupby(level=0).sum() / obs_bool.groupby(level=0).count()
WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
reading sources... [ 64%] generated/scanpy.pl.rank_genes_groups_heatmap
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_dendrogram.py:135: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  mean_df = rep_df.groupby(level=0).mean()
WARNING: Gene labels are not shown when more than 50 genes are visualized. To show gene labels set `show_gene_labels=True`
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
reading sources... [ 64%] generated/scanpy.pl.rank_genes_groups_matrixplot
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_dendrogram.py:135: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  mean_df = rep_df.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
reading sources... [ 64%] generated/scanpy.pl.rank_genes_groups_stacked_violin
reading sources... [ 65%] generated/scanpy.pl.rank_genes_groups_tracksplot
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/get/get.py:69: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  d = d.stack(level=1).reset_index()
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_dendrogram.py:135: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  mean_df = rep_df.groupby(level=0).mean()
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  color_vector = pd.Categorical(values.map(color_map))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:1234: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_anndata.py:839: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.9.x/lib/python3.9/site-packages/seaborn/_base.py:949: FutureWarning: When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas. Pass `(name,)` instead of `name` to silence this warning.
  data_subset = grouped_data.get_group(pd_key)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.9.x/lib/python3.9/site-packages/seaborn/_base.py:949: FutureWarning: When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas. Pass `(name,)` instead of `name` to silence this warning.
  data_subset = grouped_data.get_group(pd_key)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_anndata.py:839: FutureWarning: 

Passing `palette` without assigning `hue` is deprecated and will be removed in v0.14.0. Assign the `x` variable to `hue` and set `legend=False` for the same effect.

  ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_anndata.py:839: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.9.x/lib/python3.9/site-packages/seaborn/_base.py:949: FutureWarning: When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas. Pass `(name,)` instead of `name` to silence this warning.
  data_subset = grouped_data.get_group(pd_key)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_anndata.py:839: FutureWarning: 

Passing `palette` without assigning `hue` is deprecated and will be removed in v0.14.0. Assign the `x` variable to `hue` and set `legend=False` for the same effect.

  ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_anndata.py:839: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.9.x/lib/python3.9/site-packages/seaborn/_base.py:949: FutureWarning: When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas. Pass `(name,)` instead of `name` to silence this warning.
  data_subset = grouped_data.get_group(pd_key)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_anndata.py:839: FutureWarning: 

Passing `palette` without assigning `hue` is deprecated and will be removed in v0.14.0. Assign the `x` variable to `hue` and set `legend=False` for the same effect.

  ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_anndata.py:839: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.9.x/lib/python3.9/site-packages/seaborn/_base.py:949: FutureWarning: When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas. Pass `(name,)` instead of `name` to silence this warning.
  data_subset = grouped_data.get_group(pd_key)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_anndata.py:839: FutureWarning: 

Passing `palette` without assigning `hue` is deprecated and will be removed in v0.14.0. Assign the `x` variable to `hue` and set `legend=False` for the same effect.

  ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_anndata.py:839: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.9.x/lib/python3.9/site-packages/seaborn/_base.py:949: FutureWarning: When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas. Pass `(name,)` instead of `name` to silence this warning.
  data_subset = grouped_data.get_group(pd_key)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_anndata.py:839: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.9.x/lib/python3.9/site-packages/seaborn/_base.py:949: FutureWarning: When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas. Pass `(name,)` instead of `name` to silence this warning.
  data_subset = grouped_data.get_group(pd_key)
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  warnings.warn(
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/external/pp/_scrublet.py:docstring of scanpy.external.pp._scrublet.scrublet:93: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/external/pp/_scrublet.py:docstring of scanpy.external.pp._scrublet.scrublet_simulate_doublets:23: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/external/tl/_palantir.py:docstring of scanpy.external.tl._palantir.palantir_results:32: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/preprocessing/_pca.py:docstring of scanpy.preprocessing._pca.pca:68: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/preprocessing/_pca.py:docstring of scanpy.preprocessing._pca.pca:70: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_ingest.py:docstring of scanpy.tools._ingest.ingest:56: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_ingest.py:docstring of scanpy.tools._ingest.ingest:57: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_leiden.py:docstring of scanpy.tools._leiden.leiden:58: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_leiden.py:docstring of scanpy.tools._leiden.leiden:60: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_louvain.py:docstring of scanpy.tools._louvain.louvain:55: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_paga.py:docstring of scanpy.tools._paga.paga:51: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_paga.py:docstring of scanpy.tools._paga.paga:53: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/preprocessing/_pca.py:docstring of scanpy.preprocessing._pca.pca:68: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/preprocessing/_pca.py:docstring of scanpy.preprocessing._pca.pca:70: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_rank_genes_groups.py:docstring of scanpy.tools._rank_genes_groups.rank_genes_groups:53: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_rank_genes_groups.py:docstring of scanpy.tools._rank_genes_groups.rank_genes_groups:55: WARNING: Block quote ends without a blank line; unexpected unindent.
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