Read the Docs build information
Build id: 1868068
Project: icb-scanpy
Version: 2590
Commit: 9c7db293c32e2fdce259bf5be253a5647b54dbca
Date: 2023-11-28T16:44:40.651560Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-11-28T16:44:41.787813Z, end-time: 2023-11-28T16:44:43.092644Z, duration: 1, 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 pull/2590/head:external-2590
From https://github.com/scverse/scanpy
 * [new ref]         refs/pull/2590/head -> external-2590

[rtd-command-info] start-time: 2023-11-28T16:44:44.234007Z, end-time: 2023-11-28T16:44:44.398476Z, duration: 0, exit-code: 0
git checkout --force 9c7db293c32e2fdce259bf5be253a5647b54dbca
Note: switching to '9c7db293c32e2fdce259bf5be253a5647b54dbca'.

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 9c7db29 Fix variance calculation

[rtd-command-info] start-time: 2023-11-28T16:44:44.480332Z, end-time: 2023-11-28T16:44:44.535894Z, duration: 0, exit-code: 0
git clean -d -f -f


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cat .readthedocs.yml
version: 2
build:
  os: ubuntu-20.04
  tools:
    python: '3.11'
sphinx:
  fail_on_warning: true # do not change or you will be fired
  configuration: docs/conf.py
python:
  install:
  - method: pip
    path: .
    extra_requirements:
    - doc
    - leiden

[rtd-command-info] start-time: 2023-11-28T16:44:51.281209Z, end-time: 2023-11-28T16:44:51.356376Z, duration: 0, exit-code: 0
asdf global python 3.11.6


[rtd-command-info] start-time: 2023-11-28T16:44:51.731990Z, end-time: 2023-11-28T16:44:52.853050Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.11.6.final.0-64 in 793ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2590, 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: 2023-11-28T16:44:52.925006Z, end-time: 2023-11-28T16:45:04.767641Z, duration: 11, 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/2590/lib/python3.11/site-packages (23.1)
Collecting pip
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2590/lib/python3.11/site-packages (67.6.1)
Collecting setuptools
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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-23.3.1 setuptools-69.0.2

[rtd-command-info] start-time: 2023-11-28T16:45:04.838778Z, end-time: 2023-11-28T16:45:13.469886Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext
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Installing collected packages: snowballstemmer, urllib3, sphinxcontrib-jsmath, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, readthedocs-sphinx-ext, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, sphinx
Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.3 Pygments-2.17.2 alabaster-0.7.13 babel-2.13.1 certifi-2023.11.17 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.6 imagesize-1.4.1 packaging-23.2 readthedocs-sphinx-ext-2.2.3 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.7 sphinxcontrib-devhelp-1.0.5 sphinxcontrib-htmlhelp-2.0.4 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.6 sphinxcontrib-serializinghtml-1.1.9 urllib3-2.1.0

[rtd-command-info] start-time: 2023-11-28T16:45:13.553997Z, end-time: 2023-11-28T16:46:52.388442Z, duration: 98, exit-code: 0
python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc,leiden]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
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  Stored in directory: /tmp/pip-ephem-wheel-cache-a930ngv6/wheels/0c/4e/72/438a6a71defb1c2ba8e15e371bbdc31e5c9ea3ae0084a38911
  Building wheel for scanpy (pyproject.toml): started
  Building wheel for scanpy (pyproject.toml): finished with status 'done'
  Created wheel for scanpy: filename=scanpy-0.1.dev137+g9c7db29-py3-none-any.whl size=2058321 sha256=9a52c8b2fe72ea69fc37de63e1c08279131c89530a476788f49315b4176ba7e2
  Stored in directory: /tmp/pip-ephem-wheel-cache-a930ngv6/wheels/45/43/b0/b9cec9996666837918e3c24aea798393f9db61589940bff213
  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=8026 sha256=fb3908804205c9fe934f9b2999563aad52603474b2961d2d99eecc8056d547c2
  Stored in directory: /tmp/pip-ephem-wheel-cache-a930ngv6/wheels/4e/56/35/a748fc57279a4b84d0b332879445fed1ad8478e7257986b015
  Building wheel for hnswlib (pyproject.toml): started
  Building wheel for hnswlib (pyproject.toml): finished with status 'done'
  Created wheel for hnswlib: filename=hnswlib-0.7.0-cp311-cp311-linux_x86_64.whl size=2177214 sha256=0cd268911eb2321b95e2ec74b7d522153059cad516de6c3baf3294f7315a1bba
  Stored in directory: /tmp/pip-ephem-wheel-cache-a930ngv6/wheels/fd/ea/08/149cab5879745530dcf6e264a61e0cc54a4e2e291247bb99ab
Successfully built umap-learn sam-algorithm scanpy session-info hnswlib
Installing collected packages: webencodings, wcwidth, texttable, pytz, pure-eval, ptyprocess, fastjsonschema, zipp, tzdata, typing-extensions, traitlets, tqdm, tornado, tinycss2, threadpoolctl, tabulate, stdlib_list, soupsieve, six, rpds-py, pyzmq, pyyaml, pyparsing, psutil, prompt-toolkit, platformdirs, pillow, pexpect, parso, pandocfilters, numpy, networkx, nest-asyncio, natsort, mistune, mdurl, llvmlite, kiwisolver, jupyterlab-pygments, joblib, igraph, greenlet, fonttools, executing, docutils, dill, defusedxml, decorator, debugpy, cycler, click, attrs, array-api-compat, accessible-pygments, sqlalchemy, session-info, scipy, referencing, python-dateutil, patsy, numba, matplotlib-inline, markdown-it-py, leidenalg, jupyter-core, jedi, importlib_metadata, hnswlib, h5py, contourpy, comm, bleach, beautifulsoup4, asttokens, stack-data, scikit-learn, pandas, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, statsmodels, seaborn, pynndescent, jsonschema, ipython, harmonypy, anndata, umap-learn, nbformat, ipykernel, scanpy, sam-algorithm, nbclient, nbconvert, jupyter-cache, sphinx, pydata-sphinx-theme, myst-parser, sphinxext-opengraph, sphinx-design, sphinx-copybutton, sphinx-book-theme, sphinx-autodoc-typehints, scanpydoc, nbsphinx, myst-nb
  Attempting uninstall: docutils
    Found existing installation: docutils 0.20.1
    Uninstalling docutils-0.20.1:
      Successfully uninstalled docutils-0.20.1
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 7.2.6
    Uninstalling Sphinx-7.2.6:
      Successfully uninstalled Sphinx-7.2.6
Successfully installed accessible-pygments-0.0.4 anndata-0.10.3 array-api-compat-1.4 asttokens-2.4.1 attrs-23.1.0 beautifulsoup4-4.12.2 bleach-6.1.0 click-8.1.7 comm-0.2.0 contourpy-1.2.0 cycler-0.12.1 debugpy-1.8.0 decorator-5.1.1 defusedxml-0.7.1 dill-0.3.7 docutils-0.19 executing-2.0.1 fastjsonschema-2.19.0 fonttools-4.45.1 greenlet-3.0.1 h5py-3.10.0 harmonypy-0.0.9 hnswlib-0.7.0 igraph-0.10.8 importlib_metadata-6.8.0 ipykernel-6.27.1 ipython-8.18.1 jedi-0.19.1 joblib-1.3.2 jsonschema-4.20.0 jsonschema-specifications-2023.11.1 jupyter-cache-1.0.0 jupyter-client-8.6.0 jupyter-core-5.5.0 jupyterlab-pygments-0.3.0 kiwisolver-1.4.5 leidenalg-0.10.1 llvmlite-0.41.1 markdown-it-py-3.0.0 matplotlib-3.8.2 matplotlib-inline-0.1.6 mdit-py-plugins-0.4.0 mdurl-0.1.2 mistune-3.0.2 myst-nb-1.0.0 myst-parser-2.0.0 natsort-8.4.0 nbclient-0.9.0 nbconvert-7.11.0 nbformat-5.9.2 nbsphinx-0.9.3 nest-asyncio-1.5.8 networkx-3.2.1 numba-0.58.1 numpy-1.26.2 pandas-2.1.3 pandocfilters-1.5.0 parso-0.8.3 patsy-0.5.3 pexpect-4.9.0 pillow-10.1.0 platformdirs-4.0.0 prompt-toolkit-3.0.41 psutil-5.9.6 ptyprocess-0.7.0 pure-eval-0.2.2 pydata-sphinx-theme-0.14.4 pynndescent-0.5.11 pyparsing-3.1.1 python-dateutil-2.8.2 pytz-2023.3.post1 pyyaml-6.0.1 pyzmq-25.1.1 referencing-0.31.0 rpds-py-0.13.1 sam-algorithm-1.0.2 scanpy-0.1.dev137+g9c7db29 scanpydoc-0.9.5 scikit-learn-1.3.2 scipy-1.11.4 seaborn-0.13.0 session-info-1.0.0 six-1.16.0 soupsieve-2.5 sphinx-6.2.1 sphinx-autodoc-typehints-1.23.0 sphinx-book-theme-1.0.1 sphinx-copybutton-0.5.2 sphinx-design-0.5.0 sphinxext-opengraph-0.9.0 sqlalchemy-2.0.23 stack-data-0.6.3 statsmodels-0.14.0 stdlib_list-0.10.0 tabulate-0.9.0 texttable-1.7.0 threadpoolctl-3.2.0 tinycss2-1.2.1 tornado-6.3.3 tqdm-4.66.1 traitlets-5.14.0 typing-extensions-4.8.0 tzdata-2023.3 umap-learn-0.5.5 wcwidth-0.2.12 webencodings-0.5.1 zipp-3.17.0

[rtd-command-info] start-time: 2023-11-28T16:46:52.975342Z, end-time: 2023-11-28T16:46:53.035801Z, duration: 0, exit-code: 0
cat docs/conf.py
from __future__ import annotations

import sys
from datetime import datetime
from pathlib import Path
from typing import TYPE_CHECKING

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

if TYPE_CHECKING:
    from sphinx.application import Sphinx


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


nitpicky = True  # Warn about broken links. This is here for a reason: Do not change.
needs_sphinx = "4.0"  # 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"
repository_url = "https://github.com/scverse/scanpy"
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", "**.ipynb_checkpoints"]

extensions = [
    "myst_nb",
    "sphinx_copybutton",
    "sphinx.ext.autodoc",
    "sphinx.ext.intersphinx",
    "sphinx.ext.doctest",
    "sphinx.ext.coverage",
    "sphinx.ext.mathjax",
    "sphinx.ext.napoleon",
    "sphinx.ext.autosummary",
    "sphinx.ext.extlinks",
    "matplotlib.sphinxext.plot_directive",
    "sphinx_autodoc_typehints",  # needs to be after napoleon
    "git_ref",  # needs to be before scanpydoc.rtd_github_links
    "scanpydoc",  # needs to be before sphinx.ext.linkcode
    "sphinx.ext.linkcode",
    "sphinx_design",
    "sphinxext.opengraph",
    *[p.stem for p in (HERE / "extensions").glob("*.py") if p.stem not in {"git_ref"}],
]

# 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
myst_enable_extensions = [
    "amsmath",
    "colon_fence",
    "deflist",
    "dollarmath",
    "html_image",
    "html_admonition",
]
myst_url_schemes = ("http", "https", "mailto")
nb_output_stderr = "remove"
nb_execution_mode = "off"
nb_merge_streams = True


ogp_site_url = "https://scanpy.readthedocs.io/en/stable/"
ogp_image = "https://scanpy.readthedocs.io/en/stable/_static/Scanpy_Logo_BrightFG.svg"

typehints_defaults = "braces"

pygments_style = "default"
pygments_dark_style = "native"

intersphinx_mapping = dict(
    anndata=("https://anndata.readthedocs.io/en/stable/", None),
    bbknn=("https://bbknn.readthedocs.io/en/latest/", None),
    cuml=("https://docs.rapids.ai/api/cuml/stable/", None),
    cycler=("https://matplotlib.org/cycler/", None),
    dask=("https://docs.dask.org/en/stable/", None),
    dask_ml=("https://ml.dask.org/", None),
    h5py=("https://docs.h5py.org/en/stable/", None),
    ipython=("https://ipython.readthedocs.io/en/stable/", None),
    igraph=("https://python.igraph.org/en/stable/api/", 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),
    pynndescent=("https://pynndescent.readthedocs.io/en/latest/", None),
    pytest=("https://docs.pytest.org/en/latest/", None),
    python=("https://docs.python.org/3", None),
    rapids_singlecell=("https://rapids-singlecell.readthedocs.io/en/latest/", None),
    scipy=("https://docs.scipy.org/doc/scipy/", None),
    seaborn=("https://seaborn.pydata.org/", None),
    sklearn=("https://scikit-learn.org/stable/", None),
    tutorials=("https://scanpy-tutorials.readthedocs.io/en/latest/", None),
)


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

html_theme = "sphinx_book_theme"
html_theme_options = {
    "repository_url": repository_url,
    "use_repository_button": True,
}
html_static_path = ["_static"]
html_css_files = ["css/override.css"]
html_show_sphinx = False
html_logo = "_static/img/Scanpy_Logo_BrightFG.svg"
html_title = "scanpy"


def setup(app: Sphinx):
    """App setup hook."""
    app.add_config_value(
        "recommonmark_config",
        {
            "auto_toc_tree_section": "Contents",
            "enable_auto_toc_tree": True,
            "enable_math": True,
            "enable_inline_math": False,
            "enable_eval_rst": True,
        },
        True,
    )


# -- 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.metrics.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"),
    ("py:class", "scanpy.neighbors.OnFlySymMatrix"),
    # Currently undocumented
    # https://github.com/mwaskom/seaborn/issues/1810
    ("py:class", "seaborn.ClusterGrid"),
    ("py:class", "samalg.SAM"),
    # Won’t be documented
    ("py:class", "scanpy.plotting._utils._AxesSubplot"),
    ("py:class", "scanpy._utils.Empty"),
    ("py:class", "numpy.random.mtrand.RandomState"),
    ("py:class", "scanpy.neighbors._types.KnnTransformerLike"),
    # 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

# extlinks config
extlinks = {
    "issue": ("https://github.com/scverse/scanpy/issues/%s", "issue%s"),
    "pr": ("https://github.com/scverse/scanpy/pull/%s", "pr%s"),
}




###########################################################################
#          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': "2590",
    'version_slug': "2590",
    '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': '9c7db293c32e2fdce259bf5be253a5647b54dbca',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '9c7db293c32e2fdce259bf5be253a5647b54dbca',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '9c7db293c32e2fdce259bf5be253a5647b54dbca',
    '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': '9c7db293',
}

# 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 'external' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'https://github.com/scverse/scanpy/pull/2590'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/1868068/'

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: 2023-11-28T16:46:53.125420Z, end-time: 2023-11-28T16:55:42.104040Z, duration: 528, exit-code: 0
python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v6.2.1
Matplotlib is building the font cache; this may take a moment.
making output directory... done
myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'amsmath', 'dollarmath', 'deflist', 'html_image', 'html_admonition', 'colon_fence'}, disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
myst-nb v1.0.0: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', execution_mode='off', execution_cache_path='', execution_excludepatterns=(), execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=True, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='remove', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/_readthedocs/.jupyter_cache
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://docs.rapids.ai/api/cuml/stable/objects.inv...
loading intersphinx inventory from https://matplotlib.org/cycler/objects.inv...
loading intersphinx inventory from https://docs.dask.org/en/stable/objects.inv...
loading intersphinx inventory from https://ml.dask.org/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://python.igraph.org/en/stable/api/objects.inv...
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[autosummary] generating autosummary for: _tutorials.md, api/classes.md, api/datasets.md, api/deprecated.md, api/experimental.md, api/get.md, api/index.md, api/metrics.md, api/plotting.md, api/preprocessing.md, ..., release-notes/1.9.0.md, release-notes/1.9.1.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, usage-principles.md
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/scanpy.pl.embedding_density.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/scanpy.pl.filter_genes_dispersion.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy.tl.leiden.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy.tl.umap.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/docs/generated/scanpy._settings.ScanpyConfig.writedir.rst
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_matrixplot.py:148: 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/2590/scanpy/plotting/_matrixplot.py:148: 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/2590/scanpy/plotting/_matrixplot.py:148: 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/2590/scanpy/plotting/_tools/scatterplots.py:1251: 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/2590/scanpy/plotting/_tools/scatterplots.py:402: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
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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/2590/scanpy/plotting/_tools/scatterplots.py:1251: 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/2590/scanpy/plotting/_tools/scatterplots.py:402: 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/2590/scanpy/plotting/_tools/scatterplots.py:1251: 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/2590/scanpy/plotting/_tools/scatterplots.py:402: 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/2590/scanpy/plotting/_tools/scatterplots.py:402: 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/2590/scanpy/plotting/_tools/scatterplots.py:1251: 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/2590/scanpy/plotting/_tools/scatterplots.py:402: 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/2590/scanpy/plotting/_tools/scatterplots.py:1251: 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/2590/scanpy/plotting/_tools/scatterplots.py:402: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
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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/2590/scanpy/plotting/_dotplot.py:179: 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/2590/scanpy/plotting/_dotplot.py:189: 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/2590/scanpy/tools/_dendrogram.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.
  mean_df = rep_df.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_dotplot.py:757: 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/2590/scanpy/plotting/_dotplot.py:179: 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/2590/scanpy/plotting/_dotplot.py:189: 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/2590/scanpy/plotting/_dotplot.py:757: 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/2590/scanpy/plotting/_dotplot.py:179: 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/2590/scanpy/plotting/_dotplot.py:757: 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/2590/scanpy/plotting/_dotplot.py:179: 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/2590/scanpy/plotting/_dotplot.py:757: 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/2590/scanpy/plotting/_dotplot.py:179: 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/2590/scanpy/plotting/_dotplot.py:757: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
reading sources... [ 32%] api/generated/scanpy.pl.rank_genes_groups_heatmap
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
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/2590/scanpy/tools/_dendrogram.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.
  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`
reading sources... [ 32%] api/generated/scanpy.pl.rank_genes_groups_matrixplot
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
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/2590/scanpy/tools/_dendrogram.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.
  mean_df = rep_df.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
reading sources... [ 32%] api/generated/scanpy.pl.rank_genes_groups_stacked_violin
reading sources... [ 33%] api/generated/scanpy.pl.rank_genes_groups_tracksplot
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
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/2590/scanpy/tools/_dendrogram.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.
  mean_df = rep_df.groupby(level=0).mean()
reading sources... [ 33%] api/generated/scanpy.pl.rank_genes_groups_violin
reading sources... [ 33%] api/generated/scanpy.pl.sim
reading sources... [ 34%] api/generated/scanpy.pl.spatial
reading sources... [ 34%] api/generated/scanpy.pl.tsne
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_tools/scatterplots.py:1251: 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/2590/scanpy/plotting/_tools/scatterplots.py:402: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 34%] api/generated/scanpy.pl.umap
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_tools/scatterplots.py:402: 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/2590/scanpy/plotting/_tools/scatterplots.py:1251: 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/2590/scanpy/plotting/_tools/scatterplots.py:402: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 35%] api/generated/scanpy.pp.combat
reading sources... [ 35%] api/generated/scanpy.pp.neighbors
reading sources... [ 35%] api/generated/scanpy.pp.recipe_seurat
reading sources... [ 35%] api/generated/scanpy.pp.recipe_weinreb17
reading sources... [ 36%] api/generated/scanpy.pp.recipe_zheng17
reading sources... [ 36%] api/get
reading sources... [ 36%] api/index
reading sources... [ 37%] api/metrics
:17: (ERROR/3) no path specified
reading sources... [ 37%] api/plotting
:65: (ERROR/3) no path specified
:75: (ERROR/3) no path specified
:82: (ERROR/3) no path specified
reading sources... [ 37%] api/preprocessing
reading sources... [ 37%] api/queries
reading sources... [ 38%] api/reading
reading sources... [ 38%] api/settings
reading sources... [ 38%] api/tools
reading sources... [ 39%] basic_usage
reading sources... [ 39%] community
reading sources... [ 39%] contributors
reading sources... [ 40%] dev/ci
reading sources... [ 40%] dev/code
reading sources... [ 40%] dev/documentation
reading sources... [ 40%] dev/getting-set-up
reading sources... [ 41%] dev/index
reading sources... [ 41%] dev/release
reading sources... [ 41%] dev/testing
reading sources... [ 42%] dev/versioning
reading sources... [ 42%] ecosystem
reading sources... [ 42%] external/exporting
reading sources... [ 43%] external/generated/scanpy.external.tl.cyclone
reading sources... [ 43%] external/generated/scanpy.external.tl.harmony_timeseries
reading sources... [ 43%] external/generated/scanpy.external.tl.palantir
reading sources... [ 43%] external/generated/scanpy.external.tl.palantir_results
reading sources... [ 44%] external/generated/scanpy.external.tl.phate
reading sources... [ 44%] external/generated/scanpy.external.tl.phenograph
reading sources... [ 44%] external/generated/scanpy.external.tl.sam
reading sources... [ 45%] external/generated/scanpy.external.tl.sandbag
reading sources... [ 45%] external/generated/scanpy.external.tl.trimap
reading sources... [ 45%] external/generated/scanpy.external.tl.wishbone
reading sources... [ 45%] external/index
reading sources... [ 46%] external/plotting
reading sources... [ 46%] external/preprocessing
reading sources... [ 46%] external/tools
reading sources... [ 47%] generated/scanpy.Neighbors
reading sources... [ 47%] generated/scanpy.Neighbors.compute_eigen
reading sources... [ 47%] generated/scanpy.Neighbors.compute_neighbors
reading sources... [ 48%] generated/scanpy.Neighbors.compute_transitions
reading sources... [ 48%] generated/scanpy.Neighbors.connectivities
reading sources... [ 48%] generated/scanpy.Neighbors.distances
reading sources... [ 48%] generated/scanpy.Neighbors.distances_dpt
reading sources... [ 49%] generated/scanpy.Neighbors.eigen_basis
reading sources... [ 49%] generated/scanpy.Neighbors.eigen_values
reading sources... [ 49%] generated/scanpy.Neighbors.getdoc
reading sources... [ 50%] generated/scanpy.Neighbors.rp_forest
reading sources... [ 50%] generated/scanpy.Neighbors.to_igraph
reading sources... [ 50%] generated/scanpy.Neighbors.transitions
reading sources... [ 51%] generated/scanpy.Neighbors.transitions_sym
reading sources... [ 51%] generated/scanpy._settings.ScanpyConfig
reading sources... [ 51%] generated/scanpy._settings.ScanpyConfig.N_PCS
reading sources... [ 51%] generated/scanpy._settings.ScanpyConfig.autosave
reading sources... [ 52%] generated/scanpy._settings.ScanpyConfig.autoshow
reading sources... [ 52%] generated/scanpy._settings.ScanpyConfig.cache_compression
reading sources... [ 52%] generated/scanpy._settings.ScanpyConfig.cachedir
reading sources... [ 53%] generated/scanpy._settings.ScanpyConfig.categories_to_ignore
reading sources... [ 53%] generated/scanpy._settings.ScanpyConfig.datasetdir
reading sources... [ 53%] generated/scanpy._settings.ScanpyConfig.figdir
reading sources... [ 54%] generated/scanpy._settings.ScanpyConfig.file_format_data
reading sources... [ 54%] generated/scanpy._settings.ScanpyConfig.file_format_figs
reading sources... [ 54%] generated/scanpy._settings.ScanpyConfig.logfile
reading sources... [ 54%] generated/scanpy._settings.ScanpyConfig.logpath
reading sources... [ 55%] generated/scanpy._settings.ScanpyConfig.max_memory
reading sources... [ 55%] generated/scanpy._settings.ScanpyConfig.n_jobs
reading sources... [ 55%] generated/scanpy._settings.ScanpyConfig.plot_suffix
reading sources... [ 56%] generated/scanpy._settings.ScanpyConfig.set_figure_params
reading sources... [ 56%] generated/scanpy._settings.ScanpyConfig.verbosity
reading sources... [ 56%] generated/scanpy._settings.ScanpyConfig.writedir
reading sources... [ 56%] generated/scanpy.datasets.blobs
reading sources... [ 57%] generated/scanpy.datasets.ebi_expression_atlas
reading sources... [ 57%] generated/scanpy.datasets.krumsiek11
reading sources... [ 57%] generated/scanpy.datasets.moignard15
reading sources... [ 58%] generated/scanpy.datasets.paul15
reading sources... [ 58%] generated/scanpy.datasets.pbmc3k
reading sources... [ 58%] generated/scanpy.datasets.pbmc3k_processed
reading sources... [ 59%] generated/scanpy.datasets.pbmc68k_reduced
reading sources... [ 59%] generated/scanpy.datasets.toggleswitch
reading sources... [ 59%] generated/scanpy.datasets.visium_sge
reading sources... [ 59%] generated/scanpy.experimental.pp.highly_variable_genes
reading sources... [ 60%] generated/scanpy.experimental.pp.normalize_pearson_residuals
reading sources... [ 60%] generated/scanpy.experimental.pp.normalize_pearson_residuals_pca
reading sources... [ 60%] generated/scanpy.experimental.pp.recipe_pearson_residuals
reading sources... [ 61%] generated/scanpy.external.exporting.cellbrowser
reading sources... [ 61%] generated/scanpy.external.exporting.spring_project
reading sources... [ 61%] generated/scanpy.external.pl.phate
reading sources... [ 62%] generated/scanpy.external.pl.sam
reading sources... [ 62%] generated/scanpy.external.pl.scrublet_score_distribution
reading sources... [ 62%] generated/scanpy.external.pl.trimap
reading sources... [ 62%] generated/scanpy.external.pl.wishbone_marker_trajectory
reading sources... [ 63%] generated/scanpy.external.pp.bbknn
reading sources... [ 63%] generated/scanpy.external.pp.dca
reading sources... [ 63%] generated/scanpy.external.pp.harmony_integrate
reading sources... [ 64%] generated/scanpy.external.pp.hashsolo
reading sources... [ 64%] generated/scanpy.external.pp.magic
reading sources... [ 64%] generated/scanpy.external.pp.mnn_correct
reading sources... [ 64%] generated/scanpy.external.pp.scanorama_integrate
reading sources... [ 65%] generated/scanpy.external.pp.scrublet
reading sources... [ 65%] generated/scanpy.external.pp.scrublet_simulate_doublets
reading sources... [ 65%] generated/scanpy.get.aggregated
reading sources... [ 66%] generated/scanpy.get.obs_df
reading sources... [ 66%] generated/scanpy.get.rank_genes_groups_df
reading sources... [ 66%] generated/scanpy.get.var_df
reading sources... [ 67%] generated/scanpy.logging.print_header
reading sources... [ 67%] generated/scanpy.logging.print_versions
reading sources... [ 67%] generated/scanpy.metrics.confusion_matrix
:17: (ERROR/3) no path specified
reading sources... [ 67%] generated/scanpy.metrics.gearys_c
reading sources... [ 68%] generated/scanpy.metrics.morans_i
reading sources... [ 68%] generated/scanpy.pl.clustermap
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2590/lib/python3.11/site-packages/anndata/_core/anndata.py:1897: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
reading sources... [ 68%] generated/scanpy.pl.dendrogram
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/tools/_dendrogram.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.
  mean_df = rep_df.groupby(level=0).mean()
reading sources... [ 69%] generated/scanpy.pl.dotplot
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_dotplot.py:179: 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/2590/scanpy/plotting/_dotplot.py:189: 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/2590/scanpy/tools/_dendrogram.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.
  mean_df = rep_df.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_dotplot.py:757: 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/2590/scanpy/plotting/_dotplot.py:179: 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/2590/scanpy/plotting/_dotplot.py:189: 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/2590/scanpy/plotting/_dotplot.py:757: 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/2590/scanpy/plotting/_dotplot.py:179: 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/2590/scanpy/plotting/_dotplot.py:189: 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/2590/scanpy/plotting/_dotplot.py:757: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
reading sources... [ 69%] generated/scanpy.pl.heatmap
reading sources... [ 69%] generated/scanpy.pl.matrixplot
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_matrixplot.py:148: 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/2590/scanpy/tools/_dendrogram.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.
  mean_df = rep_df.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_matrixplot.py:148: 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/2590/scanpy/plotting/_matrixplot.py:148: 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... [ 70%] generated/scanpy.pl.ranking
reading sources... [ 70%] generated/scanpy.pl.scatter
reading sources... [ 70%] generated/scanpy.pl.stacked_violin
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/2590/scanpy/tools/_dendrogram.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.
  mean_df = rep_df.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:331: 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.
  _color_df = _matrix.groupby(level=0).median()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
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/2590/scanpy/plotting/_stacked_violin.py:331: 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.
  _color_df = _matrix.groupby(level=0).median()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:331: 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.
  _color_df = _matrix.groupby(level=0).median()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: 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.

  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: UserWarning: Numpy array is not a supported type for `palette`. Please convert your palette to a list. This will become an error in v0.14
  row_ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2590/scanpy/plotting/_stacked_violin.py:468: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  row_ax = sns.violinplot(
reading sources... [ 70%] generated/scanpy.pl.tracksplot
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/2590/scanpy/tools/_dendrogram.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.
  mean_df = rep_df.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
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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/checkouts/2590/scanpy/plotting/_anndata.py:851: 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/2590/scanpy/plotting/_anndata.py:851: 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/checkouts/2590/scanpy/plotting/_anndata.py:851: 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/2590/scanpy/plotting/_anndata.py:851: 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/checkouts/2590/scanpy/plotting/_anndata.py:851: 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/2590/scanpy/plotting/_anndata.py:851: 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/checkouts/2590/scanpy/plotting/_anndata.py:851: 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/2590/scanpy/plotting/_anndata.py:851: 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/checkouts/2590/scanpy/plotting/_anndata.py:851: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
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