Read the Docs build information
Build id: 1952350
Project: icb-scanpy
Version: latest
Commit: 4f4b1c3a655546d981360bcce625d354a4291385
Date: 2024-01-16T11:13:46.605283Z
State: finished
Success: False


[rtd-command-info] start-time: 2024-01-16T11:13:47.846094Z, end-time: 2024-01-16T11:13:49.184517Z, duration: 1, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-01-16T11:13:49.268288Z, end-time: 2024-01-16T11:13:49.950227Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 refs/heads/master:refs/remotes/origin/master


[rtd-command-info] start-time: 2024-01-16T11:13:50.099976Z, end-time: 2024-01-16T11:13:50.310756Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to 'origin/master'.

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 4f4b1c3 [pre-commit.ci] pre-commit autoupdate (#2811)

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git clean -d -f -f


[rtd-command-info] start-time: 2024-01-16T11:13:50.514432Z, end-time: 2024-01-16T11:13:50.570402Z, duration: 0, exit-code: 0
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: 2024-01-16T11:13:57.186250Z, end-time: 2024-01-16T11:13:57.265491Z, duration: 0, exit-code: 0
asdf global python 3.11.6


[rtd-command-info] start-time: 2024-01-16T11:13:57.637819Z, end-time: 2024-01-16T11:13:58.712142Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.11.6.final.0-64 in 769ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2024-01-16T11:13:58.783256Z, end-time: 2024-01-16T11:14:09.366252Z, duration: 10, 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/latest/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/latest/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-23.3.2 setuptools-69.0.3

[rtd-command-info] start-time: 2024-01-16T11:14:09.438399Z, end-time: 2024-01-16T11:14:15.516092Z, duration: 6, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext
Collecting sphinx
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Downloading MarkupSafe-2.1.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (28 kB)
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Installing collected packages: snowballstemmer, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx, readthedocs-sphinx-ext
Successfully installed Jinja2-3.1.3 MarkupSafe-2.1.3 Pygments-2.17.2 alabaster-0.7.16 babel-2.14.0 certifi-2023.11.17 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.6 imagesize-1.4.1 packaging-23.2 readthedocs-sphinx-ext-2.2.5 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.8 sphinxcontrib-devhelp-1.0.6 sphinxcontrib-htmlhelp-2.0.5 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.7 sphinxcontrib-serializinghtml-1.1.10 urllib3-2.1.0

[rtd-command-info] start-time: 2024-01-16T11:14:15.583122Z, end-time: 2024-01-16T11:15:41.824204Z, duration: 86, 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/latest
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting anndata>=0.7.4 (from scanpy==0.1.dev50+g4f4b1c3)
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Collecting h5py>=3 (from scanpy==0.1.dev50+g4f4b1c3)
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  Downloading joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB)
Collecting legacy-api-wrap>=1.4 (from scanpy==0.1.dev50+g4f4b1c3)
  Downloading legacy_api_wrap-1.4-py3-none-any.whl.metadata (1.8 kB)
Collecting matplotlib>=3.6 (from scanpy==0.1.dev50+g4f4b1c3)
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Collecting numba>=0.41.0 (from scanpy==0.1.dev50+g4f4b1c3)
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Successfully built scanpy umap-learn sam-algorithm 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, readthedocs-sphinx-search, pyzmq, pyyaml, pyparsing, psutil, prompt-toolkit, platformdirs, pillow, pexpect, parso, pandocfilters, numpy, networkx, nest-asyncio, natsort, mistune, mdurl, llvmlite, legacy-api-wrap, kiwisolver, jupyterlab-pygments, joblib, igraph, greenlet, fonttools, executing, 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, sphinxext-opengraph, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, scikit-learn, scanpydoc, pydata-sphinx-theme, pandas, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, statsmodels, sphinx-book-theme, seaborn, pynndescent, myst-parser, jsonschema, ipython, harmonypy, anndata, umap-learn, nbformat, ipykernel, scanpy, sam-algorithm, nbclient, nbconvert, jupyter-cache, nbsphinx, myst-nb
Successfully installed accessible-pygments-0.0.4 anndata-0.10.4 array-api-compat-1.4 asttokens-2.4.1 attrs-23.2.0 beautifulsoup4-4.12.2 bleach-6.1.0 click-8.1.7 comm-0.2.1 contourpy-1.2.0 cycler-0.12.1 debugpy-1.8.0 decorator-5.1.1 defusedxml-0.7.1 dill-0.3.7 executing-2.0.1 fastjsonschema-2.19.1 fonttools-4.47.2 greenlet-3.0.3 h5py-3.10.0 harmonypy-0.0.9 hnswlib-0.8.0 igraph-0.10.8 importlib_metadata-7.0.1 ipykernel-6.28.0 ipython-8.20.0 jedi-0.19.1 joblib-1.3.2 jsonschema-4.20.0 jsonschema-specifications-2023.12.1 jupyter-cache-1.0.0 jupyter-client-8.6.0 jupyter-core-5.7.1 jupyterlab-pygments-0.3.0 kiwisolver-1.4.5 legacy-api-wrap-1.4 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-7.14.1 nbformat-5.9.2 nbsphinx-0.9.3 nest-asyncio-1.5.9 networkx-3.2.1 numba-0.58.1 numpy-1.26.3 pandas-2.1.4 pandocfilters-1.5.0 parso-0.8.3 patsy-0.5.6 pexpect-4.9.0 pillow-10.2.0 platformdirs-4.1.0 prompt-toolkit-3.0.43 psutil-5.9.7 ptyprocess-0.7.0 pure-eval-0.2.2 pydata-sphinx-theme-0.15.1 pynndescent-0.5.11 pyparsing-3.1.1 python-dateutil-2.8.2 pytz-2023.3.post1 pyyaml-6.0.1 pyzmq-25.1.2 readthedocs-sphinx-search-0.3.2 referencing-0.32.1 rpds-py-0.17.1 sam-algorithm-1.0.2 scanpy-0.1.dev50+g4f4b1c3 scanpydoc-0.13.4 scikit-learn-1.3.2 scipy-1.11.4 seaborn-0.13.1 session-info-1.0.0 six-1.16.0 soupsieve-2.5 sphinx-autodoc-typehints-1.25.2 sphinx-book-theme-1.1.0 sphinx-copybutton-0.5.2 sphinx-design-0.5.0 sphinxext-opengraph-0.9.1 sqlalchemy-2.0.25 stack-data-0.6.3 statsmodels-0.14.1 stdlib_list-0.10.0 tabulate-0.9.0 texttable-1.7.0 threadpoolctl-3.2.0 tinycss2-1.2.1 tornado-6.4 tqdm-4.66.1 traitlets-5.14.1 typing-extensions-4.9.0 tzdata-2023.4 umap-learn-0.5.5 wcwidth-0.2.13 webencodings-0.5.1 zipp-3.17.0

[rtd-command-info] start-time: 2024-01-16T11:15:42.395121Z, end-time: 2024-01-16T11:15:42.461166Z, 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",
    "sphinx_search.extension",
    "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 ----------------------------------------------

# The theme is sphinx-book-theme, with patches for readthedocs-sphinx-search
html_theme = "scanpydoc"
html_theme_options = {
    "repository_url": repository_url,
    "use_repository_button": True,
}
html_static_path = ["_static"]
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",
    "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 = [
    # Technical issues
    ("py:class", "numpy.int64"),  # documented as “attribute”
    # Will probably be documented
    ("py:class", "scanpy._settings.Verbosity"),
    ("py:class", "scanpy.neighbors.OnFlySymMatrix"),
    ("py:class", "scanpy.plotting._baseplot_class.BasePlot"),
    # Currently undocumented
    # https://github.com/mwaskom/seaborn/issues/1810
    ("py:class", "seaborn.matrix.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': "latest",
    'version_slug': "latest",
    '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': 'master',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'master',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'master',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '4f4b1c3a',
}

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





if 'html_context' in globals():
    for key in context:
        if key not in html_context:
            html_context[key] = context[key]
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/1952350/'

project_language = 'en'

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

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

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

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

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

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

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

[rtd-command-info] start-time: 2024-01-16T11:15:42.530916Z, end-time: 2024-01-16T11:19:06.198272Z, duration: 203, exit-code: 1
python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v7.2.6
making output directory... done
myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'colon_fence', 'html_image', 'html_admonition', 'deflist', 'dollarmath', 'amsmath'}, disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
myst-nb v1.0.0: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', 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/latest/_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...
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loading intersphinx inventory from https://python.igraph.org/en/stable/api/objects.inv...
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loading intersphinx inventory from https://seaborn.pydata.org/objects.inv...
loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv...
loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv...
[autosummary] generating autosummary for: _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/latest/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.embedding_density.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.filter_genes_dispersion.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.leiden.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.umap.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.writedir.rst
The default value for `navigation_with_keys` will change to `False` in the next release. If you wish to preserve the old behavior for your site, set `navigation_with_keys=True` in the `html_theme_options` dict in your `conf.py` file. Be aware that `navigation_with_keys = True` has negative accessibility implications: https://github.com/pydata/pydata-sphinx-theme/issues/1492
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 81 source files that are out of date
updating environment: [new config] 336 added, 0 changed, 0 removed
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:401: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
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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/latest/scanpy/plotting/_tools/scatterplots.py:401: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:401: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
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:65: (ERROR/3) no path specified
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:401: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
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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/latest/scanpy/plotting/_dotplot.py:811: 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/latest/scanpy/plotting/_dotplot.py:811: 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/latest/scanpy/plotting/_dotplot.py:811: 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/latest/scanpy/plotting/_dotplot.py:811: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
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/latest/scanpy/plotting/_dotplot.py:811: 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.
WARNING: Gene labels are not shown when more than 50 genes are visualized. To show gene labels set `show_gene_labels=True`
reading sources... [ 33%] 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.
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... [ 33%] 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.
reading sources... [ 34%] api/generated/scanpy.pl.rank_genes_groups_violin
reading sources... [ 34%] api/generated/scanpy.pl.sim
reading sources... [ 34%] api/generated/scanpy.pl.spatial
reading sources... [ 35%] api/generated/scanpy.pl.tsne
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:401: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 35%] api/generated/scanpy.pl.umap
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:401: 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/latest/scanpy/plotting/_tools/scatterplots.py:401: 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... [ 36%] api/generated/scanpy.pp.recipe_seurat
reading sources... [ 36%] api/generated/scanpy.pp.recipe_weinreb17
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reading sources... [ 37%] api/get
reading sources... [ 37%] api/index
reading sources... [ 37%] api/metrics
:17: (ERROR/3) no path specified
reading sources... [ 38%] api/plotting
:65: (ERROR/3) no path specified
:75: (ERROR/3) no path specified
:82: (ERROR/3) no path specified
reading sources... [ 38%] api/preprocessing
reading sources... [ 38%] api/queries
reading sources... [ 38%] api/reading
reading sources... [ 39%] api/settings
reading sources... [ 39%] api/tools
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reading sources... [ 44%] external/generated/scanpy.external.tl.palantir_results
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reading sources... [ 47%] generated/scanpy.Neighbors
reading sources... [ 48%] generated/scanpy.Neighbors.compute_eigen
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reading sources... [ 51%] generated/scanpy._settings.ScanpyConfig
reading sources... [ 52%] generated/scanpy._settings.ScanpyConfig.N_PCS
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reading sources... [ 54%] generated/scanpy._settings.ScanpyConfig.datasetdir
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reading sources... [ 55%] generated/scanpy._settings.ScanpyConfig.logfile
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reading sources... [ 56%] generated/scanpy._settings.ScanpyConfig.plot_suffix
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reading sources... [ 57%] generated/scanpy.datasets.blobs
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reading sources... [ 59%] generated/scanpy.datasets.pbmc3k_processed
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reading sources... [ 60%] generated/scanpy.datasets.visium_sge
reading sources... [ 60%] generated/scanpy.experimental.pp.highly_variable_genes
reading sources... [ 60%] generated/scanpy.experimental.pp.normalize_pearson_residuals
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reading sources... [ 61%] generated/scanpy.experimental.pp.recipe_pearson_residuals
reading sources... [ 61%] generated/scanpy.external.exporting.cellbrowser
reading sources... [ 62%] generated/scanpy.external.exporting.spring_project
reading sources... [ 62%] 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... [ 63%] generated/scanpy.external.pl.trimap
reading sources... [ 63%] generated/scanpy.external.pl.wishbone_marker_trajectory
reading sources... [ 63%] generated/scanpy.external.pp.bbknn
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reading sources... [ 64%] generated/scanpy.external.pp.harmony_integrate
reading sources... [ 64%] generated/scanpy.external.pp.hashsolo
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reading sources... [ 65%] generated/scanpy.external.pp.mnn_correct
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reading sources... [ 66%] generated/scanpy.external.pp.scrublet_simulate_doublets
reading sources... [ 66%] generated/scanpy.get.obs_df
reading sources... [ 66%] generated/scanpy.get.rank_genes_groups_df
reading sources... [ 67%] generated/scanpy.get.var_df
reading sources... [ 67%] generated/scanpy.logging.print_header
reading sources... [ 67%] generated/scanpy.logging.print_versions
reading sources... [ 68%] generated/scanpy.metrics.confusion_matrix
:17: (ERROR/3) no path specified
reading sources... [ 68%] 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/latest/lib/python3.11/site-packages/anndata/_core/anndata.py:1906: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
reading sources... [ 69%] generated/scanpy.pl.dendrogram
reading sources... [ 69%] generated/scanpy.pl.dotplot
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/latest/scanpy/plotting/_dotplot.py:811: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
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/latest/scanpy/plotting/_dotplot.py:811: 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/latest/scanpy/plotting/_dotplot.py:811: 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... [ 70%] generated/scanpy.pl.matrixplot
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.
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... [ 70%] generated/scanpy.pl.ranking
reading sources... [ 70%] generated/scanpy.pl.scatter
reading sources... [ 71%] 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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/latest/scanpy/plotting/_stacked_violin.py:503: 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... [ 71%] 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.
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... [ 71%] generated/scanpy.pl.violin
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:906: 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/latest/scanpy/plotting/_anndata.py:906: 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/latest/scanpy/plotting/_anndata.py:906: 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/latest/scanpy/plotting/_anndata.py:906: 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/latest/scanpy/plotting/_anndata.py:906: 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/latest/scanpy/plotting/_anndata.py:906: 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/latest/scanpy/plotting/_anndata.py:906: 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/latest/scanpy/plotting/_anndata.py:906: 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/latest/scanpy/plotting/_anndata.py:906: 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/latest/scanpy/plotting/_anndata.py:906: 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(
reading sources... [ 71%] generated/scanpy.pp.calculate_qc_metrics

  0%|          | 0.00/5.58M [00:00<?, ?B/s]
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  2%|▏         | 96.0k/5.58M [00:00<00:27, 211kB/s] 
  3%|▎         | 200k/5.58M [00:00<00:16, 352kB/s] 
  7%|▋         | 416k/5.58M [00:00<00:08, 649kB/s]
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 30%|██▉       | 1.67M/5.58M [00:01<00:01, 2.37MB/s]
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 86%|████████▌ | 4.80M/5.58M [00:01<00:00, 5.75MB/s]
100%|██████████| 5.58M/5.58M [00:01<00:00, 3.40MB/s]
reading sources... [ 72%] generated/scanpy.pp.downsample_counts
reading sources... [ 72%] generated/scanpy.pp.filter_cells
reading sources... [ 72%] generated/scanpy.pp.filter_genes
reading sources... [ 73%] generated/scanpy.pp.filter_genes_dispersion
reading sources... [ 73%] generated/scanpy.pp.highly_variable_genes
reading sources... [ 73%] generated/scanpy.pp.log1p
reading sources... [ 74%] generated/scanpy.pp.normalize_per_cell
reading sources... [ 74%] generated/scanpy.pp.normalize_total
reading sources... [ 74%] generated/scanpy.pp.pca
reading sources... [ 74%] generated/scanpy.pp.regress_out
reading sources... [ 75%] generated/scanpy.pp.scale
reading sources... [ 75%] generated/scanpy.pp.subsample
reading sources... [ 75%] generated/scanpy.queries.biomart_annotations
reading sources... [ 76%] generated/scanpy.queries.enrich
reading sources... [ 76%] generated/scanpy.queries.gene_coordinates
reading sources... [ 76%] generated/scanpy.queries.mitochondrial_genes
reading sources... [ 76%] generated/scanpy.read
reading sources... [ 77%] generated/scanpy.read_10x_h5
reading sources... [ 77%] generated/scanpy.read_10x_mtx
reading sources... [ 77%] generated/scanpy.read_csv
reading sources... [ 78%] generated/scanpy.read_excel
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reading sources... [ 78%] generated/scanpy.read_hdf
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/paga.py:docstring of scanpy.plotting._tools.paga.paga:120: WARNING: Exception occurred in plotting scanpy-pl-paga-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.paga.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/datasets/_utils.py", line 33, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/datasets/_utils.py", line 16, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/datasets/_datasets.py", line 318, in pbmc3k_processed
    return read(
           ^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/readwrite.py", line 124, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/readwrite.py", line 759, in _read
    return read_h5ad(filename, backed=backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/anndata/_io/h5ad.py", line 237, in read_h5ad
    with h5py.File(filename, "r") as f:
         ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/h5py/_hl/files.py", line 562, in __init__
    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/h5py/_hl/files.py", line 235, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5f.pyx", line 102, in h5py.h5f.open
OSError: Unable to synchronously open file (truncated file: eof = 32768, sblock->base_addr = 0, stored_eof = 24653425)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/paga.py:docstring of scanpy.plotting._tools.paga.paga:130: WARNING: Exception occurred in plotting scanpy-pl-paga-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.paga.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/paga.py", line 531, in paga
    groups_key = adata.uns["paga"]["groups"]
                 ~~~~~~~~~^^^^^^^^
KeyError: 'paga'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:docstring of scanpy.plotting._tools.scatterplots.pca:139: WARNING: Exception occurred in plotting scanpy-pl-pca-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.pca.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/datasets/_utils.py", line 33, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/datasets/_utils.py", line 16, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/datasets/_datasets.py", line 318, in pbmc3k_processed
    return read(
           ^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/readwrite.py", line 124, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/readwrite.py", line 759, in _read
    return read_h5ad(filename, backed=backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/anndata/_io/h5ad.py", line 237, in read_h5ad
    with h5py.File(filename, "r") as f:
         ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/h5py/_hl/files.py", line 562, in __init__
    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/h5py/_hl/files.py", line 235, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5f.pyx", line 102, in h5py.h5f.open
OSError: Unable to synchronously open file (truncated file: eof = 32768, sblock->base_addr = 0, stored_eof = 24653425)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.pca_loadings:21: WARNING: Exception occurred in plotting scanpy-pl-pca_loadings-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.pca_loadings.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/datasets/_utils.py", line 33, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/datasets/_utils.py", line 16, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/datasets/_datasets.py", line 318, in pbmc3k_processed
    return read(
           ^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/readwrite.py", line 124, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/readwrite.py", line 759, in _read
    return read_h5ad(filename, backed=backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/anndata/_io/h5ad.py", line 237, in read_h5ad
    with h5py.File(filename, "r") as f:
         ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/h5py/_hl/files.py", line 562, in __init__
    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/h5py/_hl/files.py", line 235, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5f.pyx", line 102, in h5py.h5f.open
OSError: Unable to synchronously open file (truncated file: eof = 32768, sblock->base_addr = 0, stored_eof = 24653425)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.pca_loadings:29: WARNING: Exception occurred in plotting scanpy-pl-pca_loadings-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.pca_loadings.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py", line 164, in pca_loadings
    ranking(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py", line 659, in ranking
    plt.ylim(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/matplotlib/pyplot.py", line 1983, in ylim
    ret = ax.set_ylim(*args, **kwargs)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/matplotlib/axes/_base.py", line 3898, in set_ylim
    return self.yaxis._set_lim(bottom, top, emit=emit, auto=auto)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/matplotlib/axis.py", line 1211, in _set_lim
    v1 = self.axes._validate_converted_limits(v1, self.convert_units)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/matplotlib/axes/_base.py", line 3585, in _validate_converted_limits
    raise ValueError("Axis limits cannot be NaN or Inf")
ValueError: Axis limits cannot be NaN or Inf
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.pca_overview:91: WARNING: Exception occurred in plotting scanpy-pl-pca_overview-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.pca_overview.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/datasets/_utils.py", line 33, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/datasets/_utils.py", line 16, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/datasets/_datasets.py", line 318, in pbmc3k_processed
    return read(
           ^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/readwrite.py", line 124, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/readwrite.py", line 759, in _read
    return read_h5ad(filename, backed=backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/anndata/_io/h5ad.py", line 237, in read_h5ad
    with h5py.File(filename, "r") as f:
         ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/h5py/_hl/files.py", line 562, in __init__
    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.11/site-packages/h5py/_hl/files.py", line 235, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5f.pyx", line 102, in h5py.h5f.open
OSError: Unable to synchronously open file (truncated file: eof = 32768, sblock->base_addr = 0, stored_eof = 24653425)
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
copying assets... copying static files... done
copying extra files... done
done
writing output... [  0%] _tutorials
writing output... [  1%] api/classes
writing output... [  1%] api/datasets
writing output... [  1%] api/deprecated
writing output... [  1%] api/experimental
writing output... [  2%] api/generated/classes/scanpy.pl.DotPlot
writing output... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT
writing output... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_WSPACE
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.MAX_NUM_CATEGORIES
writing output... [  8%] api/generated/classes/scanpy.pl.DotPlot.MIN_FIGURE_HEIGHT
writing output... [  8%] api/generated/classes/scanpy.pl.DotPlot.add_dendrogram
writing output... [  8%] api/generated/classes/scanpy.pl.DotPlot.add_totals
writing output... [  9%] api/generated/classes/scanpy.pl.DotPlot.get_axes
writing output... [  9%] api/generated/classes/scanpy.pl.DotPlot.getdoc
writing output... [  9%] api/generated/classes/scanpy.pl.DotPlot.legend
writing output... [ 10%] api/generated/classes/scanpy.pl.DotPlot.make_figure
writing output... [ 10%] api/generated/classes/scanpy.pl.DotPlot.savefig
writing output... [ 10%] api/generated/classes/scanpy.pl.DotPlot.show
writing output... [ 10%] api/generated/classes/scanpy.pl.DotPlot.style
writing output... [ 11%] api/generated/classes/scanpy.pl.DotPlot.swap_axes
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dumping search index in English (code: en)... done
dumping object inventory... done
Updating searchtools for Read the Docs search... build finished with problems, 6 warnings.