Read the Docs build information
Build id: 1841400
Project: icb-scanpy
Version: 1.9.x
Commit: 70d55d5564e8442015341344582f98f69a466a1e
Date: 2023-11-13T15:57:54.093507Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-11-13T15:57:55.399801Z, end-time: 2023-11-13T15:57:56.558742Z, duration: 1, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy.git .
Cloning into '.'...

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git fetch origin --force --prune --prune-tags --depth 50 refs/heads/1.9.x:refs/remotes/origin/1.9.x
From https://github.com/scverse/scanpy
 * [new branch]      1.9.x      -> origin/1.9.x
 * [new tag]         1.9.2      -> 1.9.2
 * [new tag]         1.9.3      -> 1.9.3
 * [new tag]         1.9.4      -> 1.9.4
 * [new tag]         1.9.5      -> 1.9.5
 * [new tag]         1.9.6      -> 1.9.6

[rtd-command-info] start-time: 2023-11-13T15:57:58.156564Z, end-time: 2023-11-13T15:57:58.349466Z, duration: 0, exit-code: 0
git checkout --force origin/1.9.x
Note: switching to 'origin/1.9.x'.

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

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

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

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

HEAD is now at 70d55d5 Backport PR #2739 on branch 1.9.x (Catplot fix) (#2752)

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git clean -d -f -f


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

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asdf global python 3.9.18


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python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.9.18.final.0-64 in 866ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.9.x, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator

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python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.9.x/lib/python3.9/site-packages (23.1)
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Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 67.6.1
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      Successfully uninstalled setuptools-67.6.1
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    Found existing installation: pip 23.1
    Uninstalling pip-23.1:
      Successfully uninstalled pip-23.1
Successfully installed pip-23.3.1 setuptools-68.2.2

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python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext
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Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.3 Pygments-2.16.1 alabaster-0.7.13 babel-2.13.1 certifi-2023.7.22 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.4 imagesize-1.4.1 importlib-metadata-6.8.0 packaging-23.2 readthedocs-sphinx-ext-2.2.3 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.7 sphinxcontrib-devhelp-1.0.5 sphinxcontrib-htmlhelp-2.0.4 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.6 sphinxcontrib-serializinghtml-1.1.9 urllib3-2.1.0 zipp-3.17.0

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python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x
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  Created wheel for umap-learn: filename=umap_learn-0.5.4-py3-none-any.whl size=86777 sha256=1d15de8c0d9ff28a9c2742b32594135cd2bcd1a265fbac92804c0ac659ca5221
  Stored in directory: /tmp/pip-ephem-wheel-cache-tdzk_er4/wheels/e1/8b/ec/51afd5b0c041b6a7dd5777ceb58cc0d645ba9454cc5a923e96
  Building wheel for scanpy (pyproject.toml): started
  Building wheel for scanpy (pyproject.toml): finished with status 'done'
  Created wheel for scanpy: filename=scanpy-1.9.7.dev5+g70d55d5-py3-none-any.whl size=2034112 sha256=b2ec3a8b3c282f4c86682e04dffde10015d56d65b7819d407075140d4c8eef2b
  Stored in directory: /tmp/pip-ephem-wheel-cache-tdzk_er4/wheels/6a/38/46/29c747133e331f5aadf58ef1079a12176bb985d3018161ab34
  Building wheel for session-info (setup.py): started
  Building wheel for session-info (setup.py): finished with status 'done'
  Created wheel for session-info: filename=session_info-1.0.0-py3-none-any.whl size=8026 sha256=9e4f2ca2552c4cbe2cdf2f51544d2bce790df0200739c8377b9df9c63c370268
  Stored in directory: /tmp/pip-ephem-wheel-cache-tdzk_er4/wheels/d4/fc/2e/00ca60bac7954b84907efd41baa9b4853500eaeec4228410c6
  Building wheel for pynndescent (setup.py): started
  Building wheel for pynndescent (setup.py): finished with status 'done'
  Created wheel for pynndescent: filename=pynndescent-0.5.10-py3-none-any.whl size=55622 sha256=f40d5278803c9546347c0f1a81093a5daf708cfabde1b7d22fcb31a908527192
  Stored in directory: /tmp/pip-ephem-wheel-cache-tdzk_er4/wheels/12/f9/4d/ec5ad1c823c710fcc4473669fdcffc8891f4bc398c841af22e
Successfully built umap-learn scanpy session-info pynndescent
Installing collected packages: texttable, tbb, pytz, tzdata, tqdm, threadpoolctl, stdlib_list, six, pyyaml, pyparsing, pillow, numpy, networkx, natsort, mdurl, llvmlite, kiwisolver, joblib, importlib-resources, igraph, get-annotations, fonttools, exceptiongroup, docutils, cycler, array-api-compat, session-info, scipy, python-dateutil, patsy, numba, markdown-it-py, h5py, contourpy, scikit-learn, pandas, mdit-py-plugins, matplotlib, statsmodels, seaborn, pynndescent, anndata, umap-learn, scanpy, sphinxcontrib-jquery, sphinx-autodoc-typehints, scanpydoc, sphinx-rtd-theme, myst-parser
  Attempting uninstall: docutils
    Found existing installation: docutils 0.20.1
    Uninstalling docutils-0.20.1:
      Successfully uninstalled docutils-0.20.1
Successfully installed anndata-0.10.3 array-api-compat-1.4 contourpy-1.2.0 cycler-0.12.1 docutils-0.18.1 exceptiongroup-1.1.3 fonttools-4.44.0 get-annotations-0.1.2 h5py-3.10.0 igraph-0.11.2 importlib-resources-6.1.1 joblib-1.3.2 kiwisolver-1.4.5 llvmlite-0.41.1 markdown-it-py-3.0.0 matplotlib-3.8.1 mdit-py-plugins-0.4.0 mdurl-0.1.2 myst-parser-2.0.0 natsort-8.4.0 networkx-3.2.1 numba-0.58.1 numpy-1.26.2 pandas-2.1.3 patsy-0.5.3 pillow-10.1.0 pynndescent-0.5.10 pyparsing-3.1.1 python-dateutil-2.8.2 pytz-2023.3.post1 pyyaml-6.0.1 scanpy-1.9.7.dev5+g70d55d5 scanpydoc-0.7.11 scikit-learn-1.3.2 scipy-1.11.3 seaborn-0.13.0 session-info-1.0.0 six-1.16.0 sphinx-autodoc-typehints-1.25.2 sphinx-rtd-theme-1.3.0 sphinxcontrib-jquery-4.1 statsmodels-0.14.0 stdlib_list-0.9.0 tbb-2021.10.0 texttable-1.7.0 threadpoolctl-3.2.0 tqdm-4.66.1 tzdata-2023.3 umap-learn-0.5.4

[rtd-command-info] start-time: 2023-11-13T15:59:05.792892Z, end-time: 2023-11-13T15:59:05.868137Z, duration: 0, exit-code: 0
cat docs/conf.py
import os
import sys
from pathlib import Path
from datetime import datetime

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

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

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

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

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


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

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

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

release = version

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

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

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

typehints_defaults = 'braces'

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

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


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


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


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


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

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


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

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

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

# Options for plot examples

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




###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

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

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')

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

#Add project information to the template context.
context = {
    'html_theme': html_theme,
    'current_version': "1.9.x",
    'version_slug': "1.9.x",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ("1.9.x", "/en/1.9.x/"),
    ("1.8.x", "/en/1.8.x/"),
    ("1.7.x", "/en/1.7.x/"),
    ("1.6.x", "/en/1.6.x/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-scanpy',
    'name': u'scanpy',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': '',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'scverse',
    'proxied_api_host': '/_',
    'github_repo': 'scanpy',
    'github_version': '1.9.x',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '1.9.x',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '1.9.x',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '70d55d55',
}

# 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/1841400/'

project_language = 'en'

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

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

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

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

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

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

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

[rtd-command-info] start-time: 2023-11-13T15:59:05.947419Z, end-time: 2023-11-13T16:01:14.252875Z, duration: 128, exit-code: 0
python -m sphinx -T -E -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=set(), disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
loading intersphinx inventory from https://anndata.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://matplotlib.org/cycler/objects.inv...
loading intersphinx inventory from https://docs.h5py.org/en/stable/objects.inv...
loading intersphinx inventory from https://ipython.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://leidenalg.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://louvain-igraph.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://matplotlib.org/stable/objects.inv...
loading intersphinx inventory from https://networkx.org/documentation/stable/objects.inv...
loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv...
loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv...
loading intersphinx inventory from https://docs.pytest.org/en/latest/objects.inv...
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/scipy/objects.inv...
loading intersphinx inventory from https://seaborn.pydata.org/objects.inv...
loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv...
loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv...
[autosummary] generating autosummary for: _key_contributors.rst, api.md, basic_usage.md, community.md, contributors.md, dev/ci.md, dev/code.md, dev/documentation.md, dev/external-tools.md, dev/getting-set-up.md, ..., release-notes/1.9.2.md, release-notes/1.9.3.md, release-notes/1.9.4.md, release-notes/1.9.5.md, release-notes/1.9.6.md, release-notes/1.9.7.md, release-notes/index.md, release-notes/release-latest.md, tutorials.md, usage-principles.md
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.datasets.moignard15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.datasets.paul15.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.pca.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy.tl.umap.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/docs/generated/scanpy._settings.ScanpyConfig.writedir.rst
building [mo]: targets for 0 po files that are out of date
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_matrixplot.py:143: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  values_df = self.obs_tidy.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_matrixplot.py:143: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  values_df = self.obs_tidy.groupby(level=0).mean()
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_matrixplot.py:143: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  values_df = self.obs_tidy.groupby(level=0).mean()
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_dendrogram.py:135: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  mean_df = rep_df.groupby(level=0).mean()
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:1234: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:168: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  obs_bool.groupby(level=0).sum() / obs_bool.groupby(level=0).count()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:178: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  dot_color_df = self.obs_tidy.groupby(level=0).mean()
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_dendrogram.py:135: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  mean_df = rep_df.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:168: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  obs_bool.groupby(level=0).sum() / obs_bool.groupby(level=0).count()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:178: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  dot_color_df = self.obs_tidy.groupby(level=0).mean()
WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:168: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  obs_bool.groupby(level=0).sum() / obs_bool.groupby(level=0).count()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:178: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  dot_color_df = self.obs_tidy.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
reading sources... [ 58%] generated/scanpy.pl.dpt_groups_pseudotime
reading sources... [ 58%] generated/scanpy.pl.dpt_timeseries
reading sources... [ 58%] generated/scanpy.pl.draw_graph
WARNING: Package 'fa2' is not installed, falling back to layout 'fr'.To use the faster and better ForceAtlas2 layout, install package 'fa2' (`pip install fa2`).
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:1234: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:1234: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 59%] generated/scanpy.pl.embedding
reading sources... [ 59%] generated/scanpy.pl.embedding_density
:65: (ERROR/3) no path specified
:75: (ERROR/3) no path specified
:82: (ERROR/3) no path specified
reading sources... [ 59%] generated/scanpy.pl.filter_genes_dispersion
reading sources... [ 60%] generated/scanpy.pl.heatmap
reading sources... [ 60%] generated/scanpy.pl.highest_expr_genes
reading sources... [ 60%] generated/scanpy.pl.highly_variable_genes
reading sources... [ 61%] generated/scanpy.pl.matrixplot
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_matrixplot.py:143: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  values_df = self.obs_tidy.groupby(level=0).mean()
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_dendrogram.py:135: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  mean_df = rep_df.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_matrixplot.py:143: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  values_df = self.obs_tidy.groupby(level=0).mean()
WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_matrixplot.py:143: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  values_df = self.obs_tidy.groupby(level=0).mean()
reading sources... [ 61%] generated/scanpy.pl.paga

  0%|          | 0.00/23.5M [00:00<?, ?B/s]
 71%|███████   | 16.6M/23.5M [00:00<00:00, 174MB/s]
100%|██████████| 23.5M/23.5M [00:00<00:00, 190MB/s]
reading sources... [ 61%] generated/scanpy.pl.paga_compare
reading sources... [ 61%] generated/scanpy.pl.paga_path
reading sources... [ 62%] generated/scanpy.pl.pca
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  cax = scatter(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:1234: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 62%] generated/scanpy.pl.pca_loadings
reading sources... [ 62%] generated/scanpy.pl.pca_overview
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:1234: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 63%] generated/scanpy.pl.pca_variance_ratio
reading sources... [ 63%] generated/scanpy.pl.rank_genes_groups
reading sources... [ 63%] generated/scanpy.pl.rank_genes_groups_dotplot
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:168: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  obs_bool.groupby(level=0).sum() / obs_bool.groupby(level=0).count()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:178: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  dot_color_df = self.obs_tidy.groupby(level=0).mean()
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_dendrogram.py:135: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  mean_df = rep_df.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:168: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  obs_bool.groupby(level=0).sum() / obs_bool.groupby(level=0).count()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:178: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  dot_color_df = self.obs_tidy.groupby(level=0).mean()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:168: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  obs_bool.groupby(level=0).sum() / obs_bool.groupby(level=0).count()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:168: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  obs_bool.groupby(level=0).sum() / obs_bool.groupby(level=0).count()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:168: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  obs_bool.groupby(level=0).sum() / obs_bool.groupby(level=0).count()
WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
reading sources... [ 64%] generated/scanpy.pl.rank_genes_groups_heatmap
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_dendrogram.py:135: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  mean_df = rep_df.groupby(level=0).mean()
WARNING: Gene labels are not shown when more than 50 genes are visualized. To show gene labels set `show_gene_labels=True`
reading sources... [ 64%] generated/scanpy.pl.rank_genes_groups_matrixplot
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_dendrogram.py:135: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  mean_df = rep_df.groupby(level=0).mean()
WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
reading sources... [ 64%] generated/scanpy.pl.rank_genes_groups_stacked_violin
reading sources... [ 65%] generated/scanpy.pl.rank_genes_groups_tracksplot
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_dendrogram.py:135: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  mean_df = rep_df.groupby(level=0).mean()
reading sources... [ 65%] generated/scanpy.pl.rank_genes_groups_violin
reading sources... [ 65%] generated/scanpy.pl.ranking
reading sources... [ 66%] generated/scanpy.pl.scatter
reading sources... [ 66%] generated/scanpy.pl.sim
reading sources... [ 66%] generated/scanpy.pl.spatial
reading sources... [ 66%] generated/scanpy.pl.stacked_violin
reading sources... [ 67%] generated/scanpy.pl.tracksplot
reading sources... [ 67%] generated/scanpy.pl.tsne
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:1234: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 67%] generated/scanpy.pl.umap
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  cax = scatter(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:1234: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
  color_vector = pd.Categorical(values.map(color_map))
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_tools/scatterplots.py:394: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 68%] generated/scanpy.pl.violin
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_anndata.py:839: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_anndata.py:839: FutureWarning: 

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

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

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_anndata.py:839: FutureWarning: 

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

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

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_anndata.py:839: FutureWarning: 

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

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

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_anndata.py:839: FutureWarning: 

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

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

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  ax = sns.violinplot(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/plotting/_anndata.py:839: FutureWarning: 

The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='width'` for the same effect.
  ax = sns.violinplot(
reading sources... [ 68%] generated/scanpy.pp.calculate_qc_metrics

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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.9.x/lib/python3.9/site-packages/anndata/__init__.py:51: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024.
  warnings.warn(
reading sources... [ 68%] generated/scanpy.pp.combat
reading sources... [ 69%] generated/scanpy.pp.downsample_counts
reading sources... [ 69%] generated/scanpy.pp.filter_cells
reading sources... [ 69%] generated/scanpy.pp.filter_genes
reading sources... [ 70%] generated/scanpy.pp.filter_genes_dispersion
reading sources... [ 70%] generated/scanpy.pp.highly_variable_genes
reading sources... [ 70%] generated/scanpy.pp.log1p
reading sources... [ 70%] generated/scanpy.pp.neighbors
reading sources... [ 71%] generated/scanpy.pp.normalize_per_cell
reading sources... [ 71%] generated/scanpy.pp.normalize_total
reading sources... [ 71%] generated/scanpy.pp.pca
reading sources... [ 72%] generated/scanpy.pp.recipe_seurat
reading sources... [ 72%] generated/scanpy.pp.recipe_weinreb17
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reading sources... [ 73%] generated/scanpy.pp.regress_out
reading sources... [ 73%] generated/scanpy.pp.scale
reading sources... [ 73%] generated/scanpy.pp.subsample
reading sources... [ 74%] generated/scanpy.queries.biomart_annotations
reading sources... [ 74%] generated/scanpy.queries.enrich
reading sources... [ 74%] generated/scanpy.queries.gene_coordinates
reading sources... [ 75%] generated/scanpy.queries.mitochondrial_genes
reading sources... [ 75%] generated/scanpy.read
reading sources... [ 75%] generated/scanpy.read_10x_h5
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/external/pp/_mnn_correct.py:docstring of scanpy.external.pp._mnn_correct.mnn_correct:78: ERROR: Unexpected indentation.
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/external/pp/_scrublet.py:docstring of scanpy.external.pp._scrublet.scrublet:93: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/external/pp/_scrublet.py:docstring of scanpy.external.pp._scrublet.scrublet_simulate_doublets:23: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/external/tl/_palantir.py:docstring of scanpy.external.tl._palantir.palantir_results:32: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/preprocessing/_pca.py:docstring of scanpy.preprocessing._pca.pca:68: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/preprocessing/_pca.py:docstring of scanpy.preprocessing._pca.pca:70: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_ingest.py:docstring of scanpy.tools._ingest.ingest:56: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_ingest.py:docstring of scanpy.tools._ingest.ingest:57: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_leiden.py:docstring of scanpy.tools._leiden.leiden:58: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_leiden.py:docstring of scanpy.tools._leiden.leiden:60: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_louvain.py:docstring of scanpy.tools._louvain.louvain:55: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_paga.py:docstring of scanpy.tools._paga.paga:51: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_paga.py:docstring of scanpy.tools._paga.paga:53: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/preprocessing/_pca.py:docstring of scanpy.preprocessing._pca.pca:68: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/preprocessing/_pca.py:docstring of scanpy.preprocessing._pca.pca:70: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_rank_genes_groups.py:docstring of scanpy.tools._rank_genes_groups.rank_genes_groups:53: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.9.x/scanpy/tools/_rank_genes_groups.py:docstring of scanpy.tools._rank_genes_groups.rank_genes_groups:55: WARNING: Block quote ends without a blank line; unexpected unindent.
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