Read the Docs build information
Build id: 3261558
Project: icb-scanpy
Version: 3757
Commit: 56fc82f477ff86ea807f8943b34e3ce1af9d04df
Date: 2025-08-08T08:42:26.122407Z
State: finished
Success: False


[rtd-command-info] start-time: 2025-08-08T08:42:26.991159Z, end-time: 2025-08-08T08:42:28.007416Z, duration: 1, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy.git .
Cloning into '.'...

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git fetch origin --force --prune --prune-tags --depth 50 pull/3757/head:external-3757
From https://github.com/scverse/scanpy
 * [new ref]         refs/pull/3757/head -> external-3757

[rtd-command-info] start-time: 2025-08-08T08:42:29.311886Z, end-time: 2025-08-08T08:42:29.361265Z, duration: 0, exit-code: 0
git checkout --force 56fc82f477ff86ea807f8943b34e3ce1af9d04df
Note: switching to '56fc82f477ff86ea807f8943b34e3ce1af9d04df'.

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 56fc82f Merge branch 'main' into fix-issue-3718

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cat .readthedocs.yml
version: 2
submodules:
  include: all
build:
  os: ubuntu-24.04
  tools:
    python: '3.13'
  jobs:
    post_checkout:
      # unshallow so version can be derived from tag
      - git fetch --unshallow || true
    pre_build:
      # run towncrier to preview the next version’s release notes
      - ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true
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
    - dev  # for towncrier
    - leiden

[rtd-command-info] start-time: 2025-08-08T08:42:29.632687Z, end-time: 2025-08-08T08:42:29.701442Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2025-08-08T08:42:29.796536Z, end-time: 2025-08-08T08:42:48.999130Z, duration: 19, exit-code: 0
git submodule update --init --force --
Submodule 'notebooks' (https://github.com/scverse/scanpy-tutorials/) registered for path 'notebooks'
Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/notebooks'...
Submodule path 'notebooks': checked out '86e1dd78bd12990f265a2f6d6eeae9b505804616'

[rtd-command-info] start-time: 2025-08-08T08:42:49.092871Z, end-time: 2025-08-08T08:42:53.550426Z, duration: 4, exit-code: 0
git fetch --unshallow || true
From https://github.com/scverse/scanpy
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 * [new tag]           1.9.0.dev0  -> 1.9.0.dev0
Fetching submodule notebooks
From https://github.com/scverse/scanpy-tutorials
 * branch            26e16f83387caef76abdd42afda3c7c13f7139f1 -> FETCH_HEAD

[rtd-command-info] start-time: 2025-08-08T08:42:59.375054Z, end-time: 2025-08-08T08:42:59.434969Z, duration: 0, exit-code: 0
asdf global python 3.13.3


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python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.13.3.final.0-64 in 828ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757, 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: 2025-08-08T08:43:01.116611Z, end-time: 2025-08-08T08:43:10.172355Z, duration: 9, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/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/3757/lib/python3.13/site-packages (67.6.1)
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Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 67.6.1
    Uninstalling setuptools-67.6.1:
      Successfully uninstalled setuptools-67.6.1
  Attempting uninstall: pip
    Found existing installation: pip 23.1
    Uninstalling pip-23.1:
      Successfully uninstalled pip-23.1
Successfully installed pip-25.2 setuptools-80.9.0

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python -m pip install --upgrade --no-cache-dir sphinx
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Installing collected packages: urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, roman-numerals-py, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset_normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx

Successfully installed Jinja2-3.1.6 MarkupSafe-3.0.2 Pygments-2.19.2 alabaster-1.0.0 babel-2.17.0 certifi-2025.8.3 charset_normalizer-3.4.2 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-25.0 requests-2.32.4 roman-numerals-py-3.1.0 snowballstemmer-3.0.1 sphinx-8.2.3 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.5.0

[rtd-command-info] start-time: 2025-08-08T08:43:15.071496Z, end-time: 2025-08-08T08:44:29.583351Z, duration: 74, exit-code: 0
python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc,dev,leiden]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757
  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'
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Collecting fast-array-utils>=1.2.1 (from fast-array-utils[accel,sparse]>=1.2.1->scanpy==1.12.0.dev107+g56fc82f4)
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Collecting matplotlib>=3.7.5 (from scanpy==1.12.0.dev107+g56fc82f4)
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Collecting networkx>=2.8.8 (from scanpy==1.12.0.dev107+g56fc82f4)
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Requirement already satisfied: packaging>=21.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages (from scanpy==1.12.0.dev107+g56fc82f4) (25.0)
Collecting pandas>=2.0.3 (from scanpy==1.12.0.dev107+g56fc82f4)
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Collecting statsmodels>=0.14.5 (from scanpy==1.12.0.dev107+g56fc82f4)
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Building wheels for collected packages: scanpy, sam-algorithm, hnswlib
  Building wheel for scanpy (pyproject.toml): started
  Building wheel for scanpy (pyproject.toml): finished with status 'done'
  Created wheel for scanpy: filename=scanpy-1.12.0.dev107+g56fc82f4-py3-none-any.whl size=2101369 sha256=7981d70d116587b667c0d9881aff8bb0ce6ace4ee8077c65421df764110e4dda
  Stored in directory: /tmp/pip-ephem-wheel-cache-0pa21kpk/wheels/25/c0/dc/6d224a242e4c6c35e42c90524326e9214664ccd103f0b4a8c2
  DEPRECATION: Building 'sam-algorithm' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'sam-algorithm'. Discussion can be found at https://github.com/pypa/pip/issues/6334
  Building wheel for sam-algorithm (setup.py): started
  Building wheel for sam-algorithm (setup.py): finished with status 'done'
  Created wheel for sam-algorithm: filename=sam_algorithm-1.0.2-py3-none-any.whl size=34665 sha256=ce58ad855207fa318ad4d29fd35d3164e043c2d001b6176fdb75eaed85c366a5
  Stored in directory: /tmp/pip-ephem-wheel-cache-0pa21kpk/wheels/b7/67/70/67ec89004e1dccab383c317142419fd53d7b55316b2fa46d24
  Building wheel for hnswlib (pyproject.toml): started
  Building wheel for hnswlib (pyproject.toml): finished with status 'done'
  Created wheel for hnswlib: filename=hnswlib-0.8.0-cp313-cp313-linux_x86_64.whl size=2405496 sha256=628d96a6304e069bd1a71e04fceaca34a31d9cbf356b13c61a7e6a8bb1edbaf2
  Stored in directory: /tmp/pip-ephem-wheel-cache-0pa21kpk/wheels/35/04/88/b31765a4b9957705e18065db4657e61fc8da54f50e3ef0b67e
Successfully built scanpy sam-algorithm hnswlib
Installing collected packages: webencodings, wcwidth, trove-classifiers, texttable, sortedcontainers, pytz, pure-eval, ptyprocess, multipledispatch, fastjsonschema, distlib, zipp, zict, tzdata, typing-extensions, traitlets, tqdm, tornado, toolz, tinycss2, threadpoolctl, tblib, tabulate, soupsieve, six, setuptools-scm, session-info2, rpds-py, pyzmq, pyyaml, pyparsing, pyarrow, psutil, prompt_toolkit, pluggy, platformdirs, pillow, pexpect, pathspec, parso, pandocfilters, optype, numpy, nodeenv, networkx, nest-asyncio, natsort, msgpack, mistune, mdurl, locket, llvmlite, legacy-api-wrap, latexcodec, kiwisolver, jupyterlab-pygments, joblib, ipython-pygments-lexers, igraph, identify, greenlet, fsspec, fonttools, filelock, executing, dill, defusedxml, decorator, debugpy, cycler, comm, cloudpickle, click, cfgv, bleach, attrs, asttokens, array-api-compat, accessible-pygments, virtualenv, towncrier, stack_data, sqlalchemy, scipy, referencing, python-dateutil, pybtex, patsy, partd, numpy-typing-compat, numba, matplotlib-inline, markdown-it-py, leidenalg, jupyter-core, jedi, importlib_metadata, hnswlib, hatchling, h5py, fast-array-utils, contourpy, beautifulsoup4, sphinxext-opengraph, sphinx-tabs, sphinx-issues, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, sparse, scikit-learn, scanpydoc, pydata-sphinx-theme, pybtex-docutils, pre-commit, pandas, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, ipython, hatch-vcs, dask, statsmodels, sphinxcontrib-bibtex, sphinx-book-theme, seaborn, scipy-stubs, pynndescent, myst-parser, jsonschema, ipykernel, harmonypy, distributed, anndata, umap-learn, nbformat, dask-glm, scanpy, sam-algorithm, nbclient, dask-ml, nbconvert, jupyter-cache, nbsphinx, myst-nb

Successfully installed accessible-pygments-0.0.5 anndata-0.11.3 array-api-compat-1.12.0 asttokens-3.0.0 attrs-25.3.0 beautifulsoup4-4.13.4 bleach-6.2.0 cfgv-3.4.0 click-8.2.1 cloudpickle-3.1.1 comm-0.2.3 contourpy-1.3.3 cycler-0.12.1 dask-2025.7.0 dask-glm-0.3.2 dask-ml-2025.1.0 debugpy-1.8.16 decorator-5.2.1 defusedxml-0.7.1 dill-0.4.0 distlib-0.4.0 distributed-2025.7.0 executing-2.2.0 fast-array-utils-1.2.1 fastjsonschema-2.21.1 filelock-3.18.0 fonttools-4.59.0 fsspec-2025.7.0 greenlet-3.2.4 h5py-3.14.0 harmonypy-0.0.10 hatch-vcs-0.5.0 hatchling-1.27.0 hnswlib-0.8.0 identify-2.6.12 igraph-0.11.9 importlib_metadata-8.7.0 ipykernel-6.30.1 ipython-9.4.0 ipython-pygments-lexers-1.1.1 jedi-0.19.2 joblib-1.5.1 jsonschema-4.25.0 jsonschema-specifications-2025.4.1 jupyter-cache-1.0.1 jupyter-client-8.6.3 jupyter-core-5.8.1 jupyterlab-pygments-0.3.0 kiwisolver-1.4.8 latexcodec-3.0.1 legacy-api-wrap-1.4.1 leidenalg-0.10.2 llvmlite-0.44.0 locket-1.0.0 markdown-it-py-3.0.0 matplotlib-3.10.5 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.2 mdurl-0.1.2 mistune-3.1.3 msgpack-1.1.1 multipledispatch-1.0.0 myst-nb-1.3.0 myst-parser-4.0.1 natsort-8.4.0 nbclient-0.10.2 nbconvert-7.16.6 nbformat-5.10.4 nbsphinx-0.9.6 nest-asyncio-1.6.0 networkx-3.5 nodeenv-1.9.1 numba-0.61.2 numpy-2.2.6 numpy-typing-compat-2.2.20250730 optype-0.13.1 pandas-2.3.1 pandocfilters-1.5.1 parso-0.8.4 partd-1.4.2 pathspec-0.12.1 patsy-1.0.1 pexpect-4.9.0 pillow-11.3.0 platformdirs-4.3.8 pluggy-1.6.0 pre-commit-4.2.0 prompt_toolkit-3.0.51 psutil-7.0.0 ptyprocess-0.7.0 pure-eval-0.2.3 pyarrow-21.0.0 pybtex-0.25.1 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.15.4 pynndescent-0.5.13 pyparsing-3.2.3 python-dateutil-2.9.0.post0 pytz-2025.2 pyyaml-6.0.2 pyzmq-27.0.1 referencing-0.36.2 rpds-py-0.27.0 sam-algorithm-1.0.2 scanpy-1.12.0.dev107+g56fc82f4 scanpydoc-0.15.4 scikit-learn-1.7.1 scipy-1.16.1 scipy-stubs-1.16.1.0 seaborn-0.13.2 session-info2-0.2 setuptools-scm-8.3.1 six-1.17.0 sortedcontainers-2.4.0 soupsieve-2.7 sparse-0.17.0 sphinx-autodoc-typehints-3.2.0 sphinx-book-theme-1.1.4 sphinx-copybutton-0.5.2 sphinx-design-0.6.1 sphinx-issues-5.0.1 sphinx-tabs-3.4.7 sphinxcontrib-bibtex-2.6.5 sphinxext-opengraph-0.12.0 sqlalchemy-2.0.42 stack_data-0.6.3 statsmodels-0.14.5 tabulate-0.9.0 tblib-3.1.0 texttable-1.7.0 threadpoolctl-3.6.0 tinycss2-1.4.0 toolz-1.0.0 tornado-6.5.1 towncrier-24.8.0 tqdm-4.67.1 traitlets-5.14.3 trove-classifiers-2025.8.6.13 typing-extensions-4.14.1 tzdata-2025.2 umap-learn-0.5.9.post2 virtualenv-20.33.1 wcwidth-0.2.13 webencodings-0.5.1 zict-3.0.0 zipp-3.23.0

[rtd-command-info] start-time: 2025-08-08T08:44:29.752847Z, end-time: 2025-08-08T08:44:29.945491Z, duration: 0, exit-code: 0
( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true
Loading template...
Finding news fragments...
Rendering news fragments...
Writing to newsfile...
Staging newsfile...
Keeping the following files:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/release-notes/3564.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/release-notes/3598.dev.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/release-notes/3724.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/release-notes/3700.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/release-notes/2803.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/release-notes/3563.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/release-notes/3485.breaking.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/release-notes/3658.misc.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/release-notes/3498.feature.md
Done!

[rtd-command-info] start-time: 2025-08-08T08:44:30.069353Z, end-time: 2025-08-08T08:44:30.114068Z, duration: 0, exit-code: 0
cat docs/conf.py
"""Configuration for Scanpy’s Sphinx documentation."""

from __future__ import annotations

import os
import sys
from datetime import datetime
from functools import partial
from pathlib import Path, PurePosixPath
from typing import TYPE_CHECKING

import matplotlib  # noqa
from docutils import nodes
from packaging.version import 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")]
os.environ["SPHINX_RUNNING"] = "1"  # for scanpy._singleton
import scanpy

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 = [
    "myst.header",  # https://github.com/executablebooks/MyST-Parser/issues/262
    "mystnb.unknown_mime_type",  # application/vnd.microsoft.datawrangler.viewer.v0+json
]

# General information
project = "Scanpy"
author = "Scanpy development team"
repository_url = "https://github.com/scverse/scanpy"
copyright = f"{datetime.now():%Y}, scverse"
version = scanpy.__version__.replace(".dirty", "")

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

release = version

# Bibliography settings
bibtex_bibfiles = ["references.bib"]
bibtex_reference_style = "author_year"


# default settings
templates_path = ["_templates"]
master_doc = "index"
default_role = "literal"
exclude_patterns = [
    "_build",
    "Thumbs.db",
    ".DS_Store",
    "**.ipynb_checkpoints",
    # exclude all 0.x.y.md files, but not index.md
    "release-notes/[!i]*.md",
]

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",
    "sphinxcontrib.bibtex",
    "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_issues",
    "sphinx_tabs.tabs",
    "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_options = {
    # Don’t show members in addition to the autosummary table added by `_templates/class.rst`
    "members": False,
    # show “Bases: SomeClass” at the top of class docs
    "show-inheritance": True,
}
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", "ftp")
myst_heading_anchors = 3
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),
    fast_array_utils=(
        "https://icb-fast-array-utils.readthedocs-hosted.com/en/stable/",
        None,
    ),
    h5py=("https://docs.h5py.org/en/stable/", None),
    zarr=("https://zarr.readthedocs.io/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),
    session_info2=("https://session-info2.readthedocs.io/en/stable/", None),
    squidpy=("https://squidpy.readthedocs.io/en/stable/", None),
    sklearn=("https://scikit-learn.org/stable/", 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_generic_role("small", partial(nodes.inline, classes=["small"]))
    app.add_generic_role("smaller", partial(nodes.inline, classes=["smaller"]))
    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,  # noqa: FBT003
    )


# -- 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 = {
    "pathlib._local.Path": "pathlib.Path",
    "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",
    "numpy.bool_": "numpy.bool",  # Since numpy 2, numpy.bool is the canonical dtype
}

nitpick_ignore = [
    # Technical issues
    ("py:class", "numpy.int64"),  # documented as “attribute”
    ("py:class", "numpy._typing._dtype_like._SupportsDType"),
    ("py:class", "numpy._typing._dtype_like._DTypeDict"),
    # 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"),
]

# 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

# link config
issues_github_path = "scverse/scanpy"
rtd_links_prefix = PurePosixPath("src")

[rtd-command-info] start-time: 2025-08-08T08:44:30.195958Z, end-time: 2025-08-08T08:47:21.078173Z, duration: 170, exit-code: 1
python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v8.2.3
loading translations [en]... done
making output directory... done
checking bibtex cache... out of date
parsing bibtex file /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/references.bib... parsed 78 entries
myst v4.0.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'html_image', 'colon_fence', 'deflist', 'dollarmath', 'amsmath', 'html_admonition'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
myst-nb v1.3.0: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', 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, scroll_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/3757/_readthedocs/.jupyter_cache
loading intersphinx inventory 'anndata' from https://anndata.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'bbknn' from https://bbknn.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'cuml' from https://docs.rapids.ai/api/cuml/stable/objects.inv ...
loading intersphinx inventory 'cycler' from https://matplotlib.org/cycler/objects.inv ...
loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable/objects.inv ...
loading intersphinx inventory 'dask_ml' from https://ml.dask.org/objects.inv ...
loading intersphinx inventory 'fast_array_utils' from https://icb-fast-array-utils.readthedocs-hosted.com/en/stable/objects.inv ...
loading intersphinx inventory 'h5py' from https://docs.h5py.org/en/stable/objects.inv ...
loading intersphinx inventory 'zarr' from https://zarr.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'ipython' from https://ipython.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'igraph' from https://python.igraph.org/en/stable/api/objects.inv ...
loading intersphinx inventory 'leidenalg' from https://leidenalg.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'louvain' from https://louvain-igraph.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'matplotlib' from https://matplotlib.org/stable/objects.inv ...
loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv ...
loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ...
loading intersphinx inventory 'pandas' from https://pandas.pydata.org/pandas-docs/stable/objects.inv ...
loading intersphinx inventory 'pynndescent' from https://pynndescent.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'pytest' from https://docs.pytest.org/en/latest/objects.inv ...
loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ...
loading intersphinx inventory 'rapids_singlecell' from https://rapids-singlecell.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv ...
loading intersphinx inventory 'seaborn' from https://seaborn.pydata.org/objects.inv ...
loading intersphinx inventory 'session_info2' from https://session-info2.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'squidpy' from https://squidpy.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'sklearn' from https://scikit-learn.org/stable/objects.inv ...
[autosummary] generating autosummary for: api/classes.md, api/datasets.md, api/deprecated.md, api/experimental.md, api/get.md, api/index.md, api/io.md, api/metrics.md, api/plotting.md, api/preprocessing.md, ..., tutorials/experimental/dask.ipynb, tutorials/experimental/index.md, tutorials/experimental/pearson_residuals.ipynb, tutorials/index.md, tutorials/plotting/advanced.ipynb, tutorials/plotting/core.ipynb, tutorials/plotting/index.md, tutorials/trajectories/index.md, tutorials/trajectories/paga-paul15.ipynb, usage-principles.md
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/scanpy.pl.embedding_density.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/scanpy.pl.filter_genes_dispersion.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.tl.umap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.write.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.settings.figdir.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.settings.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.settings.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.settings.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.settings.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.settings.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.settings.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.settings.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.settings.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.settings.writedir.rst
building [mo]: targets for 0 po files that are out of date
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building [html]: targets for 52 source files that are out of date
updating environment: [new config] 273 added, 0 changed, 0 removed
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
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Package 'fa2-modified' is not installed, falling back to layout 'fr'.To use the faster and better ForceAtlas2 layout, install package 'fa2-modified' (`pip install fa2-modified`).
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
reading sources... [ 24%] api/generated/scanpy.pl.rank_genes_groups_heatmap
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.
Gene labels are not shown when more than 50 genes are visualized. To show gene labels set `show_gene_labels=True`
reading sources... [ 24%] api/generated/scanpy.pl.rank_genes_groups_matrixplot
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
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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... [ 25%] api/generated/scanpy.pl.rank_genes_groups_violin
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:17: (ERROR/3) no path specified
reading sources... [ 63%] generated/scanpy.metrics.gearys_c
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reading sources... [ 64%] generated/scanpy.pl.clustermap
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py:1756: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
reading sources... [ 64%] generated/scanpy.pl.dendrogram
reading sources... [ 65%] generated/scanpy.pl.dotplot
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
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/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
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/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
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/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
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/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
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/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
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/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
reading sources... [ 67%] generated/scanpy.pl.tracksplot
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.
Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.rank_genes_groups_dotplot:63: WARNING: Exception occurred in plotting scanpy-pl-rank_genes_groups_dotplot-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/scanpy.pl.rank_genes_groups_dotplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/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/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py", line 971, in rank_genes_groups_dotplot
    return _rank_genes_groups_plot(
        adata,
    ...<12 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py", line 613, in _rank_genes_groups_plot
    _pl = dotplot(
        adata,
    ...<5 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_dotplot.py", line 965, in dotplot
    dp = DotPlot(
        adata,
    ...<22 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_dotplot.py", line 161, in __init__
    BasePlot.__init__(
    ~~~~~~~~~~~~~~~~~^
        self,
        ^^^^^
    ...<19 lines>...
        **kwds,
        ^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_baseplot_class.py", line 166, in __init__
    self._view = AnnData(
                 ~~~~~~~^
        X=obs_tidy.values,
        ^^^^^^^^^^^^^^^^^^
        obs=obs_tidy.index.to_frame(index=False),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        var=pd.DataFrame(index=var_names),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py", line 252, in __init__
    self._init_as_actual(
    ~~~~~~~~~~~~~~~~~~~~^
        X=X,
        ^^^^
    ...<12 lines>...
        filemode=filemode,
        ^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py", line 427, in _init_as_actual
    self._var = _gen_dataframe(
                ~~~~~~~~~~~~~~^
        var, ["var_names", "col_names"], source=source, attr="var", length=n_vars
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/functools.py", line 934, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py", line 65, in _gen_dataframe_df
    raise _mk_df_error(source, attr, length, len(anno))
ValueError: Observations annot. `var` must have as many rows as `X` has columns (20), but has 10 rows. [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.rank_genes_groups_dotplot:70: WARNING: Exception occurred in plotting scanpy-pl-rank_genes_groups_dotplot-3
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/scanpy.pl.rank_genes_groups_dotplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/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/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py", line 971, in rank_genes_groups_dotplot
    return _rank_genes_groups_plot(
        adata,
    ...<12 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py", line 613, in _rank_genes_groups_plot
    _pl = dotplot(
        adata,
    ...<5 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_dotplot.py", line 965, in dotplot
    dp = DotPlot(
        adata,
    ...<22 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_dotplot.py", line 161, in __init__
    BasePlot.__init__(
    ~~~~~~~~~~~~~~~~~^
        self,
        ^^^^^
    ...<19 lines>...
        **kwds,
        ^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_baseplot_class.py", line 166, in __init__
    self._view = AnnData(
                 ~~~~~~~^
        X=obs_tidy.values,
        ^^^^^^^^^^^^^^^^^^
        obs=obs_tidy.index.to_frame(index=False),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        var=pd.DataFrame(index=var_names),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py", line 252, in __init__
    self._init_as_actual(
    ~~~~~~~~~~~~~~~~~~~~^
        X=X,
        ^^^^
    ...<12 lines>...
        filemode=filemode,
        ^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py", line 427, in _init_as_actual
    self._var = _gen_dataframe(
                ~~~~~~~~~~~~~~^
        var, ["var_names", "col_names"], source=source, attr="var", length=n_vars
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/functools.py", line 934, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py", line 65, in _gen_dataframe_df
    raise _mk_df_error(source, attr, length, len(anno))
ValueError: Observations annot. `var` must have as many rows as `X` has columns (20), but has 10 rows. [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.rank_genes_groups_dotplot:80: WARNING: Exception occurred in plotting scanpy-pl-rank_genes_groups_dotplot-4
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/scanpy.pl.rank_genes_groups_dotplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/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/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py", line 971, in rank_genes_groups_dotplot
    return _rank_genes_groups_plot(
        adata,
    ...<12 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py", line 613, in _rank_genes_groups_plot
    _pl = dotplot(
        adata,
    ...<5 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_dotplot.py", line 965, in dotplot
    dp = DotPlot(
        adata,
    ...<22 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_dotplot.py", line 161, in __init__
    BasePlot.__init__(
    ~~~~~~~~~~~~~~~~~^
        self,
        ^^^^^
    ...<19 lines>...
        **kwds,
        ^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_baseplot_class.py", line 166, in __init__
    self._view = AnnData(
                 ~~~~~~~^
        X=obs_tidy.values,
        ^^^^^^^^^^^^^^^^^^
        obs=obs_tidy.index.to_frame(index=False),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        var=pd.DataFrame(index=var_names),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py", line 252, in __init__
    self._init_as_actual(
    ~~~~~~~~~~~~~~~~~~~~^
        X=X,
        ^^^^
    ...<12 lines>...
        filemode=filemode,
        ^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py", line 427, in _init_as_actual
    self._var = _gen_dataframe(
                ~~~~~~~~~~~~~~^
        var, ["var_names", "col_names"], source=source, attr="var", length=n_vars
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/functools.py", line 934, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py", line 65, in _gen_dataframe_df
    raise _mk_df_error(source, attr, length, len(anno))
ValueError: Observations annot. `var` must have as many rows as `X` has columns (40), but has 10 rows. [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.rank_genes_groups_dotplot:96: WARNING: Exception occurred in plotting scanpy-pl-rank_genes_groups_dotplot-5
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/scanpy.pl.rank_genes_groups_dotplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/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/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py", line 971, in rank_genes_groups_dotplot
    return _rank_genes_groups_plot(
        adata,
    ...<12 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py", line 613, in _rank_genes_groups_plot
    _pl = dotplot(
        adata,
    ...<5 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_dotplot.py", line 965, in dotplot
    dp = DotPlot(
        adata,
    ...<22 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_dotplot.py", line 161, in __init__
    BasePlot.__init__(
    ~~~~~~~~~~~~~~~~~^
        self,
        ^^^^^
    ...<19 lines>...
        **kwds,
        ^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_baseplot_class.py", line 166, in __init__
    self._view = AnnData(
                 ~~~~~~~^
        X=obs_tidy.values,
        ^^^^^^^^^^^^^^^^^^
        obs=obs_tidy.index.to_frame(index=False),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        var=pd.DataFrame(index=var_names),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py", line 252, in __init__
    self._init_as_actual(
    ~~~~~~~~~~~~~~~~~~~~^
        X=X,
        ^^^^
    ...<12 lines>...
        filemode=filemode,
        ^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py", line 427, in _init_as_actual
    self._var = _gen_dataframe(
                ~~~~~~~~~~~~~~^
        var, ["var_names", "col_names"], source=source, attr="var", length=n_vars
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/functools.py", line 934, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py", line 65, in _gen_dataframe_df
    raise _mk_df_error(source, attr, length, len(anno))
ValueError: Observations annot. `var` must have as many rows as `X` has columns (40), but has 10 rows. [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.rank_genes_groups_dotplot:113: WARNING: Exception occurred in plotting scanpy-pl-rank_genes_groups_dotplot-6
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/scanpy.pl.rank_genes_groups_dotplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
    ~~~~^^^^^^^^^^
  File "<string>", line 4, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py", line 971, in rank_genes_groups_dotplot
    return _rank_genes_groups_plot(
        adata,
    ...<12 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py", line 613, in _rank_genes_groups_plot
    _pl = dotplot(
        adata,
    ...<5 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_dotplot.py", line 965, in dotplot
    dp = DotPlot(
        adata,
    ...<22 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_dotplot.py", line 161, in __init__
    BasePlot.__init__(
    ~~~~~~~~~~~~~~~~~^
        self,
        ^^^^^
    ...<19 lines>...
        **kwds,
        ^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_baseplot_class.py", line 166, in __init__
    self._view = AnnData(
                 ~~~~~~~^
        X=obs_tidy.values,
        ^^^^^^^^^^^^^^^^^^
        obs=obs_tidy.index.to_frame(index=False),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        var=pd.DataFrame(index=var_names),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py", line 252, in __init__
    self._init_as_actual(
    ~~~~~~~~~~~~~~~~~~~~^
        X=X,
        ^^^^
    ...<12 lines>...
        filemode=filemode,
        ^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py", line 427, in _init_as_actual
    self._var = _gen_dataframe(
                ~~~~~~~~~~~~~~^
        var, ["var_names", "col_names"], source=source, attr="var", length=n_vars
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/functools.py", line 934, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py", line 65, in _gen_dataframe_df
    raise _mk_df_error(source, attr, length, len(anno))
ValueError: Observations annot. `var` must have as many rows as `X` has columns (8), but has 3 rows. [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.rank_genes_groups_matrixplot:66: WARNING: Exception occurred in plotting scanpy-pl-rank_genes_groups_matrixplot-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/scanpy.pl.rank_genes_groups_matrixplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/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/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py", line 1180, in rank_genes_groups_matrixplot
    return _rank_genes_groups_plot(
        adata,
    ...<12 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py", line 627, in _rank_genes_groups_plot
    _pl = matrixplot(
        adata,
    ...<5 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_matrixplot.py", line 410, in matrixplot
    mp = MatrixPlot(
        adata,
    ...<20 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_matrixplot.py", line 140, in __init__
    BasePlot.__init__(
    ~~~~~~~~~~~~~~~~~^
        self,
        ^^^^^
    ...<19 lines>...
        **kwds,
        ^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_baseplot_class.py", line 166, in __init__
    self._view = AnnData(
                 ~~~~~~~^
        X=obs_tidy.values,
        ^^^^^^^^^^^^^^^^^^
        obs=obs_tidy.index.to_frame(index=False),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        var=pd.DataFrame(index=var_names),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py", line 252, in __init__
    self._init_as_actual(
    ~~~~~~~~~~~~~~~~~~~~^
        X=X,
        ^^^^
    ...<12 lines>...
        filemode=filemode,
        ^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py", line 427, in _init_as_actual
    self._var = _gen_dataframe(
                ~~~~~~~~~~~~~~^
        var, ["var_names", "col_names"], source=source, attr="var", length=n_vars
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/functools.py", line 934, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py", line 65, in _gen_dataframe_df
    raise _mk_df_error(source, attr, length, len(anno))
ValueError: Observations annot. `var` must have as many rows as `X` has columns (40), but has 10 rows. [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.rank_genes_groups_matrixplot:83: WARNING: Exception occurred in plotting scanpy-pl-rank_genes_groups_matrixplot-3
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/scanpy.pl.rank_genes_groups_matrixplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/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/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py", line 1180, in rank_genes_groups_matrixplot
    return _rank_genes_groups_plot(
        adata,
    ...<12 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py", line 627, in _rank_genes_groups_plot
    _pl = matrixplot(
        adata,
    ...<5 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_matrixplot.py", line 410, in matrixplot
    mp = MatrixPlot(
        adata,
    ...<20 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_matrixplot.py", line 140, in __init__
    BasePlot.__init__(
    ~~~~~~~~~~~~~~~~~^
        self,
        ^^^^^
    ...<19 lines>...
        **kwds,
        ^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_baseplot_class.py", line 166, in __init__
    self._view = AnnData(
                 ~~~~~~~^
        X=obs_tidy.values,
        ^^^^^^^^^^^^^^^^^^
        obs=obs_tidy.index.to_frame(index=False),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        var=pd.DataFrame(index=var_names),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py", line 252, in __init__
    self._init_as_actual(
    ~~~~~~~~~~~~~~~~~~~~^
        X=X,
        ^^^^
    ...<12 lines>...
        filemode=filemode,
        ^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py", line 427, in _init_as_actual
    self._var = _gen_dataframe(
                ~~~~~~~~~~~~~~^
        var, ["var_names", "col_names"], source=source, attr="var", length=n_vars
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/functools.py", line 934, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py", line 65, in _gen_dataframe_df
    raise _mk_df_error(source, attr, length, len(anno))
ValueError: Observations annot. `var` must have as many rows as `X` has columns (40), but has 10 rows. [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.rank_genes_groups_matrixplot:100: WARNING: Exception occurred in plotting scanpy-pl-rank_genes_groups_matrixplot-4
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/api/generated/scanpy.pl.rank_genes_groups_matrixplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
    ~~~~^^^^^^^^^^
  File "<string>", line 4, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py", line 1180, in rank_genes_groups_matrixplot
    return _rank_genes_groups_plot(
        adata,
    ...<12 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_tools/__init__.py", line 627, in _rank_genes_groups_plot
    _pl = matrixplot(
        adata,
    ...<5 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_matrixplot.py", line 410, in matrixplot
    mp = MatrixPlot(
        adata,
    ...<20 lines>...
        **kwds,
    )
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_matrixplot.py", line 140, in __init__
    BasePlot.__init__(
    ~~~~~~~~~~~~~~~~~^
        self,
        ^^^^^
    ...<19 lines>...
        **kwds,
        ^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/scanpy/plotting/_baseplot_class.py", line 166, in __init__
    self._view = AnnData(
                 ~~~~~~~^
        X=obs_tidy.values,
        ^^^^^^^^^^^^^^^^^^
        obs=obs_tidy.index.to_frame(index=False),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        var=pd.DataFrame(index=var_names),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py", line 252, in __init__
    self._init_as_actual(
    ~~~~~~~~~~~~~~~~~~~~^
        X=X,
        ^^^^
    ...<12 lines>...
        filemode=filemode,
        ^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/anndata.py", line 427, in _init_as_actual
    self._var = _gen_dataframe(
                ~~~~~~~~~~~~~~^
        var, ["var_names", "col_names"], source=source, attr="var", length=n_vars
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/docs/.asdf/installs/python/3.13.3/lib/python3.13/functools.py", line 934, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3757/lib/python3.13/site-packages/anndata/_core/aligned_df.py", line 65, in _gen_dataframe_df
    raise _mk_df_error(source, attr, length, len(anno))
ValueError: Observations annot. `var` must have as many rows as `X` has columns (8), but has 3 rows. [docutils]
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3757/docs/generated/scanpy.pp.pca.rst: document is referenced in multiple toctrees: ['api/preprocessing', 'api/tools'], selecting: api/tools <- generated/scanpy.pp.pca
done
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dumping search index in English (code: en)... done
dumping object inventory... done
build finished with problems, 8 warnings (with warnings treated as errors).