Read the Docs build information
Build id: 2628342
Project: icb-scanpy
Version: 3365
Commit: 3d2f06f70d5471314fe2848b0905d813cb2f6ff3
Date: 2024-11-20T03:09:38.911622Z
State: finished
Success: False


[rtd-command-info] start-time: 2024-11-20T03:09:40.077934Z, end-time: 2024-11-20T03:09:41.129773Z, duration: 1, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-11-20T03:09:41.213506Z, end-time: 2024-11-20T03:09:41.859192Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/3365/head:external-3365
From https://github.com/scverse/scanpy
 * [new ref]         refs/pull/3365/head -> external-3365

[rtd-command-info] start-time: 2024-11-20T03:09:42.003192Z, end-time: 2024-11-20T03:09:42.215758Z, duration: 0, exit-code: 0
git checkout --force 3d2f06f70d5471314fe2848b0905d813cb2f6ff3
Note: switching to '3d2f06f70d5471314fe2848b0905d813cb2f6ff3'.

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 3d2f06f default backed value

[rtd-command-info] start-time: 2024-11-20T03:09:42.303489Z, end-time: 2024-11-20T03:09:42.364250Z, duration: 0, exit-code: 0
cat .readthedocs.yml
version: 2
submodules:
  include: all
build:
  os: ubuntu-24.04
  tools:
    python: '3.12'
  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: 2024-11-20T03:09:42.504856Z, end-time: 2024-11-20T03:09:42.580207Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2024-11-20T03:09:42.649906Z, end-time: 2024-11-20T03:09:58.243383Z, duration: 15, 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/3365/notebooks'...
Submodule path 'notebooks': checked out '3385df77ce0f63987104bc644562a811c5d1b441'

[rtd-command-info] start-time: 2024-11-20T03:09:58.332815Z, end-time: 2024-11-20T03:10:01.333045Z, duration: 3, exit-code: 0
git fetch --unshallow || true
From https://github.com/scverse/scanpy
 * [new tag]           0.0         -> 0.0
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 * [new tag]           0.4.2.post1 -> 0.4.2.post1
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 * [new tag]           1.4.5.post1 -> 1.4.5.post1
 * [new tag]           1.4.5.post2 -> 1.4.5.post2
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 * [new tag]           1.9.0       -> 1.9.0
 * [new tag]           1.9.0.dev0  -> 1.9.0.dev0

[rtd-command-info] start-time: 2024-11-20T03:10:07.833270Z, end-time: 2024-11-20T03:10:07.925970Z, duration: 0, exit-code: 0
asdf global python 3.12.7


[rtd-command-info] start-time: 2024-11-20T03:10:08.374210Z, end-time: 2024-11-20T03:10:09.577407Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.12.7.final.0-64 in 816ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2024-11-20T03:10:09.664002Z, end-time: 2024-11-20T03:10:25.073340Z, duration: 15, 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/3365/lib/python3.12/site-packages (23.1)
Collecting pip
  Downloading pip-24.3.1-py3-none-any.whl (1.8 MB)
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages (67.6.1)
Collecting setuptools
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Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 67.6.1
    Uninstalling setuptools-67.6.1:
      Successfully uninstalled setuptools-67.6.1
  Attempting uninstall: pip
    Found existing installation: pip 23.1
    Uninstalling pip-23.1:
      Successfully uninstalled pip-23.1
Successfully installed pip-24.3.1 setuptools-75.5.0

[rtd-command-info] start-time: 2024-11-20T03:10:25.163659Z, end-time: 2024-11-20T03:10:36.704745Z, duration: 11, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx
Collecting sphinx
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Collecting MarkupSafe>=2.0 (from Jinja2>=3.1->sphinx)
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Downloading urllib3-2.2.3-py3-none-any.whl (126 kB)
Installing collected packages: snowballstemmer, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx
Successfully installed Jinja2-3.1.4 MarkupSafe-3.0.2 Pygments-2.18.0 alabaster-1.0.0 babel-2.16.0 certifi-2024.8.30 charset-normalizer-3.4.0 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-24.2 requests-2.32.3 snowballstemmer-2.2.0 sphinx-8.1.3 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 urllib3-2.2.3

[rtd-command-info] start-time: 2024-11-20T03:10:36.802271Z, end-time: 2024-11-20T03:12:17.542885Z, duration: 100, 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/3365
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting anndata>=0.8 (from scanpy==1.11.0.dev157+g3d2f06f7)
  Downloading anndata-0.11.1-py3-none-any.whl.metadata (8.2 kB)
Collecting h5py>=3.6 (from scanpy==1.11.0.dev157+g3d2f06f7)
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Collecting legacy-api-wrap>=1.4 (from scanpy==1.11.0.dev157+g3d2f06f7)
  Downloading legacy_api_wrap-1.4-py3-none-any.whl.metadata (1.8 kB)
Collecting matplotlib>=3.6 (from scanpy==1.11.0.dev157+g3d2f06f7)
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Collecting networkx>=2.7 (from scanpy==1.11.0.dev157+g3d2f06f7)
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Collecting numba>=0.56 (from scanpy==1.11.0.dev157+g3d2f06f7)
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Collecting numpy>=1.23 (from scanpy==1.11.0.dev157+g3d2f06f7)
  Downloading numpy-2.1.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
Requirement already satisfied: packaging>=21.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages (from scanpy==1.11.0.dev157+g3d2f06f7) (24.2)
Collecting pandas>=1.5 (from scanpy==1.11.0.dev157+g3d2f06f7)
  Downloading pandas-2.2.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (89 kB)
Collecting patsy (from scanpy==1.11.0.dev157+g3d2f06f7)
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Collecting pynndescent>=0.5 (from scanpy==1.11.0.dev157+g3d2f06f7)
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Collecting scikit-learn>=1.1 (from scanpy==1.11.0.dev157+g3d2f06f7)
  Downloading scikit_learn-1.5.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
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  Preparing metadata (setup.py): started
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Collecting statsmodels>=0.13 (from scanpy==1.11.0.dev157+g3d2f06f7)
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Collecting umap-learn!=0.5.0,>=0.5 (from scanpy==1.11.0.dev157+g3d2f06f7)
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Collecting pre-commit (from scanpy==1.11.0.dev157+g3d2f06f7)
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Collecting setuptools-scm (from scanpy==1.11.0.dev157+g3d2f06f7)
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Building wheels for collected packages: scanpy, sam-algorithm, session-info, hnswlib
  Building wheel for scanpy (pyproject.toml): started
  Building wheel for scanpy (pyproject.toml): finished with status 'done'
  Created wheel for scanpy: filename=scanpy-1.11.0.dev157+g3d2f06f7-py3-none-any.whl size=2092328 sha256=4eb9bc0e9b74033772e28f75fa7772f658705c2de02b49ea8ed3481574f58d04
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  Building wheel for sam-algorithm (setup.py): started
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  Building wheel for session-info (setup.py): finished with status 'done'
  Created wheel for session-info: filename=session_info-1.0.0-py3-none-any.whl size=8024 sha256=ea6f1115a445fe30726ca12b9a55dc0fbf741fb27de5da71e1af4658bf99800e
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  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-cp312-cp312-linux_x86_64.whl size=2289013 sha256=9c3b33e62d7955f4209380fc347732786379b3725638f47b76eb6b8bcea854d0
  Stored in directory: /tmp/pip-ephem-wheel-cache-_7rrobmz/wheels/ac/39/b3/cbd7f9cbb76501d2d5fbc84956e70d0b94e788aac87bda465e
Successfully built scanpy sam-algorithm session-info hnswlib
Installing collected packages: webencodings, wcwidth, texttable, sortedcontainers, pytz, pure-eval, ptyprocess, multipledispatch, fastjsonschema, distlib, zipp, zict, tzdata, typing-extensions, traitlets, tqdm, tornado, toolz, tinycss2, threadpoolctl, tblib, tabulate, stdlib_list, soupsieve, six, setuptools-scm, rpds-py, readthedocs-sphinx-search, pyzmq, pyyaml, pyparsing, pyarrow, psutil, prompt-toolkit, platformdirs, pillow, pexpect, parso, pandocfilters, numpy, nodeenv, networkx, nest-asyncio, natsort, msgpack, mistune, mdurl, locket, llvmlite, legacy-api-wrap, latexcodec, kiwisolver, jupyterlab-pygments, joblib, igraph, identify, greenlet, fsspec, fonttools, filelock, executing, dill, defusedxml, decorator, debugpy, cycler, cloudpickle, click, cfgv, bleach, attrs, array-api-compat, accessible-pygments, virtualenv, towncrier, sqlalchemy, session-info, scipy, referencing, python-dateutil, pybtex, patsy, partd, numba, matplotlib-inline, markdown-it-py, leidenalg, jupyter-core, jedi, importlib_metadata, hnswlib, h5py, contourpy, comm, beautifulsoup4, asttokens, stack-data, sphinxext-opengraph, sphinx-tabs, 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, dask, statsmodels, sphinxcontrib-bibtex, sphinx-book-theme, seaborn, pynndescent, myst-parser, jsonschema, ipython, harmonypy, distributed, dask-expr, anndata, umap-learn, nbformat, ipykernel, dask-glm, scanpy, sam-algorithm, nbclient, dask-ml, nbconvert, jupyter-cache, nbsphinx, myst-nb
Successfully installed accessible-pygments-0.0.5 anndata-0.11.1 array-api-compat-1.9.1 asttokens-2.4.1 attrs-24.2.0 beautifulsoup4-4.12.3 bleach-6.2.0 cfgv-3.4.0 click-8.1.7 cloudpickle-3.1.0 comm-0.2.2 contourpy-1.3.1 cycler-0.12.1 dask-2024.7.1 dask-expr-1.1.9 dask-glm-0.3.2 dask-ml-2024.4.4 debugpy-1.8.8 decorator-5.1.1 defusedxml-0.7.1 dill-0.3.9 distlib-0.3.9 distributed-2024.7.1 executing-2.1.0 fastjsonschema-2.20.0 filelock-3.16.1 fonttools-4.55.0 fsspec-2024.10.0 greenlet-3.1.1 h5py-3.12.1 harmonypy-0.0.10 hnswlib-0.8.0 identify-2.6.2 igraph-0.11.8 importlib_metadata-8.5.0 ipykernel-6.29.5 ipython-8.29.0 jedi-0.19.2 joblib-1.4.2 jsonschema-4.23.0 jsonschema-specifications-2024.10.1 jupyter-cache-1.0.1 jupyter-client-8.6.3 jupyter-core-5.7.2 jupyterlab-pygments-0.3.0 kiwisolver-1.4.7 latexcodec-3.0.0 legacy-api-wrap-1.4 leidenalg-0.10.2 llvmlite-0.43.0 locket-1.0.0 markdown-it-py-3.0.0 matplotlib-3.9.2 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.2 mdurl-0.1.2 mistune-3.0.2 msgpack-1.1.0 multipledispatch-1.0.0 myst-nb-1.1.2 myst-parser-4.0.0 natsort-8.4.0 nbclient-0.10.0 nbconvert-7.16.4 nbformat-5.10.4 nbsphinx-0.9.5 nest-asyncio-1.6.0 networkx-3.4.2 nodeenv-1.9.1 numba-0.60.0 numpy-2.0.2 pandas-2.2.3 pandocfilters-1.5.1 parso-0.8.4 partd-1.4.2 patsy-1.0.1 pexpect-4.9.0 pillow-11.0.0 platformdirs-4.3.6 pre-commit-4.0.1 prompt-toolkit-3.0.48 psutil-6.1.0 ptyprocess-0.7.0 pure-eval-0.2.3 pyarrow-18.0.0 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.16.0 pynndescent-0.5.13 pyparsing-3.2.0 python-dateutil-2.9.0.post0 pytz-2024.2 pyyaml-6.0.2 pyzmq-26.2.0 readthedocs-sphinx-search-0.3.2 referencing-0.35.1 rpds-py-0.21.0 sam-algorithm-1.0.2 scanpy-1.11.0.dev157+g3d2f06f7 scanpydoc-0.14.1 scikit-learn-1.5.2 scipy-1.14.1 seaborn-0.13.2 session-info-1.0.0 setuptools-scm-8.1.0 six-1.16.0 sortedcontainers-2.4.0 soupsieve-2.6 sparse-0.15.4 sphinx-autodoc-typehints-2.5.0 sphinx-book-theme-1.1.3 sphinx-copybutton-0.5.2 sphinx-design-0.6.1 sphinx-tabs-3.4.7 sphinxcontrib-bibtex-2.6.3 sphinxext-opengraph-0.9.1 sqlalchemy-2.0.36 stack-data-0.6.3 statsmodels-0.14.4 stdlib_list-0.11.0 tabulate-0.9.0 tblib-3.0.0 texttable-1.7.0 threadpoolctl-3.5.0 tinycss2-1.4.0 toolz-1.0.0 tornado-6.4.1 towncrier-24.8.0 tqdm-4.67.0 traitlets-5.14.3 typing-extensions-4.12.2 tzdata-2024.2 umap-learn-0.5.7 virtualenv-20.27.1 wcwidth-0.2.13 webencodings-0.5.1 zict-3.0.0 zipp-3.21.0

[rtd-command-info] start-time: 2024-11-20T03:12:17.822356Z, end-time: 2024-11-20T03:12:37.656599Z, duration: 19, exit-code: 0
( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true
Loading template...
Finding news fragments...
Rendering news fragments...
Matplotlib is building the font cache; this may take a moment.
Writing to newsfile...
Staging newsfile...
Keeping the following files:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3267.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3264.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3206.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3155.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3275.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3307.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3263.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3180.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/2921.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3184.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3302.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3286.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3243.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3296.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3244.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3283.breaking.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3324.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/release-notes/3299.bugfix.md
Done!

[rtd-command-info] start-time: 2024-11-20T03:12:37.735539Z, end-time: 2024-11-20T03:12:37.793062Z, duration: 0, exit-code: 0
cat docs/conf.py
from __future__ import annotations

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")]
import scanpy  # noqa

if TYPE_CHECKING:
    from sphinx.application import Sphinx


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

nitpicky = True  # Warn about broken links. This is here for a reason: Do not change.
needs_sphinx = "4.0"  # Nicer param docs
suppress_warnings = [
    "myst.header",  # https://github.com/executablebooks/MyST-Parser/issues/262
]

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

# Bumping the version updates all docs, so don't do that
if 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",
    "sphinx.ext.extlinks",
    "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_tabs.tabs",
    "sphinx_search.extension",
    "sphinxext.opengraph",
    *[p.stem for p in (HERE / "extensions").glob("*.py") if p.stem not in {"git_ref"}],
]

# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = "bysource"
# autodoc_default_flags = ['members']
napoleon_google_docstring = False
napoleon_numpy_docstring = True
napoleon_include_init_with_doc = False
napoleon_use_rtype = True  # having a separate entry generally helps readability
napoleon_use_param = True
napoleon_custom_sections = [("Params", "Parameters")]
todo_include_todos = False
api_dir = HERE / "api"  # function_images
myst_enable_extensions = [
    "amsmath",
    "colon_fence",
    "deflist",
    "dollarmath",
    "html_image",
    "html_admonition",
]
myst_url_schemes = ("http", "https", "mailto", "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),
    h5py=("https://docs.h5py.org/en/stable/", None),
    ipython=("https://ipython.readthedocs.io/en/stable/", None),
    igraph=("https://python.igraph.org/en/stable/api/", None),
    leidenalg=("https://leidenalg.readthedocs.io/en/latest/", None),
    louvain=("https://louvain-igraph.readthedocs.io/en/latest/", None),
    matplotlib=("https://matplotlib.org/stable/", None),
    networkx=("https://networkx.org/documentation/stable/", None),
    numpy=("https://numpy.org/doc/stable/", None),
    pandas=("https://pandas.pydata.org/pandas-docs/stable/", None),
    pynndescent=("https://pynndescent.readthedocs.io/en/latest/", None),
    pytest=("https://docs.pytest.org/en/latest/", None),
    python=("https://docs.python.org/3", None),
    rapids_singlecell=("https://rapids-singlecell.readthedocs.io/en/latest/", None),
    scipy=("https://docs.scipy.org/doc/scipy/", None),
    seaborn=("https://seaborn.pydata.org/", None),
    sklearn=("https://scikit-learn.org/stable/", None),
)


# -- 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 = {
    "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"),
    # 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

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

[rtd-command-info] start-time: 2024-11-20T03:12:37.873622Z, end-time: 2024-11-20T03:14:46.164506Z, duration: 128, exit-code: 1
python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v8.1.3
loading translations [en]... done
making output directory... done
checking bibtex cache... out of date
parsing bibtex file /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/references.bib... parsed 66 entries
myst v4.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'html_admonition', 'dollarmath', 'colon_fence', 'deflist', 'amsmath', 'html_image'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
myst-nb v1.1.2: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', execution_mode='off', execution_cache_path='', execution_excludepatterns=(), execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=True, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='remove', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/_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 'h5py' from https://docs.h5py.org/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 '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/metrics.md, api/plotting.md, api/preprocessing.md, api/queries.md, ..., tutorials/index.md, tutorials/plotting/advanced.ipynb, tutorials/plotting/core.ipynb, tutorials/plotting/index.md, tutorials/spatial/basic-analysis.ipynb, tutorials/spatial/index.md, tutorials/spatial/integration-scanorama.ipynb, 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/3365/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.embedding_density.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.filter_genes_dispersion.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.tl.leiden.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.tl.umap.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy._settings.ScanpyConfig.writedir.rst
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 55 source files that are out of date
updating environment: [new config] 311 added, 0 changed, 0 removed
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py:docstring of scanpy.plotting._matrixplot.MatrixPlot:85: WARNING: Exception occurred in plotting scanpy-pl-MatrixPlot-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py:docstring of scanpy.plotting._matrixplot.MatrixPlot:96: WARNING: Exception occurred in plotting scanpy-pl-MatrixPlot-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py:docstring of scanpy.plotting._matrixplot.MatrixPlot.style:18: WARNING: Exception occurred in plotting scanpy-pl-MatrixPlot-style-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/classes/scanpy.pl.MatrixPlot.style.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 3, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py:docstring of scanpy.plotting._matrixplot.MatrixPlot.style:28: WARNING: Exception occurred in plotting scanpy-pl-MatrixPlot-style-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/classes/scanpy.pl.MatrixPlot.style.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/scatterplots.py:docstring of scanpy.plotting._tools.scatterplots.diffmap:135: WARNING: Exception occurred in plotting scanpy-pl-diffmap-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.diffmap.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/scatterplots.py:docstring of scanpy.plotting._tools.scatterplots.draw_graph:154: WARNING: Exception occurred in plotting scanpy-pl-draw_graph-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.draw_graph.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.embedding_density:66: WARNING: Exception occurred in plotting scanpy-pl-embedding_density-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.embedding_density.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.embedding_density:76: WARNING: Exception occurred in plotting scanpy-pl-embedding_density-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.embedding_density.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.embedding_density:83: WARNING: Exception occurred in plotting scanpy-pl-embedding_density-3
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.embedding_density.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/paga.py:docstring of scanpy.plotting._tools.paga.paga:120: WARNING: Exception occurred in plotting scanpy-pl-paga-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.paga.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 24, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 452, in pbmc3k_processed
    return read(settings.datasetdir / "pbmc3k_processed.h5ad", backup_url=url)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/paga.py:docstring of scanpy.plotting._tools.paga.paga:130: WARNING: Exception occurred in plotting scanpy-pl-paga-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.paga.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/scatterplots.py:docstring of scanpy.plotting._tools.scatterplots.pca:139: WARNING: Exception occurred in plotting scanpy-pl-pca-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.pca.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 24, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 452, in pbmc3k_processed
    return read(settings.datasetdir / "pbmc3k_processed.h5ad", backup_url=url)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/scatterplots.py:docstring of scanpy.plotting._tools.scatterplots.pca:148: WARNING: Exception occurred in plotting scanpy-pl-pca-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.pca.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/scatterplots.py:docstring of scanpy.plotting._tools.scatterplots.pca:155: WARNING: Exception occurred in plotting scanpy-pl-pca-3
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.pca.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.pca_loadings:21: WARNING: Exception occurred in plotting scanpy-pl-pca_loadings-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.pca_loadings.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 24, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 452, in pbmc3k_processed
    return read(settings.datasetdir / "pbmc3k_processed.h5ad", backup_url=url)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.pca_loadings:29: WARNING: Exception occurred in plotting scanpy-pl-pca_loadings-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.pca_loadings.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.pca_overview:91: WARNING: Exception occurred in plotting scanpy-pl-pca_overview-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.pca_overview.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 24, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 452, in pbmc3k_processed
    return read(settings.datasetdir / "pbmc3k_processed.h5ad", backup_url=url)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.rank_genes_groups:30: WARNING: Exception occurred in plotting scanpy-pl-rank_genes_groups-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.rank_genes_groups.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.rank_genes_groups:39: WARNING: Exception occurred in plotting scanpy-pl-rank_genes_groups-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.rank_genes_groups.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.rank_genes_groups_dotplot:54: WARNING: Exception occurred in plotting scanpy-pl-rank_genes_groups_dotplot-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/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/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/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/3365/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/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/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/3365/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/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/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/3365/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/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/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/3365/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/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/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/3365/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/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 5, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.rank_genes_groups_heatmap:43: WARNING: Exception occurred in plotting scanpy-pl-rank_genes_groups_heatmap-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.rank_genes_groups_heatmap.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.rank_genes_groups_heatmap:53: WARNING: Exception occurred in plotting scanpy-pl-rank_genes_groups_heatmap-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.rank_genes_groups_heatmap.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.rank_genes_groups_heatmap:60: WARNING: Exception occurred in plotting scanpy-pl-rank_genes_groups_heatmap-3
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.rank_genes_groups_heatmap.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.rank_genes_groups_matrixplot:54: WARNING: Exception occurred in plotting scanpy-pl-rank_genes_groups_matrixplot-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/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/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/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/3365/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/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/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/3365/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/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/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/3365/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/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 5, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py:docstring of scanpy.plotting._tools.rank_genes_groups_tracksplot:43: WARNING: Exception occurred in plotting scanpy-pl-rank_genes_groups_tracksplot-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.rank_genes_groups_tracksplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/scatterplots.py:docstring of scanpy.plotting._tools.scatterplots.tsne:151: WARNING: Exception occurred in plotting scanpy-pl-tsne-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.tsne.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/scatterplots.py:docstring of scanpy.plotting._tools.scatterplots.umap:151: WARNING: Exception occurred in plotting scanpy-pl-umap-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.umap.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/scatterplots.py:docstring of scanpy.plotting._tools.scatterplots.umap:160: WARNING: Exception occurred in plotting scanpy-pl-umap-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.umap.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/scatterplots.py:docstring of scanpy.plotting._tools.scatterplots.umap:167: WARNING: Exception occurred in plotting scanpy-pl-umap-3
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.umap.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/scatterplots.py:docstring of scanpy.plotting._tools.scatterplots.umap:174: WARNING: Exception occurred in plotting scanpy-pl-umap-4
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/api/generated/scanpy.pl.umap.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
NameError: name 'adata' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/metrics/_metrics.py:docstring of scanpy.metrics._metrics.confusion_matrix:18: WARNING: Exception occurred in plotting scanpy-metrics-confusion_matrix-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.metrics.confusion_matrix.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py:docstring of scanpy.plotting._anndata.dendrogram:32: WARNING: Exception occurred in plotting scanpy-pl-dendrogram-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.dendrogram.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_dotplot.py:docstring of scanpy.plotting._dotplot.dotplot:148: WARNING: Exception occurred in plotting scanpy-pl-dotplot-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.dotplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_dotplot.py:docstring of scanpy.plotting._dotplot.dotplot:158: WARNING: Exception occurred in plotting scanpy-pl-dotplot-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.dotplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_dotplot.py", line 991, in dotplot
    dp = DotPlot(
         ^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_dotplot.py", line 168, in __init__
    BasePlot.__init__(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_baseplot_class.py", line 144, in __init__
    self.categories, self.obs_tidy = _prepare_dataframe(
                                     ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py", line 2057, in _prepare_dataframe
    raise ValueError(
ValueError: groupby has to be a valid observation. Given bulk_labels, is not in observations: ['cell_type'] [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_dotplot.py:docstring of scanpy.plotting._dotplot.dotplot:166: WARNING: Exception occurred in plotting scanpy-pl-dotplot-3
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.dotplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/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/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_dotplot.py", line 991, in dotplot
    dp = DotPlot(
         ^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_dotplot.py", line 168, in __init__
    BasePlot.__init__(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_baseplot_class.py", line 144, in __init__
    self.categories, self.obs_tidy = _prepare_dataframe(
                                     ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py", line 2057, in _prepare_dataframe
    raise ValueError(
ValueError: groupby has to be a valid observation. Given bulk_labels, is not in observations: ['cell_type'] [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py:docstring of scanpy.plotting._anndata.heatmap:95: WARNING: Exception occurred in plotting scanpy-pl-heatmap-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.heatmap.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py:docstring of scanpy.plotting._matrixplot.matrixplot:112: WARNING: Exception occurred in plotting scanpy-pl-matrixplot-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.matrixplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py:docstring of scanpy.plotting._matrixplot.matrixplot:122: WARNING: Exception occurred in plotting scanpy-pl-matrixplot-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.matrixplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py", line 435, in matrixplot
    mp = MatrixPlot(
         ^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py", line 147, in __init__
    BasePlot.__init__(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_baseplot_class.py", line 144, in __init__
    self.categories, self.obs_tidy = _prepare_dataframe(
                                     ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py", line 2057, in _prepare_dataframe
    raise ValueError(
ValueError: groupby has to be a valid observation. Given bulk_labels, is not in observations: ['cell_type'] [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py:docstring of scanpy.plotting._matrixplot.matrixplot:130: WARNING: Exception occurred in plotting scanpy-pl-matrixplot-3
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.matrixplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/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/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py", line 435, in matrixplot
    mp = MatrixPlot(
         ^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py", line 147, in __init__
    BasePlot.__init__(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_baseplot_class.py", line 144, in __init__
    self.categories, self.obs_tidy = _prepare_dataframe(
                                     ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py", line 2057, in _prepare_dataframe
    raise ValueError(
ValueError: groupby has to be a valid observation. Given bulk_labels, is not in observations: ['cell_type'] [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py:docstring of scanpy.plotting._matrixplot.matrixplot:138: WARNING: Exception occurred in plotting scanpy-pl-matrixplot-4
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.matrixplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
NameError: name 'mp' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_stacked_violin.py:docstring of scanpy.plotting._stacked_violin.stacked_violin:143: WARNING: Exception occurred in plotting scanpy-pl-stacked_violin-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.stacked_violin.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_stacked_violin.py:docstring of scanpy.plotting._stacked_violin.stacked_violin:154: WARNING: Exception occurred in plotting scanpy-pl-stacked_violin-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.stacked_violin.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_stacked_violin.py", line 814, in stacked_violin
    vp = StackedViolin(
         ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_stacked_violin.py", line 202, in __init__
    BasePlot.__init__(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_baseplot_class.py", line 144, in __init__
    self.categories, self.obs_tidy = _prepare_dataframe(
                                     ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py", line 2057, in _prepare_dataframe
    raise ValueError(
ValueError: groupby has to be a valid observation. Given bulk_labels, is not in observations: ['cell_type'] [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_stacked_violin.py:docstring of scanpy.plotting._stacked_violin.stacked_violin:162: WARNING: Exception occurred in plotting scanpy-pl-stacked_violin-3
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.stacked_violin.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/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/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_stacked_violin.py", line 814, in stacked_violin
    vp = StackedViolin(
         ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_stacked_violin.py", line 202, in __init__
    BasePlot.__init__(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_baseplot_class.py", line 144, in __init__
    self.categories, self.obs_tidy = _prepare_dataframe(
                                     ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py", line 2057, in _prepare_dataframe
    raise ValueError(
ValueError: groupby has to be a valid observation. Given bulk_labels, is not in observations: ['cell_type'] [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py:docstring of scanpy.plotting._anndata.tracksplot:75: WARNING: Exception occurred in plotting scanpy-pl-tracksplot-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.tracksplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py:docstring of scanpy.plotting._anndata.tracksplot:85: WARNING: Exception occurred in plotting scanpy-pl-tracksplot-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.tracksplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py", line 1558, in tracksplot
    raise ValueError(
ValueError: groupby has to be a valid categorical observation. Given value: bulk_labels, valid categorical observations: ['cell_type'] [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py:docstring of scanpy.plotting._anndata.violin:61: WARNING: Exception occurred in plotting scanpy-pl-violin-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.violin.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py:docstring of scanpy.plotting._anndata.violin:70: WARNING: Exception occurred in plotting scanpy-pl-violin-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.violin.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/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/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py", line 857, in violin
    obs_df = get.obs_df(adata, keys=[groupby] + keys, layer=layer, use_raw=use_raw)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/get/get.py", line 292, in obs_df
    obs_cols, var_idx_keys, var_symbols = _check_indices(
                                          ^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/get/get.py", line 183, in _check_indices
    raise KeyError(
KeyError: "Could not find keys '['bulk_labels', 'S_score']' in columns of `adata.obs` or in adata.var_names." [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py:docstring of scanpy.plotting._anndata.violin:77: WARNING: Exception occurred in plotting scanpy-pl-violin-3
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.violin.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py", line 857, in violin
    obs_df = get.obs_df(adata, keys=[groupby] + keys, layer=layer, use_raw=use_raw)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/get/get.py", line 292, in obs_df
    obs_cols, var_idx_keys, var_symbols = _check_indices(
                                          ^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/get/get.py", line 183, in _check_indices
    raise KeyError(
KeyError: "Could not find keys '['bulk_labels', 'S_score']' in columns of `adata.obs` or in adata.var_names." [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py:docstring of scanpy.plotting._anndata.violin:86: WARNING: Exception occurred in plotting scanpy-pl-violin-4
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.violin.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/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/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py", line 857, in violin
    obs_df = get.obs_df(adata, keys=[groupby] + keys, layer=layer, use_raw=use_raw)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/get/get.py", line 292, in obs_df
    obs_cols, var_idx_keys, var_symbols = _check_indices(
                                          ^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/get/get.py", line 183, in _check_indices
    raise KeyError(
KeyError: "Could not find keys '['bulk_labels', 'S_score', 'G2M_score']' in columns of `adata.obs` or in adata.var_names." [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py:docstring of scanpy.plotting._anndata.violin:94: WARNING: Exception occurred in plotting scanpy-pl-violin-5
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pl.violin.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/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/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_anndata.py", line 870, in violin
    obs_df = get.obs_df(adata, keys=keys, layer=layer, use_raw=use_raw)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/get/get.py", line 292, in obs_df
    obs_cols, var_idx_keys, var_symbols = _check_indices(
                                          ^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/get/get.py", line 183, in _check_indices
    raise KeyError(
KeyError: "Could not find keys '['S_score']' in columns of `adata.obs` or in adata.var_names." [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/preprocessing/_qc.py:docstring of scanpy.preprocessing._qc.calculate_qc_metrics:75: WARNING: Exception occurred in plotting scanpy-pp-calculate_qc_metrics-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pp.calculate_qc_metrics.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/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/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 24, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 410, in pbmc3k
    adata = read(settings.datasetdir / "pbmc3k_raw.h5ad", backup_url=url)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/preprocessing/_qc.py:docstring of scanpy.preprocessing._qc.calculate_qc_metrics:91: WARNING: Exception occurred in plotting scanpy-pp-calculate_qc_metrics-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pp.calculate_qc_metrics.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 1, in <module>
NameError: name 'pbmc' is not defined [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/tools/_embedding_density.py:docstring of scanpy.tools._embedding_density.embedding_density:43: WARNING: Exception occurred in plotting scanpy-tl-embedding_density-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.tl.embedding_density.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_utils.py", line 41, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/datasets/_datasets.py", line 359, in pbmc68k_reduced
    return read(filename)
           ^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 260, in read
    return _read(
           ^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 895, in _read
    return fastload(filename, backed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/readwrite.py", line 123, in fastload
    rows = f['obs'][ list(f['obs'].keys())[0] ].size
                          ^^^^^^^^^^^^^
AttributeError: 'Dataset' object has no attribute 'keys' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/tools/_embedding_density.py:docstring of scanpy.tools._embedding_density.embedding_density:54: WARNING: Exception occurred in plotting scanpy-tl-embedding_density-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.tl.embedding_density.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/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/3365/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3365/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 1538, in embedding_density
    raise ValueError(
ValueError: Cannot find the embedded representation `adata.obsm[X_'umap']`. Compute the embedding first. [docutils]
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/external/generated/scanpy.external.tl.palantir.rst: document is referenced in multiple toctrees: ['external/tools', 'external/tools'], selecting: external/tools <- external/generated/scanpy.external.tl.palantir
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/docs/generated/scanpy.pp.pca.rst: document is referenced in multiple toctrees: ['api/preprocessing', 'api/tools'], selecting: api/tools <- generated/scanpy.pp.pca
done
preparing documents... done
copying assets... 
copying static files... 
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/_readthedocs/html/_static/basic.css
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/_readthedocs/html/_static/language_data.js
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/_readthedocs/html/_static/documentation_options.js
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/_readthedocs/html/_static/copybutton.js
copying static files: done
copying extra files... 
copying extra files: done
copying assets: done
writing output... [  0%] api/classes
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dumping search index in English (code: en)... done
dumping object inventory... done
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3365/_readthedocs/html/_static/js/rtd_search_config.js
build finished with problems, 62 warnings (with warnings treated as errors).