Read the Docs build information
Build id: 2493223
Project: icb-scanpy
Version: 3209
Commit: bba9f70a97cb1d3c23957248f742b36d4aa7eb73
Date: 2024-09-19T09:01:40.034698Z
State: finished
Success: False


[rtd-command-info] start-time: 2024-09-19T09:01:41.182534Z, end-time: 2024-09-19T09:01:42.219604Z, duration: 1, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-09-19T09:01:42.300907Z, end-time: 2024-09-19T09:01:42.942913Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/3209/head:external-3209
From https://github.com/scverse/scanpy
 * [new ref]         refs/pull/3209/head -> external-3209

[rtd-command-info] start-time: 2024-09-19T09:01:43.089041Z, end-time: 2024-09-19T09:01:43.296534Z, duration: 0, exit-code: 0
git checkout --force bba9f70a97cb1d3c23957248f742b36d4aa7eb73
Note: switching to 'bba9f70a97cb1d3c23957248f742b36d4aa7eb73'.

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 bba9f70 Merge branch 'fix-style' into unhack-plotting

[rtd-command-info] start-time: 2024-09-19T09:01:43.369688Z, end-time: 2024-09-19T09:01:43.434118Z, 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: 2024-09-19T09:01:43.568197Z, end-time: 2024-09-19T09:01:43.651167Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2024-09-19T09:01:43.722014Z, end-time: 2024-09-19T09:01:58.609460Z, duration: 14, 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/3209/notebooks'...
Submodule path 'notebooks': checked out '3385df77ce0f63987104bc644562a811c5d1b441'

[rtd-command-info] start-time: 2024-09-19T09:01:58.689272Z, end-time: 2024-09-19T09:02:01.482721Z, duration: 2, 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]           1.10.0rc1   -> 1.10.0rc1
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 * [new tag]           1.4.5.1     -> 1.4.5.1
 * [new tag]           1.4.5.post1 -> 1.4.5.post1
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 * [new tag]           1.7.0rc1    -> 1.7.0rc1
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 * [new tag]           1.8.0.dev0  -> 1.8.0.dev0
 * [new tag]           1.9.0       -> 1.9.0
 * [new tag]           1.9.0.dev0  -> 1.9.0.dev0

[rtd-command-info] start-time: 2024-09-19T09:02:07.846336Z, end-time: 2024-09-19T09:02:07.929623Z, duration: 0, exit-code: 0
asdf global python 3.12.3


[rtd-command-info] start-time: 2024-09-19T09:02:08.385261Z, end-time: 2024-09-19T09:02:09.505902Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.12.3.final.0-64 in 751ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209, 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: 2024-09-19T09:02:09.587684Z, end-time: 2024-09-19T09:02:21.165482Z, duration: 11, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages (23.1)
Collecting pip
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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-24.2 setuptools-75.1.0

[rtd-command-info] start-time: 2024-09-19T09:02:21.287942Z, end-time: 2024-09-19T09:02:30.245107Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext
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, readthedocs-sphinx-ext
Successfully installed Jinja2-3.1.4 MarkupSafe-2.1.5 Pygments-2.18.0 alabaster-1.0.0 babel-2.16.0 certifi-2024.8.30 charset-normalizer-3.3.2 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-24.1 readthedocs-sphinx-ext-2.2.5 requests-2.32.3 snowballstemmer-2.2.0 sphinx-8.0.2 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: 2024-09-19T09:02:30.320532Z, end-time: 2024-09-19T09:04:03.800568Z, duration: 93, 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/3209
  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.dev131+gbba9f70a)
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Collecting h5py>=3.1 (from scanpy==1.11.0.dev131+gbba9f70a)
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Collecting legacy-api-wrap>=1.4 (from scanpy==1.11.0.dev131+gbba9f70a)
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Collecting matplotlib>=3.6 (from scanpy==1.11.0.dev131+gbba9f70a)
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Collecting numba>=0.56 (from scanpy==1.11.0.dev131+gbba9f70a)
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Collecting numpy>=1.23 (from scanpy==1.11.0.dev131+gbba9f70a)
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Requirement already satisfied: packaging>=21.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages (from scanpy==1.11.0.dev131+gbba9f70a) (24.1)
Collecting pandas>=1.5 (from scanpy==1.11.0.dev131+gbba9f70a)
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Collecting scikit-learn>=0.24 (from scanpy==1.11.0.dev131+gbba9f70a)
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  Preparing metadata (setup.py): started
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Collecting statsmodels>=0.13 (from scanpy==1.11.0.dev131+gbba9f70a)
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Collecting umap-learn!=0.5.0,>=0.5 (from scanpy==1.11.0.dev131+gbba9f70a)
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Collecting pre-commit (from scanpy==1.11.0.dev131+gbba9f70a)
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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.dev131+gbba9f70a-py3-none-any.whl size=2086438 sha256=df5a45d7e43e21741ac0e24f66bff943113748fd270eb86f33c43fba8f88c80b
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  Building wheel for sam-algorithm (setup.py): finished with status 'done'
  Created wheel for sam-algorithm: filename=sam_algorithm-1.0.2-py3-none-any.whl size=34579 sha256=30186ad2ceb992bebee60fdb48992dc6c51d7c640f2843c04775a70933e5ce0d
  Stored in directory: /tmp/pip-ephem-wheel-cache-1awf235u/wheels/57/54/be/ca87c5831826023e1d64b77d6680c582ff898a13844a7ed4ed
  Building wheel for session-info (setup.py): started
  Building wheel for session-info (setup.py): finished with status 'done'
  Created wheel for session-info: filename=session_info-1.0.0-py3-none-any.whl size=8023 sha256=83ae2e2ba7b177a44e5a115d370b118b3e2714345e0e0c1bd450491ae6f4241c
  Stored in directory: /tmp/pip-ephem-wheel-cache-1awf235u/wheels/23/da/7c/868424f4a5845ab58cd8686e0eb405e9e1e2d4152bf702c39d
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Successfully built scanpy sam-algorithm session-info hnswlib
Installing collected packages: webencodings, wcwidth, texttable, pytz, pure-eval, ptyprocess, fastjsonschema, distlib, array-api-compat, zipp, tzdata, typing-extensions, traitlets, tqdm, tornado, toolz, tinycss2, threadpoolctl, tabulate, stdlib_list, soupsieve, six, setuptools-scm, rpds-py, readthedocs-sphinx-search, pyzmq, pyyaml, pyparsing, psutil, prompt-toolkit, platformdirs, pillow, pexpect, parso, pandocfilters, numpy, nodeenv, networkx, nest-asyncio, natsort, 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, attrs, 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, bleach, beautifulsoup4, asttokens, stack-data, sphinxext-opengraph, sphinx-tabs, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, 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, anndata, umap-learn, nbformat, ipykernel, scanpy, sam-algorithm, nbclient, nbconvert, jupyter-cache, nbsphinx, myst-nb
Successfully installed accessible-pygments-0.0.5 anndata-0.10.9 array-api-compat-1.8 asttokens-2.4.1 attrs-24.2.0 beautifulsoup4-4.12.3 bleach-6.1.0 cfgv-3.4.0 click-8.1.7 cloudpickle-3.0.0 comm-0.2.2 contourpy-1.3.0 cycler-0.12.1 dask-2024.9.0 debugpy-1.8.5 decorator-5.1.1 defusedxml-0.7.1 dill-0.3.8 distlib-0.3.8 executing-2.1.0 fastjsonschema-2.20.0 filelock-3.16.1 fonttools-4.53.1 fsspec-2024.9.0 greenlet-3.1.0 h5py-3.11.0 harmonypy-0.0.10 hnswlib-0.8.0 identify-2.6.1 igraph-0.11.6 importlib_metadata-8.5.0 ipykernel-6.29.5 ipython-8.27.0 jedi-0.19.1 joblib-1.4.2 jsonschema-4.23.0 jsonschema-specifications-2023.12.1 jupyter-cache-1.0.0 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 myst-nb-1.1.1 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-3.3 nodeenv-1.9.1 numba-0.60.0 numpy-2.0.2 pandas-2.2.2 pandocfilters-1.5.1 parso-0.8.4 partd-1.4.2 patsy-0.5.6 pexpect-4.9.0 pillow-10.4.0 platformdirs-4.3.6 pre-commit-3.8.0 prompt-toolkit-3.0.47 psutil-6.0.0 ptyprocess-0.7.0 pure-eval-0.2.3 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.15.4 pynndescent-0.5.13 pyparsing-3.1.4 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-0.20.0 sam-algorithm-1.0.2 scanpy-1.11.0.dev131+gbba9f70a 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 soupsieve-2.6 sphinx-autodoc-typehints-2.4.4 sphinx-book-theme-1.1.3 sphinx-copybutton-0.5.2 sphinx-design-0.6.1 sphinx-tabs-3.4.5 sphinxcontrib-bibtex-2.6.3 sphinxext-opengraph-0.9.1 sqlalchemy-2.0.35 stack-data-0.6.3 statsmodels-0.14.3 stdlib_list-0.10.0 tabulate-0.9.0 texttable-1.7.0 threadpoolctl-3.5.0 tinycss2-1.3.0 toolz-0.12.1 tornado-6.4.1 towncrier-24.8.0 tqdm-4.66.5 traitlets-5.14.3 typing-extensions-4.12.2 tzdata-2024.1 umap-learn-0.5.6 virtualenv-20.26.5 wcwidth-0.2.13 webencodings-0.5.1 zipp-3.20.2

[rtd-command-info] start-time: 2024-09-19T09:04:04.030312Z, end-time: 2024-09-19T09:04:09.471538Z, duration: 5, exit-code: 0
( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true
Loading template...
Finding news fragments...
Rendering news fragments...
Writing to newsfile...
Staging newsfile...
Keeping the following files:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/release-notes/3206.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/release-notes/3155.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/release-notes/3180.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/release-notes/2921.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/release-notes/3184.feature.md
Done!

[rtd-command-info] start-time: 2024-09-19T09:04:09.899858Z, end-time: 2024-09-19T09:04:09.954783Z, 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")




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


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

import importlib
import sys
import os.path

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

from sphinx import version_info

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

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

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

#Add project information to the template context.
context = {
    'html_theme': html_theme,
    'current_version': "3209",
    'version_slug': "3209",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ("1.10.x", "/en/1.10.x/"),
    ("1.9.x", "/en/1.9.x/"),
    ("1.8.x", "/en/1.8.x/"),
    ("1.7.x", "/en/1.7.x/"),
    ("1.6.x", "/en/1.6.x/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-scanpy',
    'name': u'scanpy',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': '',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
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    'github_repo': 'scanpy',
    'github_version': 'bba9f70a97cb1d3c23957248f742b36d4aa7eb73',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'bba9f70a97cb1d3c23957248f742b36d4aa7eb73',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'bba9f70a97cb1d3c23957248f742b36d4aa7eb73',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'bba9f70a',
}

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





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

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

# Add External version warning banner to the external version documentation
if 'external' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'https://github.com/scverse/scanpy/pull/3209'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/2493223/'

project_language = 'en'

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

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

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

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

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

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

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

[rtd-command-info] start-time: 2024-09-19T09:04:10.074181Z, end-time: 2024-09-19T09:08:54.246504Z, duration: 284, exit-code: 1
python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v8.0.2
loading translations [en]... done
making output directory... done
checking bibtex cache... out of date
parsing bibtex file /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/references.bib... parsed 66 entries
myst v4.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'deflist', 'html_image', 'amsmath', 'html_admonition', 'colon_fence', 'dollarmath'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
myst-nb v1.1.1: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', 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/3209/_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 ...
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intersphinx inventory has moved: https://bbknn.readthedocs.io/en/latest//objects.inv -> https://bbknn.readthedocs.io/en/latest/objects.inv
loading intersphinx inventory 'ipython' from https://ipython.readthedocs.io/en/stable//objects.inv ...
intersphinx inventory has moved: https://docs.dask.org/en/stable//objects.inv -> https://docs.dask.org/en/stable/objects.inv
intersphinx inventory has moved: https://anndata.readthedocs.io/en/stable//objects.inv -> https://anndata.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 ...
intersphinx inventory has moved: https://docs.h5py.org/en/stable//objects.inv -> https://docs.h5py.org/en/stable/objects.inv
loading intersphinx inventory 'matplotlib' from https://matplotlib.org/stable//objects.inv ...
intersphinx inventory has moved: https://louvain-igraph.readthedocs.io/en/latest//objects.inv -> https://louvain-igraph.readthedocs.io/en/latest/objects.inv
intersphinx inventory has moved: https://leidenalg.readthedocs.io/en/latest//objects.inv -> https://leidenalg.readthedocs.io/en/latest/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 ...
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loading intersphinx inventory 'pandas' from https://pandas.pydata.org/pandas-docs/stable//objects.inv ...
intersphinx inventory has moved: https://ipython.readthedocs.io/en/stable//objects.inv -> https://ipython.readthedocs.io/en/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 ...
intersphinx inventory has moved: https://docs.pytest.org/en/latest//objects.inv -> https://docs.pytest.org/en/latest/objects.inv
intersphinx inventory has moved: https://pynndescent.readthedocs.io/en/latest//objects.inv -> https://pynndescent.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 ...
intersphinx inventory has moved: https://rapids-singlecell.readthedocs.io/en/latest//objects.inv -> https://rapids-singlecell.readthedocs.io/en/latest/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/3209/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/scanpy.pl.embedding_density.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/scanpy.pl.filter_genes_dispersion.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy.tl.leiden.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy.tl.umap.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/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] 452 added, 0 changed, 0 removed
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/myst_nb/core/read.py:71: RemovedInSphinx90Warning: Sphinx 9 will drop support for representing paths as strings. Use "pathlib.Path" or "os.fspath" instead.
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WARNING: Gene labels are not shown when more than 50 genes are visualized. To show gene labels set `show_gene_labels=True`
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WARNING: Cannot resolve forward reference in type annotations of "scanpy.pl.DotPlot": name 'InitVar' is not defined
WARNING: Cannot resolve forward reference in type annotations of "scanpy.pl.MatrixPlot": name 'Figure' is not defined
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py:docstring of scanpy.plotting._matrixplot.MatrixPlot:86: WARNING: Exception occurred in plotting scanpy-pl-MatrixPlot-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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 "<string>", line 38, in __init__
TypeError: MatrixPlot.__post_init__() takes 3 positional arguments but 4 were given [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py:docstring of scanpy.plotting._matrixplot.MatrixPlot:97: WARNING: Exception occurred in plotting scanpy-pl-MatrixPlot-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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 "<string>", line 38, in __init__
TypeError: MatrixPlot.__post_init__() takes 3 positional arguments but 4 were given [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py:docstring of scanpy.plotting._matrixplot.MatrixPlot.style:25: WARNING: Exception occurred in plotting scanpy-pl-MatrixPlot-style-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/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/3209/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 "<string>", line 38, in __init__
TypeError: MatrixPlot.__post_init__() takes 3 positional arguments but 4 were given [docutils]
WARNING: Cannot resolve forward reference in type annotations of "scanpy.pl.StackedViolin": name 'Figure' is not defined
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/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/3209/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/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 964, in rank_genes_groups_dotplot
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 603, in _rank_genes_groups_plot
    _pl = dotplot(
          ^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_dotplot.py", line 967, in dotplot
    dp = DotPlot(
         ^^^^^^^^
  File "<string>", line 53, in __init__
TypeError: DotPlot.__post_init__() takes 2 positional arguments but 3 were given [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/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/3209/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/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 964, in rank_genes_groups_dotplot
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 603, in _rank_genes_groups_plot
    _pl = dotplot(
          ^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_dotplot.py", line 967, in dotplot
    dp = DotPlot(
         ^^^^^^^^
  File "<string>", line 53, in __init__
TypeError: DotPlot.__post_init__() takes 2 positional arguments but 3 were given [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/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/3209/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/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 964, in rank_genes_groups_dotplot
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 603, in _rank_genes_groups_plot
    _pl = dotplot(
          ^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_dotplot.py", line 967, in dotplot
    dp = DotPlot(
         ^^^^^^^^
  File "<string>", line 53, in __init__
TypeError: DotPlot.__post_init__() takes 2 positional arguments but 3 were given [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/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/3209/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/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 964, in rank_genes_groups_dotplot
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 603, in _rank_genes_groups_plot
    _pl = dotplot(
          ^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_dotplot.py", line 967, in dotplot
    dp = DotPlot(
         ^^^^^^^^
  File "<string>", line 53, in __init__
TypeError: DotPlot.__post_init__() takes 2 positional arguments but 3 were given [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/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/3209/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/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 964, in rank_genes_groups_dotplot
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 603, in _rank_genes_groups_plot
    _pl = dotplot(
          ^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_dotplot.py", line 967, in dotplot
    dp = DotPlot(
         ^^^^^^^^
  File "<string>", line 53, in __init__
TypeError: DotPlot.__post_init__() takes 2 positional arguments but 3 were given [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/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/3209/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/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 1174, in rank_genes_groups_matrixplot
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 617, in _rank_genes_groups_plot
    _pl = matrixplot(
          ^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py", line 370, in matrixplot
    mp = MatrixPlot(
         ^^^^^^^^^^^
  File "<string>", line 38, in __init__
TypeError: MatrixPlot.__post_init__() takes 3 positional arguments but 4 were given [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/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/3209/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/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 1174, in rank_genes_groups_matrixplot
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 617, in _rank_genes_groups_plot
    _pl = matrixplot(
          ^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py", line 370, in matrixplot
    mp = MatrixPlot(
         ^^^^^^^^^^^
  File "<string>", line 38, in __init__
TypeError: MatrixPlot.__post_init__() takes 3 positional arguments but 4 were given [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/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/3209/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/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 1174, in rank_genes_groups_matrixplot
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 617, in _rank_genes_groups_plot
    _pl = matrixplot(
          ^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py", line 370, in matrixplot
    mp = MatrixPlot(
         ^^^^^^^^^^^
  File "<string>", line 38, in __init__
TypeError: MatrixPlot.__post_init__() takes 3 positional arguments but 4 were given [docutils]
WARNING: Cannot resolve forward reference in type annotations of "scanpy.pl.DotPlot": name 'InitVar' is not defined
WARNING: Cannot resolve forward reference in type annotations of "scanpy.pl.MatrixPlot": name 'Figure' is not defined
WARNING: Cannot resolve forward reference in type annotations of "scanpy.pl.StackedViolin": name 'Figure' is not defined
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/docs/generated/scanpy.pl.dotplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_dotplot.py", line 967, in dotplot
    dp = DotPlot(
         ^^^^^^^^
  File "<string>", line 53, in __init__
TypeError: DotPlot.__post_init__() takes 2 positional arguments but 3 were given [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/docs/generated/scanpy.pl.dotplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_dotplot.py", line 967, in dotplot
    dp = DotPlot(
         ^^^^^^^^
  File "<string>", line 53, in __init__
TypeError: DotPlot.__post_init__() takes 2 positional arguments but 3 were given [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/docs/generated/scanpy.pl.dotplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_dotplot.py", line 967, in dotplot
    dp = DotPlot(
         ^^^^^^^^
  File "<string>", line 53, in __init__
TypeError: DotPlot.__post_init__() takes 2 positional arguments but 3 were given [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py:docstring of scanpy.plotting._matrixplot.matrixplot:111: WARNING: Exception occurred in plotting scanpy-pl-matrixplot-1
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy.pl.matrixplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py", line 370, in matrixplot
    mp = MatrixPlot(
         ^^^^^^^^^^^
  File "<string>", line 38, in __init__
TypeError: MatrixPlot.__post_init__() takes 3 positional arguments but 4 were given [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py:docstring of scanpy.plotting._matrixplot.matrixplot:121: WARNING: Exception occurred in plotting scanpy-pl-matrixplot-2
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy.pl.matrixplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py", line 370, in matrixplot
    mp = MatrixPlot(
         ^^^^^^^^^^^
  File "<string>", line 38, in __init__
TypeError: MatrixPlot.__post_init__() takes 3 positional arguments but 4 were given [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py:docstring of scanpy.plotting._matrixplot.matrixplot:129: WARNING: Exception occurred in plotting scanpy-pl-matrixplot-3
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy.pl.matrixplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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/3209/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/3209/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py", line 370, in matrixplot
    mp = MatrixPlot(
         ^^^^^^^^^^^
  File "<string>", line 38, in __init__
TypeError: MatrixPlot.__post_init__() takes 3 positional arguments but 4 were given [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/scanpy/plotting/_matrixplot.py:docstring of scanpy.plotting._matrixplot.matrixplot:137: WARNING: Exception occurred in plotting scanpy-pl-matrixplot-4
 from /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3209/docs/generated/scanpy.pl.matrixplot.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/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]
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
copying assets... 
copying static files... done
copying extra files... done
copying assets: done
writing output... [  0%] api/classes
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/readthedocs_ext/readthedocs.py:106: RemovedInSphinx90Warning: 'sphinx.builders.html.StandaloneHTMLBuilder.css_files' is deprecated. Check CHANGES for Sphinx API modifications.
  if inject_css and theme_css not in app.builder.css_files:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/readthedocs_ext/readthedocs.py:106: RemovedInSphinx90Warning: The str interface for _CascadingStyleSheet objects is deprecated. Use css.filename instead.
  if inject_css and theme_css not in app.builder.css_files:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/readthedocs_ext/readthedocs.py:120: RemovedInSphinx90Warning: 'sphinx.builders.html.StandaloneHTMLBuilder.script_files' is deprecated. Check CHANGES for Sphinx API modifications.
  hasattr(app.builder, 'script_files'),
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/readthedocs_ext/readthedocs.py:121: RemovedInSphinx90Warning: 'sphinx.builders.html.StandaloneHTMLBuilder.script_files' is deprecated. Check CHANGES for Sphinx API modifications.
  js_file not in app.builder.script_files,
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/readthedocs_ext/readthedocs.py:121: RemovedInSphinx90Warning: The str interface for _JavaScript objects is deprecated. Use js.filename instead.
  js_file not in app.builder.script_files,
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/sphinx_tabs/tabs.py:335: RemovedInSphinx90Warning: The str interface for _JavaScript objects is deprecated. Use js.filename instead.
  if path.suffix == ".js" and path.as_posix() in context["script_files"]:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3209/lib/python3.12/site-packages/sphinx_tabs/tabs.py:336: RemovedInSphinx90Warning: The str interface for _JavaScript objects is deprecated. Use js.filename instead.
  context["script_files"].remove(path.as_posix())
writing output... [  0%] api/datasets
writing output... [  1%] api/deprecated
writing output... [  1%] api/experimental
writing output... [  1%] api/generated/classes/scanpy.pl.DotPlot
writing output... [  1%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT
writing output... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH
writing output... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP
writing output... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE
writing output... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON
writing output... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_WSPACE
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.MAX_NUM_CATEGORIES
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.MIN_FIGURE_HEIGHT
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.add_dendrogram
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.add_totals
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.are_axes_swapped
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.ax
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.ax_dict
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.categories_order
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.category_height
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.category_width
writing output... [  8%] api/generated/classes/scanpy.pl.DotPlot.cmap
writing output... [  8%] api/generated/classes/scanpy.pl.DotPlot.color_legend_title
writing output... [  8%] api/generated/classes/scanpy.pl.DotPlot.color_on
writing output... [  8%] api/generated/classes/scanpy.pl.DotPlot.dendrogram
writing output... [  8%] api/generated/classes/scanpy.pl.DotPlot.dot_color_df
writing output... [  9%] api/generated/classes/scanpy.pl.DotPlot.dot_edge_color
writing output... [  9%] api/generated/classes/scanpy.pl.DotPlot.dot_edge_lw
writing output... [  9%] api/generated/classes/scanpy.pl.DotPlot.dot_max
writing output... [  9%] api/generated/classes/scanpy.pl.DotPlot.dot_min
writing output... [ 10%] api/generated/classes/scanpy.pl.DotPlot.dot_size_df
writing output... [ 10%] api/generated/classes/scanpy.pl.DotPlot.expression_cutoff
writing output... [ 10%] api/generated/classes/scanpy.pl.DotPlot.fig
writing output... [ 10%] api/generated/classes/scanpy.pl.DotPlot.fig_title
writing output... [ 10%] api/generated/classes/scanpy.pl.DotPlot.figsize
writing output... [ 11%] api/generated/classes/scanpy.pl.DotPlot.gene_symbols
writing output... [ 11%] api/generated/classes/scanpy.pl.DotPlot.get_axes
writing output... [ 11%] api/generated/classes/scanpy.pl.DotPlot.getdoc
writing output... [ 11%] api/generated/classes/scanpy.pl.DotPlot.grid
writing output... [ 12%] api/generated/classes/scanpy.pl.DotPlot.group_extra_size
writing output... [ 12%] api/generated/classes/scanpy.pl.DotPlot.has_var_groups
writing output... [ 12%] api/generated/classes/scanpy.pl.DotPlot.height
writing output... [ 12%] api/generated/classes/scanpy.pl.DotPlot.largest_dot
writing output... [ 12%] api/generated/classes/scanpy.pl.DotPlot.layer
writing output... [ 13%] api/generated/classes/scanpy.pl.DotPlot.legend
writing output... [ 13%] api/generated/classes/scanpy.pl.DotPlot.legends_width
writing output... [ 13%] api/generated/classes/scanpy.pl.DotPlot.log
writing output... [ 13%] api/generated/classes/scanpy.pl.DotPlot.make_figure
writing output... [ 13%] api/generated/classes/scanpy.pl.DotPlot.mean_only_expressed
writing output... [ 14%] api/generated/classes/scanpy.pl.DotPlot.min_figure_height
writing output... [ 14%] api/generated/classes/scanpy.pl.DotPlot.norm
writing output... [ 14%] api/generated/classes/scanpy.pl.DotPlot.num_categories
writing output... [ 14%] api/generated/classes/scanpy.pl.DotPlot.plot_group_extra
writing output... [ 15%] api/generated/classes/scanpy.pl.DotPlot.plot_x_padding
writing output... [ 15%] api/generated/classes/scanpy.pl.DotPlot.plot_y_padding
writing output... [ 15%] api/generated/classes/scanpy.pl.DotPlot.savefig
writing output... [ 15%] api/generated/classes/scanpy.pl.DotPlot.show
writing output... [ 15%] api/generated/classes/scanpy.pl.DotPlot.show_colorbar
writing output... [ 16%] api/generated/classes/scanpy.pl.DotPlot.show_size_legend
writing output... [ 16%] api/generated/classes/scanpy.pl.DotPlot.size_exponent
writing output... [ 16%] api/generated/classes/scanpy.pl.DotPlot.size_title
writing output... [ 16%] api/generated/classes/scanpy.pl.DotPlot.smallest_dot
writing output... [ 17%] api/generated/classes/scanpy.pl.DotPlot.standard_scale
writing output... [ 17%] api/generated/classes/scanpy.pl.DotPlot.style
writing output... [ 17%] api/generated/classes/scanpy.pl.DotPlot.swap_axes
writing output... [ 17%] api/generated/classes/scanpy.pl.DotPlot.title
writing output... [ 17%] api/generated/classes/scanpy.pl.DotPlot.use_raw
writing output... [ 18%] api/generated/classes/scanpy.pl.DotPlot.var_group_labels
writing output... [ 18%] api/generated/classes/scanpy.pl.DotPlot.var_group_positions
writing output... [ 18%] api/generated/classes/scanpy.pl.DotPlot.var_group_rotation
writing output... [ 18%] api/generated/classes/scanpy.pl.DotPlot.var_names_idx_order
writing output... [ 19%] api/generated/classes/scanpy.pl.DotPlot.vboundnorm
writing output... [ 19%] api/generated/classes/scanpy.pl.DotPlot.vcenter
writing output... [ 19%] api/generated/classes/scanpy.pl.DotPlot.vmax
writing output... [ 19%] api/generated/classes/scanpy.pl.DotPlot.vmin
writing output... [ 19%] api/generated/classes/scanpy.pl.DotPlot.width
writing output... [ 20%] api/generated/classes/scanpy.pl.DotPlot.with_swapped_axes
writing output... [ 20%] api/generated/classes/scanpy.pl.DotPlot.wspace
writing output... [ 20%] api/generated/classes/scanpy.pl.MatrixPlot
writing output... [ 20%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_HEIGHT
writing output... [ 21%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_WIDTH
writing output... [ 21%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLORMAP
writing output... [ 21%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLOR_LEGEND_TITLE
writing output... [ 21%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_COLOR
writing output... [ 21%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_LW
writing output... [ 22%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_LEGENDS_WIDTH
writing output... [ 22%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_SAVE_PREFIX
writing output... [ 22%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_WSPACE
writing output... [ 22%] api/generated/classes/scanpy.pl.MatrixPlot.MAX_NUM_CATEGORIES
writing output... [ 23%] api/generated/classes/scanpy.pl.MatrixPlot.MIN_FIGURE_HEIGHT
writing output... [ 23%] api/generated/classes/scanpy.pl.MatrixPlot.add_dendrogram
writing output... [ 23%] api/generated/classes/scanpy.pl.MatrixPlot.add_totals
writing output... [ 23%] api/generated/classes/scanpy.pl.MatrixPlot.are_axes_swapped
writing output... [ 23%] api/generated/classes/scanpy.pl.MatrixPlot.ax
writing output... [ 24%] api/generated/classes/scanpy.pl.MatrixPlot.ax_dict
writing output... [ 24%] api/generated/classes/scanpy.pl.MatrixPlot.categories_order
writing output... [ 24%] api/generated/classes/scanpy.pl.MatrixPlot.category_height
writing output... [ 24%] api/generated/classes/scanpy.pl.MatrixPlot.category_width
writing output... [ 25%] api/generated/classes/scanpy.pl.MatrixPlot.cmap
writing output... [ 25%] api/generated/classes/scanpy.pl.MatrixPlot.color_legend_title
writing output... [ 25%] api/generated/classes/scanpy.pl.MatrixPlot.colorbar_title
writing output... [ 25%] api/generated/classes/scanpy.pl.MatrixPlot.dendrogram
writing output... [ 25%] api/generated/classes/scanpy.pl.MatrixPlot.edge_color
writing output... [ 26%] api/generated/classes/scanpy.pl.MatrixPlot.edge_lw
writing output... [ 26%] api/generated/classes/scanpy.pl.MatrixPlot.fig
writing output... [ 26%] api/generated/classes/scanpy.pl.MatrixPlot.fig_title
writing output... [ 26%] api/generated/classes/scanpy.pl.MatrixPlot.figsize
writing output... [ 27%] api/generated/classes/scanpy.pl.MatrixPlot.gene_symbols
writing output... [ 27%] api/generated/classes/scanpy.pl.MatrixPlot.get_axes
writing output... [ 27%] api/generated/classes/scanpy.pl.MatrixPlot.getdoc
writing output... [ 27%] api/generated/classes/scanpy.pl.MatrixPlot.group_extra_size
writing output... [ 27%] api/generated/classes/scanpy.pl.MatrixPlot.has_var_groups
writing output... [ 28%] api/generated/classes/scanpy.pl.MatrixPlot.height
writing output... [ 28%] api/generated/classes/scanpy.pl.MatrixPlot.layer
writing output... [ 28%] api/generated/classes/scanpy.pl.MatrixPlot.legend
writing output... [ 28%] api/generated/classes/scanpy.pl.MatrixPlot.legends_width
writing output... [ 29%] api/generated/classes/scanpy.pl.MatrixPlot.log
writing output... [ 29%] api/generated/classes/scanpy.pl.MatrixPlot.make_figure
writing output... [ 29%] api/generated/classes/scanpy.pl.MatrixPlot.min_figure_height
writing output... [ 29%] api/generated/classes/scanpy.pl.MatrixPlot.norm
writing output... [ 29%] api/generated/classes/scanpy.pl.MatrixPlot.num_categories
writing output... [ 30%] api/generated/classes/scanpy.pl.MatrixPlot.plot_group_extra
writing output... [ 30%] api/generated/classes/scanpy.pl.MatrixPlot.savefig
writing output... [ 30%] api/generated/classes/scanpy.pl.MatrixPlot.show
writing output... [ 30%] api/generated/classes/scanpy.pl.MatrixPlot.standard_scale
writing output... [ 31%] api/generated/classes/scanpy.pl.MatrixPlot.style
writing output... [ 31%] api/generated/classes/scanpy.pl.MatrixPlot.swap_axes
writing output... [ 31%] api/generated/classes/scanpy.pl.MatrixPlot.title
writing output... [ 31%] api/generated/classes/scanpy.pl.MatrixPlot.use_raw
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writing output... [ 32%] api/generated/classes/scanpy.pl.MatrixPlot.var_group_labels
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writing output... [ 32%] api/generated/classes/scanpy.pl.MatrixPlot.var_group_rotation
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writing output... [ 33%] api/generated/classes/scanpy.pl.MatrixPlot.vboundnorm
writing output... [ 33%] api/generated/classes/scanpy.pl.MatrixPlot.vcenter
writing output... [ 33%] api/generated/classes/scanpy.pl.MatrixPlot.vmax
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writing output... [ 33%] api/generated/classes/scanpy.pl.MatrixPlot.width
writing output... [ 34%] api/generated/classes/scanpy.pl.MatrixPlot.with_swapped_axes
writing output... [ 34%] api/generated/classes/scanpy.pl.MatrixPlot.wspace
writing output... [ 34%] api/generated/classes/scanpy.pl.StackedViolin
writing output... [ 34%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_HEIGHT
writing output... [ 35%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_WIDTH
writing output... [ 35%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP
writing output... [ 35%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE
writing output... [ 35%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT
writing output... [ 35%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_DENSITY_NORM
writing output... [ 36%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER
writing output... [ 36%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER
writing output... [ 36%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE
writing output... [ 36%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LEGENDS_WIDTH
writing output... [ 37%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH
writing output... [ 37%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING
writing output... [ 37%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS
writing output... [ 37%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING
writing output... [ 37%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE
writing output... [ 38%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX
writing output... [ 38%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT
writing output... [ 38%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_WSPACE
writing output... [ 38%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM
writing output... [ 38%] api/generated/classes/scanpy.pl.StackedViolin.MAX_NUM_CATEGORIES
writing output... [ 39%] api/generated/classes/scanpy.pl.StackedViolin.MIN_FIGURE_HEIGHT
writing output... [ 39%] api/generated/classes/scanpy.pl.StackedViolin.add_dendrogram
writing output... [ 39%] api/generated/classes/scanpy.pl.StackedViolin.add_totals
writing output... [ 39%] api/generated/classes/scanpy.pl.StackedViolin.are_axes_swapped
writing output... [ 40%] api/generated/classes/scanpy.pl.StackedViolin.ax
writing output... [ 40%] api/generated/classes/scanpy.pl.StackedViolin.ax_dict
writing output... [ 40%] api/generated/classes/scanpy.pl.StackedViolin.categories_order
writing output... [ 40%] api/generated/classes/scanpy.pl.StackedViolin.category_height
writing output... [ 40%] api/generated/classes/scanpy.pl.StackedViolin.category_width
writing output... [ 41%] api/generated/classes/scanpy.pl.StackedViolin.cmap
writing output... [ 41%] api/generated/classes/scanpy.pl.StackedViolin.color_legend_title
writing output... [ 41%] api/generated/classes/scanpy.pl.StackedViolin.dendrogram
writing output... [ 41%] api/generated/classes/scanpy.pl.StackedViolin.fig
writing output... [ 42%] api/generated/classes/scanpy.pl.StackedViolin.fig_title
writing output... [ 42%] api/generated/classes/scanpy.pl.StackedViolin.figsize
writing output... [ 42%] api/generated/classes/scanpy.pl.StackedViolin.gene_symbols
writing output... [ 42%] api/generated/classes/scanpy.pl.StackedViolin.get_axes
writing output... [ 42%] api/generated/classes/scanpy.pl.StackedViolin.getdoc
writing output... [ 43%] api/generated/classes/scanpy.pl.StackedViolin.group_extra_size
writing output... [ 43%] api/generated/classes/scanpy.pl.StackedViolin.has_var_groups
writing output... [ 43%] api/generated/classes/scanpy.pl.StackedViolin.height
writing output... [ 43%] api/generated/classes/scanpy.pl.StackedViolin.jitter
writing output... [ 44%] api/generated/classes/scanpy.pl.StackedViolin.jitter_size
writing output... [ 44%] api/generated/classes/scanpy.pl.StackedViolin.layer
writing output... [ 44%] api/generated/classes/scanpy.pl.StackedViolin.legend
writing output... [ 44%] api/generated/classes/scanpy.pl.StackedViolin.legends_width
writing output... [ 44%] api/generated/classes/scanpy.pl.StackedViolin.log
writing output... [ 45%] api/generated/classes/scanpy.pl.StackedViolin.make_figure
writing output... [ 45%] api/generated/classes/scanpy.pl.StackedViolin.min_figure_height
writing output... [ 45%] api/generated/classes/scanpy.pl.StackedViolin.norm
writing output... [ 45%] api/generated/classes/scanpy.pl.StackedViolin.num_categories
writing output... [ 46%] api/generated/classes/scanpy.pl.StackedViolin.plot_group_extra
writing output... [ 46%] api/generated/classes/scanpy.pl.StackedViolin.plot_x_padding
writing output... [ 46%] api/generated/classes/scanpy.pl.StackedViolin.plot_y_padding
writing output... [ 46%] api/generated/classes/scanpy.pl.StackedViolin.plot_yticklabels
writing output... [ 46%] api/generated/classes/scanpy.pl.StackedViolin.row_palette
writing output... [ 47%] api/generated/classes/scanpy.pl.StackedViolin.savefig
writing output... [ 47%] api/generated/classes/scanpy.pl.StackedViolin.show
writing output... [ 47%] api/generated/classes/scanpy.pl.StackedViolin.standard_scale
writing output... [ 47%] api/generated/classes/scanpy.pl.StackedViolin.stripplot
writing output... [ 48%] api/generated/classes/scanpy.pl.StackedViolin.style
writing output... [ 48%] api/generated/classes/scanpy.pl.StackedViolin.swap_axes
writing output... [ 48%] api/generated/classes/scanpy.pl.StackedViolin.title
writing output... [ 48%] api/generated/classes/scanpy.pl.StackedViolin.use_raw
writing output... [ 48%] api/generated/classes/scanpy.pl.StackedViolin.var_group_labels
writing output... [ 49%] api/generated/classes/scanpy.pl.StackedViolin.var_group_positions
writing output... [ 49%] api/generated/classes/scanpy.pl.StackedViolin.var_group_rotation
writing output... [ 49%] api/generated/classes/scanpy.pl.StackedViolin.var_names_idx_order
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