Read the Docs build information
Build id: 2592002
Project: icb-scanpy
Version: 3335
Commit: 42b2041eb67c903da44b12b671c0eb96cd0ee72f
Date: 2024-11-05T10:27:25.413812Z
State: finished
Success: False


[rtd-command-info] start-time: 2024-11-05T10:27:26.638401Z, end-time: 2024-11-05T10:27:28.072623Z, duration: 1, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-11-05T10:27:28.158092Z, end-time: 2024-11-05T10:27:28.876399Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/3335/head:external-3335
From https://github.com/scverse/scanpy
 * [new ref]         refs/pull/3335/head -> external-3335

[rtd-command-info] start-time: 2024-11-05T10:27:29.018073Z, end-time: 2024-11-05T10:27:29.165728Z, duration: 0, exit-code: 0
git checkout --force 42b2041eb67c903da44b12b671c0eb96cd0ee72f
Note: switching to '42b2041eb67c903da44b12b671c0eb96cd0ee72f'.

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 42b2041 no class

[rtd-command-info] start-time: 2024-11-05T10:27:29.241517Z, end-time: 2024-11-05T10:27:29.303813Z, 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: 2024-11-05T10:27:29.438090Z, end-time: 2024-11-05T10:27:29.524204Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2024-11-05T10:27:29.601123Z, end-time: 2024-11-05T10:27:45.686596Z, duration: 16, 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/3335/notebooks'...
Submodule path 'notebooks': checked out '3385df77ce0f63987104bc644562a811c5d1b441'

[rtd-command-info] start-time: 2024-11-05T10:27:45.751262Z, end-time: 2024-11-05T10:27:48.847889Z, 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]           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.dev0  -> 1.9.0.dev0

[rtd-command-info] start-time: 2024-11-05T10:27:55.115985Z, end-time: 2024-11-05T10:27:55.194748Z, duration: 0, exit-code: 0
asdf global python 3.12.3


[rtd-command-info] start-time: 2024-11-05T10:27:55.628638Z, end-time: 2024-11-05T10:27:56.813638Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.12.3.final.0-64 in 835ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335, 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: 2024-11-05T10:27:56.894909Z, end-time: 2024-11-05T10:28:10.480511Z, duration: 13, 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/3335/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/3335/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-75.3.0

[rtd-command-info] start-time: 2024-11-05T10:28:10.556626Z, end-time: 2024-11-05T10:28:20.300608Z, duration: 9, exit-code: 0
python -m pip install --upgrade --no-cache-dir 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-24.1 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: 2024-11-05T10:28:20.365811Z, end-time: 2024-11-05T10:29:55.222566Z, duration: 94, 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/3335
  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
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Collecting anndata>=0.8 (from scanpy==1.11.0.dev151+g42b2041e)
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Collecting legacy-api-wrap>=1.4 (from scanpy==1.11.0.dev151+g42b2041e)
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Collecting matplotlib>=3.6 (from scanpy==1.11.0.dev151+g42b2041e)
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Collecting numba>=0.56 (from scanpy==1.11.0.dev151+g42b2041e)
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Collecting numpy>=1.23 (from scanpy==1.11.0.dev151+g42b2041e)
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Requirement already satisfied: packaging>=21.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages (from scanpy==1.11.0.dev151+g42b2041e) (24.1)
Collecting pandas>=1.5 (from scanpy==1.11.0.dev151+g42b2041e)
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Collecting scikit-learn>=1.1 (from scanpy==1.11.0.dev151+g42b2041e)
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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.dev151+g42b2041e-py3-none-any.whl size=2090617 sha256=a672b6ddcf2fc1a1d278a6159657a52876f79876c44d8c0419dd4758889a2f4d
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  Building wheel for sam-algorithm (setup.py): started
  Building wheel for sam-algorithm (setup.py): finished with status 'done'
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  Stored in directory: /tmp/pip-ephem-wheel-cache-h8b049a1/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=e1e4281d3c5ce6a66047e133ea4a452842029c50dced255c5ae2a978c7cd8853
  Stored in directory: /tmp/pip-ephem-wheel-cache-h8b049a1/wheels/23/da/7c/868424f4a5845ab58cd8686e0eb405e9e1e2d4152bf702c39d
  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=2288948 sha256=2e318d247cac2f04d077c7014daef8b37ede3cc817e9387b32e4a8c5c20bfa5a
  Stored in directory: /tmp/pip-ephem-wheel-cache-h8b049a1/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-0.10.9 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-1.3.0 cycler-0.12.1 dask-2024.7.1 dask-expr-1.1.9 dask-glm-0.3.2 dask-ml-2024.4.4 debugpy-1.8.7 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-4.54.1 fsspec-2024.10.0 greenlet-3.1.1 h5py-3.12.1 harmonypy-0.0.10 hnswlib-0.8.0 identify-2.6.1 igraph-0.11.8 importlib_metadata-8.5.0 ipykernel-6.29.5 ipython-8.29.0 jedi-0.19.1 joblib-1.4.2 jsonschema-4.23.0 jsonschema-specifications-2024.10.1 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 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-0.5.6 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-0.20.1 sam-algorithm-1.0.2 scanpy-1.11.0.dev151+g42b2041e 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-4.66.6 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-3.20.2

[rtd-command-info] start-time: 2024-11-05T10:29:55.489229Z, end-time: 2024-11-05T10:30:03.826915Z, duration: 8, 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/3335/docs/release-notes/3267.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/release-notes/3264.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/release-notes/3206.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/release-notes/3155.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/release-notes/3275.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/release-notes/3263.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/release-notes/3180.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/release-notes/2921.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/release-notes/3184.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/release-notes/3302.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/release-notes/3286.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/release-notes/3243.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/release-notes/3296.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/release-notes/3244.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/release-notes/3283.breaking.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/release-notes/3324.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/release-notes/3299.bugfix.md
Done!

[rtd-command-info] start-time: 2024-11-05T10:30:03.897254Z, end-time: 2024-11-05T10:30:03.956808Z, 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: 2024-11-05T10:30:04.037889Z, end-time: 2024-11-05T10:32:47.507041Z, duration: 163, exit-code: 1
python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v8.1.3
loading translations [en]... done
making output directory... done
checking bibtex cache... out of date
parsing bibtex file /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/references.bib... parsed 66 entries
myst v4.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'amsmath', 'dollarmath', 'html_admonition', 'html_image', 'colon_fence', 'deflist'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
myst-nb v1.1.2: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', 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/3335/_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/3335/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/scanpy.pl.embedding_density.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/scanpy.pl.filter_genes_dispersion.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy.tl.leiden.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy.tl.umap.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/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/3335/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/3335/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/3335/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/3335/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/3335/lib/python3.12/site-packages/scanpy/tools/_rank_genes_groups.py", line 676, in rank_genes_groups
    test_obj.compute_statistics(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/tools/_rank_genes_groups.py", line 413, in compute_statistics
    for group_index, scores, pvals in generate_test_results:
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/tools/_rank_genes_groups.py", line 230, in t_test
    self._basic_stats()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/tools/_rank_genes_groups.py", line 210, in _basic_stats
    self.means[group_index], self.vars[group_index] = _get_mean_var(X_mask)
                                                      ^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/preprocessing/_utils.py", line 38, in _get_mean_var
    mean, var = sparse_mean_variance_axis(X, axis=axis)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/preprocessing/_utils.py", line 77, in sparse_mean_variance_axis
    return sparse_mean_var_minor_axis(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/numba/core/dispatcher.py", line 426, in _compile_for_args
    error_rewrite(e, 'unsupported_error')
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/numba/core/dispatcher.py", line 364, in error_rewrite
    raise e.with_traceback(None)
numba.core.errors.UnsupportedError: Failed in nopython mode pipeline (step: analyzing bytecode)
Use of unsupported opcode (DICT_MERGE) found

File "../../envs/3335/lib/python3.12/site-packages/scanpy/_compat.py", line 117:
        def wrapper(*args: P.args, **kwargs: P.kwargs) -> R:
            return fns[True](*args, **kwargs)
            ^ [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/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/3335/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/3335/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/3335/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/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 956, in rank_genes_groups_dotplot
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 534, in _rank_genes_groups_plot
    group_names = adata.uns[key]["names"].dtype.names if groups is None else groups
                  ~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'names' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/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/3335/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/3335/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/3335/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/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 956, in rank_genes_groups_dotplot
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 534, in _rank_genes_groups_plot
    group_names = adata.uns[key]["names"].dtype.names if groups is None else groups
                  ~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'names' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/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/3335/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/3335/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/3335/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/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 956, in rank_genes_groups_dotplot
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 534, in _rank_genes_groups_plot
    group_names = adata.uns[key]["names"].dtype.names if groups is None else groups
                  ~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'names' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/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/3335/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/3335/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/3335/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/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 956, in rank_genes_groups_dotplot
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 534, in _rank_genes_groups_plot
    group_names = adata.uns[key]["names"].dtype.names if groups is None else groups
                  ~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'names' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/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/3335/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/3335/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/3335/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/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 956, in rank_genes_groups_dotplot
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 534, in _rank_genes_groups_plot
    group_names = adata.uns[key]["names"].dtype.names if groups is None else groups
                  ~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'names' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/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/3335/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/3335/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/3335/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/3335/lib/python3.12/site-packages/scanpy/tools/_rank_genes_groups.py", line 676, in rank_genes_groups
    test_obj.compute_statistics(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/tools/_rank_genes_groups.py", line 413, in compute_statistics
    for group_index, scores, pvals in generate_test_results:
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/tools/_rank_genes_groups.py", line 230, in t_test
    self._basic_stats()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/tools/_rank_genes_groups.py", line 210, in _basic_stats
    self.means[group_index], self.vars[group_index] = _get_mean_var(X_mask)
                                                      ^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/preprocessing/_utils.py", line 38, in _get_mean_var
    mean, var = sparse_mean_variance_axis(X, axis=axis)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/preprocessing/_utils.py", line 77, in sparse_mean_variance_axis
    return sparse_mean_var_minor_axis(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/numba/core/dispatcher.py", line 426, in _compile_for_args
    error_rewrite(e, 'unsupported_error')
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/numba/core/dispatcher.py", line 364, in error_rewrite
    raise e.with_traceback(None)
numba.core.errors.UnsupportedError: Failed in nopython mode pipeline (step: analyzing bytecode)
Use of unsupported opcode (DICT_MERGE) found

File "../../envs/3335/lib/python3.12/site-packages/scanpy/_compat.py", line 117:
        def wrapper(*args: P.args, **kwargs: P.kwargs) -> R:
            return fns[True](*args, **kwargs)
            ^ [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/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/3335/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/3335/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/3335/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/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 731, in rank_genes_groups_heatmap
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 534, in _rank_genes_groups_plot
    group_names = adata.uns[key]["names"].dtype.names if groups is None else groups
                  ~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'names' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/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/3335/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/3335/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/3335/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/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 731, in rank_genes_groups_heatmap
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 534, in _rank_genes_groups_plot
    group_names = adata.uns[key]["names"].dtype.names if groups is None else groups
                  ~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'names' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/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/3335/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/3335/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/3335/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/3335/lib/python3.12/site-packages/scanpy/tools/_rank_genes_groups.py", line 676, in rank_genes_groups
    test_obj.compute_statistics(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/tools/_rank_genes_groups.py", line 413, in compute_statistics
    for group_index, scores, pvals in generate_test_results:
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/tools/_rank_genes_groups.py", line 230, in t_test
    self._basic_stats()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/tools/_rank_genes_groups.py", line 210, in _basic_stats
    self.means[group_index], self.vars[group_index] = _get_mean_var(X_mask)
                                                      ^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/preprocessing/_utils.py", line 38, in _get_mean_var
    mean, var = sparse_mean_variance_axis(X, axis=axis)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/preprocessing/_utils.py", line 77, in sparse_mean_variance_axis
    return sparse_mean_var_minor_axis(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/numba/core/dispatcher.py", line 426, in _compile_for_args
    error_rewrite(e, 'unsupported_error')
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/numba/core/dispatcher.py", line 364, in error_rewrite
    raise e.with_traceback(None)
numba.core.errors.UnsupportedError: Failed in nopython mode pipeline (step: analyzing bytecode)
Use of unsupported opcode (DICT_MERGE) found

File "../../envs/3335/lib/python3.12/site-packages/scanpy/_compat.py", line 117:
        def wrapper(*args: P.args, **kwargs: P.kwargs) -> R:
            return fns[True](*args, **kwargs)
            ^ [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/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/3335/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/3335/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/3335/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/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 1166, in rank_genes_groups_matrixplot
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 534, in _rank_genes_groups_plot
    group_names = adata.uns[key]["names"].dtype.names if groups is None else groups
                  ~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'names' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/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/3335/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/3335/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/3335/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/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 1166, in rank_genes_groups_matrixplot
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 534, in _rank_genes_groups_plot
    group_names = adata.uns[key]["names"].dtype.names if groups is None else groups
                  ~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'names' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/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/3335/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/3335/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/3335/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/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 1166, in rank_genes_groups_matrixplot
    return _rank_genes_groups_plot(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/plotting/_tools/__init__.py", line 534, in _rank_genes_groups_plot
    group_names = adata.uns[key]["names"].dtype.names if groups is None else groups
                  ~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'names' [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/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/3335/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/3335/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/3335/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/3335/lib/python3.12/site-packages/scanpy/tools/_rank_genes_groups.py", line 676, in rank_genes_groups
    test_obj.compute_statistics(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/tools/_rank_genes_groups.py", line 413, in compute_statistics
    for group_index, scores, pvals in generate_test_results:
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/tools/_rank_genes_groups.py", line 230, in t_test
    self._basic_stats()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/tools/_rank_genes_groups.py", line 210, in _basic_stats
    self.means[group_index], self.vars[group_index] = _get_mean_var(X_mask)
                                                      ^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/preprocessing/_utils.py", line 38, in _get_mean_var
    mean, var = sparse_mean_variance_axis(X, axis=axis)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/preprocessing/_utils.py", line 77, in sparse_mean_variance_axis
    return sparse_mean_var_minor_axis(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/numba/core/dispatcher.py", line 426, in _compile_for_args
    error_rewrite(e, 'unsupported_error')
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/numba/core/dispatcher.py", line 364, in error_rewrite
    raise e.with_traceback(None)
numba.core.errors.UnsupportedError: Failed in nopython mode pipeline (step: analyzing bytecode)
Use of unsupported opcode (DICT_MERGE) found

File "../../envs/3335/lib/python3.12/site-packages/scanpy/_compat.py", line 117:
        def wrapper(*args: P.args, **kwargs: P.kwargs) -> R:
            return fns[True](*args, **kwargs)
            ^ [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/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/3335/docs/generated/scanpy.pp.calculate_qc_metrics.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/matplotlib/sphinxext/plot_directive.py", line 552, in _run_code
    exec(code, ns)
  File "<string>", line 6, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/preprocessing/_qc.py", line 317, in calculate_qc_metrics
    obs_metrics = describe_obs(
                  ^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/preprocessing/_qc.py", line 123, in describe_obs
    proportions = top_segment_proportions(X, percent_top)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/scanpy/preprocessing/_qc.py", line 412, in top_segment_proportions
    return top_segment_proportions_sparse_csr(mtx.data, mtx.indptr, np.array(ns))
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/numba/core/dispatcher.py", line 426, in _compile_for_args
    error_rewrite(e, 'unsupported_error')
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/numba/core/dispatcher.py", line 364, in error_rewrite
    raise e.with_traceback(None)
numba.core.errors.UnsupportedError: Failed in nopython mode pipeline (step: analyzing bytecode)
Use of unsupported opcode (DICT_MERGE) found

File "../../envs/3335/lib/python3.12/site-packages/scanpy/_compat.py", line 117:
        def wrapper(*args: P.args, **kwargs: P.kwargs) -> R:
            return fns[True](*args, **kwargs)
            ^ [docutils]
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/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/3335/docs/generated/scanpy.pp.calculate_qc_metrics.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/pandas/core/indexes/base.py", line 3805, in get_loc
    return self._engine.get_loc(casted_key)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "index.pyx", line 167, in pandas._libs.index.IndexEngine.get_loc
  File "index.pyx", line 196, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 7081, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 7089, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'pct_counts_mito'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/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/3335/lib/python3.12/site-packages/pandas/core/frame.py", line 4102, in __getitem__
    indexer = self.columns.get_loc(key)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3335/lib/python3.12/site-packages/pandas/core/indexes/base.py", line 3812, in get_loc
    raise KeyError(key) from err
KeyError: 'pct_counts_mito' [docutils]
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/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/3335/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/3335/_readthedocs/html/_static/basic.css
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/_readthedocs/html/_static/language_data.js
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/_readthedocs/html/_static/documentation_options.js
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3335/_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/3335/_readthedocs/html/_static/js/rtd_search_config.js
build finished with problems, 16 warnings (with warnings treated as errors).