Read the Docs build information
Build id: 3484646
Project: icb-scanpy
Version: 1.11.x
Commit: 514a1847531807e09b37efad64df37987b57e89c
Date: 2025-10-30T11:12:44.890372Z
State: finished
Success: True


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git clone --depth 1 https://github.com/scverse/scanpy.git .
Cloning into '.'...

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git fetch origin --force --prune --prune-tags --depth 50 refs/heads/1.11.x:refs/remotes/origin/1.11.x
From https://github.com/scverse/scanpy
 * [new branch]      1.11.x     -> origin/1.11.x
 * [new tag]         1.11.2     -> 1.11.2
 * [new tag]         1.11.3     -> 1.11.3
 * [new tag]         1.11.4     -> 1.11.4
 * [new tag]         1.11.5     -> 1.11.5

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git checkout --force origin/1.11.x
Note: switching to 'origin/1.11.x'.

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

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

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

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

HEAD is now at 514a184 Backport PR #3852 on branch 1.11.x (chore: use `uv run`able code sample for bug reports) (#3855)

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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

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git submodule sync


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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/1.11.x/notebooks'...
Submodule path 'notebooks': checked out '897eef59b945f88f9c86715656286796eea43853'

[rtd-command-info] start-time: 2025-10-30T11:13:11.994326Z, end-time: 2025-10-30T11:13:16.195811Z, duration: 4, exit-code: 0
git fetch --unshallow || true
From https://github.com/scverse/scanpy
 * [new tag]           0.0         -> 0.0
 * [new tag]           0.1         -> 0.1
 * [new tag]           0.2         -> 0.2
 * [new tag]           0.2.1       -> 0.2.1
 * [new tag]           0.2.3       -> 0.2.3
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 * [new tag]           1.0         -> 1.0
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 * [new tag]           1.0.4       -> 1.0.4
 * [new tag]           1.1         -> 1.1
 * [new tag]           1.10.0.dev0 -> 1.10.0.dev0
 * [new tag]           1.10.0rc1   -> 1.10.0rc1
 * [new tag]           1.11.0      -> 1.11.0
 * [new tag]           1.11.0rc1   -> 1.11.0rc1
 * [new tag]           1.11.0rc2   -> 1.11.0rc2
 * [new tag]           1.11.1      -> 1.11.1
 * [new tag]           1.1a1       -> 1.1a1
 * [new tag]           1.1a2       -> 1.1a2
 * [new tag]           1.2.0       -> 1.2.0
 * [new tag]           1.2.1       -> 1.2.1
 * [new tag]           1.2.2       -> 1.2.2
 * [new tag]           1.3         -> 1.3
 * [new tag]           1.3.1       -> 1.3.1
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 * [new tag]           1.3.8       -> 1.3.8
 * [new tag]           1.4         -> 1.4
 * [new tag]           1.4.1       -> 1.4.1
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 * [new tag]           1.4.5       -> 1.4.5
 * [new tag]           1.4.5.1     -> 1.4.5.1
 * [new tag]           1.4.5.post1 -> 1.4.5.post1
 * [new tag]           1.4.5.post2 -> 1.4.5.post2
 * [new tag]           1.4.5.post3 -> 1.4.5.post3
 * [new tag]           1.4.6       -> 1.4.6
 * [new tag]           1.5.0       -> 1.5.0
 * [new tag]           1.5.0a1     -> 1.5.0a1
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 * [new tag]           1.7.0rc1    -> 1.7.0rc1
 * [new tag]           1.8.0       -> 1.8.0
 * [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
Fetching submodule notebooks
From https://github.com/scverse/scanpy-tutorials
 * branch            26e16f83387caef76abdd42afda3c7c13f7139f1 -> FETCH_HEAD

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asdf global python 3.12.10


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python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.12.10.final.0-64 in 532ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.11.x, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator

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python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.11.x/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/1.11.x/lib/python3.12/site-packages (67.6.1)
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Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 67.6.1
    Uninstalling setuptools-67.6.1:
      Successfully uninstalled setuptools-67.6.1
  Attempting uninstall: pip
    Found existing installation: pip 23.1
    Uninstalling pip-23.1:
      Successfully uninstalled pip-23.1
Successfully installed pip-25.3 setuptools-80.9.0

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

Successfully installed Jinja2-3.1.6 MarkupSafe-3.0.3 Pygments-2.19.2 alabaster-1.0.0 babel-2.17.0 certifi-2025.10.5 charset_normalizer-3.4.4 docutils-0.21.2 idna-3.11 imagesize-1.4.1 packaging-25.0 requests-2.32.5 roman-numerals-py-3.1.0 snowballstemmer-3.0.1 sphinx-8.2.3 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.5.0

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python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc,dev]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x
  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 matplotlib>=3.7.5 (from scanpy==1.12.0.dev3+g514a18475)
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Building wheels for collected packages: scanpy, sam-algorithm, hnswlib
  Building wheel for scanpy (pyproject.toml): started
  Building wheel for scanpy (pyproject.toml): finished with status 'done'
  Created wheel for scanpy: filename=scanpy-1.12.0.dev3+g514a18475-py3-none-any.whl size=2098077 sha256=5b821a144e5b978a51bfb5d0ec91b592e83babec29cda9188fdf95535f3b5357
  Stored in directory: /tmp/pip-ephem-wheel-cache-6v96ovzh/wheels/3e/cc/ac/d2d2e1ed615de3d8b01e1de0ce31b3b8dea8c050f8c52c6ad0
  Building wheel for sam-algorithm (pyproject.toml): started
  Building wheel for sam-algorithm (pyproject.toml): finished with status 'done'
  Created wheel for sam-algorithm: filename=sam_algorithm-1.0.2-py3-none-any.whl size=34665 sha256=143897f8f2362cb73b0b95679f13b666cf1408fc748be5c28fa4314fec393bdd
  Stored in directory: /tmp/pip-ephem-wheel-cache-6v96ovzh/wheels/57/54/be/ca87c5831826023e1d64b77d6680c582ff898a13844a7ed4ed
  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=2407436 sha256=de3abbf462ff8992b412b387ee8106db0fa1d0ee6f8a5828c40ec0c051be9f68
  Stored in directory: /tmp/pip-ephem-wheel-cache-6v96ovzh/wheels/ac/39/b3/cbd7f9cbb76501d2d5fbc84956e70d0b94e788aac87bda465e
Successfully built scanpy sam-algorithm hnswlib
Installing collected packages: webencodings, texttable, sortedcontainers, pytz, pure-eval, ptyprocess, multipledispatch, fastjsonschema, zipp, zict, wcwidth, tzdata, typing-extensions, traitlets, tqdm, tornado, toolz, tinycss2, threadpoolctl, tblib, tabulate, soupsieve, six, session-info2, rpds-py, pyzmq, pyyaml, pyparsing, pyarrow, psutil, platformdirs, pillow, pexpect, parso, pandocfilters, numpy, networkx, nest-asyncio, natsort, msgpack, mistune, mdurl, locket, llvmlite, legacy-api-wrap, latexcodec, kiwisolver, jupyterlab-pygments, joblib, ipython-pygments-lexers, igraph, greenlet, fsspec, fonttools, executing, dill, defusedxml, decorator, debugpy, cycler, crc32c, comm, cloudpickle, click, bleach, attrs, asttokens, array-api-compat, accessible-pygments, towncrier, stack_data, sqlalchemy, scipy, referencing, python-dateutil, pybtex, prompt_toolkit, patsy, partd, optype, numpy-typing-compat, numcodecs, numba, matplotlib-inline, markdown-it-py, leidenalg, jupyter-core, jedi, importlib_metadata, hnswlib, h5py, donfig, contourpy, beautifulsoup4, sphinxext-opengraph, sphinx-tabs, sphinx-issues, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, sparse, scikit-learn, scanpydoc, pydata-sphinx-theme, pybtex-docutils, pandas, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, ipython, dask, zarr, statsmodels, sphinxcontrib-bibtex, sphinx-book-theme, seaborn, scipy-stubs, pynndescent, myst-parser, jsonschema, ipykernel, harmonypy, distributed, umap-learn, nbformat, dask-glm, anndata, scanpy, sam-algorithm, nbclient, dask-ml, nbconvert, jupyter-cache, nbsphinx, myst-nb

Successfully installed accessible-pygments-0.0.5 anndata-0.12.4 array-api-compat-1.12.0 asttokens-3.0.0 attrs-25.4.0 beautifulsoup4-4.14.2 bleach-6.3.0 click-8.3.0 cloudpickle-3.1.1 comm-0.2.3 contourpy-1.3.3 crc32c-2.8 cycler-0.12.1 dask-2025.10.0 dask-glm-0.3.2 dask-ml-2025.1.0 debugpy-1.8.17 decorator-5.2.1 defusedxml-0.7.1 dill-0.4.0 distributed-2025.10.0 donfig-0.8.1.post1 executing-2.2.1 fastjsonschema-2.21.2 fonttools-4.60.1 fsspec-2025.9.0 greenlet-3.2.4 h5py-3.15.1 harmonypy-0.0.10 hnswlib-0.8.0 igraph-0.11.9 importlib_metadata-8.7.0 ipykernel-7.1.0 ipython-9.6.0 ipython-pygments-lexers-1.1.1 jedi-0.19.2 joblib-1.5.2 jsonschema-4.25.1 jsonschema-specifications-2025.9.1 jupyter-cache-1.0.1 jupyter-client-8.6.3 jupyter-core-5.9.1 jupyterlab-pygments-0.3.0 kiwisolver-1.4.9 latexcodec-3.0.1 legacy-api-wrap-1.4.1 leidenalg-0.10.2 llvmlite-0.45.1 locket-1.0.0 markdown-it-py-3.0.0 matplotlib-3.10.7 matplotlib-inline-0.2.1 mdit-py-plugins-0.5.0 mdurl-0.1.2 mistune-3.1.4 msgpack-1.1.2 multipledispatch-1.0.0 myst-nb-1.3.0 myst-parser-4.0.1 natsort-8.4.0 nbclient-0.10.2 nbconvert-7.16.6 nbformat-5.10.4 nbsphinx-0.9.6 nest-asyncio-1.6.0 networkx-3.5 numba-0.62.1 numcodecs-0.16.3 numpy-2.3.4 numpy-typing-compat-20250818.2.3 optype-0.14.0 pandas-2.3.3 pandocfilters-1.5.1 parso-0.8.5 partd-1.4.2 patsy-1.0.2 pexpect-4.9.0 pillow-12.0.0 platformdirs-4.5.0 prompt_toolkit-3.0.52 psutil-7.1.2 ptyprocess-0.7.0 pure-eval-0.2.3 pyarrow-22.0.0 pybtex-0.25.1 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.15.4 pynndescent-0.5.13 pyparsing-3.2.5 python-dateutil-2.9.0.post0 pytz-2025.2 pyyaml-6.0.3 pyzmq-27.1.0 referencing-0.37.0 rpds-py-0.28.0 sam-algorithm-1.0.2 scanpy-1.12.0.dev3+g514a18475 scanpydoc-0.15.4 scikit-learn-1.7.2 scipy-1.16.3 scipy-stubs-1.16.3.0 seaborn-0.13.2 session-info2-0.2.3 six-1.17.0 sortedcontainers-2.4.0 soupsieve-2.8 sparse-0.17.0 sphinx-autodoc-typehints-3.5.2 sphinx-book-theme-1.1.4 sphinx-copybutton-0.5.2 sphinx-design-0.6.1 sphinx-issues-5.0.1 sphinx-tabs-3.4.7 sphinxcontrib-bibtex-2.6.5 sphinxext-opengraph-0.13.0 sqlalchemy-2.0.44 stack_data-0.6.3 statsmodels-0.14.5 tabulate-0.9.0 tblib-3.2.0 texttable-1.7.0 threadpoolctl-3.6.0 tinycss2-1.4.0 toolz-1.1.0 tornado-6.5.2 towncrier-25.8.0 tqdm-4.67.1 traitlets-5.14.3 typing-extensions-4.15.0 tzdata-2025.2 umap-learn-0.5.9.post2 wcwidth-0.2.14 webencodings-0.5.1 zarr-3.1.3 zict-3.0.0 zipp-3.23.0

[rtd-command-info] start-time: 2025-10-30T11:14:54.040012Z, end-time: 2025-10-30T11:14:54.080753Z, duration: 0, exit-code: 0
( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true


[rtd-command-info] start-time: 2025-10-30T11:14:54.167931Z, end-time: 2025-10-30T11:14:54.206475Z, duration: 0, exit-code: 0
cat docs/conf.py
"""Configuration for Scanpy’s Sphinx documentation."""

from __future__ import annotations

import os
import sys
from datetime import datetime
from functools import partial
from importlib.metadata import version as get_version
from pathlib import Path, PurePosixPath
from typing import TYPE_CHECKING

import matplotlib  # noqa
from docutils import nodes
from packaging.version import Version

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

HERE = Path(__file__).parent
sys.path[:0] = [str(HERE.parent), str(HERE / "extensions")]
os.environ["SPHINX_RUNNING"] = "1"  # for scanpy._singleton

if TYPE_CHECKING:
    from sphinx.application import Sphinx


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

nitpicky = True  # Warn about broken links. This is here for a reason: Do not change.
needs_sphinx = "4.0"  # Nicer param docs
suppress_warnings = [
    "myst.header",  # https://github.com/executablebooks/MyST-Parser/issues/262
    "mystnb.unknown_mime_type",  # application/vnd.microsoft.datawrangler.viewer.v0+json
]

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

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

release = version

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


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

extensions = [
    "myst_nb",
    "sphinx_copybutton",
    "sphinx.ext.autodoc",
    "sphinx.ext.intersphinx",
    "sphinx.ext.doctest",
    "sphinx.ext.coverage",
    "sphinx.ext.mathjax",
    "sphinx.ext.napoleon",
    "sphinx.ext.autosummary",
    "sphinxcontrib.bibtex",
    "matplotlib.sphinxext.plot_directive",
    "sphinx_autodoc_typehints",  # needs to be after napoleon
    "git_ref",  # needs to be before scanpydoc.rtd_github_links
    "scanpydoc",  # needs to be before sphinx.ext.linkcode
    "sphinx.ext.linkcode",
    "sphinx_design",
    "sphinx_issues",
    "sphinx_tabs.tabs",
    "sphinxext.opengraph",
    *[p.stem for p in (HERE / "extensions").glob("*.py") if p.stem not in {"git_ref"}],
]

# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = "bysource"
autodoc_default_options = {
    # Don’t show members in addition to the autosummary table added by `_templates/class.rst`
    "members": False,
    # show “Bases: SomeClass” at the top of class docs
    "show-inheritance": True,
}
napoleon_google_docstring = False
napoleon_numpy_docstring = True
napoleon_include_init_with_doc = False
napoleon_use_rtype = True  # having a separate entry generally helps readability
napoleon_use_param = True
napoleon_custom_sections = [("Params", "Parameters")]
todo_include_todos = False
api_dir = HERE / "api"  # function_images
myst_enable_extensions = [
    "amsmath",
    "colon_fence",
    "deflist",
    "dollarmath",
    "html_image",
    "html_admonition",
]
myst_url_schemes = ("http", "https", "mailto", "ftp")
myst_heading_anchors = 3
nb_output_stderr = "remove"
nb_execution_mode = "off"
nb_merge_streams = True


ogp_site_url = "https://scanpy.readthedocs.io/en/stable/"
ogp_image = "https://scanpy.readthedocs.io/en/stable/_static/Scanpy_Logo_BrightFG.svg"

typehints_defaults = "braces"

pygments_style = "default"
pygments_dark_style = "native"

intersphinx_mapping = dict(
    anndata=("https://anndata.readthedocs.io/en/stable/", None),
    bbknn=("https://bbknn.readthedocs.io/en/latest/", None),
    cuml=("https://docs.rapids.ai/api/cuml/stable/", None),
    cycler=("https://matplotlib.org/cycler/", None),
    dask=("https://docs.dask.org/en/stable/", None),
    dask_ml=("https://ml.dask.org/", None),
    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/3.13", None),
    rapids_singlecell=("https://rapids-singlecell.readthedocs.io/en/latest/", None),
    scipy=("https://docs.scipy.org/doc/scipy/", None),
    seaborn=("https://seaborn.pydata.org/", None),
    session_info2=("https://session-info2.readthedocs.io/en/stable/", None),
    squidpy=("https://squidpy.readthedocs.io/en/stable/", None),
    sklearn=("https://scikit-learn.org/stable/", None),
)


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

# The theme is sphinx-book-theme, with patches for readthedocs-sphinx-search
html_theme = "scanpydoc"
html_theme_options = {
    "repository_url": repository_url,
    "use_repository_button": True,
}
html_static_path = ["_static"]
html_show_sphinx = False
html_logo = "_static/img/Scanpy_Logo_BrightFG.svg"
html_title = "scanpy"


def setup(app: Sphinx):
    """App setup hook."""
    app.add_generic_role("small", partial(nodes.inline, classes=["small"]))
    app.add_generic_role("smaller", partial(nodes.inline, classes=["smaller"]))
    app.add_config_value(
        "recommonmark_config",
        {
            "auto_toc_tree_section": "Contents",
            "enable_auto_toc_tree": True,
            "enable_math": True,
            "enable_inline_math": False,
            "enable_eval_rst": True,
        },
        True,  # noqa: FBT003
    )


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

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


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

qualname_overrides = {
    "sklearn.neighbors._dist_metrics.DistanceMetric": "sklearn.metrics.DistanceMetric",
    "scanpy.plotting._matrixplot.MatrixPlot": "scanpy.pl.MatrixPlot",
    "scanpy.plotting._dotplot.DotPlot": "scanpy.pl.DotPlot",
    "scanpy.plotting._stacked_violin.StackedViolin": "scanpy.pl.StackedViolin",
    "pandas.core.series.Series": "pandas.Series",
    "numpy.bool_": "numpy.bool",  # Since numpy 2, numpy.bool is the canonical dtype
}

nitpick_ignore = [
    # Technical issues
    ("py:class", "numpy.int64"),  # documented as “attribute”
    ("py:class", "numpy._typing._dtype_like._SupportsDType"),
    ("py:class", "numpy._typing._dtype_like._DTypeDict"),
    # Will probably be documented
    ("py:class", "scanpy._settings.Verbosity"),
    ("py:class", "scanpy.neighbors.OnFlySymMatrix"),
    ("py:class", "scanpy.plotting._baseplot_class.BasePlot"),
    # Currently undocumented
    # https://github.com/mwaskom/seaborn/issues/1810
    ("py:class", "seaborn.matrix.ClusterGrid"),
    ("py:class", "samalg.SAM"),
    # Won’t be documented
    ("py:class", "scanpy.plotting._utils._AxesSubplot"),
    ("py:class", "scanpy._utils.Empty"),
    ("py:class", "numpy.random.mtrand.RandomState"),
    ("py:class", "scanpy.neighbors._types.KnnTransformerLike"),
]

# Options for plot examples

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

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

[rtd-command-info] start-time: 2025-10-30T11:14:54.610525Z, end-time: 2025-10-30T11:18:09.157480Z, duration: 194, exit-code: 0
python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v8.2.3
loading translations [en]... done
Matplotlib is building the font cache; this may take a moment.
making output directory... done
checking bibtex cache... out of date
parsing bibtex file /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/references.bib... parsed 79 entries
myst v4.0.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'deflist', 'html_image', 'html_admonition', 'dollarmath', 'colon_fence', 'amsmath'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
myst-nb v1.3.0: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', execution_mode='off', execution_cache_path='', execution_excludepatterns=(), execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=True, render_plugin='default', remove_code_source=False, remove_code_outputs=False, scroll_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='remove', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/_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/3.13/objects.inv ...
loading intersphinx inventory 'rapids_singlecell' from https://rapids-singlecell.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv ...
loading intersphinx inventory 'seaborn' from https://seaborn.pydata.org/objects.inv ...
loading intersphinx inventory 'session_info2' from https://session-info2.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'squidpy' from https://squidpy.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'sklearn' from https://scikit-learn.org/stable/objects.inv ...
[autosummary] generating autosummary for: api/classes.md, api/datasets.md, api/deprecated.md, api/experimental.md, api/get.md, api/index.md, api/io.md, api/metrics.md, api/plotting.md, api/preprocessing.md, ..., tutorials/experimental/dask.ipynb, tutorials/experimental/index.md, tutorials/experimental/pearson_residuals.ipynb, tutorials/index.md, tutorials/plotting/advanced.ipynb, tutorials/plotting/core.ipynb, tutorials/plotting/index.md, tutorials/trajectories/index.md, tutorials/trajectories/paga-paul15.ipynb, usage-principles.md
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/scanpy.pl.correlation_matrix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/scanpy.pl.embedding_density.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.tl.umap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.write.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.settings.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.settings.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.settings.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.settings.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.settings.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.settings.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.settings.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.settings.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.settings.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.settings.writedir.rst
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 53 source files that are out of date
updating environment: [new config] 276 added, 0 changed, 0 removed
reading sources... [  0%] api/classes
reading sources... [  1%] api/datasets
reading sources... [  1%] api/deprecated
reading sources... [  1%] api/experimental
reading sources... [  2%] api/generated/classes/scanpy.pl.DotPlot
reading sources... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP
reading sources... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE
reading sources... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON
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reading sources... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW
reading sources... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX
reading sources... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN
reading sources... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT
reading sources... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH
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Package 'fa2-modified' is not installed, falling back to layout 'fr'.To use the faster and better ForceAtlas2 layout, install package 'fa2-modified' (`pip install fa2-modified`).
reading sources... [ 19%] api/generated/scanpy.pl.embedding
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:65: (ERROR/3) no path specified
:75: (ERROR/3) no path specified
:82: (ERROR/3) no path specified
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100%|██████████| 23.5M/23.5M [00:00<00:00, 264MB/s]
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reading sources... [ 23%] api/generated/scanpy.pl.rank_genes_groups_dotplot
dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
reading sources... [ 24%] api/generated/scanpy.pl.rank_genes_groups_heatmap
dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
Gene labels are not shown when more than 50 genes are visualized. To show gene labels set `show_gene_labels=True`
reading sources... [ 24%] api/generated/scanpy.pl.rank_genes_groups_matrixplot
dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
reading sources... [ 24%] api/generated/scanpy.pl.rank_genes_groups_stacked_violin
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dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
reading sources... [ 25%] api/generated/scanpy.pl.rank_genes_groups_violin
reading sources... [ 25%] api/generated/scanpy.pl.scrublet_score_distribution
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Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/docs/generated/scanpy.pp.pca.rst: document is referenced in multiple toctrees: ['api/preprocessing', 'api/tools'], selecting: api/tools <- generated/scanpy.pp.pca
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dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded.

The HTML pages are in ../_readthedocs/html.