Read the Docs build information
Build id: 3476349
Project: icb-anndata
Version: stable
Commit: 38dda6180a37d9528ad2bd16f8f1b036f38ff88b
Date: 2025-10-27T19:29:45.116266Z
State: finished
Success: True


[rtd-command-info] start-time: 2025-10-27T19:29:46.046487Z, end-time: 2025-10-27T19:29:46.582126Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/scverse/anndata.git .
Cloning into '.'...

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git fetch origin --force --prune --prune-tags --depth 50 38dda6180a37d9528ad2bd16f8f1b036f38ff88b
From https://github.com/scverse/anndata
 * branch            38dda6180a37d9528ad2bd16f8f1b036f38ff88b -> FETCH_HEAD

[rtd-command-info] start-time: 2025-10-27T19:29:48.131957Z, end-time: 2025-10-27T19:29:48.191436Z, duration: 0, exit-code: 0
git checkout --force 38dda6180a37d9528ad2bd16f8f1b036f38ff88b
Note: switching to '38dda6180a37d9528ad2bd16f8f1b036f38ff88b'.

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 38dda61 (chore): generate 0.12.4 release notes (#2181)

[rtd-command-info] start-time: 2025-10-27T19:29:48.297176Z, end-time: 2025-10-27T19:29:48.336648Z, duration: 0, exit-code: 0
cat .readthedocs.yml
version: 2
build:
  os: ubuntu-24.04
  tools:
    python: "3.13"
  jobs:
    post_checkout:
      # unshallow so version can be derived from tag
      - git fetch --unshallow || true
    pre_build:
      # run towncrier to preview the next version’s release notes
      - ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true
sphinx:
  configuration: docs/conf.py
  fail_on_warning: true # do not change or you will be fired
python:
  install:
    - method: pip
      path: .
      extra_requirements:
        - doc
submodules:
  include:
    - "docs/tutorials/notebooks"
  recursive: true

[rtd-command-info] start-time: 2025-10-27T19:29:48.482148Z, end-time: 2025-10-27T19:29:48.712087Z, duration: 0, exit-code: 0
git submodule sync


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git submodule update --init --force --recursive -- docs/tutorials/notebooks
Submodule 'docs/tutorials/notebooks' (https://github.com/scverse/anndata-tutorials) registered for path 'docs/tutorials/notebooks'
Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/tutorials/notebooks'...
Submodule path 'docs/tutorials/notebooks': checked out '0d8ffb2dc4a53de9762f76ed9030114d8aced353'

[rtd-command-info] start-time: 2025-10-27T19:29:49.717879Z, end-time: 2025-10-27T19:29:51.353105Z, duration: 1, exit-code: 0
git fetch --unshallow || true
From https://github.com/scverse/anndata
 * [new tag]         0.12.0     -> 0.12.0
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[rtd-command-info] start-time: 2025-10-27T19:29:56.974413Z, end-time: 2025-10-27T19:29:57.034661Z, duration: 0, exit-code: 0
asdf global python 3.13.3


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python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.13.3.final.0-64 in 841ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2025-10-27T19:29:58.728588Z, end-time: 2025-10-27T19:30:07.910173Z, duration: 9, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.13/site-packages (23.1)
Collecting pip
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.13/site-packages (67.6.1)
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Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 67.6.1
    Uninstalling setuptools-67.6.1:
      Successfully uninstalled setuptools-67.6.1
  Attempting uninstall: pip
    Found existing installation: pip 23.1
    Uninstalling pip-23.1:
      Successfully uninstalled pip-23.1
Successfully installed pip-25.3 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]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable
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Building wheels for collected packages: anndata
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Installing collected packages: webencodings, standard-imghdr, pytz, pure-eval, ptyprocess, fastjsonschema, zipp, wcwidth, tzdata, typing-extensions, traitlets, tornado, toolz, tabulate, soupsieve, six, ruamel.yaml.clib, rpds-py, requests, pyzmq, pyyaml, psutil, platformdirs, pexpect, parso, numpy, nest-asyncio, natsort, msgpack, more-itertools, mdurl, locket, legacy-api-wrap, ipython-pygments-lexers, greenlet, fsspec, filelock, executing, decorator, debugpy, crc32c, comm, cloudpickle, click, attrs, asttokens, array-api-compat, accessible-pygments, towncrier, stack_data, sqlalchemy, sphinx-jinja2-compat, scipy, ruamel.yaml, referencing, python-dateutil, prompt_toolkit, partd, numcodecs, matplotlib-inline, markdown-it-py, jupyter-core, jedi, importlib_metadata, html5lib, h5py, donfig, domdf-python-tools, cssutils, cachecontrol, beautifulsoup4, awkward-cpp, sphinxext-opengraph, sphinx-tabs, sphinx-prompt, sphinx-issues, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, scanpydoc, pydata-sphinx-theme, pandas, mdit-py-plugins, jupyter-client, jsonschema-specifications, ipython, dict2css, dask, awkward, autodocsumm, apeye-core, zarr, sphinx-book-theme, myst-parser, jsonschema, ipykernel, apeye, sphinx-toolbox, nbformat, anndata, nbclient, jupyter-cache, myst-nb
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Successfully installed accessible-pygments-0.0.5 anndata-0.12.4 apeye-1.4.1 apeye-core-1.1.5 array-api-compat-1.12.0 asttokens-3.0.0 attrs-25.4.0 autodocsumm-0.2.14 awkward-2.8.9 awkward-cpp-50 beautifulsoup4-4.14.2 cachecontrol-0.14.3 click-8.3.0 cloudpickle-3.1.1 comm-0.2.3 crc32c-2.8 cssutils-2.11.1 dask-2025.10.0 debugpy-1.8.17 decorator-5.2.1 dict2css-0.3.0.post1 domdf-python-tools-3.10.0 donfig-0.8.1.post1 executing-2.2.1 fastjsonschema-2.21.2 filelock-3.20.0 fsspec-2025.9.0 greenlet-3.2.4 h5py-3.15.1 html5lib-1.1 importlib_metadata-8.7.0 ipykernel-7.1.0 ipython-9.6.0 ipython-pygments-lexers-1.1.1 jedi-0.19.2 jsonschema-4.25.1 jsonschema-specifications-2025.9.1 jupyter-cache-1.0.1 jupyter-client-8.6.3 jupyter-core-5.9.1 legacy-api-wrap-1.4.1 locket-1.0.0 markdown-it-py-3.0.0 matplotlib-inline-0.2.1 mdit-py-plugins-0.5.0 mdurl-0.1.2 more-itertools-10.8.0 msgpack-1.1.2 myst-nb-1.3.0 myst-parser-4.0.1 natsort-8.4.0 nbclient-0.10.2 nbformat-5.10.4 nest-asyncio-1.6.0 numcodecs-0.16.3 numpy-2.3.4 pandas-2.3.3 parso-0.8.5 partd-1.4.2 pexpect-4.9.0 platformdirs-4.5.0 prompt_toolkit-3.0.52 psutil-7.1.2 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.15.4 python-dateutil-2.9.0.post0 pytz-2025.2 pyyaml-6.0.3 pyzmq-27.1.0 referencing-0.37.0 requests-2.32.4 rpds-py-0.28.0 ruamel.yaml-0.18.16 ruamel.yaml.clib-0.2.14 scanpydoc-0.15.4 scipy-1.16.2 six-1.17.0 soupsieve-2.8 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-jinja2-compat-0.4.1 sphinx-prompt-1.10.1 sphinx-tabs-3.4.5 sphinx-toolbox-4.0.0 sphinxext-opengraph-0.13.0 sqlalchemy-2.0.44 stack_data-0.6.3 standard-imghdr-3.10.14 tabulate-0.9.0 toolz-1.1.0 tornado-6.5.2 towncrier-25.8.0 traitlets-5.14.3 typing-extensions-4.15.0 tzdata-2025.2 wcwidth-0.2.14 webencodings-0.5.1 zarr-3.1.3 zipp-3.23.0

[rtd-command-info] start-time: 2025-10-27T19:30:46.577348Z, end-time: 2025-10-27T19:30:46.905651Z, duration: 0, exit-code: 0
( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true
Loading template...
Finding news fragments...
Rendering news fragments...
Writing to newsfile...
Staging newsfile...
No news fragments to remove. Skipping!
Done!

[rtd-command-info] start-time: 2025-10-27T19:30:47.000231Z, end-time: 2025-10-27T19:30:47.040573Z, duration: 0, exit-code: 0
cat docs/conf.py
from __future__ import annotations

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

from docutils import nodes

if TYPE_CHECKING:
    from sphinx.application import Sphinx

HERE = Path(__file__).parent
_extension_dir = HERE / "extensions"
sys.path[:0] = [str(_extension_dir)]


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

# General information
project = "anndata"
author = f"{project} developers"
copyright = f"{datetime.now():%Y}, scverse"
release = version = metadata.version("anndata")

# default settings
templates_path = ["_templates"]
html_static_path = ["_static"]
source_suffix = {".rst": "restructuredtext", ".md": "myst-nb"}
master_doc = "index"
default_role = "literal"
exclude_patterns = [
    "_build",
    "Thumbs.db",
    ".DS_Store",
    "**.ipynb_checkpoints",
    "tutorials/notebooks/*.rst",
    # exclude all 0.x.y.md files, but not index.md
    "release-notes/[!i]*.md",
    "news.md",  # is `include`d into index.md
]
pygments_style = "sphinx"

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_autodoc_typehints",  # needs to be after napoleon
    "sphinx_issues",
    "sphinx_design",
    "sphinxext.opengraph",
    "scanpydoc",  # needs to be before linkcode
    "sphinx.ext.linkcode",
    "IPython.sphinxext.ipython_console_highlighting",
    "sphinx_toolbox.more_autodoc.autoprotocol",
    *(p.stem for p in _extension_dir.glob("*.py")),
]
myst_enable_extensions = [
    "html_image",  # So README.md can be used on github and sphinx docs
    "colon_fence",
    "dollarmath",
]
myst_heading_anchors = 3
nb_execution_mode = "off"

# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = "bysource"
autodoc_mock_imports = ["torch"]
# autodoc_default_flags = ['members']
issues_github_path = "scverse/anndata"
rtd_links_prefix = PurePosixPath("src")
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")]
typehints_defaults = "braces"
todo_include_todos = False
nitpicky = True  # Report broken links
nitpick_ignore = [  # APIs without an intersphinx entry
    # This API isn’t actually documented
    ("py:class", "anndata._core.raw.Raw"),
    # TODO: remove zappy support; the zappy repo is archived
    ("py:class", "anndata.compat.ZappyArray"),
]


def setup(app: Sphinx):
    app.add_generic_role("small", partial(nodes.inline, classes=["small"]))
    app.add_generic_role("smaller", partial(nodes.inline, classes=["smaller"]))

    # TODO: move to scanpydoc
    if TYPE_CHECKING:
        from docutils.nodes import TextElement, reference
        from sphinx.addnodes import pending_xref
        from sphinx.environment import BuildEnvironment

    def res(
        app: Sphinx, env: BuildEnvironment, node: pending_xref, contnode: TextElement
    ) -> reference | None:
        return env.domains["py"].resolve_xref(
            env,
            node["refdoc"],
            app.builder,
            node["reftype"],
            node["reftarget"],
            node,
            contnode,
        )

    app.connect("missing-reference", res, priority=502)


intersphinx_mapping = dict(
    awkward=("https://awkward-array.org/doc/stable", None),
    cupy=("https://docs.cupy.dev/en/stable", None),
    dask=("https://docs.dask.org/en/stable", None),
    fsspec=("https://filesystem-spec.readthedocs.io/en/stable/", None),
    h5py=("https://docs.h5py.org/en/latest", None),
    hdf5plugin=("https://hdf5plugin.readthedocs.io/en/latest", None),
    kvikio=("https://docs.rapids.ai/api/kvikio/stable/", None),
    loompy=("https://linnarssonlab.org/loompy", None),
    numpy=("https://numpy.org/doc/stable", None),
    obstore=("https://developmentseed.org/obstore/latest/", None),
    pandas=("https://pandas.pydata.org/pandas-docs/stable", None),
    # TODO: switch to `/3` once docs are built with Python 3.14
    python=("https://docs.python.org/3.13", None),
    scipy=("https://docs.scipy.org/doc/scipy", None),
    sklearn=("https://scikit-learn.org/stable", None),
    xarray=("https://docs.xarray.dev/en/stable", None),
    zarr=("https://zarr.readthedocs.io/en/stable/", None),
    zarrs=("https://zarrs-python.readthedocs.io/en/stable/", None),
)

qualname_overrides = {
    "h5py._hl.group.Group": "h5py.Group",
    "h5py._hl.files.File": "h5py.File",
    "h5py._hl.dataset.Dataset": "h5py.Dataset",
    "anndata._core.anndata.AnnData": "anndata.AnnData",
    **{
        f"anndata._core.aligned_mapping.{cls}{kind}": "collections.abc.Mapping"
        for cls in ["Layers", "AxisArrays", "PairwiseArrays"]
        for kind in ["", "View"]
    },
    "anndata._types.ReadCallback": "anndata.experimental.ReadCallback",
    "anndata._types.WriteCallback": "anndata.experimental.WriteCallback",
    "anndata._types.Read": "anndata.experimental.Read",
    "anndata._types.Write": "anndata.experimental.Write",
    "anndata._types.Dataset2DIlocIndexer": "anndata.experimental.Dataset2DIlocIndexer",
    "zarr.core.array.Array": "zarr.Array",
    "zarr.core.group.Group": "zarr.Group",
    # Buffer is not yet exported, so the buffer class registry is the closest thing
    "zarr.core.buffer.core.Buffer": "zarr.registry.Registry",
    "zarr.storage._common.StorePath": "zarr.storage.StorePath",
    "anndata.compat.DaskArray": "dask.array.Array",
    "anndata.compat.CupyArray": "cupy.ndarray",
    "anndata.compat.CupySparseMatrix": "cupyx.scipy.sparse.spmatrix",
    "anndata.compat.XDataArray": "xarray.DataArray",
    "anndata.compat.XDataset": "xarray.Dataset",
    "awkward.highlevel.Array": "ak.Array",
    "numpy.int64": ("py:attr", "numpy.int64"),
    "pandas.DataFrame.iloc": ("py:attr", "pandas.DataFrame.iloc"),
    "pandas.DataFrame.loc": ("py:attr", "pandas.DataFrame.loc"),
    # should be fixed soon: https://github.com/tox-dev/sphinx-autodoc-typehints/pull/516
    "types.EllipsisType": ("py:data", "types.EllipsisType"),
    "pathlib._local.Path": "pathlib.Path",
}
autodoc_type_aliases = dict(
    NDArray=":data:`~numpy.typing.NDArray`",
    AxisStorable=":data:`~anndata.typing.AxisStorable`",
    **{
        f"{v}variantRWAble": ":data:`~anndata.typing.RWAble`"
        for v in ["In", "Co", "Contra"]
    },
)

# -- Social cards ---------------------------------------------------------

ogp_site_url = "https://anndata.readthedocs.io/"
ogp_image = "https://anndata.readthedocs.io/en/latest/_static/img/anndata_schema.svg"

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


# The theme is sphinx-book-theme, with patches for readthedocs-sphinx-search
html_theme = "scanpydoc"
html_theme_options = dict(
    use_repository_button=True,
    repository_url="https://github.com/scverse/anndata",
    repository_branch="main",
    navigation_with_keys=False,  # https://github.com/pydata/pydata-sphinx-theme/issues/1492
)
html_logo = "_static/img/anndata_schema.svg"
issues_github_path = "scverse/anndata"
html_show_sphinx = False


# -- 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",
    )
]

[rtd-command-info] start-time: 2025-10-27T19:30:47.127620Z, end-time: 2025-10-27T19:31:11.629578Z, duration: 24, exit-code: 0
python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v8.2.3
loading translations [en]... done
matplotlib is not installed, social cards will not be generated
making output directory... done
myst v4.0.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'html_image', 'colon_fence', 'dollarmath'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
myst-nb v1.3.0: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', 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=False, 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='show', 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-anndata/checkouts/stable/_readthedocs/.jupyter_cache
loading intersphinx inventory 'awkward' from https://awkward-array.org/doc/stable/objects.inv ...
loading intersphinx inventory 'cupy' from https://docs.cupy.dev/en/stable/objects.inv ...
loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable/objects.inv ...
loading intersphinx inventory 'fsspec' from https://filesystem-spec.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'h5py' from https://docs.h5py.org/en/latest/objects.inv ...
loading intersphinx inventory 'hdf5plugin' from https://hdf5plugin.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'kvikio' from https://docs.rapids.ai/api/kvikio/stable/objects.inv ...
loading intersphinx inventory 'loompy' from https://linnarssonlab.org/loompy/objects.inv ...
loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ...
loading intersphinx inventory 'obstore' from https://developmentseed.org/obstore/latest/objects.inv ...
loading intersphinx inventory 'pandas' from https://pandas.pydata.org/pandas-docs/stable/objects.inv ...
loading intersphinx inventory 'python' from https://docs.python.org/3.13/objects.inv ...
loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv ...
loading intersphinx inventory 'sklearn' from https://scikit-learn.org/stable/objects.inv ...
loading intersphinx inventory 'xarray' from https://docs.xarray.dev/en/stable/objects.inv ...
loading intersphinx inventory 'zarr' from https://zarr.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'zarrs' from https://zarrs-python.readthedocs.io/en/stable/objects.inv ...
[autosummary] generating autosummary for: _key_contributors.rst, api.md, benchmark-read-write.ipynb, benchmarks.md, concatenation.rst, contributing.md, fileformat-prose.md, index.md, interoperability.md, references.rst, ..., tutorials/index.md, tutorials/notebooks/anncollection-annloader.ipynb, tutorials/notebooks/anncollection.ipynb, tutorials/notebooks/anndata_dask_array.ipynb, tutorials/notebooks/annloader.ipynb, tutorials/notebooks/awkward-arrays.ipynb, tutorials/notebooks/getting-started.ipynb, tutorials/notebooks/read_lazy.ipynb, tutorials/notebooks/{read,write}_dispatched.ipynb, tutorials/zarr-v3.md
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.AnnData.write_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.ImplicitModificationWarning.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.abc.CSCDataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.abc.CSRDataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.concat.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.experimental.AnnCollection.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.io.write_elem.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.io.write_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.io.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.register_anndata_namespace.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.settings.override.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.settings.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.types.ExtensionNamespace.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.typing.AxisStorable.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.typing.Index.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.typing.RWAble.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.AnnData.layers.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.experimental.backed.Dataset2D.is_backed.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.experimental.backed.Dataset2D.keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.experimental.backed.Dataset2D.reindex.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.experimental.backed.Dataset2D.shape.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.experimental.backed.Dataset2D.to_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.experimental.backed.Dataset2D.true_index.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.experimental.backed.Dataset2D.true_index_dim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.experimental.backed.Dataset2D.true_xr_index.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.experimental.backed.Dataset2D.xr_index.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/generated/anndata.experimental.backed.MaskedArray.dtype.rst
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 21 source files that are out of date
updating environment: [new config] 137 added, 0 changed, 0 removed
reading sources... [  1%] _key_contributors
reading sources... [  1%] api
reading sources... [  2%] benchmark-read-write
reading sources... [  3%] benchmarks
reading sources... [  4%] concatenation
reading sources... [  4%] contributing
reading sources... [  5%] fileformat-prose
reading sources... [  6%] generated/anndata.AnnData
reading sources... [  7%] generated/anndata.AnnData.T
reading sources... [  7%] generated/anndata.AnnData.X
reading sources... [  8%] generated/anndata.AnnData.chunk_X
reading sources... [  9%] generated/anndata.AnnData.chunked_X
reading sources... [  9%] generated/anndata.AnnData.concatenate
reading sources... [ 10%] generated/anndata.AnnData.copy
reading sources... [ 11%] generated/anndata.AnnData.filename
reading sources... [ 12%] generated/anndata.AnnData.is_view
reading sources... [ 12%] generated/anndata.AnnData.isbacked
reading sources... [ 13%] generated/anndata.AnnData.layers
reading sources... [ 14%] generated/anndata.AnnData.n_obs
reading sources... [ 15%] generated/anndata.AnnData.n_vars
reading sources... [ 15%] generated/anndata.AnnData.obs
reading sources... [ 16%] generated/anndata.AnnData.obs_names
reading sources... [ 17%] generated/anndata.AnnData.obs_names_make_unique
reading sources... [ 18%] generated/anndata.AnnData.obs_vector
reading sources... [ 18%] generated/anndata.AnnData.obsm
reading sources... [ 19%] generated/anndata.AnnData.obsp
reading sources... [ 20%] generated/anndata.AnnData.raw
reading sources... [ 20%] generated/anndata.AnnData.rename_categories
reading sources... [ 21%] generated/anndata.AnnData.shape
reading sources... [ 22%] generated/anndata.AnnData.strings_to_categoricals
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