Read the Docs build information
Build id: 4036593
Project: icb-anndata
Version: 2467
Commit: 46e4cff071c751e1e967dbbe32b9ba2a32a2aedd
Date: 2026-05-22T15:03:55.419137Z
State: finished
Success: True


[rtd-command-info] start-time: 2026-05-22T15:03:56.251411Z, end-time: 2026-05-22T15:03:56.804248Z, 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 pull/2467/head:external-2467
From https://github.com/scverse/anndata
 * [new ref]         refs/pull/2467/head -> external-2467
 * [new tag]         0.12.10             -> 0.12.10
 * [new tag]         0.12.11             -> 0.12.11
 * [new tag]         0.12.12             -> 0.12.12
 * [new tag]         0.12.13             -> 0.12.13
 * [new tag]         0.12.14             -> 0.12.14
 * [new tag]         0.12.16             -> 0.12.16
 * [new tag]         0.12.8              -> 0.12.8
 * [new tag]         0.12.9              -> 0.12.9

[rtd-command-info] start-time: 2026-05-22T15:03:58.775179Z, end-time: 2026-05-22T15:03:58.847103Z, duration: 0, exit-code: 0
git checkout --force 46e4cff071c751e1e967dbbe32b9ba2a32a2aedd
Note: switching to '46e4cff071c751e1e967dbbe32b9ba2a32a2aedd'.

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 46e4cff Backport PR #2466: docs: Mention anndataR in interoperability section

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cat .readthedocs.yml
version: 2
build:
  os: ubuntu-24.04
  tools:
    python: "3.14"
  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: 2026-05-22T15:03:59.088735Z, end-time: 2026-05-22T15:03:59.165000Z, 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/2467/docs/tutorials/notebooks'...
Submodule path 'docs/tutorials/notebooks': checked out '3ead7c9670fa55eca4eef35067a24a03b6621ce8'

[rtd-command-info] start-time: 2026-05-22T15:04:00.095729Z, end-time: 2026-05-22T15:04:01.901960Z, duration: 1, exit-code: 0
git fetch --unshallow || true
From https://github.com/scverse/anndata
 * [new tag]         0.10.0       -> 0.10.0
 * [new tag]         0.10.0.dev0  -> 0.10.0.dev0
 * [new tag]         0.10.0rc1    -> 0.10.0rc1
 * [new tag]         0.11.0       -> 0.11.0
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 * [new tag]         0.9.0rc1     -> 0.9.0rc1

[rtd-command-info] start-time: 2026-05-22T15:04:06.685420Z, end-time: 2026-05-22T15:04:06.753682Z, duration: 0, exit-code: 0
asdf global python 3.14.0


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python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.14.0.final.0-64 in 398ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2467, 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: 2026-05-22T15:04:07.897961Z, end-time: 2026-05-22T15:04:14.161153Z, duration: 6, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2467/lib/python3.14/site-packages/pip/_vendor/pyparsing/core.py:5332: SyntaxWarning: 'return' in a 'finally' block
  return self.__class__.__name__ + ": " + retString
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2467/lib/python3.14/site-packages (23.1)
Collecting pip
  Downloading pip-26.1.1-py3-none-any.whl (1.8 MB)
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2467/lib/python3.14/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-26.1.1 setuptools-82.0.1

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python -m pip install --upgrade --no-cache-dir sphinx
Collecting sphinx
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Collecting sphinxcontrib-applehelp>=1.0.7 (from sphinx)
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Collecting idna<4,>=2.5 (from requests>=2.30.0->sphinx)
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Downloading sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl (92 kB)
Installing collected packages: urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, roman-numerals, 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-2.20.0 alabaster-1.0.0 babel-2.18.0 certifi-2026.5.20 charset_normalizer-3.4.7 docutils-0.22.4 idna-3.16 imagesize-2.0.0 packaging-26.2 requests-2.34.2 roman-numerals-4.1.0 snowballstemmer-3.0.1 sphinx-9.1.0 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 urllib3-2.7.0

[rtd-command-info] start-time: 2026-05-22T15:04:20.122649Z, end-time: 2026-05-22T15:04:56.473592Z, duration: 36, exit-code: 0
python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc]
Processing ./.
  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 array-api-compat>=1.7.1 (from anndata==0.13.0.dev3+g46e4cff07)
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Requirement already satisfied: packaging>=24.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2467/lib/python3.14/site-packages (from anndata==0.13.0.dev3+g46e4cff07) (26.2)
Collecting pandas!=2.1.2,<3,>=2.1.0 (from anndata==0.13.0.dev3+g46e4cff07)
  Downloading pandas-2.3.3-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB)
Collecting scipy!=1.17.0,>=1.12 (from anndata==0.13.0.dev3+g46e4cff07)
  Downloading scipy-1.17.1-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
Collecting scverse-misc>=0.0.3 (from anndata==0.13.0.dev3+g46e4cff07)
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Collecting zarr!=3.0.*,>=2.18.7 (from anndata==0.13.0.dev3+g46e4cff07)
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Building wheels for collected packages: anndata
  Building wheel for anndata (pyproject.toml): started
  Building wheel for anndata (pyproject.toml): finished with status 'done'
  Created wheel for anndata: filename=anndata-0.13.0.dev3+g46e4cff07-py3-none-any.whl size=175444 sha256=1d56e5f62c52b435a878d5b4dc45b13eab37a18b09a8705e83bed4c82b67684d
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Successfully built anndata
Installing collected packages: pytz, pure-eval, ptyprocess, fastjsonschema, zipp, wcwidth, tzdata, typing-extensions, traitlets, tornado, toolz, tabulate, soupsieve, six, session-info2, rpds-py, pyzmq, pyyaml, psutil, platformdirs, pexpect, parso, numpy, nest-asyncio, natsort, mdurl, locket, legacy-api-wrap, ipython-pygments-lexers, greenlet, google-crc32c, fsspec, executing, decorator, debugpy, comm, cloudpickle, click, attrs, asttokens, array-api-compat, accessible-pygments, towncrier, stack_data, sqlalchemy, scverse-misc, scipy, referencing, python-dateutil, prompt_toolkit, partd, numcodecs, matplotlib-inline, markdown-it-py, jupyter-core, jedi, importlib_metadata, h5py, donfig, beautifulsoup4, awkward-cpp, zarr, sphinxext-opengraph, sphinx-issues, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, scanpydoc, pydata-sphinx-theme, pandas, mdit-py-plugins, jupyter-client, jsonschema-specifications, ipython, dask, awkward, sphinx-book-theme, myst-parser, jsonschema, ipykernel, anndata, nbformat, nbclient, jupyter-cache, myst-nb

Successfully installed accessible-pygments-0.0.5 anndata-0.13.0.dev3+g46e4cff07 array-api-compat-1.14.0 asttokens-3.0.1 attrs-26.1.0 awkward-2.9.0 awkward-cpp-52 beautifulsoup4-4.14.3 click-8.4.1 cloudpickle-3.1.2 comm-0.2.3 dask-2026.3.0 debugpy-1.8.20 decorator-5.3.1 donfig-0.8.1.post1 executing-2.2.1 fastjsonschema-2.21.2 fsspec-2026.4.0 google-crc32c-1.8.0 greenlet-3.5.1 h5py-3.16.0 importlib_metadata-9.0.0 ipykernel-7.2.0 ipython-9.13.0 ipython-pygments-lexers-1.1.1 jedi-0.20.0 jsonschema-4.26.0 jsonschema-specifications-2025.9.1 jupyter-cache-1.0.1 jupyter-client-8.8.0 jupyter-core-5.9.1 legacy-api-wrap-1.5 locket-1.0.0 markdown-it-py-4.2.0 matplotlib-inline-0.2.2 mdit-py-plugins-0.6.1 mdurl-0.1.2 myst-nb-1.4.0 myst-parser-5.1.0 natsort-8.4.0 nbclient-0.10.4 nbformat-5.10.4 nest-asyncio-1.6.0 numcodecs-0.16.5 numpy-2.4.6 pandas-2.3.3 parso-0.8.7 partd-1.4.2 pexpect-4.9.0 platformdirs-4.9.6 prompt_toolkit-3.0.52 psutil-7.2.2 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.16.1 python-dateutil-2.9.0.post0 pytz-2026.2 pyyaml-6.0.3 pyzmq-27.1.0 referencing-0.37.0 rpds-py-0.30.0 scanpydoc-0.17.3 scipy-1.17.1 scverse-misc-0.0.7 session-info2-0.4.1 six-1.17.0 soupsieve-2.8.3 sphinx-autodoc-typehints-3.10.2 sphinx-book-theme-1.2.0 sphinx-copybutton-0.5.2 sphinx-design-0.7.0 sphinx-issues-6.0.0 sphinxext-opengraph-0.13.0 sqlalchemy-2.0.49 stack_data-0.6.3 tabulate-0.10.0 toolz-1.1.0 tornado-6.5.5 towncrier-25.8.0 traitlets-5.15.0 typing-extensions-4.15.0 tzdata-2026.2 wcwidth-0.7.0 zarr-3.2.1 zipp-4.1.0

[rtd-command-info] start-time: 2026-05-22T15:04:56.609638Z, end-time: 2026-05-22T15:04:56.653578Z, duration: 0, exit-code: 0
( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true


[rtd-command-info] start-time: 2026-05-22T15:04:56.726647Z, end-time: 2026-05-22T15:04:56.774827Z, 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",
    *(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"
always_use_bars_union = True  # use `|`, not `Union` in types even when on Python ≤3.14
todo_include_todos = False
nitpicky = True  # Report broken links
nitpick_ignore = [  # APIs without an intersphinx entry
    # These APIs aren’t actually documented
    ("py:class", "anndata._core.raw.Raw"),
    ("py:class", "pandas._libs.missing.NAType"),
    # 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/version/2.3", None),
    python=("https://docs.python.org/3", 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),
    scverse_misc=("https://scverse-misc.readthedocs.io/stable", None),
)

qualname_overrides = {
    "types.EllipsisType": ("py:data", "Ellipsis"),
    "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.StorageType": "anndata.experimental.StorageType",
    "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",
    "anndata.compat.Index": "anndata.typing.Index",
    "awkward.highlevel.Array": "ak.Array",
    "numpy.int64": ("py:attr", "numpy.int64"),
    "numpy.dtypes.StringDType": ("py:attr", "numpy.dtypes.StringDType"),
    "pandas.DataFrame.iloc": ("py:attr", "pandas.DataFrame.iloc"),
    "pandas.DataFrame.loc": ("py:attr", "pandas.DataFrame.loc"),
    "pandas.core.series.Series": "pandas.Series",
    "pandas.core.arrays.categorical.Categorical": "pandas.Categorical",
    "pandas.core.arrays.base.ExtensionArray": "pandas.api.extensions.ExtensionArray",
    "pandas.core.dtypes.dtypes.BaseMaskedDtype": "pandas.api.extensions.ExtensionDtype",
    **{
        f"anndata._types.{var}{v}": ("py:data", f"anndata.{typ}")
        for v in ["", "_co", "_contra"]
        for var, typ in [("RWAble", "typing.RWAble"), ("S", "experimental.StorageType")]
    },
}
autodoc_type_aliases = dict(
    NDArray=":data:`~numpy.typing.NDArray`",
    AxisStorable=":data:`~anndata.typing.AxisStorable`",
)

# -- 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: 2026-05-22T15:04:56.853399Z, end-time: 2026-05-22T15:05:17.944842Z, duration: 21, exit-code: 0
python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v9.1.0
loading translations [en]... done
matplotlib is not installed, social cards will not be generated
making output directory... done
myst v5.1.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'colon_fence', 'dollarmath', 'html_image'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, strikethrough_single_tilde=False, colon_fence_exact_match=False, suppress_warnings=[], highlight_code_blocks=True)
myst-nb v1.4.0: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', 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/2467/_readthedocs/.jupyter_cache
loading intersphinx inventory 'awkward' from https://awkward-array.org/doc/stable/objects.inv ...
loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable/objects.inv ...
loading intersphinx inventory 'cupy' from https://docs.cupy.dev/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/version/2.3/objects.inv ...
loading intersphinx inventory 'python' from https://docs.python.org/3/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 'zarrs' from https://zarrs-python.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'zarr' from https://zarr.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'scverse_misc' from https://scverse-misc.readthedocs.io/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
/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2467/lib/python3.14/site-packages/sphinx/ext/autosummary/__init__.py:697: FutureWarning: Importing ExtensionNamespace from `types` is deprecated. Please use scverse_misc instead.
  return getattr(mod, name_parts[-1]), mod, modname
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.AnnData.write_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.ImplicitModificationWarning.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.abc.CSCDataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.abc.CSRDataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.concat.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.experimental.AnnCollection.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.io.write_elem.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.io.write_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.io.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.register_anndata_namespace.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.settings.override.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.settings.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.types.ExtensionNamespace.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.typing.AxisStorable.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.typing.Index.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.typing.RWAble.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.AnnData.isview.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.experimental.AnnCollection.attrs_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.experimental.AnnCollection.convert.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.experimental.AnnCollection.has_backed.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.experimental.AnnCollection.lazy_attr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.experimental.AnnCollection.n_obs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.experimental.AnnCollection.n_vars.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.experimental.AnnCollection.obs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.experimental.AnnCollection.obsm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.experimental.AnnCollection.shape.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2467/docs/generated/anndata.experimental.AnnCollection.to_adata.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] 117 added, 0 changed, 0 removed
/home/docs/.asdf/installs/python/3.14.0/lib/python3.14/importlib/__init__.py:88: ZarrUserWarning: pytest not installed, skipping test suite
  return _bootstrap._gcd_import(name[level:], package, level)
reading sources... [  1%] _key_contributors
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/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2467/lib/python3.14/site-packages/sphinx/ext/autosummary/__init__.py:697: FutureWarning: Importing ExtensionNamespace from `types` is deprecated. Please use scverse_misc instead.
  return getattr(mod, name_parts[-1]), mod, modname
/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2467/lib/python3.14/site-packages/sphinx/util/inspect.py:461: FutureWarning: Importing ExtensionNamespace from `types` is deprecated. Please use scverse_misc instead.
  return getattr(obj, name, *defargs)
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