Read the Docs build information Build id: 3625827 Project: icb-anndata Version: latest Commit: ce752e5fcef470c0fc18077d2168e75e8a0646c3 Date: 2025-12-24T12:58:51.295142Z State: finished Success: True [rtd-command-info] start-time: 2025-12-24T12:58:52.365516Z, end-time: 2025-12-24T12:58:52.903854Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/scverse/anndata.git . Cloning into '.'... [rtd-command-info] start-time: 2025-12-24T12:58:53.031678Z, end-time: 2025-12-24T12:58:54.157627Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 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] 0.10.1 -> 0.10.1 * [new tag] 0.10.2 -> 0.10.2 * [new tag] 0.10.3 -> 0.10.3 * [new tag] 0.10.4 -> 0.10.4 * [new tag] 0.10.5 -> 0.10.5 * [new tag] 0.10.5.post1 -> 0.10.5.post1 * [new tag] 0.10.6 -> 0.10.6 * [new tag] 0.10.7 -> 0.10.7 * [new tag] 0.10.8 -> 0.10.8 * [new tag] 0.10.9 -> 0.10.9 * [new tag] 0.11.0 -> 0.11.0 * [new tag] 0.11.0.dev0 -> 0.11.0.dev0 * [new tag] 0.11.0rc1 -> 0.11.0rc1 * [new tag] 0.11.0rc2 -> 0.11.0rc2 * [new tag] 0.11.0rc3 -> 0.11.0rc3 * [new tag] 0.11.1 -> 0.11.1 * [new tag] 0.11.2 -> 0.11.2 * [new tag] 0.11.3 -> 0.11.3 * [new tag] 0.11.4 -> 0.11.4 * [new tag] 0.12.0 -> 0.12.0 * [new tag] 0.12.0rc1 -> 0.12.0rc1 * [new tag] 0.12.0rc2 -> 0.12.0rc2 * [new tag] 0.12.0rc3 -> 0.12.0rc3 * [new tag] 0.12.0rc4 -> 0.12.0rc4 * [new tag] 0.12.1 -> 0.12.1 * [new tag] 0.12.2 -> 0.12.2 * [new tag] 0.12.3 -> 0.12.3 * [new tag] 0.12.4 -> 0.12.4 * [new tag] 0.12.5 -> 0.12.5 * [new tag] 0.12.6 -> 0.12.6 * [new tag] 0.12.7 -> 0.12.7 * [new tag] 0.3 -> 0.3 * [new tag] 0.3.0.1 -> 0.3.0.1 * [new tag] 0.3.0.3 -> 0.3.0.3 * [new tag] 0.3.1 -> 0.3.1 * [new tag] 0.3.2 -> 0.3.2 * [new tag] 0.3.3 -> 0.3.3 * [new tag] 0.3.4 -> 0.3.4 * [new tag] 0.4.1 -> 0.4.1 * [new tag] 0.4.2 -> 0.4.2 * [new tag] 0.4.3 -> 0.4.3 * [new tag] 0.4.4 -> 0.4.4 * [new tag] 0.5 -> 0.5 * [new tag] 0.5.1 -> 0.5.1 * [new tag] 0.5.10 -> 0.5.10 * [new tag] 0.5.2 -> 0.5.2 * [new tag] 0.5.3 -> 0.5.3 * [new tag] 0.5.4 -> 0.5.4 * [new tag] 0.5.5 -> 0.5.5 * [new tag] 0.5.6 -> 0.5.6 * [new tag] 0.5.7 -> 0.5.7 * [new tag] 0.5.8 -> 0.5.8 * [new tag] 0.5.9 -> 0.5.9 * [new tag] 0.6 -> 0.6 * [new tag] 0.6.1 -> 0.6.1 * [new tag] 0.6.10 -> 0.6.10 * [new tag] 0.6.11 -> 0.6.11 * [new tag] 0.6.12 -> 0.6.12 * [new tag] 0.6.13 -> 0.6.13 * [new tag] 0.6.14 -> 0.6.14 * [new tag] 0.6.15 -> 0.6.15 * [new tag] 0.6.16 -> 0.6.16 * [new tag] 0.6.17 -> 0.6.17 * [new tag] 0.6.18 -> 0.6.18 * [new tag] 0.6.19 -> 0.6.19 * [new tag] 0.6.2 -> 0.6.2 * [new tag] 0.6.20 -> 0.6.20 * [new tag] 0.6.21 -> 0.6.21 * [new tag] 0.6.22 -> 0.6.22 * [new tag] 0.6.22.post1 -> 0.6.22.post1 * [new tag] 0.6.22rc1 -> 0.6.22rc1 * [new tag] 0.6.3 -> 0.6.3 * [new tag] 0.6.4 -> 0.6.4 * [new tag] 0.6.5 -> 0.6.5 * [new tag] 0.6.6 -> 0.6.6 * [new tag] 0.6.7 -> 0.6.7 * [new tag] 0.6.8 -> 0.6.8 * [new tag] 0.6.9 -> 0.6.9 * [new tag] 0.7 -> 0.7 * [new tag] 0.7.1 -> 0.7.1 * [new tag] 0.7.2 -> 0.7.2 * [new tag] 0.7.2a1 -> 0.7.2a1 * [new tag] 0.7.3 -> 0.7.3 * [new tag] 0.7.4 -> 0.7.4 * [new tag] 0.7.5 -> 0.7.5 * [new tag] 0.7.6 -> 0.7.6 * [new tag] 0.7.7 -> 0.7.7 * [new tag] 0.7.8 -> 0.7.8 * [new tag] 0.7rc1 -> 0.7rc1 * [new tag] 0.7rc2 -> 0.7rc2 * [new tag] 0.8.0 -> 0.8.0 * [new tag] 0.8.0.dev0 -> 0.8.0.dev0 * [new tag] 0.8.0rc1 -> 0.8.0rc1 * [new tag] 0.9.0 -> 0.9.0 * [new tag] 0.9.0.dev0 -> 0.9.0.dev0 * [new tag] 0.9.0rc1 -> 0.9.0rc1 * [new tag] 0.9.1 -> 0.9.1 * [new tag] 0.9.2 -> 0.9.2 [rtd-command-info] start-time: 2025-12-24T12:58:54.953473Z, end-time: 2025-12-24T12:58:54.997231Z, 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: 2025-12-24T12:58:55.145440Z, end-time: 2025-12-24T12:58:55.214199Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2025-12-24T12:58:55.288835Z, end-time: 2025-12-24T12:58:56.469117Z, duration: 1, exit-code: 0 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/latest/docs/tutorials/notebooks'... Submodule path 'docs/tutorials/notebooks': checked out '0d8ffb2dc4a53de9762f76ed9030114d8aced353' [rtd-command-info] start-time: 2025-12-24T12:58:56.551558Z, end-time: 2025-12-24T12:58:57.628604Z, duration: 1, exit-code: 0 git fetch --unshallow || true [rtd-command-info] start-time: 2025-12-24T12:59:03.647060Z, end-time: 2025-12-24T12:59:03.709644Z, duration: 0, exit-code: 0 asdf global python 3.13.3 [rtd-command-info] start-time: 2025-12-24T12:59:04.144644Z, end-time: 2025-12-24T12:59:05.270443Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.13.3.final.0-64 in 816ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest, 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: 2025-12-24T12:59:05.365086Z, end-time: 2025-12-24T12:59:13.502236Z, duration: 8, 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/latest/lib/python3.13/site-packages (23.1) Collecting pip Downloading pip-25.3-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 9.4 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.13/site-packages (67.6.1) Collecting setuptools Downloading setuptools-80.9.0-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 22.1 MB/s eta 0:00:00 Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: 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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-2.19.2 alabaster-1.0.0 babel-2.17.0 certifi-2025.11.12 charset_normalizer-3.4.4 docutils-0.22.4 idna-3.11 imagesize-1.4.1 packaging-25.0 requests-2.32.5 roman-numerals-4.1.0 snowballstemmer-3.0.1 sphinx-9.0.4 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 urllib3-2.6.2 [rtd-command-info] start-time: 2025-12-24T12:59:18.571831Z, end-time: 2025-12-24T12:59:52.683837Z, duration: 34, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc] Processing 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Successfully built anndata 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, roman-numerals-py, roman, pyzmq, pyyaml, psutil, platformdirs, pexpect, parso, numpy, nest-asyncio, natsort, msgpack, more-itertools, mdurl, locket, legacy-api-wrap, ipython-pygments-lexers, greenlet, google-crc32c, fsspec, filelock, executing, docutils, decorator, debugpy, comm, cloudpickle, click, attrs, asttokens, array-api-compat, accessible-pygments, towncrier, stack_data, sqlalchemy, sphinx-jinja2-compat, sphinx, 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, zarr, 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, sphinx-book-theme, myst-parser, jsonschema, ipykernel, apeye, anndata, sphinx-toolbox, nbformat, nbclient, jupyter-cache, myst-nb Attempting uninstall: docutils Found existing installation: docutils 0.22.4 Uninstalling docutils-0.22.4: Successfully uninstalled docutils-0.22.4 Attempting uninstall: sphinx Found existing installation: Sphinx 9.0.4 Uninstalling Sphinx-9.0.4: Successfully uninstalled Sphinx-9.0.4 Successfully installed accessible-pygments-0.0.5 anndata-0.13.0.dev93+gce752e5fc apeye-1.4.1 apeye-core-1.1.5 array-api-compat-1.12.0 asttokens-3.0.1 attrs-25.4.0 autodocsumm-0.2.14 awkward-2.8.11 awkward-cpp-51 beautifulsoup4-4.14.3 cachecontrol-0.14.4 click-8.3.1 cloudpickle-3.1.2 comm-0.2.3 cssutils-2.11.1 dask-2025.12.0 debugpy-1.8.19 decorator-5.2.1 dict2css-0.3.0.post1 docutils-0.21.2 domdf-python-tools-3.10.0 donfig-0.8.1.post1 executing-2.2.1 fastjsonschema-2.21.2 filelock-3.20.1 fsspec-2025.12.0 google-crc32c-1.8.0 greenlet-3.3.0 h5py-3.15.1 html5lib-1.1 importlib_metadata-8.7.1 ipykernel-7.1.0 ipython-9.8.0 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-8.7.0 jupyter-core-5.9.1 legacy-api-wrap-1.5 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-0.10.4 nbformat-5.10.4 nest-asyncio-1.6.0 numcodecs-0.16.5 numpy-2.4.0 pandas-2.3.3 parso-0.8.5 partd-1.4.2 pexpect-4.9.0 platformdirs-4.5.1 prompt_toolkit-3.0.52 psutil-7.2.0 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 roman-5.2 roman-numerals-py-4.1.0 rpds-py-0.30.0 ruamel.yaml-0.18.17 ruamel.yaml.clib-0.2.15 scanpydoc-0.16 scipy-1.16.3 six-1.17.0 soupsieve-2.8.1 sphinx-8.2.3 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-1.10.2 sphinx-tabs-3.4.5 sphinx-toolbox-4.1.0 sphinxext-opengraph-0.13.0 sqlalchemy-2.0.45 stack_data-0.6.3 standard-imghdr-3.10.14 tabulate-0.9.0 toolz-1.1.0 tornado-6.5.4 towncrier-25.8.0 traitlets-5.14.3 typing-extensions-4.15.0 tzdata-2025.3 wcwidth-0.2.14 webencodings-0.5.1 zarr-3.1.5 zipp-3.23.0 [rtd-command-info] start-time: 2025-12-24T12:59:52.870929Z, end-time: 2025-12-24T12:59:53.220666Z, 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... Keeping the following files: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/release-notes/2133.breaking.md /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/release-notes/2223.docs.md /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/release-notes/2220.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/release-notes/2218.fix.md Done! [rtd-command-info] start-time: 2025-12-24T12:59:53.315621Z, end-time: 2025-12-24T12:59:53.359359Z, 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 # 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/stable", None), # TODO: switch to `/3` once docs are built with Python 3.14 # https://github.com/readthedocs/readthedocs.org/issues/12523 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"), "numpy.dtypes.StringDType": ("py:attr", "numpy.dtypes.StringDType"), "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`", ) # -- 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: 2025-12-24T12:59:53.445962Z, end-time: 2025-12-24T13:00:18.978637Z, duration: 25, 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/latest/_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/latest/docs/generated/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.ImplicitModificationWarning.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.abc.CSCDataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.abc.CSRDataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.concat.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.io.write_elem.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.io.write_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.io.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.register_anndata_namespace.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.settings.override.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.settings.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.types.ExtensionNamespace.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.typing.AxisStorable.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.typing.Index.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.typing.RWAble.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.layers.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.backed.Dataset2D.is_backed.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.backed.Dataset2D.keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.backed.Dataset2D.reindex.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.backed.Dataset2D.shape.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.backed.Dataset2D.to_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.backed.Dataset2D.true_index.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.backed.Dataset2D.true_index_dim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.backed.Dataset2D.true_xr_index.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.backed.Dataset2D.xr_index.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/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 reading sources... [ 23%] generated/anndata.AnnData.to_df reading sources... [ 23%] generated/anndata.AnnData.to_memory reading sources... [ 24%] generated/anndata.AnnData.transpose reading sources... [ 25%] generated/anndata.AnnData.uns reading sources... [ 26%] generated/anndata.AnnData.var reading sources... [ 26%] generated/anndata.AnnData.var_names reading sources... [ 27%] generated/anndata.AnnData.var_names_make_unique reading sources... [ 28%] generated/anndata.AnnData.var_vector reading sources... [ 28%] generated/anndata.AnnData.varm reading sources... [ 29%] generated/anndata.AnnData.varp reading sources... [ 30%] generated/anndata.AnnData.write reading sources... [ 31%] generated/anndata.AnnData.write_csvs reading sources... [ 31%] generated/anndata.AnnData.write_h5ad reading sources... [ 32%] generated/anndata.AnnData.write_loom reading sources... [ 33%] generated/anndata.AnnData.write_zarr reading sources... [ 34%] generated/anndata.ImplicitModificationWarning reading sources... [ 34%] generated/anndata.abc.CSCDataset reading sources... [ 35%] generated/anndata.abc.CSCDataset.__getitem__ reading sources... [ 36%] generated/anndata.abc.CSCDataset.format reading sources... [ 36%] generated/anndata.abc.CSCDataset.to_memory reading sources... [ 37%] generated/anndata.abc.CSRDataset reading sources... [ 38%] generated/anndata.abc.CSRDataset.__getitem__ reading sources... [ 39%] generated/anndata.abc.CSRDataset.format reading sources... [ 39%] generated/anndata.abc.CSRDataset.to_memory reading sources... [ 40%] generated/anndata.concat reading sources... [ 41%] generated/anndata.experimental.AnnCollection reading sources... [ 42%] generated/anndata.experimental.AnnCollection.attrs_keys reading sources... [ 42%] generated/anndata.experimental.AnnCollection.convert reading sources... [ 43%] generated/anndata.experimental.AnnCollection.has_backed reading sources... [ 44%] generated/anndata.experimental.AnnCollection.lazy_attr reading sources... [ 45%] generated/anndata.experimental.AnnCollection.n_obs reading sources... [ 45%] generated/anndata.experimental.AnnCollection.n_vars reading sources... [ 46%] generated/anndata.experimental.AnnCollection.obs reading sources... [ 47%] generated/anndata.experimental.AnnCollection.obsm reading sources... [ 47%] generated/anndata.experimental.AnnCollection.shape reading sources... [ 48%] generated/anndata.experimental.AnnCollection.to_adata reading sources... [ 49%] generated/anndata.experimental.AnnLoader reading sources... [ 50%] generated/anndata.experimental.Dataset2DIlocIndexer reading sources... [ 50%] generated/anndata.experimental.IOSpec reading sources... [ 51%] generated/anndata.experimental.Read reading sources... [ 52%] generated/anndata.experimental.ReadCallback reading sources... [ 53%] generated/anndata.experimental.StorageType reading sources... [ 53%] generated/anndata.experimental.Write reading sources... [ 54%] generated/anndata.experimental.WriteCallback reading sources... [ 55%] generated/anndata.experimental.backed.CategoricalArray reading sources... [ 55%] generated/anndata.experimental.backed.CategoricalArray.categories reading sources... [ 56%] generated/anndata.experimental.backed.CategoricalArray.dtype reading sources... [ 57%] generated/anndata.experimental.backed.Dataset2D reading sources... [ 58%] generated/anndata.experimental.backed.Dataset2D.columns reading sources... [ 58%] generated/anndata.experimental.backed.Dataset2D.copy reading sources... [ 59%] generated/anndata.experimental.backed.Dataset2D.ds reading sources... [ 60%] generated/anndata.experimental.backed.Dataset2D.dtypes reading sources... [ 61%] generated/anndata.experimental.backed.Dataset2D.equals reading sources... [ 61%] generated/anndata.experimental.backed.Dataset2D.iloc reading sources... [ 62%] generated/anndata.experimental.backed.Dataset2D.index reading sources... [ 63%] generated/anndata.experimental.backed.Dataset2D.index_dim reading sources... [ 64%] generated/anndata.experimental.backed.Dataset2D.is_backed reading sources... [ 64%] generated/anndata.experimental.backed.Dataset2D.keys reading sources... [ 65%] generated/anndata.experimental.backed.Dataset2D.reindex reading sources... [ 66%] generated/anndata.experimental.backed.Dataset2D.shape reading sources... [ 66%] generated/anndata.experimental.backed.Dataset2D.to_memory reading sources... [ 67%] generated/anndata.experimental.backed.Dataset2D.true_index reading sources... [ 68%] generated/anndata.experimental.backed.Dataset2D.true_index_dim reading sources... [ 69%] generated/anndata.experimental.backed.Dataset2D.true_xr_index reading sources... [ 69%] generated/anndata.experimental.backed.Dataset2D.xr_index reading sources... [ 70%] generated/anndata.experimental.backed.MaskedArray reading sources... [ 71%] generated/anndata.experimental.backed.MaskedArray.dtype reading sources... [ 72%] generated/anndata.experimental.concat_on_disk reading sources... [ 72%] generated/anndata.experimental.read_dispatched reading sources... [ 73%] generated/anndata.experimental.read_elem_lazy reading sources... [ 74%] generated/anndata.experimental.read_lazy reading sources... [ 74%] generated/anndata.experimental.write_dispatched reading sources... [ 75%] generated/anndata.io.read_csv reading sources... [ 76%] generated/anndata.io.read_elem reading sources... [ 77%] generated/anndata.io.read_excel reading sources... [ 77%] generated/anndata.io.read_h5ad reading sources... [ 78%] generated/anndata.io.read_hdf reading sources... [ 79%] generated/anndata.io.read_loom reading sources... [ 80%] generated/anndata.io.read_mtx reading sources... [ 80%] generated/anndata.io.read_text reading sources... [ 81%] generated/anndata.io.read_umi_tools reading sources... [ 82%] generated/anndata.io.read_zarr reading sources... [ 82%] generated/anndata.io.sparse_dataset reading sources... [ 83%] generated/anndata.io.write_elem reading sources... [ 84%] generated/anndata.io.write_h5ad reading sources... [ 85%] generated/anndata.io.write_zarr reading sources... [ 85%] generated/anndata.register_anndata_namespace reading sources... [ 86%] generated/anndata.settings reading sources... [ 87%] generated/anndata.settings.override reading sources... [ 88%] generated/anndata.types.ExtensionNamespace reading sources... [ 88%] generated/anndata.typing.AxisStorable reading sources... [ 89%] generated/anndata.typing.Index reading sources... [ 90%] generated/anndata.typing.RWAble reading sources... [ 91%] index reading sources... [ 91%] interoperability reading sources... [ 92%] references reading sources... [ 93%] release-notes/index reading sources... [ 93%] tutorials/index reading sources... [ 94%] tutorials/notebooks/anncollection reading sources... [ 95%] tutorials/notebooks/anncollection-annloader reading sources... [ 96%] tutorials/notebooks/anndata_dask_array reading sources... [ 96%] tutorials/notebooks/annloader reading sources... [ 97%] tutorials/notebooks/awkward-arrays reading sources... 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[100%] tutorials/zarr-v3 looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write_csvs.rst: document is referenced in multiple toctrees: ['api', 'generated/anndata.AnnData'], selecting: generated/anndata.AnnData <- generated/anndata.AnnData.write_csvs /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write_h5ad.rst: document is referenced in multiple toctrees: ['api', 'generated/anndata.AnnData'], selecting: generated/anndata.AnnData <- generated/anndata.AnnData.write_h5ad /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write_zarr.rst: document is referenced in multiple toctrees: ['api', 'generated/anndata.AnnData'], selecting: generated/anndata.AnnData <- generated/anndata.AnnData.write_zarr done preparing documents... done copying assets... copying static files... Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/_readthedocs/html/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/_readthedocs/html/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/_readthedocs/html/_static/documentation_options.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/_readthedocs/html/_static/copybutton.js copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 1%] _key_contributors writing output... [ 1%] api writing output... [ 2%] benchmark-read-write writing output... [ 3%] benchmarks writing output... [ 4%] concatenation writing output... [ 4%] contributing writing output... [ 5%] fileformat-prose writing output... [ 6%] generated/anndata.AnnData writing output... [ 7%] generated/anndata.AnnData.T writing output... [ 7%] generated/anndata.AnnData.X writing output... [ 8%] generated/anndata.AnnData.chunk_X writing output... [ 9%] generated/anndata.AnnData.chunked_X writing output... [ 9%] generated/anndata.AnnData.concatenate writing output... [ 10%] generated/anndata.AnnData.copy writing output... [ 11%] generated/anndata.AnnData.filename writing output... [ 12%] generated/anndata.AnnData.is_view writing output... [ 12%] generated/anndata.AnnData.isbacked writing output... [ 13%] generated/anndata.AnnData.layers writing output... [ 14%] generated/anndata.AnnData.n_obs writing output... [ 15%] generated/anndata.AnnData.n_vars writing output... [ 15%] generated/anndata.AnnData.obs writing output... [ 16%] generated/anndata.AnnData.obs_names writing output... [ 17%] generated/anndata.AnnData.obs_names_make_unique writing output... 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