Read the Docs build information Build id: 3932574 Project: icb-anndata Version: 2390 Commit: 134e2edf017cbad5de52b56bc4d050e6bf559d92 Date: 2026-04-16T07:45:58.726927Z State: finished Success: False [rtd-command-info] start-time: 2026-04-16T07:45:59.494859Z, end-time: 2026-04-16T07:46:00.218210Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/scverse/anndata.git . Cloning into '.'... [rtd-command-info] start-time: 2026-04-16T07:46:00.295588Z, end-time: 2026-04-16T07:46:01.445238Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/2390/head:external-2390 From https://github.com/scverse/anndata * [new ref] refs/pull/2390/head -> external-2390 * [new tag] 0.12.10 -> 0.12.10 * [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] 0.12.8 -> 0.12.8 * [new tag] 0.12.9 -> 0.12.9 [rtd-command-info] start-time: 2026-04-16T07:46:02.218292Z, end-time: 2026-04-16T07:46:02.283140Z, duration: 0, exit-code: 0 git checkout --force 134e2edf017cbad5de52b56bc4d050e6bf559d92 Note: switching to '134e2edf017cbad5de52b56bc4d050e6bf559d92'. 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 Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 134e2ed fix sphinx version [rtd-command-info] start-time: 2026-04-16T07:46:02.378440Z, end-time: 2026-04-16T07:46:02.414930Z, duration: 0, exit-code: 0 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: 2026-04-16T07:46:02.564630Z, end-time: 2026-04-16T07:46:02.630014Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2026-04-16T07:46:02.717030Z, end-time: 2026-04-16T07:46:03.543746Z, duration: 0, 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/2390/docs/tutorials/notebooks'... 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psutil-7.2.2-cp36-abi3-manylinux2010_x86_64.manylinux_2_12_x86_64.manylinux_2_28_x86_64.whl (155 kB) Downloading pure_eval-0.2.3-py3-none-any.whl (11 kB) Downloading session_info2-0.4.1-py3-none-any.whl (17 kB) Downloading sphinx_copybutton-0.5.2-py3-none-any.whl (13 kB) Downloading sphinxext_opengraph-0.13.0-py3-none-any.whl (1.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 1.1 GB/s 0:00:00 Downloading wcwidth-0.6.0-py3-none-any.whl (94 kB) Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) 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.dev10+g134e2edf0-py3-none-any.whl size=173725 sha256=5d9c45e865e4af0ffd750aa6f0b7a245b98b57e82a189fa1c751e480b440f433 Stored in directory: /tmp/pip-ephem-wheel-cache-oyj6b1g9/wheels/54/2c/f8/87238450f88de42384682b97c99e030682a105b8ed72715e1b 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, session-info2, ruamel.yaml, rpds-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, decorator, debugpy, comm, cloudpickle, click, attrs, asttokens, array-api-compat, accessible-pygments, towncrier, stack_data, sqlalchemy, sphinx-jinja2-compat, scverse-misc, scipy, 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 Successfully installed accessible-pygments-0.0.5 anndata-0.13.0.dev10+g134e2edf0 apeye-1.4.1 apeye-core-1.1.5 array-api-compat-1.14.0 asttokens-3.0.1 attrs-26.1.0 autodocsumm-0.2.15 awkward-2.9.0 awkward-cpp-52 beautifulsoup4-4.14.3 cachecontrol-0.14.4 click-8.3.2 cloudpickle-3.1.2 comm-0.2.3 cssutils-2.11.1 dask-2026.3.0 debugpy-1.8.20 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-3.28.0 fsspec-2026.3.0 google-crc32c-1.8.0 greenlet-3.4.0 h5py-3.16.0 html5lib-1.1 importlib_metadata-9.0.0 ipykernel-7.2.0 ipython-9.12.0 ipython-pygments-lexers-1.1.1 jedi-0.19.2 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-4.0.0 matplotlib-inline-0.2.1 mdit-py-plugins-0.5.0 mdurl-0.1.2 more-itertools-11.0.2 msgpack-1.1.2 myst-nb-1.4.0 myst-parser-5.0.0 natsort-8.4.0 nbclient-0.10.4 nbformat-5.10.4 nest-asyncio-1.6.0 numcodecs-0.16.5 numpy-2.4.4 pandas-2.3.3 parso-0.8.6 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-2026.1.post1 pyyaml-6.0.3 pyzmq-27.1.0 referencing-0.37.0 roman-5.2 rpds-py-0.30.0 ruamel.yaml-0.18.16 scanpydoc-0.17.3 scipy-1.17.1 scverse-misc-0.0.3 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 sphinx-jinja2-compat-0.4.1 sphinx-prompt-1.10.2 sphinx-tabs-3.4.5 sphinx-toolbox-4.1.2 sphinxext-opengraph-0.13.0 sqlalchemy-2.0.49 stack_data-0.6.3 standard-imghdr-3.10.14 tabulate-0.10.0 toolz-1.1.0 tornado-6.5.5 towncrier-25.8.0 traitlets-5.14.3 typing-extensions-4.15.0 tzdata-2026.1 wcwidth-0.6.0 webencodings-0.5.1 zarr-3.1.6 zipp-3.23.1 [rtd-command-info] start-time: 2026-04-16T07:46:56.514171Z, end-time: 2026-04-16T07:46:56.810030Z, 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/2390/docs/release-notes/2358.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2390/docs/release-notes/2342.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2390/docs/release-notes/2351.fix.md Done! [rtd-command-info] start-time: 2026-04-16T07:46:56.901199Z, end-time: 2026-04-16T07:46:56.937937Z, 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" 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 = { "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"), "pandas.core.dtypes.dtypes.BaseMaskedDtype": "pandas.api.extensions.ExtensionDtype", # 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: 2026-04-16T07:46:57.022756Z, end-time: 2026-04-16T07:46:58.311679Z, duration: 1, exit-code: 2 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 Extension error! Versions ======== * Platform: linux; (Linux-6.17.0-1007-aws-x86_64-with-glibc2.39) * Python version: 3.14.0 (CPython) * Sphinx version: 9.1.0 * Docutils version: 0.22.4 * Jinja2 version: 3.1.6 * Pygments version: 2.20.0 Last Messages ============= None. Loaded Extensions ================= None. Traceback ========= Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2390/lib/python3.14/site-packages/sphinx/registry.py", line 550, in load_extension mod = import_module(extname) File "/home/docs/.asdf/installs/python/3.14.0/lib/python3.14/importlib/__init__.py", line 88, in import_module return _bootstrap._gcd_import(name[level:], package, level) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "", line 1398, in _gcd_import File "", line 1371, in _find_and_load File "", line 1314, in _find_and_load_unlocked File "", line 491, in _call_with_frames_removed File "", line 1398, in _gcd_import File "", line 1371, in _find_and_load File "", line 1314, in _find_and_load_unlocked File "", line 491, in _call_with_frames_removed File "", line 1398, in _gcd_import File "", line 1371, in _find_and_load File "", line 1342, in _find_and_load_unlocked File "", line 938, in _load_unlocked File "", line 762, in exec_module File "", line 491, in _call_with_frames_removed File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2390/lib/python3.14/site-packages/sphinx_toolbox/__init__.py", line 42, in from sphinx_toolbox import ( # noqa: F401 ...<11 lines>... ) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2390/lib/python3.14/site-packages/sphinx_toolbox/assets.py", line 110, in from sphinx_toolbox.utils import SphinxExtMetadata, metadata_add_version File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2390/lib/python3.14/site-packages/sphinx_toolbox/utils.py", line 64, in from sphinx.ext.autodoc import Documenter, logger ImportError: cannot import name 'logger' from 'sphinx.ext.autodoc' (/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2390/lib/python3.14/site-packages/sphinx/ext/autodoc/__init__.py) The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2390/lib/python3.14/site-packages/sphinx/cmd/build.py", line 414, in build_main app = Sphinx( srcdir=args.sourcedir, ...<14 lines>... exception_on_warning=args.exception_on_warning, ) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2390/lib/python3.14/site-packages/sphinx/application.py", line 299, in __init__ self.setup_extension(extension) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2390/lib/python3.14/site-packages/sphinx/application.py", line 505, in setup_extension self.registry.load_extension(self, extname) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2390/lib/python3.14/site-packages/sphinx/registry.py", line 553, in load_extension raise ExtensionError( __('Could not import extension %s') % extname, err ) from err sphinx.errors.ExtensionError: Could not import extension sphinx_toolbox.more_autodoc.autoprotocol (exception: cannot import name 'logger' from 'sphinx.ext.autodoc' (/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/2390/lib/python3.14/site-packages/sphinx/ext/autodoc/__init__.py)) The full traceback has been saved in: /tmp/sphinx-err-w_sx29kv.log To report this error to the developers, please open an issue at . Thanks! Please also report this if it was a user error, so that a better error message can be provided next time. matplotlib is not installed, social cards will not be generated