Read the Docs build information Build id: 3479061 Project: icb-anndata Version: latest Commit: 52344dbb40037704f15d79bdd9329f31ed75074d Date: 2025-10-28T15:39:55.684630Z State: finished Success: False [rtd-command-info] start-time: 2025-10-28T15:39:56.841192Z, end-time: 2025-10-28T15:39:57.348215Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/scverse/anndata.git . Cloning into '.'... [rtd-command-info] start-time: 2025-10-28T15:39:57.468952Z, end-time: 2025-10-28T15:39:58.014627Z, duration: 0, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main [rtd-command-info] start-time: 2025-10-28T15:39:58.813178Z, end-time: 2025-10-28T15:39:58.871903Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: switching to 'origin/main'. 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 52344db fix: remove `read_dataset` usage in `read_lazy{_elem}` stack (#2158) [rtd-command-info] start-time: 2025-10-28T15:39:58.962520Z, end-time: 2025-10-28T15:39:59.006216Z, duration: 0, exit-code: 0 cat .readthedocs.yml version: 2 build: os: ubuntu-24.04 tools: python: "3.13" jobs: post_checkout: # unshallow so version can be derived from tag - git fetch --unshallow || true pre_build: # run towncrier to preview the next version’s release notes - ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true sphinx: configuration: docs/conf.py fail_on_warning: true # do not change or you will be fired python: install: - method: pip path: . extra_requirements: - doc submodules: include: - "docs/tutorials/notebooks" recursive: true [rtd-command-info] start-time: 2025-10-28T15:39:59.142676Z, end-time: 2025-10-28T15:39:59.208839Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2025-10-28T15:39:59.303118Z, end-time: 2025-10-28T15:40:00.115760Z, 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/latest/docs/tutorials/notebooks'... 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sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl (98 kB) Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Downloading sphinxcontrib_qthelp-2.0.0-py3-none-any.whl (88 kB) 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-py, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset_normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx Successfully installed Jinja2-3.1.6 MarkupSafe-3.0.3 Pygments-2.19.2 alabaster-1.0.0 babel-2.17.0 certifi-2025.10.5 charset_normalizer-3.4.4 docutils-0.21.2 idna-3.11 imagesize-1.4.1 packaging-25.0 requests-2.32.5 roman-numerals-py-3.1.0 snowballstemmer-3.0.1 sphinx-8.2.3 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 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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.dev60+g52344dbb4-py3-none-any.whl size=171525 sha256=e76479d0cc80e67b8cef796ce88b7fbd6acd27d4dab33a8790f3e3dae45248f7 Stored in directory: /tmp/pip-ephem-wheel-cache-qsjtesxo/wheels/52/85/59/780c094138dfa90e5dd120c1770a029544c8dc8f0169efb02a 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, requests, pyzmq, pyyaml, psutil, platformdirs, pexpect, parso, numpy, nest-asyncio, natsort, msgpack, more-itertools, mdurl, locket, legacy-api-wrap, ipython-pygments-lexers, greenlet, fsspec, filelock, executing, decorator, debugpy, crc32c, comm, cloudpickle, click, attrs, asttokens, array-api-compat, accessible-pygments, towncrier, stack_data, sqlalchemy, sphinx-jinja2-compat, scipy, ruamel.yaml, referencing, python-dateutil, prompt_toolkit, partd, numcodecs, matplotlib-inline, markdown-it-py, jupyter-core, jedi, importlib_metadata, html5lib, h5py, donfig, domdf-python-tools, cssutils, cachecontrol, beautifulsoup4, awkward-cpp, sphinxext-opengraph, sphinx-tabs, sphinx-prompt, sphinx-issues, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, scanpydoc, pydata-sphinx-theme, pandas, mdit-py-plugins, jupyter-client, jsonschema-specifications, ipython, dict2css, dask, awkward, autodocsumm, apeye-core, zarr, sphinx-book-theme, myst-parser, jsonschema, ipykernel, apeye, sphinx-toolbox, nbformat, anndata, nbclient, jupyter-cache, myst-nb Attempting uninstall: requests Found existing installation: requests 2.32.5 Uninstalling requests-2.32.5: Successfully uninstalled requests-2.32.5 Successfully installed accessible-pygments-0.0.5 anndata-0.13.0.dev60+g52344dbb4 apeye-1.4.1 apeye-core-1.1.5 array-api-compat-1.12.0 asttokens-3.0.0 attrs-25.4.0 autodocsumm-0.2.14 awkward-2.8.10 awkward-cpp-50 beautifulsoup4-4.14.2 cachecontrol-0.14.3 click-8.3.0 cloudpickle-3.1.1 comm-0.2.3 crc32c-2.8 cssutils-2.11.1 dask-2025.10.0 debugpy-1.8.17 decorator-5.2.1 dict2css-0.3.0.post1 domdf-python-tools-3.10.0 donfig-0.8.1.post1 executing-2.2.1 fastjsonschema-2.21.2 filelock-3.20.0 fsspec-2025.9.0 greenlet-3.2.4 h5py-3.15.1 html5lib-1.1 importlib_metadata-8.7.0 ipykernel-7.1.0 ipython-9.6.0 ipython-pygments-lexers-1.1.1 jedi-0.19.2 jsonschema-4.25.1 jsonschema-specifications-2025.9.1 jupyter-cache-1.0.1 jupyter-client-8.6.3 jupyter-core-5.9.1 legacy-api-wrap-1.4.1 locket-1.0.0 markdown-it-py-3.0.0 matplotlib-inline-0.2.1 mdit-py-plugins-0.5.0 mdurl-0.1.2 more-itertools-10.8.0 msgpack-1.1.2 myst-nb-1.3.0 myst-parser-4.0.1 natsort-8.4.0 nbclient-0.10.2 nbformat-5.10.4 nest-asyncio-1.6.0 numcodecs-0.16.3 numpy-2.3.4 pandas-2.3.3 parso-0.8.5 partd-1.4.2 pexpect-4.9.0 platformdirs-4.5.0 prompt_toolkit-3.0.52 psutil-7.1.2 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.15.4 python-dateutil-2.9.0.post0 pytz-2025.2 pyyaml-6.0.3 pyzmq-27.1.0 referencing-0.37.0 requests-2.32.4 rpds-py-0.28.0 ruamel.yaml-0.18.16 ruamel.yaml.clib-0.2.14 scanpydoc-0.15.4 scipy-1.16.2 six-1.17.0 soupsieve-2.8 sphinx-autodoc-typehints-3.5.2 sphinx-book-theme-1.1.4 sphinx-copybutton-0.5.2 sphinx-design-0.6.1 sphinx-issues-5.0.1 sphinx-jinja2-compat-0.4.1 sphinx-prompt-1.10.1 sphinx-tabs-3.4.5 sphinx-toolbox-4.0.0 sphinxext-opengraph-0.13.0 sqlalchemy-2.0.44 stack_data-0.6.3 standard-imghdr-3.10.14 tabulate-0.9.0 toolz-1.1.0 tornado-6.5.2 towncrier-25.8.0 traitlets-5.14.3 typing-extensions-4.15.0 tzdata-2025.2 wcwidth-0.2.14 webencodings-0.5.1 zarr-3.1.3 zipp-3.23.0 [rtd-command-info] start-time: 2025-10-28T15:40:56.738783Z, end-time: 2025-10-28T15:40:57.070771Z, 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/2158.fix.md Done! [rtd-command-info] start-time: 2025-10-28T15:40:57.162633Z, end-time: 2025-10-28T15:40:57.206256Z, duration: 0, exit-code: 0 cat docs/conf.py from __future__ import annotations import sys from datetime import datetime from functools import partial from importlib import metadata from pathlib import Path, PurePosixPath from typing import TYPE_CHECKING from docutils import nodes if TYPE_CHECKING: from sphinx.application import Sphinx HERE = Path(__file__).parent _extension_dir = HERE / "extensions" sys.path[:0] = [str(_extension_dir)] # -- General configuration ------------------------------------------------ # General information project = "anndata" author = f"{project} developers" copyright = f"{datetime.now():%Y}, scverse" release = version = metadata.version("anndata") # default settings templates_path = ["_templates"] html_static_path = ["_static"] source_suffix = {".rst": "restructuredtext", ".md": "myst-nb"} master_doc = "index" default_role = "literal" exclude_patterns = [ "_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints", "tutorials/notebooks/*.rst", # exclude all 0.x.y.md files, but not index.md "release-notes/[!i]*.md", "news.md", # is `include`d into index.md ] pygments_style = "sphinx" extensions = [ "myst_nb", "sphinx_copybutton", "sphinx.ext.autodoc", "sphinx.ext.intersphinx", "sphinx.ext.doctest", "sphinx.ext.coverage", "sphinx.ext.mathjax", "sphinx.ext.napoleon", "sphinx.ext.autosummary", "sphinx_autodoc_typehints", # needs to be after napoleon "sphinx_issues", "sphinx_design", "sphinxext.opengraph", "scanpydoc", # needs to be before linkcode "sphinx.ext.linkcode", "IPython.sphinxext.ipython_console_highlighting", "sphinx_toolbox.more_autodoc.autoprotocol", *(p.stem for p in _extension_dir.glob("*.py")), ] myst_enable_extensions = [ "html_image", # So README.md can be used on github and sphinx docs "colon_fence", "dollarmath", ] myst_heading_anchors = 3 nb_execution_mode = "off" # Generate the API documentation when building autosummary_generate = True autodoc_member_order = "bysource" autodoc_mock_imports = ["torch"] # autodoc_default_flags = ['members'] issues_github_path = "scverse/anndata" rtd_links_prefix = PurePosixPath("src") napoleon_google_docstring = False napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_use_rtype = True # having a separate entry generally helps readability napoleon_use_param = True napoleon_custom_sections = [("Params", "Parameters")] typehints_defaults = "braces" todo_include_todos = False nitpicky = True # Report broken links nitpick_ignore = [ # APIs without an intersphinx entry # This API isn’t actually documented ("py:class", "anndata._core.raw.Raw"), # TODO: remove zappy support; the zappy repo is archived ("py:class", "anndata.compat.ZappyArray"), # TODO: remove once https://github.com/sphinx-doc/sphinx/pull/13508 is released ("py:class", "anndata.typing.TypeAliasType"), ("py:class", "anndata._types.TypeAliasType"), ("py:class", "anndata._io.specs.registry.TypeAliasType"), ] def setup(app: Sphinx): app.add_generic_role("small", partial(nodes.inline, classes=["small"])) app.add_generic_role("smaller", partial(nodes.inline, classes=["smaller"])) # TODO: move to scanpydoc if TYPE_CHECKING: from docutils.nodes import TextElement, reference from sphinx.addnodes import pending_xref from sphinx.environment import BuildEnvironment def res( app: Sphinx, env: BuildEnvironment, node: pending_xref, contnode: TextElement ) -> reference | None: return env.domains["py"].resolve_xref( env, node["refdoc"], app.builder, node["reftype"], node["reftarget"], node, contnode, ) app.connect("missing-reference", res, priority=502) intersphinx_mapping = dict( awkward=("https://awkward-array.org/doc/stable", None), cupy=("https://docs.cupy.dev/en/stable", None), dask=("https://docs.dask.org/en/stable", None), fsspec=("https://filesystem-spec.readthedocs.io/en/stable/", None), h5py=("https://docs.h5py.org/en/latest", None), hdf5plugin=("https://hdf5plugin.readthedocs.io/en/latest", None), kvikio=("https://docs.rapids.ai/api/kvikio/stable/", None), loompy=("https://linnarssonlab.org/loompy", None), numpy=("https://numpy.org/doc/stable", None), obstore=("https://developmentseed.org/obstore/latest/", None), pandas=("https://pandas.pydata.org/pandas-docs/stable", None), # TODO: switch to `/3` once docs are built with Python 3.14 python=("https://docs.python.org/3.13", None), scipy=("https://docs.scipy.org/doc/scipy", None), sklearn=("https://scikit-learn.org/stable", None), xarray=("https://docs.xarray.dev/en/stable", None), zarr=("https://zarr.readthedocs.io/en/stable/", None), zarrs=("https://zarrs-python.readthedocs.io/en/stable/", None), ) qualname_overrides = { "h5py._hl.group.Group": "h5py.Group", "h5py._hl.files.File": "h5py.File", "h5py._hl.dataset.Dataset": "h5py.Dataset", "anndata._core.anndata.AnnData": "anndata.AnnData", **{ f"anndata._core.aligned_mapping.{cls}{kind}": "collections.abc.Mapping" for cls in ["Layers", "AxisArrays", "PairwiseArrays"] for kind in ["", "View"] }, "anndata._types.ReadCallback": "anndata.experimental.ReadCallback", "anndata._types.WriteCallback": "anndata.experimental.WriteCallback", "anndata._types.Read": "anndata.experimental.Read", "anndata._types.Write": "anndata.experimental.Write", "anndata._types.Dataset2DIlocIndexer": "anndata.experimental.Dataset2DIlocIndexer", "zarr.core.array.Array": "zarr.Array", "zarr.core.group.Group": "zarr.Group", # Buffer is not yet exported, so the buffer class registry is the closest thing "zarr.core.buffer.core.Buffer": "zarr.registry.Registry", "zarr.storage._common.StorePath": "zarr.storage.StorePath", "anndata.compat.DaskArray": "dask.array.Array", "anndata.compat.CupyArray": "cupy.ndarray", "anndata.compat.CupySparseMatrix": "cupyx.scipy.sparse.spmatrix", "anndata.compat.XDataArray": "xarray.DataArray", "anndata.compat.XDataset": "xarray.Dataset", "awkward.highlevel.Array": "ak.Array", "numpy.int64": ("py:attr", "numpy.int64"), "pandas.DataFrame.iloc": ("py:attr", "pandas.DataFrame.iloc"), "pandas.DataFrame.loc": ("py:attr", "pandas.DataFrame.loc"), # should be fixed soon: https://github.com/tox-dev/sphinx-autodoc-typehints/pull/516 "types.EllipsisType": ("py:data", "types.EllipsisType"), "pathlib._local.Path": "pathlib.Path", } autodoc_type_aliases = dict( NDArray=":data:`~numpy.typing.NDArray`", AxisStorable=":data:`~anndata.typing.AxisStorable`", ) # -- 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: None, end-time: None, duration: None, exit-code: None python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html