Read the Docs build information Build id: 4389379 Project: icb-anndata Version: 2529 Commit: d39cf2547049e0232f7ee76975b5288b9ce404fc Date: 2026-09-01T20:38:02.672954Z State: finished Success: False [rtd-command-info] start-time: 2026-09-01T20:38:03.415595Z, end-time: 2026-09-01T20:38:04.191597Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/scverse/anndata.git . Cloning into '.'... [rtd-command-info] start-time: 2026-09-01T20:38:04.281505Z, end-time: 2026-09-01T20:38:05.633750Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/2529/head:external-2529 From https://github.com/scverse/anndata * [new ref] refs/pull/2529/head -> external-2529 * [new tag] 0.13.0 -> 0.13.0 * [new tag] 0.13.0rc1 -> 0.13.0rc1 * [new tag] 0.13.0rc2 -> 0.13.0rc2 * [new tag] 0.13.0rc3 -> 0.13.0rc3 [rtd-command-info] start-time: 2026-09-01T20:38:06.456912Z, end-time: 2026-09-01T20:38:06.526161Z, duration: 0, exit-code: 0 git checkout --force d39cf2547049e0232f7ee76975b5288b9ce404fc Note: switching to 'd39cf2547049e0232f7ee76975b5288b9ce404fc'. 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 d39cf25 Merge branch 'main' into ig/zarr_fused [rtd-command-info] start-time: 2026-09-01T20:38:06.604936Z, end-time: 2026-09-01T20:38:06.640576Z, duration: 0, exit-code: 0 cat .readthedocs.yml # https://docs.readthedocs.io/en/stable/config-file/v2.html version: 2 build: os: ubuntu-26.04 tools: python: "3.14" jobs: post_checkout: # unshallow so version can be derived from tag - git fetch --unshallow || true create_environment: - asdf plugin add uv - asdf install uv latest - asdf global uv latest pre_build: # run towncrier to preview the next version’s release notes - ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run docs:towncrier build --keep || true build: html: - uvx --from=hatch!=1.18.0 hatch run docs:build -T - mv docs/_build $READTHEDOCS_OUTPUT [rtd-command-info] start-time: 2026-09-01T20:38:06.733321Z, end-time: 2026-09-01T20:38:08.578309Z, 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 * [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] 0.12.0 -> 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] 0.12.15 -> 0.12.15 * [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] 0.6.17 -> 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.dev0 -> 0.9.0.dev0 * [new tag] 0.9.0rc1 -> 0.9.0rc1 [rtd-command-info] start-time: 2026-09-01T20:38:15.826107Z, end-time: 2026-09-01T20:38:15.937139Z, duration: 0, exit-code: 0 asdf global python 3.14.6 [rtd-command-info] start-time: 2026-09-01T20:38:16.559870Z, end-time: 2026-09-01T20:38:19.085513Z, duration: 2, exit-code: 0 asdf plugin add uv updating plugin repository...From https://github.com/asdf-vm/asdf-plugins c0369a1..3715919 master -> origin/master 8f55a19..035221f dependabot/github_actions/actions/checkout-6 -> origin/dependabot/github_actions/actions/checkout-6 26de994..a1633cc dependabot/github_actions/amannn/action-semantic-pull-request-6.1.1 -> origin/dependabot/github_actions/amannn/action-semantic-pull-request-6.1.1 * [new branch] tb/remove-deleted-plugins -> origin/tb/remove-deleted-plugins HEAD is now at 3715919 feat: add elp plugin (#1089) [rtd-command-info] start-time: 2026-09-01T20:38:19.160225Z, end-time: 2026-09-01T20:38:20.221039Z, duration: 1, exit-code: 0 asdf install uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.12.8 * Downloading uv release 0.12.8... uv 0.12.8 installation was successful! [rtd-command-info] start-time: 2026-09-01T20:38:20.304567Z, end-time: 2026-09-01T20:38:20.426509Z, duration: 0, exit-code: 0 asdf global uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.12.8 [rtd-command-info] start-time: 2026-09-01T20:38:20.557142Z, end-time: 2026-09-01T20:38:27.082349Z, duration: 6, exit-code: 0 ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run docs:towncrier build --keep || true Downloading cryptography (4.5MiB) Downloading uv (19.1MiB) Downloading virtualenv (5.1MiB) Downloading pygments (1.2MiB) Downloaded virtualenv Downloaded uv Downloaded cryptography Downloaded pygments Installed 42 packages in 53ms Creating environment: docs Installing project in development mode Checking dependencies Syncing dependencies 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/2529/docs/release-notes/2577.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2529/docs/release-notes/2577.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2529/docs/release-notes/2538.docs.md /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2529/docs/release-notes/2577.chore.md Done! [rtd-command-info] start-time: 2026-09-01T20:38:27.158662Z, end-time: 2026-09-01T20:38:37.755336Z, duration: 10, exit-code: 1 uvx --from=hatch!=1.18.0 hatch run docs:build -T Installed 42 packages in 19ms 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={'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, 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/2529/docs/_build/.jupyter_cache loading intersphinx inventory 'array_api' from https://array-api.readthedocs.io/en/stable/objects.inv ... 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/objects.inv ... loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv ... loading intersphinx inventory 'scverse_misc' from https://scverse-misc.readthedocs.io/stable/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 'annbatch' from https://annbatch.readthedocs.io/en/stable/objects.inv ... loading intersphinx inventory 'zarrs' from https://zarrs-python.readthedocs.io/en/stable/objects.inv ... loading intersphinx inventory 'mudata' from https://mudata.readthedocs.io/stable/objects.inv ... [autosummary] generating autosummary for: _key_contributors.rst, accessors.rst, api.md, contributing.md, fileformat-prose.md, generated/anndata.types.ExtensionNamespace.rst, index.md, interoperability.md, references.rst, release-notes/index.md, ..., tutorials/index.md, tutorials/notebooks/annbatch.ipynb, tutorials/notebooks/anncollection.ipynb, tutorials/notebooks/anndata_dask_array.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, typing.md + Exception Group Traceback (most recent call last): | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/ext/autosummary/generate.py", line 664, in generate_autosummary_docs | name, obj, parent, modname = import_by_name(entry.name) | ~~~~~~~~~~~~~~^^^^^^^^^^^^ | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/ext/autosummary/__init__.py", line 682, in import_by_name | raise ImportExceptionGroup(msg, exceptions) | sphinx.ext.autosummary.ImportExceptionGroup: could not import anndata.AnnData (4 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/ext/autodoc/_dynamic/_importer.py", line 221, in _import_module | module = importlib.import_module(modname) | File "/home/docs/.asdf/installs/python/3.14.6/lib/python3.14/importlib/__init__.py", line 88, in import_module | return _bootstrap._gcd_import(name[level:], package, level) | ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "", line 1406, 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 759, in exec_module | File "", line 491, in _call_with_frames_removed | File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2529/src/anndata/__init__.py", line 35, in | if "Batched" in old_pipeline and Version(version("zarr")) >= Version("3.3"): | ^^^^^^^ | NameError: name 'Version' is not defined +---------------- 2 ---------------- | Traceback (most recent call last): | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/ext/autodoc/_dynamic/_importer.py", line 215, in _import_module | spec = find_spec(modname) | File "", line 90, in find_spec | File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2529/src/anndata/__init__.py", line 35, in | if "Batched" in old_pipeline and Version(version("zarr")) >= Version("3.3"): | ^^^^^^^ | NameError: name 'Version' is not defined +---------------- 3 ---------------- | Traceback (most recent call last): | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/ext/autodoc/_dynamic/_importer.py", line 221, in _import_module | module = importlib.import_module(modname) | File "/home/docs/.asdf/installs/python/3.14.6/lib/python3.14/importlib/__init__.py", line 88, in import_module | return _bootstrap._gcd_import(name[level:], package, level) | ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "", line 1406, 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 759, in exec_module | File "", line 491, in _call_with_frames_removed | File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2529/src/anndata/__init__.py", line 35, in | if "Batched" in old_pipeline and Version(version("zarr")) >= Version("3.3"): | ^^^^^^^ | NameError: name 'Version' is not defined +---------------- 4 ---------------- | Traceback (most recent call last): | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/ext/autosummary/__init__.py", line 717, in _import_by_name | obj = sys.modules[modname] | ~~~~~~~~~~~^^^^^^^^^ | KeyError: 'anndata' +------------------------------------ During handling of the above exception, another exception occurred: + Exception Group Traceback (most recent call last): | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/bin/sphinx-build", line 10, in | sys.exit(main()) | ~~~~^^ | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/cmd/build.py", line 491, in main | return make_mode.run_make_mode(argv[1:]) | ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^ | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/cmd/make_mode.py", line 223, in run_make_mode | return make.run_generic_build(builder_name) | ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^ | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/cmd/make_mode.py", line 206, in run_generic_build | return build_main(args + self.opts) | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/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/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/application.py", line 340, in __init__ | self._init_builder() | ~~~~~~~~~~~~~~~~~~^^ | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/application.py", line 430, in _init_builder | self.events.emit('builder-inited') | ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/events.py", line 441, in emit | results.append(listener.handler(self._app, *args)) | ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/ext/autosummary/__init__.py", line 870, in process_generate_options | generate_autosummary_docs( | ~~~~~~~~~~~~~~~~~~~~~~~~~^ | genfiles, | ^^^^^^^^^ | ...<5 lines>... | encoding=app.config.source_encoding, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ) | ^ | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/ext/autosummary/generate.py", line 669, in generate_autosummary_docs | name, obj, parent, modname = import_ivar_by_name(entry.name) | ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/ext/autosummary/__init__.py", line 740, in import_ivar_by_name | real_name, obj, _parent, modname = import_by_name(name, prefixes) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^ | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/ext/autosummary/__init__.py", line 682, in import_by_name | raise ImportExceptionGroup(msg, exceptions) | sphinx.ext.autosummary.ImportExceptionGroup: could not import anndata (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/ext/autodoc/_dynamic/_importer.py", line 221, in _import_module | module = importlib.import_module(modname) | File "/home/docs/.asdf/installs/python/3.14.6/lib/python3.14/importlib/__init__.py", line 88, in import_module | return _bootstrap._gcd_import(name[level:], package, level) | ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "", line 1406, 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 759, in exec_module | File "", line 491, in _call_with_frames_removed | File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/2529/src/anndata/__init__.py", line 35, in | if "Batched" in old_pipeline and Version(version("zarr")) >= Version("3.3"): | ^^^^^^^ | NameError: name 'Version' is not defined +---------------- 2 ---------------- | Traceback (most recent call last): | File "/home/docs/.local/share/hatch/env/virtual/anndata/pqXiNqb9/docs/lib/python3.14/site-packages/sphinx/ext/autosummary/__init__.py", line 723, in _import_by_name | return sys.modules[modname], None, modname | ~~~~~~~~~~~^^^^^^^^^ | KeyError: 'anndata' +------------------------------------