Read the Docs build information Build id: 3704288 Project: icb-anndata Version: latest Commit: bc5cdc199b59d92c0c9dc7a7b674b1ef31c18bb2 Date: 2026-01-29T12:40:37.312505Z State: finished Success: True [rtd-command-info] start-time: 2026-01-29T12:40:38.582986Z, end-time: 2026-01-29T12:40:39.102561Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/scverse/anndata.git . Cloning into '.'... [rtd-command-info] start-time: 2026-01-29T12:40:39.329544Z, end-time: 2026-01-29T12:40:40.419398Z, 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] 0.12.8 -> 0.12.8 * [new tag] 0.12.9 -> 0.12.9 * [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: 2026-01-29T12:40:41.238546Z, end-time: 2026-01-29T12:40:41.269342Z, duration: 0, exit-code: 0 cat .readthedocs.yml # https://docs.readthedocs.io/en/stable/config-file/v2.html 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 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 . ) && towncrier build --keep || true build: html: - uvx hatch run docs:build - mv docs/_build $READTHEDOCS_OUTPUT submodules: include: - "docs/tutorials/notebooks" recursive: true [rtd-command-info] start-time: 2026-01-29T12:40:41.523085Z, end-time: 2026-01-29T12:40:41.685777Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2026-01-29T12:40:41.877982Z, end-time: 2026-01-29T12:40:42.570630Z, 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'... Submodule path 'docs/tutorials/notebooks': checked out '0d8ffb2dc4a53de9762f76ed9030114d8aced353' [rtd-command-info] start-time: 2026-01-29T12:40:42.780227Z, end-time: 2026-01-29T12:40:43.680332Z, duration: 0, exit-code: 0 git fetch --unshallow || true [rtd-command-info] start-time: 2026-01-29T12:40:48.326829Z, end-time: 2026-01-29T12:40:48.372772Z, duration: 0, exit-code: 0 asdf global python 3.14.0 [rtd-command-info] start-time: 2026-01-29T12:40:48.797411Z, end-time: 2026-01-29T12:40:50.931221Z, duration: 2, exit-code: 0 asdf plugin add uv updating plugin repository...From https://github.com/asdf-vm/asdf-plugins 8e311ee..c0369a1 master -> origin/master * [new branch] dependabot/github_actions/actions/checkout-6 -> origin/dependabot/github_actions/actions/checkout-6 * [new branch] 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] dependabot/github_actions/asdf-vm/actions-4 -> origin/dependabot/github_actions/asdf-vm/actions-4 HEAD is now at c0369a1 feat: add yasm plugin (#1087) [rtd-command-info] start-time: 2026-01-29T12:40:51.107001Z, end-time: 2026-01-29T12:40:52.095823Z, duration: 0, exit-code: 0 asdf install uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.9.27 * Downloading uv release 0.9.27... uv 0.9.27 installation was successful! [rtd-command-info] start-time: 2026-01-29T12:40:52.283073Z, end-time: 2026-01-29T12:40:52.381769Z, duration: 0, exit-code: 0 asdf global uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.9.27 [rtd-command-info] start-time: 2026-01-29T12:40:52.763757Z, end-time: 2026-01-29T12:40:52.797385Z, duration: 0, exit-code: 0 ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true /bin/sh: 1: towncrier: not found [rtd-command-info] start-time: 2026-01-29T12:40:52.999539Z, end-time: 2026-01-29T12:41:18.287365Z, duration: 25, exit-code: 0 uvx hatch run docs:build Downloading virtualenv (5.7MiB) Downloading cryptography (4.2MiB) Downloading pygments (1.2MiB) Downloading uv (21.7MiB) Downloaded uv Downloaded cryptography Downloaded virtualenv Downloaded pygments Installed 40 packages in 81ms Creating environment: docs Installing project in development mode Checking dependencies Syncing dependencies Running Sphinx v9.1.0 loading translations [en]... done matplotlib is not installed, social cards will not be generated making output directory... done myst v5.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'colon_fence', 'html_image', '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/docs/_build/.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/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.AnnCollection.attrs_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.convert.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.has_backed.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.lazy_attr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.n_obs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.n_vars.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.obs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.obsm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.shape.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.to_adata.rst building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 21 source files that are out of date updating environment: [new config] 111 added, 0 changed, 0 removed reading sources... [ 1%] _key_contributors reading sources... [ 2%] api /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config reading sources... [ 3%] benchmark-read-write /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:180: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. path = self.env.docname.split("/") reading sources... [ 4%] benchmarks /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config reading sources... [ 5%] concatenation reading sources... [ 5%] contributing /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config reading sources... [ 6%] fileformat-prose /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config reading sources... [ 7%] generated/anndata.AnnData reading sources... [ 8%] generated/anndata.AnnData.T reading sources... [ 9%] generated/anndata.AnnData.X reading sources... [ 10%] generated/anndata.AnnData.chunk_X reading sources... [ 11%] generated/anndata.AnnData.chunked_X reading sources... [ 12%] generated/anndata.AnnData.concatenate reading sources... [ 13%] generated/anndata.AnnData.copy reading sources... [ 14%] generated/anndata.AnnData.filename reading sources... [ 14%] generated/anndata.AnnData.is_view reading sources... [ 15%] generated/anndata.AnnData.isbacked reading sources... [ 16%] generated/anndata.AnnData.layers reading sources... [ 17%] generated/anndata.AnnData.n_obs reading sources... [ 18%] generated/anndata.AnnData.n_vars reading sources... [ 19%] generated/anndata.AnnData.obs reading sources... [ 20%] generated/anndata.AnnData.obs_names reading sources... [ 21%] generated/anndata.AnnData.obs_names_make_unique reading sources... [ 22%] generated/anndata.AnnData.obs_vector reading sources... [ 23%] generated/anndata.AnnData.obsm reading sources... [ 23%] generated/anndata.AnnData.obsp reading sources... [ 24%] generated/anndata.AnnData.raw reading sources... [ 25%] generated/anndata.AnnData.rename_categories reading sources... [ 26%] generated/anndata.AnnData.shape reading sources... [ 27%] generated/anndata.AnnData.strings_to_categoricals reading sources... [ 28%] generated/anndata.AnnData.to_df reading sources... [ 29%] generated/anndata.AnnData.to_memory reading sources... [ 30%] generated/anndata.AnnData.transpose reading sources... [ 31%] generated/anndata.AnnData.uns reading sources... [ 32%] generated/anndata.AnnData.var reading sources... [ 32%] generated/anndata.AnnData.var_names reading sources... [ 33%] generated/anndata.AnnData.var_names_make_unique reading sources... [ 34%] generated/anndata.AnnData.var_vector reading sources... [ 35%] generated/anndata.AnnData.varm reading sources... [ 36%] generated/anndata.AnnData.varp reading sources... [ 37%] generated/anndata.AnnData.write reading sources... [ 38%] generated/anndata.AnnData.write_csvs reading sources... [ 39%] generated/anndata.AnnData.write_h5ad reading sources... [ 40%] generated/anndata.AnnData.write_loom reading sources... [ 41%] generated/anndata.AnnData.write_zarr reading sources... [ 41%] generated/anndata.ImplicitModificationWarning reading sources... [ 42%] generated/anndata.abc.CSCDataset reading sources... [ 43%] generated/anndata.abc.CSRDataset reading sources... [ 44%] generated/anndata.concat reading sources... [ 45%] generated/anndata.experimental.AnnCollection reading sources... [ 46%] generated/anndata.experimental.AnnCollection.attrs_keys reading sources... [ 47%] generated/anndata.experimental.AnnCollection.convert reading sources... [ 48%] generated/anndata.experimental.AnnCollection.has_backed reading sources... [ 49%] generated/anndata.experimental.AnnCollection.lazy_attr reading sources... [ 50%] generated/anndata.experimental.AnnCollection.n_obs reading sources... [ 50%] generated/anndata.experimental.AnnCollection.n_vars reading sources... [ 51%] generated/anndata.experimental.AnnCollection.obs reading sources... [ 52%] generated/anndata.experimental.AnnCollection.obsm reading sources... [ 53%] generated/anndata.experimental.AnnCollection.shape reading sources... [ 54%] generated/anndata.experimental.AnnCollection.to_adata reading sources... [ 55%] generated/anndata.experimental.AnnLoader reading sources... [ 56%] generated/anndata.experimental.Dataset2DIlocIndexer reading sources... [ 57%] generated/anndata.experimental.IOSpec reading sources... [ 58%] generated/anndata.experimental.Read reading sources... [ 59%] generated/anndata.experimental.ReadCallback reading sources... [ 59%] generated/anndata.experimental.StorageType reading sources... [ 60%] generated/anndata.experimental.Write reading sources... [ 61%] generated/anndata.experimental.WriteCallback reading sources... [ 62%] generated/anndata.experimental.backed.CategoricalArray reading sources... [ 63%] generated/anndata.experimental.backed.Dataset2D reading sources... [ 64%] generated/anndata.experimental.backed.MaskedArray reading sources... [ 65%] generated/anndata.experimental.concat_on_disk reading sources... [ 66%] generated/anndata.experimental.read_dispatched reading sources... [ 67%] generated/anndata.experimental.read_elem_lazy reading sources... [ 68%] generated/anndata.experimental.read_lazy reading sources... [ 68%] generated/anndata.experimental.write_dispatched reading sources... [ 69%] generated/anndata.io.read_csv reading sources... [ 70%] generated/anndata.io.read_elem reading sources... [ 71%] generated/anndata.io.read_excel reading sources... [ 72%] generated/anndata.io.read_h5ad reading sources... [ 73%] generated/anndata.io.read_hdf reading sources... [ 74%] generated/anndata.io.read_loom reading sources... [ 75%] generated/anndata.io.read_mtx reading sources... [ 76%] generated/anndata.io.read_text reading sources... [ 77%] generated/anndata.io.read_umi_tools reading sources... [ 77%] generated/anndata.io.read_zarr reading sources... [ 78%] generated/anndata.io.sparse_dataset reading sources... [ 79%] generated/anndata.io.write_elem reading sources... [ 80%] generated/anndata.io.write_h5ad reading sources... [ 81%] generated/anndata.io.write_zarr reading sources... [ 82%] generated/anndata.register_anndata_namespace reading sources... [ 83%] generated/anndata.settings reading sources... [ 84%] generated/anndata.settings.override reading sources... [ 85%] generated/anndata.types.ExtensionNamespace reading sources... [ 86%] generated/anndata.typing.AxisStorable reading sources... [ 86%] generated/anndata.typing.Index reading sources... [ 87%] generated/anndata.typing.RWAble reading sources... [ 88%] index /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config reading sources... [ 89%] interoperability /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config reading sources... [ 90%] references reading sources... [ 91%] release-notes/index /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config reading sources... [ 92%] tutorials/index /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config reading sources... [ 93%] tutorials/notebooks/anncollection /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:180: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. path = self.env.docname.split("/") reading sources... [ 94%] tutorials/notebooks/anncollection-annloader /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:180: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. path = self.env.docname.split("/") reading sources... [ 95%] tutorials/notebooks/anndata_dask_array /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:180: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. path = self.env.docname.split("/") reading sources... [ 95%] tutorials/notebooks/annloader /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:180: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. path = self.env.docname.split("/") reading sources... [ 96%] tutorials/notebooks/awkward-arrays /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:180: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. path = self.env.docname.split("/") reading sources... [ 97%] tutorials/notebooks/getting-started /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:180: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. path = self.env.docname.split("/") reading sources... [ 98%] tutorials/notebooks/read_lazy /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:180: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. path = self.env.docname.split("/") reading sources... [ 99%] tutorials/notebooks/{read,write}_dispatched /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:180: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. path = self.env.docname.split("/") reading sources... [100%] tutorials/zarr-v3 /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:73: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. assert self.env is not None, "env not set" /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:74: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. document_path = self.env.doc2path(self.env.docname) /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:80: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. md_config: MdParserConfig = self.env.myst_config /home/docs/.local/share/hatch/env/virtual/anndata/l25kgEpZ/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py:83: RemovedInSphinx10Warning: 'myst_nb.sphinx_.Parser.env' is deprecated. Check CHANGES for Sphinx API modifications. nb_config: NbParserConfig = self.env.mystnb_config 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/docs/_build/html/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/_build/html/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/_build/html/_static/documentation_options.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/_build/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... [ 2%] api writing output... [ 3%] benchmark-read-write writing output... [ 4%] benchmarks writing output... [ 5%] concatenation writing output... [ 5%] contributing writing output... [ 6%] fileformat-prose writing output... [ 7%] generated/anndata.AnnData writing output... [ 8%] generated/anndata.AnnData.T writing output... [ 9%] generated/anndata.AnnData.X writing output... [ 10%] generated/anndata.AnnData.chunk_X writing output... [ 11%] generated/anndata.AnnData.chunked_X writing output... [ 12%] generated/anndata.AnnData.concatenate writing output... [ 13%] generated/anndata.AnnData.copy writing output... [ 14%] generated/anndata.AnnData.filename writing output... [ 14%] generated/anndata.AnnData.is_view writing output... [ 15%] generated/anndata.AnnData.isbacked writing output... [ 16%] generated/anndata.AnnData.layers writing output... [ 17%] generated/anndata.AnnData.n_obs writing output... [ 18%] generated/anndata.AnnData.n_vars writing output... [ 19%] generated/anndata.AnnData.obs writing output... [ 20%] generated/anndata.AnnData.obs_names writing output... [ 21%] generated/anndata.AnnData.obs_names_make_unique writing output... [ 22%] generated/anndata.AnnData.obs_vector writing output... [ 23%] generated/anndata.AnnData.obsm writing output... [ 23%] generated/anndata.AnnData.obsp writing output... [ 24%] generated/anndata.AnnData.raw writing output... [ 25%] generated/anndata.AnnData.rename_categories writing output... [ 26%] generated/anndata.AnnData.shape writing output... [ 27%] generated/anndata.AnnData.strings_to_categoricals writing output... [ 28%] generated/anndata.AnnData.to_df writing output... [ 29%] generated/anndata.AnnData.to_memory writing output... [ 30%] generated/anndata.AnnData.transpose writing output... [ 31%] generated/anndata.AnnData.uns writing output... [ 32%] generated/anndata.AnnData.var writing output... [ 32%] generated/anndata.AnnData.var_names writing output... [ 33%] generated/anndata.AnnData.var_names_make_unique writing output... [ 34%] generated/anndata.AnnData.var_vector writing output... [ 35%] generated/anndata.AnnData.varm writing output... [ 36%] generated/anndata.AnnData.varp writing output... [ 37%] generated/anndata.AnnData.write writing output... [ 38%] generated/anndata.AnnData.write_csvs writing output... [ 39%] generated/anndata.AnnData.write_h5ad writing output... [ 40%] generated/anndata.AnnData.write_loom writing output... [ 41%] generated/anndata.AnnData.write_zarr writing output... [ 41%] generated/anndata.ImplicitModificationWarning writing output... [ 42%] generated/anndata.abc.CSCDataset writing output... [ 43%] generated/anndata.abc.CSRDataset writing output... [ 44%] generated/anndata.concat writing output... [ 45%] generated/anndata.experimental.AnnCollection writing output... [ 46%] generated/anndata.experimental.AnnCollection.attrs_keys writing output... [ 47%] generated/anndata.experimental.AnnCollection.convert writing output... [ 48%] generated/anndata.experimental.AnnCollection.has_backed writing output... [ 49%] generated/anndata.experimental.AnnCollection.lazy_attr writing output... [ 50%] generated/anndata.experimental.AnnCollection.n_obs writing output... [ 50%] generated/anndata.experimental.AnnCollection.n_vars writing output... [ 51%] generated/anndata.experimental.AnnCollection.obs writing output... [ 52%] generated/anndata.experimental.AnnCollection.obsm writing output... [ 53%] generated/anndata.experimental.AnnCollection.shape writing output... [ 54%] generated/anndata.experimental.AnnCollection.to_adata writing output... [ 55%] generated/anndata.experimental.AnnLoader writing output... [ 56%] generated/anndata.experimental.Dataset2DIlocIndexer writing output... [ 57%] generated/anndata.experimental.IOSpec writing output... [ 58%] generated/anndata.experimental.Read writing output... [ 59%] generated/anndata.experimental.ReadCallback writing output... [ 59%] generated/anndata.experimental.StorageType writing output... [ 60%] generated/anndata.experimental.Write writing output... [ 61%] generated/anndata.experimental.WriteCallback writing output... [ 62%] generated/anndata.experimental.backed.CategoricalArray writing output... [ 63%] generated/anndata.experimental.backed.Dataset2D writing output... [ 64%] generated/anndata.experimental.backed.MaskedArray writing output... [ 65%] generated/anndata.experimental.concat_on_disk writing output... [ 66%] generated/anndata.experimental.read_dispatched writing output... [ 67%] generated/anndata.experimental.read_elem_lazy writing output... [ 68%] generated/anndata.experimental.read_lazy writing output... [ 68%] generated/anndata.experimental.write_dispatched writing output... [ 69%] generated/anndata.io.read_csv writing output... [ 70%] generated/anndata.io.read_elem writing output... [ 71%] generated/anndata.io.read_excel writing output... [ 72%] generated/anndata.io.read_h5ad writing output... [ 73%] generated/anndata.io.read_hdf writing output... [ 74%] generated/anndata.io.read_loom writing output... [ 75%] generated/anndata.io.read_mtx writing output... [ 76%] generated/anndata.io.read_text writing output... [ 77%] generated/anndata.io.read_umi_tools writing output... [ 77%] generated/anndata.io.read_zarr writing output... [ 78%] generated/anndata.io.sparse_dataset writing output... [ 79%] generated/anndata.io.write_elem writing output... [ 80%] generated/anndata.io.write_h5ad writing output... [ 81%] generated/anndata.io.write_zarr writing output... [ 82%] generated/anndata.register_anndata_namespace writing output... [ 83%] generated/anndata.settings writing output... [ 84%] generated/anndata.settings.override writing output... [ 85%] generated/anndata.types.ExtensionNamespace writing output... [ 86%] generated/anndata.typing.AxisStorable writing output... [ 86%] generated/anndata.typing.Index writing output... [ 87%] generated/anndata.typing.RWAble writing output... [ 88%] index writing output... [ 89%] interoperability writing output... [ 90%] references writing output... [ 91%] release-notes/index writing output... [ 92%] tutorials/index writing output... [ 93%] tutorials/notebooks/anncollection writing output... [ 94%] tutorials/notebooks/anncollection-annloader writing output... [ 95%] tutorials/notebooks/anndata_dask_array writing output... [ 95%] tutorials/notebooks/annloader writing output... [ 96%] tutorials/notebooks/awkward-arrays writing output... [ 97%] tutorials/notebooks/getting-started writing output... [ 98%] tutorials/notebooks/read_lazy writing output... [ 99%] tutorials/notebooks/{read,write}_dispatched writing output... [100%] tutorials/zarr-v3 generating indices... genindex py-modindex done writing additional pages... search done copying images... [ 7%] _static/img/anndata_schema.svg copying images... [ 13%] _build/jupyter_execute/6f787644a193af699d5d8f7ba77ee8efd989b4a32cfdb05c78b8a2dc977b89e8.png copying images... [ 20%] _build/jupyter_execute/7cbf3095d3b2040b1fe3a23416dbc37d2c50fd634afaf8f7aae3f1dbd0fec679.png copying images... [ 27%] tutorials/notebooks/_static/semisup_cvae.jpg copying images... [ 33%] _build/jupyter_execute/db92a59f25afcf1264f77bd0a38b5877e0b1d1438381931d2746157cd19d064f.png copying images... [ 40%] _build/jupyter_execute/9b9bd721eb3494ffe24174a5772abe9efaea9447ff2659ffd16b1483a85bedd2.png copying images... [ 47%] _build/jupyter_execute/e5650eec3a30dd58abcdb33f33c5dc93c1dee8e9e120cbb0e52aea849b75f498.png copying images... [ 53%] _build/jupyter_execute/93cef0c495665cc632acf437237e77d875a47d45bae143a3180962706ae5bc69.png copying images... [ 60%] _build/jupyter_execute/f1cd16e5436948dd1ec690ca5209004f78fbe5cafbdcaa58c49913868ea6dd0e.png copying images... [ 67%] _build/jupyter_execute/ca5b1c0712b1bc35714458bb9880dd12787013880083843a6d9e87c324a76a05.png copying images... [ 73%] tutorials/notebooks/_static/sup_cvae.jpg copying images... [ 80%] _build/jupyter_execute/b7a65145d48ac22f5832741fd20807d5041232c3850aa275a14a0991b103619d.png copying images... [ 87%] _build/jupyter_execute/7fdb31a8e84ad3126331186ad694efa5cbe5771c9ed4d50ffd5a96f5bf3ce6e9.png copying images... [ 93%] _build/jupyter_execute/67c0e73df6de3643bf564af68a80ffca6ae84a4cd6e29271f889c33e46742ea9.png copying images... [100%] _build/jupyter_execute/4aade5b748bd30e24cde99f1ae3a96cf48183e547bdb794e37fafd43c80078c2.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded. The HTML pages are in docs/_build/html. [rtd-command-info] start-time: 2026-01-29T12:41:18.499538Z, end-time: 2026-01-29T12:41:18.534871Z, duration: 0, exit-code: 0 mv docs/_build $READTHEDOCS_OUTPUT