Read the Docs build information Build id: 4330469 Project: icb-scanpy Version: 3645 Commit: e0ac683f23744a13d2309fab4213e67b441460f3 Date: 2026-08-18T14:06:15.846081Z State: finished Success: False [rtd-command-info] start-time: 2026-08-18T14:06:16.596428Z, end-time: 2026-08-18T14:06:18.443464Z, duration: 1, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2026-08-18T14:06:18.518249Z, end-time: 2026-08-18T14:06:20.008135Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/3645/head:external-3645 From https://github.com/scverse/scanpy * [new ref] refs/pull/3645/head -> external-3645 * [new tag] 1.13.0a1 -> 1.13.0a1 [rtd-command-info] start-time: 2026-08-18T14:06:20.778251Z, end-time: 2026-08-18T14:06:21.153264Z, duration: 0, exit-code: 0 git checkout --force e0ac683f23744a13d2309fab4213e67b441460f3 Note: switching to 'e0ac683f23744a13d2309fab4213e67b441460f3'. 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 e0ac683 cleanup [rtd-command-info] start-time: 2026-08-18T14:06:21.227033Z, end-time: 2026-08-18T14:06:21.264416Z, 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 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: 2026-08-18T14:06:21.344592Z, end-time: 2026-08-18T14:06:24.092920Z, duration: 2, exit-code: 0 git fetch --unshallow || true From https://github.com/scverse/scanpy * [new tag] 0.0 -> 0.0 * [new tag] 0.1 -> 0.1 * [new tag] 0.2 -> 0.2 * [new tag] 0.2.1 -> 0.2.1 * [new tag] 0.2.3 -> 0.2.3 * [new tag] 0.2.3.5 -> 0.2.3.5 * [new tag] 0.2.4 -> 0.2.4 * [new tag] 0.2.5 -> 0.2.5 * [new tag] 0.2.6 -> 0.2.6 * [new tag] 0.2.7 -> 0.2.7 * [new tag] 0.2.8 -> 0.2.8 * [new tag] 0.2.9 -> 0.2.9 * [new tag] 0.2.9.1 -> 0.2.9.1 * [new tag] 0.3 -> 0.3 * [new tag] 0.3.1 -> 0.3.1 * [new tag] 0.3.2 -> 0.3.2 * [new tag] 0.4 -> 0.4 * [new tag] 0.4.1 -> 0.4.1 * [new tag] 0.4.2 -> 0.4.2 * [new tag] 0.4.2.post1 -> 0.4.2.post1 * [new tag] 0.4.2.post2 -> 0.4.2.post2 * [new tag] 0.4.3 -> 0.4.3 * [new tag] 0.4.4 -> 0.4.4 * [new tag] 1.0 -> 1.0 * [new tag] 1.0.1 -> 1.0.1 * [new tag] 1.0.2 -> 1.0.2 * [new tag] 1.0.3 -> 1.0.3 * [new tag] 1.0.4 -> 1.0.4 * [new tag] 1.1 -> 1.1 * [new tag] 1.10.0.dev0 -> 1.10.0.dev0 * [new tag] 1.10.0rc1 -> 1.10.0rc1 * [new tag] 1.11.0 -> 1.11.0 * [new tag] 1.11.0rc1 -> 1.11.0rc1 * [new tag] 1.11.0rc2 -> 1.11.0rc2 * [new tag] 1.12.0 -> 1.12.0 * [new tag] 1.12.0rc1 -> 1.12.0rc1 * [new tag] 1.1a1 -> 1.1a1 * [new tag] 1.1a2 -> 1.1a2 * [new tag] 1.2.0 -> 1.2.0 * [new tag] 1.2.1 -> 1.2.1 * [new tag] 1.2.2 -> 1.2.2 * [new tag] 1.3 -> 1.3 * [new tag] 1.3.1 -> 1.3.1 * [new tag] 1.3.2 -> 1.3.2 * [new tag] 1.3.3 -> 1.3.3 * [new tag] 1.3.4 -> 1.3.4 * [new tag] 1.3.5 -> 1.3.5 * [new tag] 1.3.6 -> 1.3.6 * [new tag] 1.3.7 -> 1.3.7 * [new tag] 1.3.8 -> 1.3.8 * [new tag] 1.4 -> 1.4 * [new tag] 1.4.1 -> 1.4.1 * [new tag] 1.4.2 -> 1.4.2 * [new tag] 1.4.3 -> 1.4.3 * [new tag] 1.4.4 -> 1.4.4 * [new tag] 1.4.5 -> 1.4.5 * [new tag] 1.4.5.1 -> 1.4.5.1 * [new tag] 1.4.5.post1 -> 1.4.5.post1 * [new tag] 1.4.5.post2 -> 1.4.5.post2 * [new tag] 1.4.5.post3 -> 1.4.5.post3 * [new tag] 1.4.6 -> 1.4.6 * [new tag] 1.5.0 -> 1.5.0 * [new tag] 1.5.0a1 -> 1.5.0a1 * [new tag] 1.5.1 -> 1.5.1 * [new tag] 1.6.0 -> 1.6.0 * [new tag] 1.7.0rc1 -> 1.7.0rc1 * [new tag] 1.8.0 -> 1.8.0 * [new tag] 1.8.0.dev0 -> 1.8.0.dev0 * [new tag] 1.9.0 -> 1.9.0 * [new tag] 1.9.0.dev0 -> 1.9.0.dev0 [rtd-command-info] start-time: 2026-08-18T14:06:28.861459Z, end-time: 2026-08-18T14:06:28.926153Z, duration: 0, exit-code: 0 asdf global python 3.14.6 [rtd-command-info] start-time: 2026-08-18T14:06:29.421946Z, end-time: 2026-08-18T14:06:31.003981Z, duration: 1, 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: 2026-08-18T14:06:31.088042Z, end-time: 2026-08-18T14:06:31.981734Z, duration: 0, exit-code: 0 asdf install uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.12.5 * Downloading uv release 0.12.5... uv 0.12.5 installation was successful! [rtd-command-info] start-time: 2026-08-18T14:06:32.069994Z, end-time: 2026-08-18T14:06:32.176317Z, duration: 0, exit-code: 0 asdf global uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.12.5 [rtd-command-info] start-time: 2026-08-18T14:06:32.333933Z, end-time: 2026-08-18T14:06:38.819472Z, duration: 6, exit-code: 0 ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true Downloading pygments (1.2MiB) Downloading uv (22.6MiB) Downloading cryptography (4.5MiB) Downloading virtualenv (5.1MiB) Downloaded uv Downloaded cryptography Downloaded virtualenv Downloaded pygments Installed 42 packages in 21ms Creating environment: default 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-scanpy/checkouts/3645/docs/release-notes/4260.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/release-notes/4263.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/release-notes/4231.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/release-notes/4232.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/release-notes/4290.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/release-notes/3645.chore.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/release-notes/4252.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/release-notes/4299.chore.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/release-notes/4256.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/release-notes/4269.feat.md Done! [rtd-command-info] start-time: 2026-08-18T14:06:38.896706Z, end-time: 2026-08-18T14:11:12.117932Z, duration: 273, exit-code: 2 uvx --from=hatch!=1.18.0 hatch run docs:build -T Installed 42 packages in 18ms Creating environment: docs Installing project in development mode Checking dependencies Syncing dependencies Running Sphinx v9.1.0 loading translations [en]... done making output directory... done myst v5.1.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'deflist', 'html_image', 'dollarmath', 'amsmath', 'html_admonition', 'colon_fence'}, 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='cache', execution_cache_path='', execution_excludepatterns=['tutorials/*', 'tutorials/*/*', 'tutorials/*/*/*', 'how-to/*', 'how-to/*/*', 'how-to/*/*/*'], execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=True, merge_streams=True, 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-scanpy/checkouts/3645/docs/_build/.jupyter_cache loading intersphinx inventory 'anndata' from https://anndata.scverse.org/en/stable/objects.inv ... loading intersphinx inventory 'cuml' from https://docs.rapids.ai/api/cuml/stable/objects.inv ... loading intersphinx inventory 'bbknn' from https://bbknn.readthedocs.io/en/latest/objects.inv ... loading intersphinx inventory 'cycler' from https://matplotlib.org/cycler/objects.inv ... loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable/objects.inv ... loading intersphinx inventory 'decoupler' from https://decoupler.readthedocs.io/en/stable/objects.inv ... loading intersphinx inventory 'fast_array_utils' from https://fast-array-utils.scverse.org/en/stable/objects.inv ... loading intersphinx inventory 'dask_ml' from https://ml.dask.org/objects.inv ... loading intersphinx inventory 'h5py' from https://docs.h5py.org/en/stable/objects.inv ... loading intersphinx inventory 'holoviews' from https://holoviews.org/objects.inv ... loading intersphinx inventory 'hv_anndata' from https://hv-anndata.readthedocs.io/en/latest/objects.inv ... loading intersphinx inventory 'zarr' from https://zarr.readthedocs.io/en/stable/objects.inv ... loading intersphinx inventory 'ipython' from https://ipython.readthedocs.io/en/stable/objects.inv ... loading intersphinx inventory 'igraph' from https://python.igraph.org/en/stable/api/objects.inv ... loading intersphinx inventory 'leidenalg' from https://leidenalg.readthedocs.io/en/latest/objects.inv ... loading intersphinx inventory 'louvain' from https://louvain-igraph.readthedocs.io/en/latest/objects.inv ... loading intersphinx inventory 'matplotlib' from https://matplotlib.org/stable/objects.inv ... loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv ... loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ... loading intersphinx inventory 'palantir' from https://palantir.readthedocs.io/en/stable/objects.inv ... loading intersphinx inventory 'pandas' from https://pandas.pydata.org/pandas-docs/stable/objects.inv ... loading intersphinx inventory 'pydeseq2' from https://pydeseq2.readthedocs.io/en/stable/objects.inv ... loading intersphinx inventory 'pynndescent' from https://pynndescent.readthedocs.io/en/latest/objects.inv ... loading intersphinx inventory 'pytest' from https://docs.pytest.org/en/latest/objects.inv ... loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ... loading intersphinx inventory 'rapids_singlecell' from https://rapids-singlecell.readthedocs.io/en/latest/objects.inv ... loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv ... loading intersphinx inventory 'seaborn' from https://seaborn.pydata.org/objects.inv ... loading intersphinx inventory 'session_info2' from https://session-info2.readthedocs.io/en/stable/objects.inv ... loading intersphinx inventory 'squidpy' from https://squidpy.readthedocs.io/en/stable/objects.inv ... loading intersphinx inventory 'sklearn' from https://scikit-learn.org/stable/objects.inv ... [autosummary] generating autosummary for: api/classes.md, api/datasets.md, api/deprecated.md, api/experimental.md, api/get.md, api/index.md, api/io.md, api/metrics.md, api/plotting.md, api/preprocessing.md, ..., tutorials/experimental/dask.ipynb, tutorials/experimental/index.md, tutorials/experimental/pearson_residuals.ipynb, tutorials/index.md, tutorials/plotting/advanced.ipynb, tutorials/plotting/core.ipynb, tutorials/plotting/index.md, tutorials/trajectories/index.md, tutorials/trajectories/paga-paul15.ipynb, usage-principles.md /home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx/ext/autosummary/__init__.py:697: FutureWarning: `read_loom` is deprecated and will be removed, use `read_h5ad` instead return getattr(mod, name_parts[-1]), mod, modname [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.Preset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.Verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.datasets.moignard15.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/external/generated/scanpy.external.tl.cyclone.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/external/generated/scanpy.external.tl.harmony_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/external/generated/scanpy.external.tl.palantir.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/external/generated/scanpy.external.tl.palantir_results.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/external/generated/scanpy.external.tl.phate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/external/generated/scanpy.external.tl.phenograph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/external/generated/scanpy.external.tl.sam.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/external/generated/scanpy.external.tl.sandbag.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/external/generated/scanpy.external.tl.trimap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/external/generated/scanpy.external.tl.wishbone.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.Preset.scale.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.Preset.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.Preset.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.Preset.umap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.Verbosity.debug.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.Verbosity.error.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.Verbosity.hint.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.Verbosity.info.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.Verbosity.level.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/api/generated/scanpy.Verbosity.warning.rst checking bibtex cache... out of date parsing bibtex file /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3645/docs/references.bib... parsed 81 entries building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 51 source files that are out of date updating environment: [new config] 268 added, 0 changed, 0 removed /home/docs/.asdf/installs/python/3.14.6/lib/python3.14/importlib/__init__.py:88: ZarrUserWarning: pytest not installed, skipping test suite return _bootstrap._gcd_import(name[level:], package, level) reading sources... [ 0%] api/classes reading sources... [ 1%] api/datasets reading sources... [ 1%] api/deprecated /home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx/ext/autosummary/__init__.py:697: FutureWarning: `read_loom` is deprecated and will be removed, use `read_h5ad` instead return getattr(mod, name_parts[-1]), mod, modname /home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx/util/inspect.py:461: FutureWarning: `read_loom` is deprecated and will be removed, use `read_h5ad` instead return getattr(obj, name, *defargs) reading sources... [ 1%] api/experimental reading sources... [ 2%] api/generated/classes/scanpy.pl.DotPlot reading sources... [ 2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP reading sources... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON reading sources... 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[ 53%] api/generated/scanpy.pl.rank_genes_groups_stacked_violin /tmp/tmpf0q4y0b0/api/generated/scanpy.pl.rank_genes_groups_stacked_violin-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpf0q4y0b0/api/generated/scanpy.pl.rank_genes_groups_stacked_violin-exec-1.ipynb: Executed notebook in 6.39 seconds [mystnb] /tmp/tmpf0q4y0b0/api/generated/scanpy.pl.rank_genes_groups_stacked_violin-exec-1.ipynb: Cached executed notebook: ID=27 [mystnb] reading sources... [ 53%] api/generated/scanpy.pl.rank_genes_groups_tracksplot /tmp/tmpwzinv27w/api/generated/scanpy.pl.rank_genes_groups_tracksplot-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpwzinv27w/api/generated/scanpy.pl.rank_genes_groups_tracksplot-exec-1.ipynb: Executed notebook in 12.07 seconds [mystnb] /tmp/tmpwzinv27w/api/generated/scanpy.pl.rank_genes_groups_tracksplot-exec-1.ipynb: Cached executed notebook: ID=28 [mystnb] reading sources... 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[ 54%] api/generated/scanpy.pl.scatter /tmp/tmp57obgwjx/api/generated/scanpy.pl.scatter-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp57obgwjx/api/generated/scanpy.pl.scatter-exec-1.ipynb: Executed notebook in 3.75 seconds [mystnb] /tmp/tmp57obgwjx/api/generated/scanpy.pl.scatter-exec-1.ipynb: Cached executed notebook: ID=31 [mystnb] reading sources... [ 55%] api/generated/scanpy.pl.scrublet_score_distribution /tmp/tmpga45_q7o/api/generated/scanpy.pl.scrublet_score_distribution-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpga45_q7o/api/generated/scanpy.pl.scrublet_score_distribution-exec-1.ipynb: Executed notebook in 5.18 seconds [mystnb] /tmp/tmpga45_q7o/api/generated/scanpy.pl.scrublet_score_distribution-exec-1.ipynb: Cached executed notebook: ID=32 [mystnb] reading sources... [ 55%] api/generated/scanpy.pl.sim reading sources... [ 56%] api/generated/scanpy.pl.spatial reading sources... [ 56%] api/generated/scanpy.pl.stacked_violin /tmp/tmp_1juyloj/api/generated/scanpy.pl.stacked_violin-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp_1juyloj/api/generated/scanpy.pl.stacked_violin-exec-1.ipynb: Executed notebook in 21.72 seconds [mystnb] /tmp/tmp_1juyloj/api/generated/scanpy.pl.stacked_violin-exec-1.ipynb: Cached executed notebook: ID=33 [mystnb] reading sources... [ 56%] api/generated/scanpy.pl.tracksplot /tmp/tmpuushcv_1/api/generated/scanpy.pl.tracksplot-exec-1.ipynb: Executing notebook using local CWD [mystnb] Versions ======== * Platform: linux; (Linux-7.0.0-1004-aws-x86_64-with-glibc2.43) * Python version: 3.14.6 (CPython) * Sphinx version: 9.1.0 * Docutils version: 0.22.4 * Jinja2 version: 3.1.6 * Pygments version: 2.21.0 Last Messages ============= reading sources... [ 56%] api/generated/scanpy.pl.stacked_violin /tmp/tmp_1juyloj/api/generated/scanpy.pl.stacked_violin-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp_1juyloj/api/generated/scanpy.pl.stacked_violin-exec-1.ipynb: Executed notebook in 21.72 seconds [mystnb] /tmp/tmp_1juyloj/api/generated/scanpy.pl.stacked_violin-exec-1.ipynb: Cached executed notebook: ID=33 [mystnb] reading sources... [ 56%] api/generated/scanpy.pl.tracksplot /tmp/tmpuushcv_1/api/generated/scanpy.pl.tracksplot-exec-1.ipynb: Executing notebook using local CWD [mystnb] Loaded Extensions ================= * sphinx.ext.mathjax (9.1.0) * alabaster (1.0.0) * sphinxcontrib.applehelp (2.0.0) * sphinxcontrib.devhelp (2.0.0) * sphinxcontrib.htmlhelp (2.1.0) * sphinxcontrib.serializinghtml (2.0.0) * sphinxcontrib.qthelp (2.0.0) * myst_nb (1.4.0) * sphinx_copybutton (0.5.2) * sphinx.ext.autodoc (9.1.0) * sphinx.ext.intersphinx (9.1.0) * sphinx.ext.doctest (9.1.0) * sphinx.ext.coverage (9.1.0) * sphinx.ext.napoleon (9.1.0) * sphinx.ext.autosummary (9.1.0) * sphinx_exec_jupyter.holoviews (0.4.2) * sphinx_exec_jupyter (0.4.2) * sphinxcontrib.bibtex (2.7.0) * sphinxcontrib.katex (0.9.11) * sphinx_autodoc_typehints (3.13.2) * git_ref (unknown version) * scanpydoc.definition_list_typed_field (0.17.3) * scanpydoc.elegant_typehints (0.17.3) * scanpydoc.rtd_github_links (0.17.3) * scanpydoc.theme (unknown version) * scanpydoc.release_notes (0.17.3) * scanpydoc (0.17.3) * scverse_misc.sphinx_ext (0.1.3) * sphinx.ext.linkcode (9.1.0) * sphinx_design (0.7.0) * sphinx_issues (6.0.0) * sphinxext.opengraph (0.13.0) * param_police (unknown version) * array_support (unknown version) * autosummary_skip_inherited (unknown version) * debug_docstrings (unknown version) * function_images (unknown version) * autosummary_skip_deprecated (unknown version) * myst_ignore_mime_types (unknown version) * returns_prose_wrap (1) * sphinx_book_theme (unknown version) * pydata_sphinx_theme (unknown version) Traceback ========= Traceback (most recent call last): File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx/cmd/build.py", line 432, in build_main app.build(args.force_all, args.filenames) ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx/application.py", line 442, in build self.builder.build_update() ~~~~~~~~~~~~~~~~~~~~~~~~~^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx/builders/__init__.py", line 381, in build_update self.build( ~~~~~~~~~~^ to_build, ^^^^^^^^^ ...<2 lines>... method='update', ^^^^^^^^^^^^^^^^ ) ^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx/builders/__init__.py", line 409, in build updated_docnames = set(self.read()) ~~~~~~~~~^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx/builders/__init__.py", line 525, in read self._read_serial(docnames) ~~~~~~~~~~~~~~~~~^^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx/builders/__init__.py", line 590, in _read_serial self.read_doc(docname) ~~~~~~~~~~~~~^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx/builders/__init__.py", line 653, in read_doc doctree = _parse_str_to_doctree( content, ...<6 lines>... transforms=self._registry.get_transforms(), ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx/util/docutils.py", line 906, in _parse_str_to_doctree transformer.apply_transforms() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx/transforms/__init__.py", line 95, in apply_transforms super().apply_transforms() ~~~~~~~~~~~~~~~~~~~~~~~~^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/docutils/transforms/__init__.py", line 193, in apply_transforms transform.apply(**kwargs) ~~~~~~~~~~~~~~~^^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx_exec_jupyter/_resolve.py", line 41, in apply all_results = execute_cells( all_cells, self.document, kernel_name=self.config.exec_jupyter_kernel ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx_exec_jupyter/common.py", line 38, in execute_cells parser.parse(notebook_json, document) ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/myst_nb/sphinx_.py", line 156, in parse with create_client( ~~~~~~~~~~~~~^ notebook, document_path, nb_config, logger, nb_reader.read_fmt ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) as nb_client: ^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/myst_nb/core/execute/base.py", line 80, in __enter__ self.start_client() ~~~~~~~~~~~~~~~~~^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/myst_nb/core/execute/cache.py", line 73, in start_client result = single_nb_execution( self.notebook, ...<3 lines>... meta_override=True, # TODO still support this? ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution executenb( ~~~~~~~~~^ nb, ^^^ ...<4 lines>... **kwargs, ^^^^^^^^^ ) ^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/nbclient/client.py", line 1323, in execute return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped return loop.run_until_complete(inner) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^ File "/home/docs/.asdf/installs/python/3.14.6/lib/python3.14/asyncio/base_events.py", line 719, in run_until_complete return future.result() ~~~~~~~~~~~~~^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/nbclient/client.py", line 693, in async_execute async with self.async_setup_kernel(**kwargs): ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^ File "/home/docs/.asdf/installs/python/3.14.6/lib/python3.14/contextlib.py", line 214, in __aenter__ return await anext(self.gen) ^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/nbclient/client.py", line 648, in async_setup_kernel await self.async_start_new_kernel(**kwargs) File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/nbclient/client.py", line 550, in async_start_new_kernel await ensure_async(self.km.start_kernel(extra_arguments=self.extra_arguments, **kwargs)) File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/jupyter_core/utils/__init__.py", line 214, in ensure_async result = await obj ^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/jupyter_client/manager.py", line 116, in wrapper raise e File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/jupyter_client/manager.py", line 107, in wrapper out = await method(self, *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/jupyter_client/manager.py", line 527, in _async_start_kernel await self._async_launch_kernel(kernel_cmd, **kw) File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/jupyter_client/manager.py", line 431, in _async_launch_kernel connection_info = await self.provisioner.launch_kernel(kernel_cmd, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx_exec_jupyter/_kernel_mgr/__init__.py", line 282, in launch_kernel self.pid = await self.server.fork(kernel_argv, self.log_path) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx_exec_jupyter/_kernel_mgr/__init__.py", line 115, in wrapper return await method(self, *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/P65JUpYB/docs/lib/python3.14/site-packages/sphinx_exec_jupyter/_kernel_mgr/__init__.py", line 139, in fork return resp["pid"] ~~~~^^^^^^^ KeyError: 'pid' The full traceback has been saved in: /tmp/sphinx-err-o85g9tju.log To report this error to the developers, please open an issue at . Thanks! Please also report this if it was a user error, so that a better error message can be provided next time.