Read the Docs build information Build id: 4179079 Project: icb-scanpy Version: latest Commit: af6de2e90a3684862b6722694d052654fc44acec Date: 2026-07-06T20:12:03.181959Z State: finished Success: False [rtd-command-info] start-time: 2026-07-06T20:12:04.009058Z, end-time: 2026-07-06T20:12:05.012172Z, duration: 1, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2026-07-06T20:12:05.116763Z, end-time: 2026-07-06T20:12:05.612431Z, duration: 0, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 HEAD From https://github.com/scverse/scanpy * branch HEAD -> FETCH_HEAD [rtd-command-info] start-time: 2026-07-06T20:12:06.257285Z, end-time: 2026-07-06T20:12:06.295920Z, duration: 0, exit-code: 0 cat .readthedocs.yml # https://docs.readthedocs.io/en/stable/config-file/v2.html version: 2 submodules: include: all build: os: ubuntu-24.04 tools: python: '3.13' 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 hatch run docs:build -T - mv docs/_build $READTHEDOCS_OUTPUT [rtd-command-info] start-time: 2026-07-06T20:12:06.446629Z, end-time: 2026-07-06T20:12:06.571516Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2026-07-06T20:12:06.665900Z, end-time: 2026-07-06T20:12:25.581779Z, duration: 18, exit-code: 0 git submodule update --init --force -- Submodule 'notebooks' (https://github.com/scverse/scanpy-tutorials/) registered for path 'notebooks' Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/notebooks'... Submodule path 'notebooks': checked out 'ac0e94be9f36977400177dc940cbd8eac1d2297c' [rtd-command-info] start-time: 2026-07-06T20:12:25.678529Z, end-time: 2026-07-06T20:12:30.509972Z, duration: 4, 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 Fetching submodule notebooks From https://github.com/scverse/scanpy-tutorials * branch 26e16f83387caef76abdd42afda3c7c13f7139f1 -> FETCH_HEAD [rtd-command-info] start-time: 2026-07-06T20:12:35.139641Z, end-time: 2026-07-06T20:12:35.197014Z, duration: 0, exit-code: 0 asdf global python 3.13.14 [rtd-command-info] start-time: 2026-07-06T20:12:35.523811Z, end-time: 2026-07-06T20:12:36.942728Z, duration: 1, 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: 2026-07-06T20:12:37.022307Z, end-time: 2026-07-06T20:12:38.083032Z, duration: 1, exit-code: 0 asdf install uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.11.26 * Downloading uv release 0.11.26... uv 0.11.26 installation was successful! [rtd-command-info] start-time: 2026-07-06T20:12:38.174612Z, end-time: 2026-07-06T20:12:38.289407Z, duration: 0, exit-code: 0 asdf global uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.11.26 [rtd-command-info] start-time: 2026-07-06T20:12:38.434755Z, end-time: 2026-07-06T20:12:44.915899Z, duration: 6, exit-code: 0 ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true Downloading uv (25.0MiB) Downloading virtualenv (5.3MiB) Downloading pygments (1.2MiB) Downloading cryptography (4.5MiB) Downloaded virtualenv Downloaded cryptography Downloaded uv Downloaded pygments Installed 43 packages in 19ms 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/latest/docs/release-notes/4126.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4055.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4141.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4178.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4184.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/3953.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4081.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4052.breaking.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4037.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4132.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4081.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4010.chore.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4013.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4191.chore.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4147.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/3983.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4142.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4143.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4192.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4112.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4100.docs.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4039.breaking.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4036.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4079.docs.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/3999.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4017.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4062.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/3984.breaking.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4076.feat.md Done! [rtd-command-info] start-time: 2026-07-06T20:12:44.996028Z, end-time: 2026-07-06T20:14:46.186616Z, duration: 121, exit-code: 2 uvx hatch run docs:build -T Creating environment: docs Installing project in development mode Checking dependencies Syncing dependencies Running Sphinx v9.1.0 loading translations [en]... done Matplotlib is building the font cache; this may take a moment. making output directory... done myst v5.1.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'amsmath', 'deflist', 'colon_fence', 'dollarmath', 'html_admonition', 'html_image'}, 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=False, 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='remove', 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/latest/docs/_build/.jupyter_cache loading intersphinx inventory 'anndata' from https://anndata.scverse.org/en/stable/objects.inv ... loading intersphinx inventory 'bbknn' from https://bbknn.readthedocs.io/en/latest/objects.inv ... loading intersphinx inventory 'cuml' from https://docs.rapids.ai/api/cuml/stable/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 'dask_ml' from https://ml.dask.org/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 'h5py' from https://docs.h5py.org/en/stable/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 '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 [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.correlation_matrix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.embedding_density.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.umap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.write.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.Preset.scale.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.Preset.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.Preset.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.Preset.umap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.Verbosity.debug.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.Verbosity.error.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.Verbosity.hint.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.Verbosity.info.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.Verbosity.level.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.Verbosity.warning.rst checking bibtex cache... out of date parsing bibtex file /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/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] 266 added, 0 changed, 0 removed /home/docs/.asdf/installs/python/3.13.14/lib/python3.13/importlib/__init__.py:88: ZarrUserWarning: pytest not installed, skipping test suite return _bootstrap._gcd_import(name[level:], package, level) /home/docs/.asdf/installs/python/3.13.14/lib/python3.13/importlib/__init__.py:88: ZarrUserWarning: pytest not installed, skipping test suite return _bootstrap._gcd_import(name[level:], package, level) /home/docs/.asdf/installs/python/3.13.14/lib/python3.13/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 reading sources... [ 2%] 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... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR reading sources... [ 4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW reading sources... [ 4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX reading sources... [ 5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN reading sources... [ 5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT reading sources... [ 5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH reading sources... [ 6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING reading sources... [ 6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING reading sources... [ 6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX reading sources... [ 7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT reading sources... [ 7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE reading sources... [ 8%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT reading sources... [ 8%] api/generated/classes/scanpy.pl.DotPlot.legend reading sources... [ 8%] api/generated/classes/scanpy.pl.DotPlot.style reading sources... [ 9%] api/generated/classes/scanpy.pl.MatrixPlot /tmp/tmp5luoegt9/api/generated/classes/scanpy.pl.MatrixPlot-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp5luoegt9/api/generated/classes/scanpy.pl.MatrixPlot-exec-1.ipynb: Executed notebook in 10.24 seconds [mystnb] /tmp/tmp5luoegt9/api/generated/classes/scanpy.pl.MatrixPlot-exec-1.ipynb: Cached executed notebook: ID=1 [mystnb] reading sources... [ 9%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLORMAP reading sources... [ 9%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 10%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_COLOR reading sources... [ 10%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_LW reading sources... [ 11%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_SAVE_PREFIX reading sources... [ 11%] api/generated/classes/scanpy.pl.MatrixPlot.style /tmp/tmp9ime46ww/api/generated/classes/scanpy.pl.MatrixPlot.style-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp9ime46ww/api/generated/classes/scanpy.pl.MatrixPlot.style-exec-1.ipynb: Executed notebook in 0.60 seconds [mystnb] /tmp/tmp9ime46ww/api/generated/classes/scanpy.pl.MatrixPlot.style-exec-1.ipynb: Cached executed notebook: ID=2 [mystnb] reading sources... [ 11%] api/generated/classes/scanpy.pl.StackedViolin reading sources... [ 12%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP reading sources... [ 12%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 12%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT reading sources... [ 13%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_DENSITY_NORM reading sources... [ 13%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER reading sources... 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[ 18%] api/generated/scanpy.pl.correlation_matrix /tmp/tmp_6h6h7bt/api/generated/scanpy.pl.correlation_matrix-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp_6h6h7bt/api/generated/scanpy.pl.correlation_matrix-exec-1.ipynb: Executed notebook in 0.71 seconds [mystnb] /tmp/tmp_6h6h7bt/api/generated/scanpy.pl.correlation_matrix-exec-1.ipynb: Cached executed notebook: ID=3 [mystnb] reading sources... [ 18%] api/generated/scanpy.pl.diffmap /tmp/tmptfjkwjdl/api/generated/scanpy.pl.diffmap-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmptfjkwjdl/api/generated/scanpy.pl.diffmap-exec-1.ipynb: Executed notebook in 0.76 seconds [mystnb] /tmp/tmptfjkwjdl/api/generated/scanpy.pl.diffmap-exec-1.ipynb: Cached executed notebook: ID=4 [mystnb] reading sources... [ 18%] api/generated/scanpy.pl.dpt_groups_pseudotime reading sources... [ 19%] api/generated/scanpy.pl.dpt_timeseries reading sources... [ 19%] api/generated/scanpy.pl.draw_graph /tmp/tmp_e236gqw/api/generated/scanpy.pl.draw_graph-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp_e236gqw/api/generated/scanpy.pl.draw_graph-exec-1.ipynb: Executed notebook in 1.22 seconds [mystnb] /tmp/tmp_e236gqw/api/generated/scanpy.pl.draw_graph-exec-1.ipynb: Cached executed notebook: ID=5 [mystnb] reading sources... [ 20%] api/generated/scanpy.pl.embedding /tmp/tmpjdgbbh_j/api/generated/scanpy.pl.embedding-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpjdgbbh_j/api/generated/scanpy.pl.embedding-exec-1.ipynb: Executed notebook in 0.99 seconds [mystnb] /tmp/tmpjdgbbh_j/api/generated/scanpy.pl.embedding-exec-1.ipynb: Cached executed notebook: ID=6 [mystnb] reading sources... 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[ 24%] api/generated/scanpy.pl.rank_genes_groups_dotplot /tmp/tmprfjw90sv/api/generated/scanpy.pl.rank_genes_groups_dotplot-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmprfjw90sv/api/generated/scanpy.pl.rank_genes_groups_dotplot-exec-1.ipynb: Executed notebook in 4.62 seconds [mystnb] /tmp/tmprfjw90sv/api/generated/scanpy.pl.rank_genes_groups_dotplot-exec-1.ipynb: Cached executed notebook: ID=17 [mystnb] reading sources... [ 24%] api/generated/scanpy.pl.rank_genes_groups_heatmap /tmp/tmpq3ugrrzl/api/generated/scanpy.pl.rank_genes_groups_heatmap-exec-1.ipynb: Executing notebook using local CWD [mystnb] Versions ======== * Platform: linux; (Linux-7.0.0-1004-aws-x86_64-with-glibc2.39) * Python version: 3.13.14 (CPython) * Sphinx version: 9.1.0 * Docutils version: 0.22.4 * Jinja2 version: 3.1.6 * Pygments version: 2.20.0 Last Messages ============= reading sources... [ 24%] api/generated/scanpy.pl.rank_genes_groups_dotplot /tmp/tmprfjw90sv/api/generated/scanpy.pl.rank_genes_groups_dotplot-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmprfjw90sv/api/generated/scanpy.pl.rank_genes_groups_dotplot-exec-1.ipynb: Executed notebook in 4.62 seconds [mystnb] /tmp/tmprfjw90sv/api/generated/scanpy.pl.rank_genes_groups_dotplot-exec-1.ipynb: Cached executed notebook: ID=17 [mystnb] reading sources... [ 24%] api/generated/scanpy.pl.rank_genes_groups_heatmap /tmp/tmpq3ugrrzl/api/generated/scanpy.pl.rank_genes_groups_heatmap-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 (0.3.1) * sphinxcontrib.bibtex (2.7.0) * sphinxcontrib.katex (0.9.11) * sphinx_autodoc_typehints (3.12.1) * 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 (0.1.1) * 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) * canonical_tutorial (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/T0JdXacZ/docs/lib/python3.13/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/T0JdXacZ/docs/lib/python3.13/site-packages/sphinx/application.py", line 442, in build self.builder.build_update() ~~~~~~~~~~~~~~~~~~~~~~~~~^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/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/T0JdXacZ/docs/lib/python3.13/site-packages/sphinx/builders/__init__.py", line 409, in build updated_docnames = set(self.read()) ~~~~~~~~~^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/sphinx/builders/__init__.py", line 525, in read self._read_serial(docnames) ~~~~~~~~~~~~~~~~~^^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/sphinx/builders/__init__.py", line 590, in _read_serial self.read_doc(docname) ~~~~~~~~~~~~~^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/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/T0JdXacZ/docs/lib/python3.13/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/T0JdXacZ/docs/lib/python3.13/site-packages/sphinx/transforms/__init__.py", line 95, in apply_transforms super().apply_transforms() ~~~~~~~~~~~~~~~~~~~~~~~~^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/docutils/transforms/__init__.py", line 193, in apply_transforms transform.apply(**kwargs) ~~~~~~~~~~~~~~~^^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/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/T0JdXacZ/docs/lib/python3.13/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/T0JdXacZ/docs/lib/python3.13/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/T0JdXacZ/docs/lib/python3.13/site-packages/myst_nb/core/execute/base.py", line 80, in __enter__ self.start_client() ~~~~~~~~~~~~~~~~~^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/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/T0JdXacZ/docs/lib/python3.13/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/T0JdXacZ/docs/lib/python3.13/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/T0JdXacZ/docs/lib/python3.13/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped return loop.run_until_complete(inner) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^ File "/home/docs/.asdf/installs/python/3.13.14/lib/python3.13/asyncio/base_events.py", line 725, in run_until_complete return future.result() ~~~~~~~~~~~~~^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 693, in async_execute async with self.async_setup_kernel(**kwargs): ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^ File "/home/docs/.asdf/installs/python/3.13.14/lib/python3.13/contextlib.py", line 214, in __aenter__ return await anext(self.gen) ^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/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/T0JdXacZ/docs/lib/python3.13/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/T0JdXacZ/docs/lib/python3.13/site-packages/jupyter_core/utils/__init__.py", line 214, in ensure_async result = await obj ^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/jupyter_client/manager.py", line 116, in wrapper raise e File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/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/T0JdXacZ/docs/lib/python3.13/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/T0JdXacZ/docs/lib/python3.13/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/T0JdXacZ/docs/lib/python3.13/site-packages/sphinx_exec_jupyter/_kernel_mgr/__init__.py", line 279, in launch_kernel self.pid = await self.server.fork(kernel_argv, self.log_path) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/sphinx_exec_jupyter/_kernel_mgr/__init__.py", line 112, in wrapper return await method(self, *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/sphinx_exec_jupyter/_kernel_mgr/__init__.py", line 136, in fork return resp["pid"] ~~~~^^^^^^^ KeyError: 'pid' The full traceback has been saved in: /tmp/sphinx-err-6tvalhwr.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.