Read the Docs build information Build id: 4314062 Project: icb-scanpy Version: latest Commit: 6a7c727ee459e703aeb173e182a24a64235a209c Date: 2026-08-13T08:39:47.788559Z State: finished Success: False [rtd-command-info] start-time: 2026-08-13T08:39:48.891451Z, end-time: 2026-08-13T08:39:52.619218Z, duration: 3, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2026-08-13T08:39:52.703397Z, end-time: 2026-08-13T08:39:53.569937Z, 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: 2026-08-13T08:39:54.199794Z, end-time: 2026-08-13T08:39:54.231214Z, 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: '3.13' 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: 2026-08-13T08:39:54.341007Z, end-time: 2026-08-13T08:39:57.168432Z, duration: 2, exit-code: 0 git fetch --unshallow || true From https://github.com/scverse/scanpy * [new tag] 1.13.0a1 -> 1.13.0a1 * [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: 2026-08-13T08:40:00.840933Z, end-time: 2026-08-13T08:40:00.887443Z, duration: 0, exit-code: 0 asdf global python 3.13.14 [rtd-command-info] start-time: 2026-08-13T08:40:01.191547Z, end-time: 2026-08-13T08:40:03.134674Z, duration: 1, exit-code: 0 asdf plugin add uv updating plugin repository...From https://github.com/asdf-vm/asdf-plugins 8e311ee..3715919 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 * [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: 2026-08-13T08:40:03.214154Z, end-time: 2026-08-13T08:40:04.147525Z, duration: 0, exit-code: 0 asdf install uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.12.3 * Downloading uv release 0.12.3... uv 0.12.3 installation was successful! [rtd-command-info] start-time: 2026-08-13T08:40:04.301906Z, end-time: 2026-08-13T08:40:04.399910Z, duration: 0, exit-code: 0 asdf global uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.12.3 [rtd-command-info] start-time: 2026-08-13T08:40:04.557590Z, end-time: 2026-08-13T08:40:10.008128Z, duration: 5, exit-code: 0 ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true Downloading cryptography (4.5MiB) Downloading pygments (1.2MiB) Downloading uv (21.3MiB) Downloading virtualenv (5.1MiB) Downloaded uv Downloaded cryptography Downloaded virtualenv Downloaded pygments Installed 43 packages in 16ms 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/4260.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4263.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4231.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4232.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4252.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4256.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4269.feat.md Done! [rtd-command-info] start-time: 2026-08-13T08:40:10.087098Z, end-time: 2026-08-13T08:44:19.558751Z, duration: 249, exit-code: 1 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={'dollarmath', 'html_image', 'colon_fence', 'html_admonition', 'amsmath', 'deflist'}, 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/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 '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 '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 'seaborn' from https://seaborn.pydata.org/objects.inv ... loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/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.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.Preset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.Verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.datasets.moignard15.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.cyclone.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.harmony_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.palantir.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.palantir_results.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.phate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.phenograph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.sam.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.sandbag.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.trimap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.wishbone.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/api/generated/scanpy.Preset.scale.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.Preset.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.Preset.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.Preset.umap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.Verbosity.debug.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.Verbosity.error.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.Verbosity.hint.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.Verbosity.info.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.Verbosity.level.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/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/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] 268 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) reading sources... [ 0%] api/classes reading sources... [ 1%] api/datasets reading sources... [ 1%] api/deprecated 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... [ 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... [ 4%] 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... [ 7%] 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/tmpphyk_xmw/api/generated/classes/scanpy.pl.MatrixPlot-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpphyk_xmw/api/generated/classes/scanpy.pl.MatrixPlot-exec-1.ipynb: Executed notebook in 9.14 seconds [mystnb] /tmp/tmpphyk_xmw/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... [ 10%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_SAVE_PREFIX reading sources... [ 11%] api/generated/classes/scanpy.pl.MatrixPlot.style /tmp/tmpmfik1vfu/api/generated/classes/scanpy.pl.MatrixPlot.style-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpmfik1vfu/api/generated/classes/scanpy.pl.MatrixPlot.style-exec-1.ipynb: Executed notebook in 0.88 seconds [mystnb] /tmp/tmpmfik1vfu/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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[ 39%] api/generated/scanpy.pl.clustermap /tmp/tmp0x10nl0l/api/generated/scanpy.pl.clustermap-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp0x10nl0l/api/generated/scanpy.pl.clustermap-exec-1.ipynb: Executed notebook in 1.34 seconds [mystnb] /tmp/tmp0x10nl0l/api/generated/scanpy.pl.clustermap-exec-1.ipynb: Cached executed notebook: ID=4 [mystnb] reading sources... [ 40%] api/generated/scanpy.pl.correlation_matrix /tmp/tmpsaeqx6q1/api/generated/scanpy.pl.correlation_matrix-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpsaeqx6q1/api/generated/scanpy.pl.correlation_matrix-exec-1.ipynb: Executed notebook in 0.86 seconds [mystnb] /tmp/tmpsaeqx6q1/api/generated/scanpy.pl.correlation_matrix-exec-1.ipynb: Cached executed notebook: ID=5 [mystnb] reading sources... 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[100%] usage-principles /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.get.pca-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc sc.settings.preset = sc.Preset.ScanpyV2Preview adata = sc.datasets.pbmc68k_reduced() sc.get.pca(adata) ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[1], line 2  1 import scanpy as sc ----> 2 sc.settings.preset = sc.Preset.ScanpyV2Preview  3 adata = sc.datasets.pbmc68k_reduced()  4 sc.get.pca(adata) File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.get.pca-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.get.pca-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.diffmap-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() sc.tl.diffmap(adata) sc.pl.diffmap(adata, color=A.obs["bulk_labels"]).opts( cmap="tab10", show_legend=False ) ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 2  1 import scanpy as sc ----> 2 sc.settings.preset = sc.Preset.ScanpyV2Preview  3 A = sc.pl.hv_init(FAKE_BACKEND)  4  5 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.diffmap-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.diffmap-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.dotplot-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() markers = ["C1QA", "PSAP", "CD79A", "CD79B", "CST3", "LYZ"] sc.pl.dotplot(adata[:, markers], A.obs["bulk_labels"]) ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 3  1 import scanpy as sc  2 ----> 3 sc.settings.preset = sc.Preset.ScanpyV2Preview  4 A = sc.pl.hv_init(FAKE_BACKEND)  5  6 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.dotplot-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.dotplot-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.draw_graph-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() sc.pp.neighbors(adata) sc.pl.draw_graph( adata, A.obsm["umap"], "distances", [A.obs["bulk_labels"]] ).opts( node_color=A.obs["bulk_labels"], node_cmap="tab10", aspect="square", show_legend=True, legend_position="right", ) ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 3  1 import scanpy as sc  2 ----> 3 sc.settings.preset = sc.Preset.ScanpyV2Preview  4 A = sc.pl.hv_init(FAKE_BACKEND)  5  6 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.draw_graph-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.draw_graph-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.embedding_density-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() sc.tl.embedding_density(adata, basis="umap", groupby="phase") sc.pl.embedding_density(adata, A.obsm["umap"], groupby="phase") ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 3  1 import scanpy as sc  2 ----> 3 sc.settings.preset = sc.Preset.ScanpyV2Preview  4 A = sc.pl.hv_init(FAKE_BACKEND)  5  6 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.embedding_density-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.embedding_density-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.heatmap-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc import holoviews as hv sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() markers = ["C1QA", "PSAP", "CD79A", "CD79B", "CST3", "LYZ"] sc.pl.heatmap( adata[:, markers], A.X, [A.obs["n_counts"]] ).opts(hv.opts.HeatMap(xticks=0, aspect=2)) ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 4  1 import scanpy as sc  2 import holoviews as hv  3 ----> 4 sc.settings.preset = sc.Preset.ScanpyV2Preview  5 A = sc.pl.hv_init(FAKE_BACKEND)  6  7 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.heatmap-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.heatmap-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.highest_expr_genes-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() sc.pl.highest_expr_genes(adata, layer="counts") ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 3  1 import scanpy as sc  2 ----> 3 sc.settings.preset = sc.Preset.ScanpyV2Preview  4 A = sc.pl.hv_init(FAKE_BACKEND)  5  6 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.highest_expr_genes-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.highest_expr_genes-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.highly_variable_genes-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() sc.pp.highly_variable_genes(adata, layer="counts") # TODO: this should be the default sc.pl.highly_variable_genes(adata) ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 3  1 import scanpy as sc  2 ----> 3 sc.settings.preset = sc.Preset.ScanpyV2Preview  4 A = sc.pl.hv_init(FAKE_BACKEND)  5  6 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.highly_variable_genes-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.highly_variable_genes-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.matrixplot-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() markers = ["C1QA", "PSAP", "CD79A", "CD79B", "CST3", "LYZ"] sc.pl.matrixplot( adata[:, markers], A.obs["bulk_labels"], data=A.layers["counts"], add_totals=True ) ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 3  1 import scanpy as sc  2 ----> 3 sc.settings.preset = sc.Preset.ScanpyV2Preview  4 A = sc.pl.hv_init(FAKE_BACKEND)  5  6 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.matrixplot-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.matrixplot-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.pca-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() sc.tl.pca(adata) sc.pl.pca(adata, color=A.obs["bulk_labels"]).opts( cmap="tab10", show_legend=False ) ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 2  1 import scanpy as sc ----> 2 sc.settings.preset = sc.Preset.ScanpyV2Preview  3 A = sc.pl.hv_init(FAKE_BACKEND)  4  5 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.pca-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.pca-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.ranking-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc import holoviews as hv sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() hv.Layout([ sc.pl.ranking(adata, A.varm["PCs"][0]).opts(aspect=1.2), sc.pl.ranking(adata, A.varm["PCs"][0], include_lowest=False).opts(aspect=0.6), ]).opts(shared_axes=False) ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 4  1 import scanpy as sc  2 import holoviews as hv  3 ----> 4 sc.settings.preset = sc.Preset.ScanpyV2Preview  5 A = sc.pl.hv_init(FAKE_BACKEND)  6  7 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.ranking-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.ranking-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.scatter-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() sc.pl.scatter(adata, A.X[:, ["PSAP", "C1QA"]], color=A.obs["bulk_labels"]).opts( cmap="tab10", show_legend=False ) ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 2  1 import scanpy as sc ----> 2 sc.settings.preset = sc.Preset.ScanpyV2Preview  3 A = sc.pl.hv_init(FAKE_BACKEND)  4  5 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.scatter-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.scatter-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.scrublet_score_distribution-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() adata_sim = sc.pp.scrublet_simulate_doublets(adata) sc.pp.scrublet(adata, adata_sim) sc.pl.scrublet_score_distribution(adata) ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 3  1 import scanpy as sc  2 ----> 3 sc.settings.preset = sc.Preset.ScanpyV2Preview  4 A = sc.pl.hv_init(FAKE_BACKEND)  5  6 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.scrublet_score_distribution-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.scrublet_score_distribution-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.stacked_violin-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc import holoviews as hv sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() markers = ["C1QA", "PSAP", "CD79A", "CD79B", "CST3", "LYZ"] sc.pl.stacked_violin(adata[:, markers], A.var.index, A.obs["bulk_labels"]) ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 4  1 import scanpy as sc  2 import holoviews as hv  3 ----> 4 sc.settings.preset = sc.Preset.ScanpyV2Preview  5 A = sc.pl.hv_init(FAKE_BACKEND)  6  7 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.stacked_violin-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.stacked_violin-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.tracksplot-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc import holoviews as hv sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() markers = ["C1QA", "PSAP", "CD79A", "CD79B", "CST3", "LYZ"] sc.pl.tracksplot( adata, A.X[:, markers], color=A.obs["bulk_labels"] ).opts(hv.opts.Curve(aspect=20)) ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 4  1 import scanpy as sc  2 import holoviews as hv  3 ----> 4 sc.settings.preset = sc.Preset.ScanpyV2Preview  5 A = sc.pl.hv_init(FAKE_BACKEND)  6  7 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.tracksplot-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.tracksplot-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.tsne-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() sc.tl.tsne(adata) sc.pl.tsne(adata, color=A.obs["bulk_labels"]).opts( cmap="tab10", show_legend=False ) ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 2  1 import scanpy as sc ----> 2 sc.settings.preset = sc.Preset.ScanpyV2Preview  3 A = sc.pl.hv_init(FAKE_BACKEND)  4  5 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.tsne-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.tsne-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.umap-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() sc.tl.umap(adata) sc.pl.umap(adata, color=A.obs["bulk_labels"]).opts( cmap="tab10", show_legend=False ) ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 2  1 import scanpy as sc ----> 2 sc.settings.preset = sc.Preset.ScanpyV2Preview  3 A = sc.pl.hv_init(FAKE_BACKEND)  4  5 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.umap-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.umap-exec-1.err.log [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.violin-exec-1.rst: WARNING: Executing notebook failed: CellExecutionError Traceback (most recent call last): 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 709, in async_execute await self.async_execute_cell( cell, index, execution_count=self.code_cells_executed + 1 ) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 1062, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/nbclient/client.py", line 918, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import scanpy as sc import holoviews as hv sc.settings.preset = sc.Preset.ScanpyV2Preview A = sc.pl.hv_init(FAKE_BACKEND) adata = sc.datasets.pbmc68k_reduced() sc.pl.violin(adata, A.obs[["percent_mito", "n_counts", "n_genes"]]).opts( hv.opts.Violin(ylim=(0, None)) ) ------------------ --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 4  1 import scanpy as sc  2 import holoviews as hv  3 ----> 4 sc.settings.preset = sc.Preset.ScanpyV2Preview  5 A = sc.pl.hv_init(FAKE_BACKEND)  6  7 adata = sc.datasets.pbmc68k_reduced() File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:1049, in BaseModel.__setattr__(self, name, value)  1047 # if None is returned from _setattr_handler, the attribute was set directly  1048 elif (setattr_handler := self._setattr_handler(name, value)) is not None: -> 1049 setattr_handler(self, name, value) # call here to not memo on possibly unknown fields  1050 self.__pydantic_setattr_handlers__[name] = setattr_handler File ~/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs/lib/python3.13/site-packages/pydantic/main.py:112, in (model, name, val)  106 object.__setattr__(model, '__pydantic_private__', {})  107 model.__pydantic_private__[name] = val # pyright: ignore[reportOptionalSubscript]  110 _SIMPLE_SETATTR_HANDLERS: Mapping[str, Callable[[BaseModel, str, Any], None]] = {  111 'model_field': _model_field_setattr_handler, --> 112 'validate_assignment': lambda model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val), # pyright: ignore[reportAssignmentType]  113 'private': _private_setattr_handler,  114 'cached_property': lambda model, name, val: model.__dict__.__setitem__(name, val),  115 'extra_known': lambda model, name, val: _object_setattr(model, name, val),  116 }  119 class BaseModel(metaclass=_model_construction.ModelMetaclass):  120  """!!! abstract "Usage Documentation"  121  [Models](../concepts/models.md)  122  (...) 151  __pydantic_private__: Values of private attributes set on the model instance.  152  """ File ~/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/_settings/presets.py:313, in Preset.check(self)  307 missing_str = ", ".join(f"‘{m.name}’" for m in missing)  308 msg = (  309 f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "  310 f"dependencies that are not installed: {missing_str}. "  311 "Install them with: pip install `scanpy[scanpy2]`"  312 ) --> 313 raise ImportError(msg)  314 case _:  315 return self ImportError: Setting preset to requires optional dependencies that are not installed: ‘illico’. Install them with: pip install `scanpy[scanpy2]` [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.violin-exec-1.rst: WARNING: Notebook exception traceback saved in: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/_build/html/reports/api/generated/scanpy.pl.violin-exec-1.err.log [mystnb.exec] [mystnb.exec] looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.ranking.rst: document is referenced in multiple toctrees: ['api/plotting', 'api/plotting'], selecting: api/plotting <- api/generated/scanpy.pl.ranking /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pp.pca.rst: document is referenced in multiple toctrees: ['api/preprocessing', 'api/tools'], selecting: api/tools <- api/generated/scanpy.pp.pca /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.palantir.rst: document is referenced in multiple toctrees: ['external/tools', 'external/tools'], selecting: external/tools <- external/generated/scanpy.external.tl.palantir done preparing documents... done copying assets... copying static files... 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