Read the Docs build information Build id: 4245289 Project: icb-scanpy Version: 4188 Commit: 7e169440a4370b06c98ef0af63e330ec09d899d9 Date: 2026-07-23T14:59:23.858188Z State: finished Success: False [rtd-command-info] start-time: 2026-07-23T14:59:24.873079Z, end-time: 2026-07-23T14:59:26.222845Z, duration: 1, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2026-07-23T14:59:26.318448Z, end-time: 2026-07-23T14:59:26.902287Z, duration: 0, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/4188/head:external-4188 From https://github.com/scverse/scanpy * [new ref] refs/pull/4188/head -> external-4188 [rtd-command-info] start-time: 2026-07-23T14:59:27.583241Z, end-time: 2026-07-23T14:59:27.793449Z, duration: 0, exit-code: 0 git checkout --force 7e169440a4370b06c98ef0af63e330ec09d899d9 Note: switching to '7e169440a4370b06c98ef0af63e330ec09d899d9'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 7e16944 fix legacy PCA plot [rtd-command-info] start-time: 2026-07-23T14:59:27.891447Z, end-time: 2026-07-23T14:59:27.934432Z, duration: 0, exit-code: 0 cat .readthedocs.yml # https://docs.readthedocs.io/en/stable/config-file/v2.html version: 2 submodules: include: all build: os: ubuntu-24.04 tools: python: '3.13' jobs: post_checkout: # unshallow so version can be derived from tag - git fetch --unshallow || true create_environment: - asdf plugin add uv - asdf install uv latest - asdf global uv latest pre_build: # run towncrier to preview the next version’s release notes - ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true build: html: - uvx hatch run docs:build -T - mv docs/_build $READTHEDOCS_OUTPUT [rtd-command-info] start-time: 2026-07-23T14:59:28.083526Z, end-time: 2026-07-23T14:59:28.155290Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2026-07-23T14:59:28.264779Z, end-time: 2026-07-23T14:59:47.004828Z, duration: 18, exit-code: 0 git submodule update --init --force -- Submodule 'notebooks' (https://github.com/scverse/scanpy-tutorials/) registered for path 'notebooks' Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/notebooks'... Submodule path 'notebooks': checked out '4a74bcfb54ba5e016e8ab80e16457e557b4a07ab' [rtd-command-info] start-time: 2026-07-23T14:59:47.095506Z, end-time: 2026-07-23T14:59:51.504231Z, duration: 4, exit-code: 0 git fetch --unshallow || true From https://github.com/scverse/scanpy * [new tag] 0.0 -> 0.0 * [new tag] 0.1 -> 0.1 * [new tag] 0.2 -> 0.2 * [new tag] 0.2.1 -> 0.2.1 * [new tag] 0.2.3 -> 0.2.3 * [new tag] 0.2.3.5 -> 0.2.3.5 * [new tag] 0.2.4 -> 0.2.4 * [new tag] 0.2.5 -> 0.2.5 * [new tag] 0.2.6 -> 0.2.6 * [new tag] 0.2.7 -> 0.2.7 * [new tag] 0.2.8 -> 0.2.8 * [new tag] 0.2.9 -> 0.2.9 * [new tag] 0.2.9.1 -> 0.2.9.1 * [new tag] 0.3 -> 0.3 * [new tag] 0.3.1 -> 0.3.1 * [new tag] 0.3.2 -> 0.3.2 * [new tag] 0.4 -> 0.4 * [new tag] 0.4.1 -> 0.4.1 * [new tag] 0.4.2 -> 0.4.2 * [new tag] 0.4.2.post1 -> 0.4.2.post1 * [new tag] 0.4.2.post2 -> 0.4.2.post2 * [new tag] 0.4.3 -> 0.4.3 * [new tag] 0.4.4 -> 0.4.4 * [new tag] 1.0 -> 1.0 * [new tag] 1.0.1 -> 1.0.1 * [new tag] 1.0.2 -> 1.0.2 * [new tag] 1.0.3 -> 1.0.3 * [new tag] 1.0.4 -> 1.0.4 * [new tag] 1.1 -> 1.1 * [new tag] 1.10.0.dev0 -> 1.10.0.dev0 * [new tag] 1.10.0rc1 -> 1.10.0rc1 * [new tag] 1.11.0 -> 1.11.0 * [new tag] 1.11.0rc1 -> 1.11.0rc1 * [new tag] 1.11.0rc2 -> 1.11.0rc2 * [new tag] 1.12.0 -> 1.12.0 * [new tag] 1.12.0rc1 -> 1.12.0rc1 * [new tag] 1.1a1 -> 1.1a1 * [new tag] 1.1a2 -> 1.1a2 * [new tag] 1.2.0 -> 1.2.0 * [new tag] 1.2.1 -> 1.2.1 * [new tag] 1.2.2 -> 1.2.2 * [new tag] 1.3 -> 1.3 * [new tag] 1.3.1 -> 1.3.1 * [new tag] 1.3.2 -> 1.3.2 * [new tag] 1.3.3 -> 1.3.3 * [new tag] 1.3.4 -> 1.3.4 * [new tag] 1.3.5 -> 1.3.5 * [new tag] 1.3.6 -> 1.3.6 * [new tag] 1.3.7 -> 1.3.7 * [new tag] 1.3.8 -> 1.3.8 * [new tag] 1.4 -> 1.4 * [new tag] 1.4.1 -> 1.4.1 * [new tag] 1.4.2 -> 1.4.2 * [new tag] 1.4.3 -> 1.4.3 * [new tag] 1.4.4 -> 1.4.4 * [new tag] 1.4.5 -> 1.4.5 * [new tag] 1.4.5.1 -> 1.4.5.1 * [new tag] 1.4.5.post1 -> 1.4.5.post1 * [new tag] 1.4.5.post2 -> 1.4.5.post2 * [new tag] 1.4.5.post3 -> 1.4.5.post3 * [new tag] 1.4.6 -> 1.4.6 * [new tag] 1.5.0 -> 1.5.0 * [new tag] 1.5.0a1 -> 1.5.0a1 * [new tag] 1.5.1 -> 1.5.1 * [new tag] 1.6.0 -> 1.6.0 * [new tag] 1.7.0rc1 -> 1.7.0rc1 * [new tag] 1.8.0 -> 1.8.0 * [new tag] 1.8.0.dev0 -> 1.8.0.dev0 * [new tag] 1.9.0 -> 1.9.0 * [new tag] 1.9.0.dev0 -> 1.9.0.dev0 Fetching submodule notebooks From https://github.com/scverse/scanpy-tutorials * branch 26e16f83387caef76abdd42afda3c7c13f7139f1 -> FETCH_HEAD [rtd-command-info] start-time: 2026-07-23T14:59:55.837458Z, end-time: 2026-07-23T14:59:55.895195Z, duration: 0, exit-code: 0 asdf global python 3.13.14 [rtd-command-info] start-time: 2026-07-23T14:59:56.234879Z, end-time: 2026-07-23T14:59:57.226144Z, duration: 0, exit-code: 0 asdf plugin add uv updating plugin repository...From https://github.com/asdf-vm/asdf-plugins 8e311ee..c0369a1 master -> origin/master * [new branch] dependabot/github_actions/actions/checkout-6 -> origin/dependabot/github_actions/actions/checkout-6 * [new branch] dependabot/github_actions/amannn/action-semantic-pull-request-6.1.1 -> origin/dependabot/github_actions/amannn/action-semantic-pull-request-6.1.1 * [new branch] dependabot/github_actions/asdf-vm/actions-4 -> origin/dependabot/github_actions/asdf-vm/actions-4 HEAD is now at c0369a1 feat: add yasm plugin (#1087) [rtd-command-info] start-time: 2026-07-23T14:59:57.317089Z, end-time: 2026-07-23T14:59:58.464983Z, duration: 1, exit-code: 0 asdf install uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.11.31 * Downloading uv release 0.11.31... uv 0.11.31 installation was successful! [rtd-command-info] start-time: 2026-07-23T14:59:58.558384Z, end-time: 2026-07-23T14:59:58.665824Z, duration: 0, exit-code: 0 asdf global uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.11.31 [rtd-command-info] start-time: 2026-07-23T14:59:58.822755Z, end-time: 2026-07-23T15:00:05.510937Z, duration: 6, exit-code: 0 ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true Downloading cryptography (4.5MiB) Downloading virtualenv (5.3MiB) Downloading pygments (1.2MiB) Downloading uv (25.6MiB) Downloaded uv Downloaded cryptography Downloaded virtualenv Downloaded pygments Installed 43 packages in 20ms 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/4188/docs/release-notes/4126.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4055.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4141.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4178.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4204.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4184.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4188.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4205.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/3953.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4081.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4052.breaking.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4037.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4132.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4081.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4010.chore.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4208.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4013.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4191.chore.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4147.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/3653.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/3983.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4142.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4143.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4199.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4192.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4196.docs.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4038.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4112.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4100.docs.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4039.breaking.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4036.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4079.docs.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/3999.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4017.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4062.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/3984.breaking.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4076.feat.md Done! [rtd-command-info] start-time: 2026-07-23T15:00:05.590382Z, end-time: 2026-07-23T15:07:09.550852Z, duration: 423, 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 making output directory... done myst v5.1.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'amsmath', 'html_admonition', 'colon_fence', 'html_image', 'dollarmath', '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/4188/docs/_build/.jupyter_cache loading intersphinx inventory 'bbknn' from https://bbknn.readthedocs.io/en/latest/objects.inv ... loading intersphinx inventory 'anndata' from https://anndata.scverse.org/en/stable/objects.inv ... loading intersphinx inventory 'cuml' from https://docs.rapids.ai/api/cuml/stable/objects.inv ... loading intersphinx inventory '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 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv ... loading intersphinx inventory 'seaborn' from https://seaborn.pydata.org/objects.inv ... loading intersphinx inventory 'session_info2' from https://session-info2.readthedocs.io/en/stable/objects.inv ... loading intersphinx inventory 'squidpy' from https://squidpy.readthedocs.io/en/stable/objects.inv ... loading intersphinx inventory 'sklearn' from https://scikit-learn.org/stable/objects.inv ... [autosummary] generating autosummary for: api/classes.md, api/datasets.md, api/deprecated.md, api/experimental.md, api/get.md, api/index.md, api/io.md, api/metrics.md, api/plotting.md, api/preprocessing.md, ..., tutorials/experimental/dask.ipynb, tutorials/experimental/index.md, tutorials/experimental/pearson_residuals.ipynb, tutorials/index.md, tutorials/plotting/advanced.ipynb, tutorials/plotting/core.ipynb, tutorials/plotting/index.md, tutorials/trajectories/index.md, tutorials/trajectories/paga-paul15.ipynb, usage-principles.md [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/scanpy.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/scanpy.Preset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/scanpy.Verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/scanpy.datasets.moignard15.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/external/generated/scanpy.external.tl.cyclone.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/external/generated/scanpy.external.tl.harmony_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/external/generated/scanpy.external.tl.palantir.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/external/generated/scanpy.external.tl.palantir_results.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/external/generated/scanpy.external.tl.phate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/external/generated/scanpy.external.tl.phenograph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/external/generated/scanpy.external.tl.sam.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/external/generated/scanpy.external.tl.sandbag.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/external/generated/scanpy.external.tl.trimap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/external/generated/scanpy.external.tl.wishbone.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/scanpy.Preset.scale.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/scanpy.Preset.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/scanpy.Preset.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/scanpy.Preset.umap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/scanpy.Verbosity.debug.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/scanpy.Verbosity.error.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/scanpy.Verbosity.hint.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/scanpy.Verbosity.info.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/api/generated/scanpy.Verbosity.level.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/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/4188/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) /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/tmpj71pwzzl/api/generated/classes/scanpy.pl.MatrixPlot-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpj71pwzzl/api/generated/classes/scanpy.pl.MatrixPlot-exec-1.ipynb: Executed notebook in 11.18 seconds [mystnb] /tmp/tmpj71pwzzl/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/tmp_i4hgoof/api/generated/classes/scanpy.pl.MatrixPlot.style-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp_i4hgoof/api/generated/classes/scanpy.pl.MatrixPlot.style-exec-1.ipynb: Executed notebook in 0.88 seconds [mystnb] /tmp/tmp_i4hgoof/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... [ 13%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER reading sources... [ 14%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE reading sources... [ 14%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH reading sources... [ 15%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING reading sources... [ 15%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS reading sources... [ 15%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING reading sources... [ 16%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE reading sources... [ 16%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX reading sources... [ 16%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT reading sources... [ 17%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM reading sources... [ 17%] api/generated/classes/scanpy.pl.StackedViolin.style reading sources... [ 18%] api/generated/scanpy.Neighbors reading sources... [ 18%] api/generated/scanpy.Neighbors.compute_eigen reading sources... [ 18%] api/generated/scanpy.Neighbors.compute_neighbors reading sources... [ 19%] api/generated/scanpy.Neighbors.compute_transitions reading sources... [ 19%] api/generated/scanpy.Neighbors.connectivities reading sources... [ 19%] api/generated/scanpy.Neighbors.distances reading sources... [ 20%] api/generated/scanpy.Neighbors.distances_dpt reading sources... [ 20%] api/generated/scanpy.Neighbors.eigen_basis reading sources... [ 21%] api/generated/scanpy.Neighbors.eigen_values reading sources... [ 21%] api/generated/scanpy.Neighbors.rp_forest reading sources... [ 21%] api/generated/scanpy.Neighbors.to_igraph reading sources... [ 22%] api/generated/scanpy.Neighbors.transitions reading sources... [ 22%] api/generated/scanpy.Neighbors.transitions_sym reading sources... [ 22%] api/generated/scanpy.Preset reading sources... [ 23%] api/generated/scanpy.Preset.check reading sources... [ 23%] api/generated/scanpy.Preset.diffmap reading sources... [ 24%] api/generated/scanpy.Preset.draw_graph reading sources... [ 24%] api/generated/scanpy.Preset.highly_variable_genes reading sources... [ 24%] api/generated/scanpy.Preset.leiden reading sources... [ 25%] api/generated/scanpy.Preset.override reading sources... [ 25%] api/generated/scanpy.Preset.pca reading sources... [ 25%] api/generated/scanpy.Preset.rank_genes_groups reading sources... [ 26%] api/generated/scanpy.Preset.scale reading sources... [ 26%] api/generated/scanpy.Preset.score_genes reading sources... [ 26%] api/generated/scanpy.Preset.tsne reading sources... [ 27%] api/generated/scanpy.Preset.umap reading sources... [ 27%] api/generated/scanpy.Verbosity reading sources... [ 28%] api/generated/scanpy.Verbosity.debug reading sources... [ 28%] api/generated/scanpy.Verbosity.error reading sources... [ 28%] api/generated/scanpy.Verbosity.hint reading sources... [ 29%] api/generated/scanpy.Verbosity.info reading sources... [ 29%] api/generated/scanpy.Verbosity.level reading sources... [ 29%] api/generated/scanpy.Verbosity.warning reading sources... [ 30%] api/generated/scanpy.datasets.blobs reading sources... [ 30%] api/generated/scanpy.datasets.ebi_expression_atlas reading sources... [ 31%] api/generated/scanpy.datasets.krumsiek11 reading sources... [ 31%] api/generated/scanpy.datasets.moignard15 reading sources... [ 31%] api/generated/scanpy.datasets.paul15 reading sources... [ 32%] api/generated/scanpy.datasets.pbmc3k reading sources... [ 32%] api/generated/scanpy.datasets.pbmc3k_processed reading sources... [ 32%] api/generated/scanpy.datasets.pbmc68k_reduced reading sources... [ 33%] api/generated/scanpy.datasets.toggleswitch reading sources... [ 33%] api/generated/scanpy.datasets.visium_sge reading sources... [ 34%] api/generated/scanpy.experimental.pp.highly_variable_genes reading sources... [ 34%] api/generated/scanpy.experimental.pp.normalize_pearson_residuals reading sources... [ 34%] api/generated/scanpy.experimental.pp.normalize_pearson_residuals_pca reading sources... [ 35%] api/generated/scanpy.experimental.pp.recipe_pearson_residuals reading sources... [ 35%] api/generated/scanpy.get.aggregate reading sources... [ 35%] api/generated/scanpy.get.obs_df reading sources... [ 36%] api/generated/scanpy.get.pca /tmp/tmp3p1elytx/api/generated/scanpy.get.pca-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp3p1elytx/api/generated/scanpy.get.pca-exec-1.ipynb: Executed notebook in 0.57 seconds [mystnb] /tmp/tmp3p1elytx/api/generated/scanpy.get.pca-exec-1.ipynb: Cached executed notebook: ID=3 [mystnb] reading sources... [ 36%] api/generated/scanpy.get.rank_genes_groups_df reading sources... [ 37%] api/generated/scanpy.get.var_df reading sources... [ 37%] api/generated/scanpy.logging.print_header reading sources... [ 37%] api/generated/scanpy.logging.print_versions reading sources... [ 38%] api/generated/scanpy.metrics.confusion_matrix /tmp/tmp7ratyt_n/api/generated/scanpy.metrics.confusion_matrix-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp7ratyt_n/api/generated/scanpy.metrics.confusion_matrix-exec-1.ipynb: Executed notebook in 1.09 seconds [mystnb] /tmp/tmp7ratyt_n/api/generated/scanpy.metrics.confusion_matrix-exec-1.ipynb: Cached executed notebook: ID=4 [mystnb] reading sources... [ 38%] api/generated/scanpy.metrics.gearys_c reading sources... [ 38%] api/generated/scanpy.metrics.modularity reading sources... [ 39%] api/generated/scanpy.metrics.morans_i reading sources... [ 39%] api/generated/scanpy.pl.clustermap /tmp/tmpp0r2bnip/api/generated/scanpy.pl.clustermap-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpp0r2bnip/api/generated/scanpy.pl.clustermap-exec-1.ipynb: Executed notebook in 1.75 seconds [mystnb] /tmp/tmpp0r2bnip/api/generated/scanpy.pl.clustermap-exec-1.ipynb: Cached executed notebook: ID=5 [mystnb] reading sources... [ 40%] api/generated/scanpy.pl.correlation_matrix /tmp/tmpbhdwnqec/api/generated/scanpy.pl.correlation_matrix-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpbhdwnqec/api/generated/scanpy.pl.correlation_matrix-exec-1.ipynb: Executed notebook in 0.92 seconds [mystnb] /tmp/tmpbhdwnqec/api/generated/scanpy.pl.correlation_matrix-exec-1.ipynb: Cached executed notebook: ID=6 [mystnb] reading sources... [ 40%] api/generated/scanpy.pl.dendrogram /tmp/tmp3o1njtd2/api/generated/scanpy.pl.dendrogram-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp3o1njtd2/api/generated/scanpy.pl.dendrogram-exec-1.ipynb: Executed notebook in 0.85 seconds [mystnb] /tmp/tmp3o1njtd2/api/generated/scanpy.pl.dendrogram-exec-1.ipynb: Cached executed notebook: ID=7 [mystnb] reading sources... [ 40%] api/generated/scanpy.pl.diffmap /tmp/tmp0oh6wdgg/api/generated/scanpy.pl.diffmap-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp0oh6wdgg/api/generated/scanpy.pl.diffmap-exec-1.ipynb: Executed notebook in 18.28 seconds [mystnb] /tmp/tmp0oh6wdgg/api/generated/scanpy.pl.diffmap-exec-1.ipynb: Cached executed notebook: ID=8 [mystnb] reading sources... [ 41%] api/generated/scanpy.pl.dot_area reading sources... [ 41%] api/generated/scanpy.pl.dotplot /tmp/tmpvp_tur5_/api/generated/scanpy.pl.dotplot-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpvp_tur5_/api/generated/scanpy.pl.dotplot-exec-1.ipynb: Executed notebook in 3.94 seconds [mystnb] /tmp/tmpvp_tur5_/api/generated/scanpy.pl.dotplot-exec-1.ipynb: Cached executed notebook: ID=9 [mystnb] reading sources... [ 41%] api/generated/scanpy.pl.dpt_groups_pseudotime reading sources... [ 42%] api/generated/scanpy.pl.dpt_timeseries reading sources... [ 42%] api/generated/scanpy.pl.draw_graph /tmp/tmpyu67a1pp/api/generated/scanpy.pl.draw_graph-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpyu67a1pp/api/generated/scanpy.pl.draw_graph-exec-1.ipynb: Executed notebook in 47.01 seconds [mystnb] /tmp/tmpyu67a1pp/api/generated/scanpy.pl.draw_graph-exec-1.ipynb: Cached executed notebook: ID=10 [mystnb] reading sources... [ 43%] api/generated/scanpy.pl.embedding /tmp/tmpzncgg038/api/generated/scanpy.pl.embedding-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpzncgg038/api/generated/scanpy.pl.embedding-exec-1.ipynb: Executed notebook in 1.23 seconds [mystnb] /tmp/tmpzncgg038/api/generated/scanpy.pl.embedding-exec-1.ipynb: Cached executed notebook: ID=11 [mystnb] reading sources... [ 43%] api/generated/scanpy.pl.embedding_density /tmp/tmpt0dwlr98/api/generated/scanpy.pl.embedding_density-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpt0dwlr98/api/generated/scanpy.pl.embedding_density-exec-1.ipynb: Executed notebook in 4.76 seconds [mystnb] /tmp/tmpt0dwlr98/api/generated/scanpy.pl.embedding_density-exec-1.ipynb: Cached executed notebook: ID=12 [mystnb] reading sources... [ 43%] api/generated/scanpy.pl.heatmap /tmp/tmpna9kfta7/api/generated/scanpy.pl.heatmap-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpna9kfta7/api/generated/scanpy.pl.heatmap-exec-1.ipynb: Executed notebook in 13.60 seconds [mystnb] /tmp/tmpna9kfta7/api/generated/scanpy.pl.heatmap-exec-1.ipynb: Cached executed notebook: ID=13 [mystnb] reading sources... [ 44%] api/generated/scanpy.pl.highest_expr_genes /tmp/tmpv7py8m6y/api/generated/scanpy.pl.highest_expr_genes-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpv7py8m6y/api/generated/scanpy.pl.highest_expr_genes-exec-1.ipynb: Executed notebook in 5.98 seconds [mystnb] /tmp/tmpv7py8m6y/api/generated/scanpy.pl.highest_expr_genes-exec-1.ipynb: Cached executed notebook: ID=14 [mystnb] reading sources... [ 44%] api/generated/scanpy.pl.highly_variable_genes /tmp/tmpc3k4p7me/api/generated/scanpy.pl.highly_variable_genes-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpc3k4p7me/api/generated/scanpy.pl.highly_variable_genes-exec-1.ipynb: Executed notebook in 8.19 seconds [mystnb] /tmp/tmpc3k4p7me/api/generated/scanpy.pl.highly_variable_genes-exec-1.ipynb: Cached executed notebook: ID=15 [mystnb] reading sources... [ 44%] api/generated/scanpy.pl.matrixplot /tmp/tmpj_nwus22/api/generated/scanpy.pl.matrixplot-exec-1.ipynb: Executing notebook using local CWD [mystnb] reading sources... [ 45%] api/generated/scanpy.pl.paga /tmp/tmpauxxr6pz/api/generated/scanpy.pl.paga-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpauxxr6pz/api/generated/scanpy.pl.paga-exec-1.ipynb: Executed notebook in 1.22 seconds [mystnb] /tmp/tmpauxxr6pz/api/generated/scanpy.pl.paga-exec-1.ipynb: Cached executed notebook: ID=16 [mystnb] reading sources... [ 45%] api/generated/scanpy.pl.paga_compare /tmp/tmpmfzbtcg_/api/generated/scanpy.pl.paga_compare-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpmfzbtcg_/api/generated/scanpy.pl.paga_compare-exec-1.ipynb: Executed notebook in 0.96 seconds [mystnb] /tmp/tmpmfzbtcg_/api/generated/scanpy.pl.paga_compare-exec-1.ipynb: Cached executed notebook: ID=17 [mystnb] reading sources... [ 46%] api/generated/scanpy.pl.paga_path reading sources... [ 46%] api/generated/scanpy.pl.pca /tmp/tmp9dnhgzxx/api/generated/scanpy.pl.pca-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp9dnhgzxx/api/generated/scanpy.pl.pca-exec-1.ipynb: Executed notebook in 4.25 seconds [mystnb] /tmp/tmp9dnhgzxx/api/generated/scanpy.pl.pca-exec-1.ipynb: Cached executed notebook: ID=18 [mystnb] reading sources... [ 46%] api/generated/scanpy.pl.pca_loadings /tmp/tmpe4e1u34o/api/generated/scanpy.pl.pca_loadings-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpe4e1u34o/api/generated/scanpy.pl.pca_loadings-exec-1.ipynb: Executed notebook in 1.28 seconds [mystnb] /tmp/tmpe4e1u34o/api/generated/scanpy.pl.pca_loadings-exec-1.ipynb: Cached executed notebook: ID=19 [mystnb] reading sources... [ 47%] api/generated/scanpy.pl.pca_overview /tmp/tmpl04f66f8/api/generated/scanpy.pl.pca_overview-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpl04f66f8/api/generated/scanpy.pl.pca_overview-exec-1.ipynb: Executed notebook in 1.49 seconds [mystnb] /tmp/tmpl04f66f8/api/generated/scanpy.pl.pca_overview-exec-1.ipynb: Cached executed notebook: ID=20 [mystnb] reading sources... [ 47%] api/generated/scanpy.pl.pca_variance_ratio /tmp/tmp6s8fopxo/api/generated/scanpy.pl.pca_variance_ratio-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp6s8fopxo/api/generated/scanpy.pl.pca_variance_ratio-exec-1.ipynb: Executed notebook in 1.22 seconds [mystnb] /tmp/tmp6s8fopxo/api/generated/scanpy.pl.pca_variance_ratio-exec-1.ipynb: Cached executed notebook: ID=21 [mystnb] reading sources... [ 47%] api/generated/scanpy.pl.rank_genes_groups /tmp/tmpxef2z0n3/api/generated/scanpy.pl.rank_genes_groups-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpxef2z0n3/api/generated/scanpy.pl.rank_genes_groups-exec-1.ipynb: Executed notebook in 2.96 seconds [mystnb] /tmp/tmpxef2z0n3/api/generated/scanpy.pl.rank_genes_groups-exec-1.ipynb: Cached executed notebook: ID=22 [mystnb] reading sources... [ 48%] api/generated/scanpy.pl.rank_genes_groups_dotplot /tmp/tmpcvwxgbrc/api/generated/scanpy.pl.rank_genes_groups_dotplot-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpcvwxgbrc/api/generated/scanpy.pl.rank_genes_groups_dotplot-exec-1.ipynb: Executed notebook in 6.62 seconds [mystnb] /tmp/tmpcvwxgbrc/api/generated/scanpy.pl.rank_genes_groups_dotplot-exec-1.ipynb: Cached executed notebook: ID=23 [mystnb] reading sources... [ 48%] api/generated/scanpy.pl.rank_genes_groups_heatmap /tmp/tmp7lgm2a0e/api/generated/scanpy.pl.rank_genes_groups_heatmap-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp7lgm2a0e/api/generated/scanpy.pl.rank_genes_groups_heatmap-exec-1.ipynb: Executed notebook in 3.95 seconds [mystnb] /tmp/tmp7lgm2a0e/api/generated/scanpy.pl.rank_genes_groups_heatmap-exec-1.ipynb: Cached executed notebook: ID=24 [mystnb] reading sources... [ 49%] api/generated/scanpy.pl.rank_genes_groups_matrixplot /tmp/tmphjpqdob1/api/generated/scanpy.pl.rank_genes_groups_matrixplot-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmphjpqdob1/api/generated/scanpy.pl.rank_genes_groups_matrixplot-exec-1.ipynb: Executed notebook in 3.64 seconds [mystnb] /tmp/tmphjpqdob1/api/generated/scanpy.pl.rank_genes_groups_matrixplot-exec-1.ipynb: Cached executed notebook: ID=25 [mystnb] reading sources... [ 49%] api/generated/scanpy.pl.rank_genes_groups_stacked_violin /tmp/tmpp7_tgvxv/api/generated/scanpy.pl.rank_genes_groups_stacked_violin-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpp7_tgvxv/api/generated/scanpy.pl.rank_genes_groups_stacked_violin-exec-1.ipynb: Executed notebook in 6.51 seconds [mystnb] /tmp/tmpp7_tgvxv/api/generated/scanpy.pl.rank_genes_groups_stacked_violin-exec-1.ipynb: Cached executed notebook: ID=26 [mystnb] reading sources... [ 49%] api/generated/scanpy.pl.rank_genes_groups_tracksplot /tmp/tmpbecz3tdf/api/generated/scanpy.pl.rank_genes_groups_tracksplot-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpbecz3tdf/api/generated/scanpy.pl.rank_genes_groups_tracksplot-exec-1.ipynb: Executed notebook in 11.88 seconds [mystnb] /tmp/tmpbecz3tdf/api/generated/scanpy.pl.rank_genes_groups_tracksplot-exec-1.ipynb: Cached executed notebook: ID=27 [mystnb] reading sources... [ 50%] api/generated/scanpy.pl.rank_genes_groups_violin /tmp/tmpwyhrvzkd/api/generated/scanpy.pl.rank_genes_groups_violin-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpwyhrvzkd/api/generated/scanpy.pl.rank_genes_groups_violin-exec-1.ipynb: Executed notebook in 2.40 seconds [mystnb] /tmp/tmpwyhrvzkd/api/generated/scanpy.pl.rank_genes_groups_violin-exec-1.ipynb: Cached executed notebook: ID=28 [mystnb] reading sources... [ 50%] api/generated/scanpy.pl.ranking /tmp/tmpl6duoxbs/api/generated/scanpy.pl.ranking-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpl6duoxbs/api/generated/scanpy.pl.ranking-exec-1.ipynb: Executed notebook in 4.19 seconds [mystnb] /tmp/tmpl6duoxbs/api/generated/scanpy.pl.ranking-exec-1.ipynb: Cached executed notebook: ID=29 [mystnb] reading sources... [ 50%] api/generated/scanpy.pl.scatter /tmp/tmp8g4znvkx/api/generated/scanpy.pl.scatter-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp8g4znvkx/api/generated/scanpy.pl.scatter-exec-1.ipynb: Executed notebook in 3.80 seconds [mystnb] /tmp/tmp8g4znvkx/api/generated/scanpy.pl.scatter-exec-1.ipynb: Cached executed notebook: ID=30 [mystnb] reading sources... [ 51%] api/generated/scanpy.pl.scrublet_score_distribution /tmp/tmp9q8xw8ic/api/generated/scanpy.pl.scrublet_score_distribution-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp9q8xw8ic/api/generated/scanpy.pl.scrublet_score_distribution-exec-1.ipynb: Executed notebook in 5.05 seconds [mystnb] /tmp/tmp9q8xw8ic/api/generated/scanpy.pl.scrublet_score_distribution-exec-1.ipynb: Cached executed notebook: ID=31 [mystnb] reading sources... [ 51%] api/generated/scanpy.pl.sim reading sources... [ 51%] api/generated/scanpy.pl.spatial reading sources... [ 52%] api/generated/scanpy.pl.stacked_violin /tmp/tmp6ntlpxuu/api/generated/scanpy.pl.stacked_violin-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmp6ntlpxuu/api/generated/scanpy.pl.stacked_violin-exec-1.ipynb: Executed notebook in 22.87 seconds [mystnb] /tmp/tmp6ntlpxuu/api/generated/scanpy.pl.stacked_violin-exec-1.ipynb: Cached executed notebook: ID=32 [mystnb] reading sources... [ 52%] api/generated/scanpy.pl.tracksplot /tmp/tmpl6kl9jz5/api/generated/scanpy.pl.tracksplot-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpl6kl9jz5/api/generated/scanpy.pl.tracksplot-exec-1.ipynb: Executed notebook in 17.21 seconds [mystnb] /tmp/tmpl6kl9jz5/api/generated/scanpy.pl.tracksplot-exec-1.ipynb: Cached executed notebook: ID=33 [mystnb] reading sources... [ 53%] api/generated/scanpy.pl.tsne /tmp/tmpx_7iwzqb/api/generated/scanpy.pl.tsne-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpx_7iwzqb/api/generated/scanpy.pl.tsne-exec-1.ipynb: Executed notebook in 11.11 seconds [mystnb] /tmp/tmpx_7iwzqb/api/generated/scanpy.pl.tsne-exec-1.ipynb: Cached executed notebook: ID=34 [mystnb] reading sources... [ 53%] api/generated/scanpy.pl.umap /tmp/tmpw0d967y7/api/generated/scanpy.pl.umap-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpw0d967y7/api/generated/scanpy.pl.umap-exec-1.ipynb: Executed notebook in 6.32 seconds [mystnb] /tmp/tmpw0d967y7/api/generated/scanpy.pl.umap-exec-1.ipynb: Cached executed notebook: ID=35 [mystnb] reading sources... [ 53%] api/generated/scanpy.pl.violin /tmp/tmpb8bj_4xw/api/generated/scanpy.pl.violin-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpb8bj_4xw/api/generated/scanpy.pl.violin-exec-1.ipynb: Executed notebook in 10.34 seconds [mystnb] /tmp/tmpb8bj_4xw/api/generated/scanpy.pl.violin-exec-1.ipynb: Cached executed notebook: ID=36 [mystnb] reading sources... [ 54%] api/generated/scanpy.pp.calculate_qc_metrics /tmp/tmps191d9i8/api/generated/scanpy.pp.calculate_qc_metrics-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmps191d9i8/api/generated/scanpy.pp.calculate_qc_metrics-exec-1.ipynb: Executed notebook in 16.52 seconds [mystnb] /tmp/tmps191d9i8/api/generated/scanpy.pp.calculate_qc_metrics-exec-1.ipynb: Cached executed notebook: ID=37 [mystnb] reading sources... [ 54%] api/generated/scanpy.pp.combat reading sources... [ 54%] api/generated/scanpy.pp.downsample_counts reading sources... [ 55%] api/generated/scanpy.pp.filter_cells reading sources... [ 55%] api/generated/scanpy.pp.filter_genes reading sources... [ 56%] api/generated/scanpy.pp.harmony_integrate reading sources... [ 56%] api/generated/scanpy.pp.highly_variable_genes reading sources... [ 56%] api/generated/scanpy.pp.log1p reading sources... [ 57%] api/generated/scanpy.pp.neighbors reading sources... [ 57%] api/generated/scanpy.pp.normalize_total reading sources... [ 57%] api/generated/scanpy.pp.pca reading sources... [ 58%] api/generated/scanpy.pp.recipe_seurat reading sources... [ 58%] api/generated/scanpy.pp.recipe_weinreb17 reading sources... [ 59%] api/generated/scanpy.pp.recipe_zheng17 reading sources... [ 59%] api/generated/scanpy.pp.regress_out reading sources... [ 59%] api/generated/scanpy.pp.sample reading sources... [ 60%] api/generated/scanpy.pp.scale reading sources... [ 60%] api/generated/scanpy.pp.scrublet reading sources... [ 60%] api/generated/scanpy.pp.scrublet_simulate_doublets reading sources... [ 61%] api/generated/scanpy.pp.subsample reading sources... [ 61%] api/generated/scanpy.queries.biomart_annotations reading sources... [ 62%] api/generated/scanpy.queries.enrich reading sources... [ 62%] api/generated/scanpy.queries.gene_coordinates reading sources... [ 62%] api/generated/scanpy.queries.mitochondrial_genes reading sources... [ 63%] api/generated/scanpy.read reading sources... [ 63%] api/generated/scanpy.read_10x_h5 reading sources... [ 63%] api/generated/scanpy.read_10x_mtx reading sources... [ 64%] api/generated/scanpy.read_csv reading sources... [ 64%] api/generated/scanpy.read_excel reading sources... [ 65%] api/generated/scanpy.read_h5ad reading sources... [ 65%] api/generated/scanpy.read_hdf reading sources... [ 65%] api/generated/scanpy.read_loom reading sources... [ 66%] api/generated/scanpy.read_mtx reading sources... [ 66%] api/generated/scanpy.read_text reading sources... [ 66%] api/generated/scanpy.read_umi_tools reading sources... [ 67%] api/generated/scanpy.read_visium reading sources... [ 67%] api/generated/scanpy.set_figure_params reading sources... [ 68%] api/generated/scanpy.settings reading sources... [ 68%] api/generated/scanpy.settings.override reading sources... [ 68%] api/generated/scanpy.tl.dendrogram reading sources... [ 69%] api/generated/scanpy.tl.diffmap reading sources... [ 69%] api/generated/scanpy.tl.dpt reading sources... [ 69%] api/generated/scanpy.tl.draw_graph reading sources... [ 70%] api/generated/scanpy.tl.embedding_density /tmp/tmpif08iuv9/api/generated/scanpy.tl.embedding_density-exec-1.ipynb: Executing notebook using local CWD [mystnb] /tmp/tmpif08iuv9/api/generated/scanpy.tl.embedding_density-exec-1.ipynb: Executed notebook in 2.27 seconds [mystnb] /tmp/tmpif08iuv9/api/generated/scanpy.tl.embedding_density-exec-1.ipynb: Cached executed notebook: ID=38 [mystnb] reading sources... [ 70%] api/generated/scanpy.tl.filter_rank_genes_groups reading sources... [ 71%] api/generated/scanpy.tl.ingest reading sources... [ 71%] api/generated/scanpy.tl.leiden reading sources... [ 71%] api/generated/scanpy.tl.louvain reading sources... [ 72%] api/generated/scanpy.tl.marker_gene_overlap reading sources... [ 72%] api/generated/scanpy.tl.paga reading sources... [ 72%] api/generated/scanpy.tl.rank_genes_groups reading sources... [ 73%] api/generated/scanpy.tl.score_genes reading sources... [ 73%] api/generated/scanpy.tl.score_genes_cell_cycle reading sources... [ 74%] api/generated/scanpy.tl.sim reading sources... [ 74%] api/generated/scanpy.tl.tsne reading sources... [ 74%] api/generated/scanpy.tl.umap reading sources... [ 75%] api/generated/scanpy.write reading sources... [ 75%] api/get reading sources... [ 75%] api/index reading sources... [ 76%] api/io reading sources... [ 76%] api/metrics reading sources... [ 76%] api/plotting reading sources... [ 77%] api/preprocessing reading sources... [ 77%] api/queries reading sources... [ 78%] api/settings reading sources... [ 78%] api/tools reading sources... [ 78%] basic_usage reading sources... [ 79%] community reading sources... [ 79%] contributors reading sources... [ 79%] dev/ci reading sources... [ 80%] dev/code reading sources... [ 80%] dev/documentation reading sources... [ 81%] dev/getting-set-up reading sources... [ 81%] dev/index reading sources... [ 81%] dev/release reading sources... [ 82%] dev/testing reading sources... [ 82%] dev/versioning reading sources... [ 82%] external/exporting reading sources... [ 83%] external/generated/scanpy.external.exporting.cellbrowser reading sources... [ 83%] external/generated/scanpy.external.exporting.spring_project reading sources... [ 84%] external/generated/scanpy.external.pl.phate reading sources... [ 84%] external/generated/scanpy.external.pl.sam reading sources... [ 84%] external/generated/scanpy.external.pl.trimap reading sources... [ 85%] external/generated/scanpy.external.pl.wishbone_marker_trajectory reading sources... [ 85%] external/generated/scanpy.external.pp.bbknn reading sources... [ 85%] external/generated/scanpy.external.pp.hashsolo reading sources... [ 86%] external/generated/scanpy.external.pp.magic reading sources... [ 86%] external/generated/scanpy.external.pp.mnn_correct reading sources... [ 87%] external/generated/scanpy.external.pp.scanorama_integrate reading sources... [ 87%] external/generated/scanpy.external.tl.cyclone reading sources... [ 87%] external/generated/scanpy.external.tl.harmony_timeseries reading sources... [ 88%] external/generated/scanpy.external.tl.palantir reading sources... [ 88%] external/generated/scanpy.external.tl.palantir_results reading sources... [ 88%] external/generated/scanpy.external.tl.phate reading sources... [ 89%] external/generated/scanpy.external.tl.phenograph reading sources... [ 89%] external/generated/scanpy.external.tl.sam reading sources... [ 90%] external/generated/scanpy.external.tl.sandbag reading sources... [ 90%] external/generated/scanpy.external.tl.trimap reading sources... [ 90%] external/generated/scanpy.external.tl.wishbone reading sources... [ 91%] external/index reading sources... [ 91%] external/plotting reading sources... [ 91%] external/preprocessing reading sources... [ 92%] external/tools reading sources... [ 92%] how-to/cell-cycle /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/how-to/cell-cycle.ipynb: Excluded from execution by pattern: 'how-to/*' [mystnb] reading sources... [ 93%] how-to/index reading sources... [ 93%] how-to/knn-transformers /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/how-to/knn-transformers.ipynb: Excluded from execution by pattern: 'how-to/*' [mystnb] reading sources... [ 93%] how-to/plotting-with-marsilea /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/how-to/plotting-with-marsilea.ipynb: Excluded from execution by pattern: 'how-to/*' [mystnb] reading sources... [ 94%] index reading sources... [ 94%] installation reading sources... [ 94%] references reading sources... [ 95%] release-notes/index reading sources... [ 95%] tutorials/basics/clustering /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/tutorials/basics/clustering.ipynb: Excluded from execution by pattern: 'tutorials/*/*' [mystnb] reading sources... [ 96%] tutorials/basics/clustering-2017 /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/tutorials/basics/clustering-2017.ipynb: Excluded from execution by pattern: 'tutorials/*/*' [mystnb] reading sources... [ 96%] tutorials/basics/index reading sources... [ 96%] tutorials/basics/integrating-data-using-ingest /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/tutorials/basics/integrating-data-using-ingest.ipynb: Excluded from execution by pattern: 'tutorials/*/*' [mystnb] reading sources... [ 97%] tutorials/experimental/dask /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/tutorials/experimental/dask.ipynb: Excluded from execution by pattern: 'tutorials/*/*' [mystnb] reading sources... [ 97%] tutorials/experimental/index reading sources... [ 97%] tutorials/experimental/pearson_residuals /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/tutorials/experimental/pearson_residuals.ipynb: Excluded from execution by pattern: 'tutorials/*/*' [mystnb] reading sources... [ 98%] tutorials/index reading sources... [ 98%] tutorials/plotting/advanced /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/tutorials/plotting/advanced.ipynb: Excluded from execution by pattern: 'tutorials/*/*' [mystnb] reading sources... [ 99%] tutorials/plotting/core /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/tutorials/plotting/core.ipynb: Excluded from execution by pattern: 'tutorials/*/*' [mystnb] reading sources... [ 99%] tutorials/plotting/index reading sources... [ 99%] tutorials/trajectories/index reading sources... [100%] tutorials/trajectories/paga-paul15 /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/tutorials/trajectories/paga-paul15.ipynb: Excluded from execution by pattern: 'tutorials/*/*' [mystnb] reading sources... [100%] usage-principles /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/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/TCvYOmNh/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/TCvYOmNh/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/TCvYOmNh/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/TCvYOmNh/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/TCvYOmNh/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/TCvYOmNh/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 ) ------------------ [31m---------------------------------------------------------------------------[39m [31mValueError[39m Traceback (most recent call last) [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/core/dimension.py:1491[39m, in [36mDimensioned._repr_mimebundle_[39m[34m(self, include, exclude)[39m [32m 1484[39m [38;5;28;01mdef[39;00m[38;5;250m [39m[34m_repr_mimebundle_[39m([38;5;28mself[39m, include=[38;5;28;01mNone[39;00m, exclude=[38;5;28;01mNone[39;00m): [32m 1485[39m [38;5;250m [39m[33;03m"""Resolves the class hierarchy for the class rendering the[39;00m [32m 1486[39m [33;03m object using any display hooks registered on Store.display[39;00m [32m 1487[39m [33;03m hooks. The output of all registered display_hooks is then[39;00m [32m 1488[39m [33;03m combined and returned.[39;00m [32m 1489[39m [32m 1490[39m [33;03m """[39;00m [32m-> [39m[32m1491[39m [38;5;28;01mreturn[39;00m [30;43mStore[39;49m[30;43m.[39;49m[30;43mrender[39;49m[30;43m([39;49m[30;43mself[39;49m[30;43m)[39;49m [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/core/options.py:1517[39m, in [36mStore.render[39m[34m(cls, obj)[39m [32m 1515[39m data, metadata = {}, {} [32m 1516[39m [38;5;28;01mfor[39;00m hook [38;5;129;01min[39;00m hooks: [32m-> [39m[32m1517[39m ret = [30;43mhook[39;49m[30;43m([39;49m[30;43mobj[39;49m[30;43m)[39;49m [32m 1518[39m [38;5;28;01mif[39;00m ret [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m: [32m 1519[39m [38;5;28;01mcontinue[39;00m [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/ipython/display_hooks.py:330[39m, in [36mpprint_display[39m[34m(obj)[39m [32m 328[39m [38;5;28;01mif[39;00m [38;5;129;01mnot[39;00m ip.display_formatter.formatters[[33m"[39m[33mtext/plain[39m[33m"[39m].pprint: [32m 329[39m [38;5;28;01mreturn[39;00m [38;5;28;01mNone[39;00m [32m--> [39m[32m330[39m [38;5;28;01mreturn[39;00m [30;43mdisplay[39;49m[30;43m([39;49m[30;43mobj[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mraw_output[39;49m[30;43m=[39;49m[30;43;01mTrue[39;49;00m[30;43m)[39;49m [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/ipython/display_hooks.py:301[39m, in [36mdisplay[39m[34m(obj, raw_output, **kwargs)[39m [32m 299[39m [38;5;28;01melif[39;00m [38;5;28misinstance[39m(obj, (Layout, NdLayout, AdjointLayout)): [32m 300[39m [38;5;28;01mwith[39;00m option_state(obj): [32m--> [39m[32m301[39m output = [30;43mlayout_display[39;49m[30;43m([39;49m[30;43mobj[39;49m[30;43m)[39;49m [32m 302[39m [38;5;28;01melif[39;00m [38;5;28misinstance[39m(obj, (HoloMap, DynamicMap)): [32m 303[39m [38;5;28;01mwith[39;00m option_state(obj): [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/ipython/display_hooks.py:193[39m, in [36mdisplay_hook..wrapped[39m[34m(element)[39m [32m 191[39m [38;5;28;01mtry[39;00m: [32m 192[39m max_frames = OutputSettings.options[[33m"[39m[33mmax_frames[39m[33m"[39m] [32m--> [39m[32m193[39m mimebundle = [30;43mfn[39;49m[30;43m([39;49m[30;43melement[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mmax_frames[39;49m[30;43m=[39;49m[30;43mmax_frames[39;49m[30;43m)[39;49m [32m 194[39m [38;5;28;01mif[39;00m mimebundle [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m: [32m 195[39m [38;5;28;01mreturn[39;00m {}, {} [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/ipython/display_hooks.py:261[39m, in [36mlayout_display[39m[34m(layout, max_frames)[39m [32m 258[39m max_frame_warning(max_frames) [32m 259[39m [38;5;28;01mreturn[39;00m [38;5;28;01mNone[39;00m [32m--> [39m[32m261[39m [38;5;28;01mreturn[39;00m [30;43mrender[39;49m[30;43m([39;49m[30;43mlayout[39;49m[30;43m)[39;49m [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/ipython/display_hooks.py:62[39m, in [36mrender[39m[34m(obj, **kwargs)[39m [32m 59[39m [38;5;28;01mif[39;00m renderer.fig == [33m"[39m[33mpdf[39m[33m"[39m: [32m 60[39m renderer = renderer.instance(fig=[33m"[39m[33mpng[39m[33m"[39m) [32m---> [39m[32m62[39m [38;5;28;01mreturn[39;00m [30;43mrenderer[39;49m[30;43m.[39;49m[30;43mcomponents[39;49m[30;43m([39;49m[30;43mobj[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43m*[39;49m[30;43m*[39;49m[30;43mkwargs[39;49m[30;43m)[39;49m [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/plotting/renderer.py:450[39m, in [36mRenderer.components[39m[34m(self, obj, fmt, comm, **kwargs)[39m [32m 448[39m embed = [38;5;129;01mnot[39;00m (dynamic [38;5;129;01mor[39;00m streams [38;5;129;01mor[39;00m [38;5;28mself[39m.widget_mode == [33m"[39m[33mlive[39m[33m"[39m) [38;5;129;01mor[39;00m config.embed [32m 449[39m [38;5;28;01mif[39;00m embed [38;5;129;01mor[39;00m config.comms == [33m"[39m[33mdefault[39m[33m"[39m: [32m--> [39m[32m450[39m [38;5;28;01mreturn[39;00m [30;43mself[39;49m[30;43m.[39;49m[30;43m_render_panel[39;49m[30;43m([39;49m[30;43mplot[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43membed[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mcomm[39;49m[30;43m)[39;49m [32m 451[39m [38;5;28;01mreturn[39;00m [38;5;28mself[39m._render_ipywidget(plot) [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/plotting/renderer.py:457[39m, in [36mRenderer._render_panel[39m[34m(self, plot, embed, comm)[39m [32m 455[39m doc = Document() [32m 456[39m [38;5;28;01mwith[39;00m config.set(embed=embed): [32m--> [39m[32m457[39m model = [30;43mplot[39;49m[30;43m.[39;49m[30;43mlayout[39;49m[30;43m.[39;49m[30;43m_render_model[39;49m[30;43m([39;49m[30;43mdoc[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mcomm[39;49m[30;43m)[39;49m [32m 458[39m [38;5;28;01mif[39;00m embed: [32m 459[39m [38;5;28;01mreturn[39;00m render_model(model, comm) [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/panel/viewable.py:775[39m, in [36mViewable._render_model[39m[34m(self, doc, comm)[39m [32m 773[39m [38;5;28;01mif[39;00m comm [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m: [32m 774[39m comm = state._comm_manager.get_server_comm() [32m--> [39m[32m775[39m model = [30;43mself[39;49m[30;43m.[39;49m[30;43mget_root[39;49m[30;43m([39;49m[30;43mdoc[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mcomm[39;49m[30;43m)[39;49m [32m 777[39m [38;5;28;01mif[39;00m [38;5;28mself[39m._design [38;5;129;01mand[39;00m [38;5;28mself[39m._design.theme.bokeh_theme: [32m 778[39m doc.theme = [38;5;28mself[39m._design.theme.bokeh_theme [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/panel/layout/base.py:332[39m, in [36mPanel.get_root[39m[34m(self, doc, comm, preprocess)[39m [32m 328[39m [38;5;28;01mdef[39;00m[38;5;250m [39m[34mget_root[39m( [32m 329[39m [38;5;28mself[39m, doc: Document | [38;5;28;01mNone[39;00m = [38;5;28;01mNone[39;00m, comm: Comm | [38;5;28;01mNone[39;00m = [38;5;28;01mNone[39;00m, [32m 330[39m preprocess: [38;5;28mbool[39m = [38;5;28;01mTrue[39;00m [32m 331[39m ) -> Model: [32m--> [39m[32m332[39m root = [30;43msuper[39;49m[30;43m([39;49m[30;43m)[39;49m[30;43m.[39;49m[30;43mget_root[39;49m[30;43m([39;49m[30;43mdoc[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mcomm[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mpreprocess[39;49m[30;43m)[39;49m [32m 333[39m [38;5;66;03m# ALERT: Find a better way to handle this[39;00m [32m 334[39m [38;5;28;01mif[39;00m [38;5;28mhasattr[39m(root, [33m'[39m[33mstyles[39m[33m'[39m) [38;5;129;01mand[39;00m [33m'[39m[33moverflow-x[39m[33m'[39m [38;5;129;01min[39;00m root.styles: [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/panel/viewable.py:705[39m, in [36mRenderable.get_root[39m[34m(self, doc, comm, preprocess)[39m [32m 703[39m wrapper = [38;5;28mself[39m._design._wrapper([38;5;28mself[39m) [32m 704[39m [38;5;28;01mif[39;00m wrapper [38;5;129;01mis[39;00m [38;5;28mself[39m: [32m--> [39m[32m705[39m root = [30;43mself[39;49m[30;43m.[39;49m[30;43m_get_model[39;49m[30;43m([39;49m[30;43mdoc[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mcomm[39;49m[30;43m=[39;49m[30;43mcomm[39;49m[30;43m)[39;49m [32m 706[39m [38;5;28;01mif[39;00m preprocess: [32m 707[39m [38;5;28mself[39m._preprocess(root) [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/panel/layout/base.py:316[39m, in [36mPanel._get_model[39m[34m(self, doc, root, parent, comm)[39m [32m 314[39m root = root [38;5;129;01mor[39;00m model [32m 315[39m [38;5;28mself[39m._models[root.ref[[33m'[39m[33mid[39m[33m'[39m]] = (model, parent) [32m--> [39m[32m316[39m objects, _ = [30;43mself[39;49m[30;43m.[39;49m[30;43m_get_objects[39;49m[30;43m([39;49m[30;43mmodel[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43m[[39;49m[30;43m][39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mdoc[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mroot[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mcomm[39;49m[30;43m)[39;49m [32m 317[39m props = [38;5;28mself[39m._get_properties(doc) [32m 318[39m props[[38;5;28mself[39m._property_mapping[[33m'[39m[33mobjects[39m[33m'[39m]] = objects [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/panel/layout/base.py:298[39m, in [36mPanel._get_objects[39m[34m(self, model, old_objects, doc, root, comm)[39m [32m 296[39m [38;5;28;01melse[39;00m: [32m 297[39m [38;5;28;01mtry[39;00m: [32m--> [39m[32m298[39m child = [30;43mpane[39;49m[30;43m.[39;49m[30;43m_get_model[39;49m[30;43m([39;49m[30;43mdoc[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mroot[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mmodel[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mcomm[39;49m[30;43m)[39;49m [32m 299[39m [38;5;28;01mexcept[39;00m RerenderError [38;5;28;01mas[39;00m e: [32m 300[39m [38;5;28;01mif[39;00m e.layout [38;5;129;01mis[39;00m [38;5;129;01mnot[39;00m [38;5;28;01mNone[39;00m [38;5;129;01mand[39;00m e.layout [38;5;129;01mis[39;00m [38;5;129;01mnot[39;00m [38;5;28mself[39m: [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/panel/pane/holoviews.py:494[39m, in [36mHoloViews._get_model[39m[34m(self, doc, root, parent, comm)[39m [32m 492[39m plot = [38;5;28mself[39m.object [32m 493[39m [38;5;28;01melse[39;00m: [32m--> [39m[32m494[39m plot = [30;43mself[39;49m[30;43m.[39;49m[30;43m_render[39;49m[30;43m([39;49m[30;43mdoc[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mcomm[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mroot[39;49m[30;43m)[39;49m [32m 496[39m plot.pane = [38;5;28mself[39m [32m 497[39m backend = plot.renderer.backend [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/panel/pane/holoviews.py:588[39m, in [36mHoloViews._render[39m[34m(self, doc, comm, root)[39m [32m 585[39m [38;5;28;01mif[39;00m comm: [32m 586[39m kwargs[[33m'[39m[33mcomm[39m[33m'[39m] = comm [32m--> [39m[32m588[39m [38;5;28;01mreturn[39;00m [30;43mrenderer[39;49m[30;43m.[39;49m[30;43mget_plot[39;49m[30;43m([39;49m[30;43mself[39;49m[30;43m.[39;49m[30;43mobject[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43m*[39;49m[30;43m*[39;49m[30;43mkwargs[39;49m[30;43m)[39;49m [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/plotting/bokeh/renderer.py:77[39m, in [36mBokehRenderer.get_plot[39m[34m(self_or_cls, obj, doc, renderer, **kwargs)[39m [32m 70[39m [38;5;129m@bothmethod[39m [32m 71[39m [38;5;28;01mdef[39;00m[38;5;250m [39m[34mget_plot[39m(self_or_cls, obj, doc=[38;5;28;01mNone[39;00m, renderer=[38;5;28;01mNone[39;00m, **kwargs): [32m 72[39m [38;5;250m [39m[33;03m"""Given a HoloViews Viewable return a corresponding plot instance.[39;00m [32m 73[39m [33;03m Allows supplying a document attach the plot to, useful when[39;00m [32m 74[39m [33;03m combining the bokeh model with another plot.[39;00m [32m 75[39m [32m 76[39m [33;03m """[39;00m [32m---> [39m[32m77[39m plot = [30;43msuper[39;49m[30;43m([39;49m[30;43m)[39;49m[30;43m.[39;49m[30;43mget_plot[39;49m[30;43m([39;49m[30;43mobj[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mdoc[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mrenderer[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43m*[39;49m[30;43m*[39;49m[30;43mkwargs[39;49m[30;43m)[39;49m [32m 78[39m [38;5;28;01mif[39;00m plot.document [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m: [32m 79[39m plot.document = Document() [38;5;28;01mif[39;00m self_or_cls.notebook_context [38;5;28;01melse[39;00m curdoc() [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/plotting/renderer.py:286[39m, in [36mRenderer.get_plot[39m[34m(self_or_cls, obj, doc, renderer, comm, **kwargs)[39m [32m 284[39m [38;5;28;01mif[39;00m [38;5;28misinstance[39m(obj, AdjointLayout): [32m 285[39m obj = Layout(obj) [32m--> [39m[32m286[39m plot = [30;43mself_or_cls[39;49m[30;43m.[39;49m[30;43mplotting_class[39;49m[30;43m([39;49m[30;43mobj[39;49m[30;43m)[39;49m[30;43m([39;49m[30;43mobj[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mrenderer[39;49m[30;43m=[39;49m[30;43mrenderer[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43m*[39;49m[30;43m*[39;49m[30;43mplot_opts[39;49m[30;43m)[39;49m [32m 287[39m defaults = [kd.default [38;5;28;01mfor[39;00m kd [38;5;129;01min[39;00m plot.dimensions] [32m 288[39m init_key = [38;5;28mtuple[39m( [32m 289[39m v [38;5;28;01mif[39;00m d [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m [38;5;28;01melse[39;00m d [38;5;28;01mfor[39;00m v, d [38;5;129;01min[39;00m [38;5;28mzip[39m(plot.keys[[32m0[39m], defaults, strict=[38;5;28;01mNone[39;00m) [32m 290[39m ) [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/plotting/bokeh/plot.py:863[39m, in [36mLayoutPlot.__init__[39m[34m(self, layout, keys, **params)[39m [32m 861[39m [38;5;28;01mdef[39;00m[38;5;250m [39m[34m__init__[39m([38;5;28mself[39m, layout, keys=[38;5;28;01mNone[39;00m, **params): [32m 862[39m [38;5;28msuper[39m().[34m__init__[39m(layout, keys=keys, **params) [32m--> [39m[32m863[39m [38;5;28mself[39m.layout, [38;5;28mself[39m.subplots, [38;5;28mself[39m.paths = [30;43mself[39;49m[30;43m.[39;49m[30;43m_init_layout[39;49m[30;43m([39;49m[30;43mlayout[39;49m[30;43m)[39;49m [32m 864[39m [38;5;28;01mif[39;00m [38;5;28mself[39m.top_level: [32m 865[39m [38;5;28mself[39m.traverse([38;5;28;01mlambda[39;00m x: attach_streams([38;5;28mself[39m, x.hmap, [32m2[39m), [GenericElementPlot]) [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/plotting/bokeh/plot.py:914[39m, in [36mLayoutPlot._init_layout[39m[34m(self, layout)[39m [32m 912[39m layout_count += [32m1[39m [32m 913[39m num = [32m0[39m [38;5;28;01mif[39;00m empty [38;5;28;01melse[39;00m layout_count [32m--> [39m[32m914[39m subplots, adjoint_layout = [30;43mself[39;49m[30;43m.[39;49m[30;43m_create_subplots[39;49m[30;43m([39;49m [32m 915[39m [30;43m [39;49m[30;43mview[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mpositions[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mlayout_dimensions[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mframe_ranges[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mnum[39;49m[30;43m=[39;49m[30;43mnum[39;49m [32m 916[39m [30;43m[39;49m[30;43m)[39;49m [32m 918[39m [38;5;66;03m# Generate the AdjointLayoutsPlot which will coordinate[39;00m [32m 919[39m [38;5;66;03m# plotting of AdjointLayouts in the larger grid[39;00m [32m 920[39m plotopts = [38;5;28mself[39m.lookup_options(view, [33m"[39m[33mplot[39m[33m"[39m).options [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/plotting/bokeh/plot.py:994[39m, in [36mLayoutPlot._create_subplots[39m[34m(self, layout, positions, layout_dimensions, ranges, num)[39m [32m 992[39m [38;5;28;01mcontinue[39;00m [32m 993[39m num = num [38;5;28;01mif[39;00m [38;5;28mlen[39m([38;5;28mself[39m.coords) > [32m1[39m [38;5;28;01melse[39;00m [32m0[39m [32m--> [39m[32m994[39m subplot = [30;43mplot_type[39;49m[30;43m([39;49m [32m 995[39m [30;43m [39;49m[30;43melement[39;49m[30;43m,[39;49m [32m 996[39m [30;43m [39;49m[30;43mkeys[39;49m[30;43m=[39;49m[30;43mself[39;49m[30;43m.[39;49m[30;43mkeys[39;49m[30;43m,[39;49m [32m 997[39m [30;43m [39;49m[30;43mdimensions[39;49m[30;43m=[39;49m[30;43mself[39;49m[30;43m.[39;49m[30;43mdimensions[39;49m[30;43m,[39;49m [32m 998[39m [30;43m [39;49m[30;43mlayout_dimensions[39;49m[30;43m=[39;49m[30;43mlayout_dimensions[39;49m[30;43m,[39;49m [32m 999[39m [30;43m [39;49m[30;43mranges[39;49m[30;43m=[39;49m[30;43mranges[39;49m[30;43m,[39;49m [32m 1000[39m [30;43m [39;49m[30;43msubplot[39;49m[30;43m=[39;49m[30;43;01mTrue[39;49;00m[30;43m,[39;49m [32m 1001[39m [30;43m [39;49m[30;43mroot[39;49m[30;43m=[39;49m[30;43mself[39;49m[30;43m.[39;49m[30;43mroot[39;49m[30;43m,[39;49m [32m 1002[39m [30;43m [39;49m[30;43muniform[39;49m[30;43m=[39;49m[30;43mself[39;49m[30;43m.[39;49m[30;43muniform[39;49m[30;43m,[39;49m [32m 1003[39m [30;43m [39;49m[30;43mlayout_num[39;49m[30;43m=[39;49m[30;43mnum[39;49m[30;43m,[39;49m [32m 1004[39m [30;43m [39;49m[30;43mrenderer[39;49m[30;43m=[39;49m[30;43mself[39;49m[30;43m.[39;49m[30;43mrenderer[39;49m[30;43m,[39;49m [32m 1005[39m [30;43m [39;49m[30;43m*[39;49m[30;43m*[39;49m[30;43mdict[39;49m[30;43m([39;49m[30;43m{[39;49m[30;43m"[39;49m[30;43mshared_axes[39;49m[30;43m"[39;49m[30;43m:[39;49m[30;43m [39;49m[30;43mself[39;49m[30;43m.[39;49m[30;43mshared_axes[39;49m[30;43m}[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43m*[39;49m[30;43m*[39;49m[30;43mplotopts[39;49m[30;43m)[39;49m[30;43m,[39;49m [32m 1006[39m [30;43m[39;49m[30;43m)[39;49m [32m 1007[39m subplots[pos] = subplot [32m 1008[39m [38;5;28;01mif[39;00m [38;5;28misinstance[39m(plot_type, [38;5;28mtype[39m) [38;5;129;01mand[39;00m [38;5;28missubclass[39m(plot_type, GenericCompositePlot): [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/plotting/plot.py:355[39m, in [36mPlotSelector.__call__[39m[34m(self, obj, **kwargs)[39m [32m 353[39m [38;5;28;01mdef[39;00m[38;5;250m [39m[34m__call__[39m([38;5;28mself[39m, obj, **kwargs): [32m 354[39m plot_class = [38;5;28mself[39m.get_plot_class(obj) [32m--> [39m[32m355[39m [38;5;28;01mreturn[39;00m [30;43mplot_class[39;49m[30;43m([39;49m[30;43mobj[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43m*[39;49m[30;43m*[39;49m[30;43mkwargs[39;49m[30;43m)[39;49m [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/plotting/bokeh/heatmap.py:87[39m, in [36mHeatMapPlot.__init__[39m[34m(self, element, plot, **params)[39m [32m 86[39m [38;5;28;01mdef[39;00m[38;5;250m [39m[34m__init__[39m([38;5;28mself[39m, element, plot=[38;5;28;01mNone[39;00m, **params): [32m---> [39m[32m87[39m [30;43msuper[39;49m[30;43m([39;49m[30;43m)[39;49m[30;43m.[39;49m[30;43m__init__[39;49m[30;43m([39;49m[30;43melement[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mplot[39;49m[30;43m=[39;49m[30;43mplot[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43m*[39;49m[30;43m*[39;49m[30;43mparams[39;49m[30;43m)[39;49m [32m 88[39m [38;5;28mself[39m._is_contiguous_gridded = [38;5;28;01mFalse[39;00m [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/plotting/bokeh/element.py:500[39m, in [36mElementPlot.__init__[39m[34m(self, element, plot, **params)[39m [32m 498[39m [38;5;28mself[39m._subcoord_standalone_ = [38;5;28;01mNone[39;00m [32m 499[39m [38;5;28mself[39m.current_ranges = [38;5;28;01mNone[39;00m [32m--> [39m[32m500[39m [30;43msuper[39;49m[30;43m([39;49m[30;43m)[39;49m[30;43m.[39;49m[30;43m__init__[39;49m[30;43m([39;49m[30;43melement[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43m*[39;49m[30;43m*[39;49m[30;43mparams[39;49m[30;43m)[39;49m [32m 501[39m [38;5;28mself[39m.handles = {} [38;5;28;01mif[39;00m plot [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m [38;5;28;01melse[39;00m [38;5;28mself[39m.handles[[33m"[39m[33mplot[39m[33m"[39m] [32m 502[39m [38;5;28mself[39m.static = [38;5;28mlen[39m([38;5;28mself[39m.hmap) == [32m1[39m [38;5;129;01mand[39;00m [38;5;28mlen[39m([38;5;28mself[39m.keys) == [38;5;28mlen[39m([38;5;28mself[39m.hmap) [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/plotting/plot.py:1427[39m, in [36mGenericElementPlot.__init__[39m[34m(self, element, keys, ranges, dimensions, batched, overlaid, cyclic_index, zorder, style, overlay_dims, stream_sources, streams, **params)[39m [32m 1424[39m plot_opts.update(**{k: v[[32m0[39m] [38;5;28;01mfor[39;00m k, v [38;5;129;01min[39;00m inherited.items() [38;5;28;01mif[39;00m k [38;5;129;01mnot[39;00m [38;5;129;01min[39;00m plot_opts}) [32m 1426[39m applied_params = [38;5;28mdict[39m(params, **plot_opts) [32m-> [39m[32m1427[39m [30;43msuper[39;49m[30;43m([39;49m[30;43m)[39;49m[30;43m.[39;49m[30;43m__init__[39;49m[30;43m([39;49m[30;43mkeys[39;49m[30;43m=[39;49m[30;43mkeys[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mdimensions[39;49m[30;43m=[39;49m[30;43mdimensions[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mdynamic[39;49m[30;43m=[39;49m[30;43mdynamic[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43m*[39;49m[30;43m*[39;49m[30;43mapplied_params[39;49m[30;43m)[39;49m [32m 1428[39m [38;5;28mself[39m.batched = batched [32m 1429[39m [38;5;28mself[39m.streams = get_nested_streams([38;5;28mself[39m.hmap) [38;5;28;01mif[39;00m streams [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m [38;5;28;01melse[39;00m streams [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/plotting/plot.py:489[39m, in [36mDimensionedPlot.__init__[39m[34m(self, keys, dimensions, layout_dimensions, uniform, subplot, adjoined, layout_num, style, subplots, dynamic, **params)[39m [32m 487[39m [38;5;28mself[39m.ranges = {} [32m 488[39m [38;5;28mself[39m._updated = [38;5;28;01mFalse[39;00m [38;5;66;03m# Whether the plot should be marked as updated[39;00m [32m--> [39m[32m489[39m [30;43msuper[39;49m[30;43m([39;49m[30;43m)[39;49m[30;43m.[39;49m[30;43m__init__[39;49m[30;43m([39;49m[30;43m*[39;49m[30;43m*[39;49m[30;43mparams[39;49m[30;43m)[39;49m [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/holoviews/plotting/plot.py:71[39m, in [36mPlot.__init__[39m[34m(self, renderer, root, **params)[39m [32m 69[39m [38;5;28;01mdef[39;00m[38;5;250m [39m[34m__init__[39m([38;5;28mself[39m, renderer=[38;5;28;01mNone[39;00m, root=[38;5;28;01mNone[39;00m, **params): [32m 70[39m params = {k: v [38;5;28;01mfor[39;00m k, v [38;5;129;01min[39;00m params.items() [38;5;28;01mif[39;00m k [38;5;129;01min[39;00m [38;5;28mself[39m.param} [32m---> [39m[32m71[39m [30;43msuper[39;49m[30;43m([39;49m[30;43m)[39;49m[30;43m.[39;49m[30;43m__init__[39;49m[30;43m([39;49m[30;43m*[39;49m[30;43m*[39;49m[30;43mparams[39;49m[30;43m)[39;49m [32m 72[39m [38;5;28mself[39m.renderer = renderer [38;5;28;01mif[39;00m renderer [38;5;28;01melse[39;00m Store.renderers[[38;5;28mself[39m.backend].instance() [32m 73[39m [38;5;28mself[39m._force = [38;5;28;01mFalse[39;00m [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/param/parameterized.py:5879[39m, in [36mParameterized.__init__[39m[34m(self, **params)[39m [32m 5877[39m [38;5;28;01mif[39;00m [38;5;28mself[39m.param.name.default == [38;5;28mself[39m.[34m__class__[39m.[34m__name__[39m: [32m 5878[39m [38;5;28mself[39m.param._generate_name() [32m-> [39m[32m5879[39m refs, deps = [30;43mself[39;49m[30;43m.[39;49m[30;43mparam[39;49m[30;43m.[39;49m[30;43m_setup_params[39;49m[30;43m([39;49m[30;43m*[39;49m[30;43m*[39;49m[30;43mparams[39;49m[30;43m)[39;49m [32m 5880[39m object_count += [32m1[39m [32m 5882[39m [38;5;28mself[39m._param__private.initialized = [38;5;28;01mTrue[39;00m [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/param/parameterized.py:2316[39m, in [36mas_uninitialized..override_initialization[39m[34m(self_, *args, **kw)[39m [32m 2314[39m original_initialized = parameterized_instance._param__private.initialized [32m 2315[39m parameterized_instance._param__private.initialized = [38;5;28;01mFalse[39;00m [32m-> [39m[32m2316[39m ret = [30;43mfn[39;49m[30;43m([39;49m[30;43mself_[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43m*[39;49m[30;43margs[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43m*[39;49m[30;43m*[39;49m[30;43mkw[39;49m[30;43m)[39;49m [32m 2317[39m parameterized_instance._param__private.initialized = original_initialized [32m 2318[39m [38;5;28;01mreturn[39;00m ret [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/param/parameterized.py:2646[39m, in [36mParameters._setup_params[39m[34m(self_, **params)[39m [32m 2634[39m [38;5;28;01mif[39;00m ref: [32m 2635[39m warnings.warn( [32m 2636[39m [33mf[39m[33m"[39m[33mParameter [39m[38;5;132;01m{[39;00mname[38;5;132;01m!r}[39;00m[33m on [39m[38;5;132;01m{[39;00mpobj.owner[38;5;132;01m}[39;00m[33m is being given a valid parameter [39m[33m"[39m [32m 2637[39m [33mf[39m[33m"[39m[33mreference [39m[38;5;132;01m{[39;00mval[38;5;132;01m}[39;00m[33m but is implicitly allow_refs=False. [39m[33m"[39m [32m (...)[39m[32m 2644[39m stacklevel=_find_stack_level(), [32m 2645[39m ) [32m-> [39m[32m2646[39m [30;43msetattr[39;49m[30;43m([39;49m[30;43mself[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mname[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mval[39;49m[30;43m)[39;49m [32m 2647[39m [38;5;28;01mcontinue[39;00m [32m 2649[39m [38;5;66;03m# Resolve references[39;00m [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/param/parameterized.py:679[39m, in [36minstance_descriptor.._f[39m[34m(self, obj, val)[39m [32m 677[39m instance_param.[34m__set__[39m(obj, val) [32m 678[39m [38;5;28;01mreturn[39;00m [32m--> [39m[32m679[39m [38;5;28;01mreturn[39;00m [30;43mf[39;49m[30;43m([39;49m[30;43mself[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mobj[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mval[39;49m[30;43m)[39;49m [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/param/parameterized.py:1992[39m, in [36mParameter.__set__[39m[34m(self, obj, val)[39m [32m 1989[39m [38;5;28;01mif[39;00m is_async [38;5;129;01mor[39;00m val [38;5;129;01mis[39;00m Undefined: [32m 1990[39m [38;5;28;01mreturn[39;00m [32m-> [39m[32m1992[39m [30;43mself[39;49m[30;43m.[39;49m[30;43m_validate[39;49m[30;43m([39;49m[30;43mval[39;49m[30;43m)[39;49m [32m 1994[39m _old = [38;5;28mNotImplemented[39m [32m 1995[39m [38;5;66;03m# obj can be None if __set__ is called for a Parameterized class[39;00m [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/param/parameters.py:3687[39m, in [36mList._validate[39m[34m(self, val)[39m [32m 3682[39m [38;5;28;01mdef[39;00m[38;5;250m [39m[34m_validate[39m([38;5;28mself[39m, val): [32m 3683[39m [38;5;250m [39m[33;03m"""[39;00m [32m 3684[39m [33;03m Check that the value is numeric and that it is within the hard[39;00m [32m 3685[39m [33;03m bounds; if not, an exception is raised.[39;00m [32m 3686[39m [33;03m """[39;00m [32m-> [39m[32m3687[39m [30;43mself[39;49m[30;43m.[39;49m[30;43m_validate_value[39;49m[30;43m([39;49m[30;43mval[39;49m[30;43m,[39;49m[30;43m [39;49m[30;43mself[39;49m[30;43m.[39;49m[30;43mallow_None[39;49m[30;43m)[39;49m [32m 3688[39m [38;5;28mself[39m._validate_bounds(val, [38;5;28mself[39m.bounds) [32m 3689[39m [38;5;28mself[39m._validate_item_type(val, [38;5;28mself[39m.item_type, [38;5;28mself[39m.is_instance) [36mFile [39m[32m~/.local/share/hatch/env/virtual/scanpy/TCvYOmNh/docs/lib/python3.13/site-packages/param/parameters.py:3720[39m, in [36mList._validate_value[39m[34m(self, value, allow_None)[39m [32m 3718[39m [38;5;28;01mreturn[39;00m [32m 3719[39m [38;5;28;01mif[39;00m [38;5;129;01mnot[39;00m [38;5;28misinstance[39m(value, [38;5;28mlist[39m): [32m-> [39m[32m3720[39m [38;5;28;01mraise[39;00m [38;5;167;01mValueError[39;00m( [32m 3721[39m [33mf[39m[33m"[39m[38;5;132;01m{[39;00m_validate_error_prefix([38;5;28mself[39m)[38;5;132;01m}[39;00m[33m must be a list, not an [39m[33m"[39m [32m 3722[39m [33mf[39m[33m"[39m[33mobject of [39m[38;5;132;01m{[39;00m[38;5;28mtype[39m(value)[38;5;132;01m}[39;00m[33m.[39m[33m"[39m [32m 3723[39m ) [31mValueError[39m: List parameter 'ElementPlot.tools' must be a list, not an object of . [mystnb.exec] [mystnb.exec] /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/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/4188/docs/_build/html/reports/api/generated/scanpy.pl.matrixplot-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/4188/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/4188/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/4188/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... Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/_build/html/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/_build/html/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/_build/html/_static/documentation_options.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/_build/html/_static/copybutton.js copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 0%] api/classes writing output... [ 1%] api/datasets writing output... [ 1%] api/deprecated writing output... [ 1%] api/experimental writing output... [ 2%] api/generated/classes/scanpy.pl.DotPlot writing output... [ 2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP writing output... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE writing output... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON writing output... [ 3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR writing output... [ 4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW writing output... [ 4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX writing output... [ 4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN writing output... [ 5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT writing output... [ 5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH writing output... [ 6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING writing output... [ 6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING writing output... [ 6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX writing output... [ 7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT writing output... [ 7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE writing output... [ 7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT writing output... [ 8%] api/generated/classes/scanpy.pl.DotPlot.legend writing output... [ 8%] api/generated/classes/scanpy.pl.DotPlot.style writing output... [ 9%] api/generated/classes/scanpy.pl.MatrixPlot writing output... [ 9%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLORMAP writing output... [ 9%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLOR_LEGEND_TITLE writing output... [ 10%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_COLOR writing output... [ 10%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_LW writing output... [ 10%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_SAVE_PREFIX writing output... [ 11%] api/generated/classes/scanpy.pl.MatrixPlot.style writing output... [ 11%] api/generated/classes/scanpy.pl.StackedViolin writing output... [ 12%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP writing output... [ 12%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE writing output... [ 12%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT writing output... [ 13%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_DENSITY_NORM writing output... [ 13%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER writing output... [ 13%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER writing output... [ 14%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE writing output... [ 14%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH writing output... [ 15%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING writing output... [ 15%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS writing output... [ 15%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING writing output... [ 16%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE writing output... [ 16%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX writing output... [ 16%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT writing output... [ 17%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM writing output... [ 17%] api/generated/classes/scanpy.pl.StackedViolin.style writing output... [ 18%] api/generated/scanpy.Neighbors writing output... [ 18%] api/generated/scanpy.Neighbors.compute_eigen writing output... [ 18%] api/generated/scanpy.Neighbors.compute_neighbors writing output... [ 19%] api/generated/scanpy.Neighbors.compute_transitions writing output... [ 19%] api/generated/scanpy.Neighbors.connectivities writing output... [ 19%] api/generated/scanpy.Neighbors.distances writing output... [ 20%] api/generated/scanpy.Neighbors.distances_dpt writing output... [ 20%] api/generated/scanpy.Neighbors.eigen_basis writing output... [ 21%] api/generated/scanpy.Neighbors.eigen_values writing output... [ 21%] api/generated/scanpy.Neighbors.rp_forest writing output... [ 21%] api/generated/scanpy.Neighbors.to_igraph writing output... [ 22%] api/generated/scanpy.Neighbors.transitions writing output... [ 22%] api/generated/scanpy.Neighbors.transitions_sym writing output... [ 22%] api/generated/scanpy.Preset writing output... [ 23%] api/generated/scanpy.Preset.check writing output... [ 23%] api/generated/scanpy.Preset.diffmap writing output... [ 24%] api/generated/scanpy.Preset.draw_graph writing output... [ 24%] api/generated/scanpy.Preset.highly_variable_genes writing output... [ 24%] api/generated/scanpy.Preset.leiden writing output... [ 25%] api/generated/scanpy.Preset.override writing output... [ 25%] api/generated/scanpy.Preset.pca writing output... [ 25%] api/generated/scanpy.Preset.rank_genes_groups writing output... [ 26%] api/generated/scanpy.Preset.scale writing output... [ 26%] api/generated/scanpy.Preset.score_genes writing output... [ 26%] api/generated/scanpy.Preset.tsne writing output... [ 27%] api/generated/scanpy.Preset.umap writing output... [ 27%] api/generated/scanpy.Verbosity writing output... [ 28%] api/generated/scanpy.Verbosity.debug writing output... [ 28%] api/generated/scanpy.Verbosity.error writing output... [ 28%] api/generated/scanpy.Verbosity.hint writing output... [ 29%] api/generated/scanpy.Verbosity.info writing output... [ 29%] api/generated/scanpy.Verbosity.level writing output... [ 29%] api/generated/scanpy.Verbosity.warning writing output... [ 30%] api/generated/scanpy.datasets.blobs writing output... [ 30%] api/generated/scanpy.datasets.ebi_expression_atlas writing output... [ 31%] api/generated/scanpy.datasets.krumsiek11 writing output... [ 31%] api/generated/scanpy.datasets.moignard15 writing output... [ 31%] api/generated/scanpy.datasets.paul15 writing output... [ 32%] api/generated/scanpy.datasets.pbmc3k writing output... [ 32%] api/generated/scanpy.datasets.pbmc3k_processed writing output... [ 32%] api/generated/scanpy.datasets.pbmc68k_reduced writing output... [ 33%] api/generated/scanpy.datasets.toggleswitch writing output... [ 33%] api/generated/scanpy.datasets.visium_sge writing output... [ 34%] api/generated/scanpy.experimental.pp.highly_variable_genes writing output... [ 34%] api/generated/scanpy.experimental.pp.normalize_pearson_residuals writing output... [ 34%] api/generated/scanpy.experimental.pp.normalize_pearson_residuals_pca writing output... [ 35%] api/generated/scanpy.experimental.pp.recipe_pearson_residuals writing output... [ 35%] api/generated/scanpy.get.aggregate writing output... [ 35%] api/generated/scanpy.get.obs_df writing output... [ 36%] api/generated/scanpy.get.pca writing output... [ 36%] api/generated/scanpy.get.rank_genes_groups_df writing output... [ 37%] api/generated/scanpy.get.var_df writing output... [ 37%] api/generated/scanpy.logging.print_header writing output... [ 37%] api/generated/scanpy.logging.print_versions writing output... [ 38%] api/generated/scanpy.metrics.confusion_matrix writing output... [ 38%] api/generated/scanpy.metrics.gearys_c writing output... [ 38%] api/generated/scanpy.metrics.modularity writing output... [ 39%] api/generated/scanpy.metrics.morans_i writing output... [ 39%] api/generated/scanpy.pl.clustermap writing output... [ 40%] api/generated/scanpy.pl.correlation_matrix writing output... [ 40%] api/generated/scanpy.pl.dendrogram writing output... [ 40%] api/generated/scanpy.pl.diffmap writing output... [ 41%] api/generated/scanpy.pl.dot_area writing output... [ 41%] api/generated/scanpy.pl.dotplot writing output... [ 41%] api/generated/scanpy.pl.dpt_groups_pseudotime writing output... [ 42%] api/generated/scanpy.pl.dpt_timeseries writing output... [ 42%] api/generated/scanpy.pl.draw_graph writing output... [ 43%] api/generated/scanpy.pl.embedding writing output... [ 43%] api/generated/scanpy.pl.embedding_density writing output... [ 43%] api/generated/scanpy.pl.heatmap writing output... [ 44%] api/generated/scanpy.pl.highest_expr_genes writing output... [ 44%] api/generated/scanpy.pl.highly_variable_genes writing output... [ 44%] api/generated/scanpy.pl.matrixplot writing output... [ 45%] api/generated/scanpy.pl.paga writing output... [ 45%] api/generated/scanpy.pl.paga_compare writing output... [ 46%] api/generated/scanpy.pl.paga_path writing output... [ 46%] api/generated/scanpy.pl.pca writing output... [ 46%] api/generated/scanpy.pl.pca_loadings writing output... [ 47%] api/generated/scanpy.pl.pca_overview writing output... [ 47%] api/generated/scanpy.pl.pca_variance_ratio writing output... [ 47%] api/generated/scanpy.pl.rank_genes_groups writing output... [ 48%] api/generated/scanpy.pl.rank_genes_groups_dotplot writing output... [ 48%] api/generated/scanpy.pl.rank_genes_groups_heatmap writing output... [ 49%] api/generated/scanpy.pl.rank_genes_groups_matrixplot writing output... [ 49%] api/generated/scanpy.pl.rank_genes_groups_stacked_violin writing output... [ 49%] api/generated/scanpy.pl.rank_genes_groups_tracksplot writing output... [ 50%] api/generated/scanpy.pl.rank_genes_groups_violin writing output... [ 50%] api/generated/scanpy.pl.ranking writing output... [ 50%] api/generated/scanpy.pl.scatter writing output... [ 51%] api/generated/scanpy.pl.scrublet_score_distribution writing output... [ 51%] api/generated/scanpy.pl.sim writing output... [ 51%] api/generated/scanpy.pl.spatial writing output... [ 52%] api/generated/scanpy.pl.stacked_violin writing output... [ 52%] api/generated/scanpy.pl.tracksplot writing output... [ 53%] api/generated/scanpy.pl.tsne writing output... [ 53%] api/generated/scanpy.pl.umap writing output... [ 53%] api/generated/scanpy.pl.violin writing output... [ 54%] api/generated/scanpy.pp.calculate_qc_metrics writing output... [ 54%] api/generated/scanpy.pp.combat writing output... [ 54%] api/generated/scanpy.pp.downsample_counts writing output... [ 55%] api/generated/scanpy.pp.filter_cells writing output... [ 55%] api/generated/scanpy.pp.filter_genes writing output... [ 56%] api/generated/scanpy.pp.harmony_integrate writing output... [ 56%] api/generated/scanpy.pp.highly_variable_genes writing output... [ 56%] api/generated/scanpy.pp.log1p writing output... [ 57%] api/generated/scanpy.pp.neighbors writing output... [ 57%] api/generated/scanpy.pp.normalize_total writing output... [ 57%] api/generated/scanpy.pp.pca writing output... [ 58%] api/generated/scanpy.pp.recipe_seurat writing output... [ 58%] api/generated/scanpy.pp.recipe_weinreb17 writing output... [ 59%] api/generated/scanpy.pp.recipe_zheng17 writing output... [ 59%] api/generated/scanpy.pp.regress_out writing output... [ 59%] api/generated/scanpy.pp.sample writing output... [ 60%] api/generated/scanpy.pp.scale writing output... [ 60%] api/generated/scanpy.pp.scrublet writing output... [ 60%] api/generated/scanpy.pp.scrublet_simulate_doublets writing output... [ 61%] api/generated/scanpy.pp.subsample writing output... [ 61%] api/generated/scanpy.queries.biomart_annotations writing output... [ 62%] api/generated/scanpy.queries.enrich writing output... [ 62%] api/generated/scanpy.queries.gene_coordinates writing output... [ 62%] api/generated/scanpy.queries.mitochondrial_genes writing output... [ 63%] api/generated/scanpy.read writing output... [ 63%] api/generated/scanpy.read_10x_h5 writing output... [ 63%] api/generated/scanpy.read_10x_mtx writing output... [ 64%] api/generated/scanpy.read_csv writing output... [ 64%] api/generated/scanpy.read_excel writing output... [ 65%] api/generated/scanpy.read_h5ad writing output... [ 65%] api/generated/scanpy.read_hdf writing output... [ 65%] api/generated/scanpy.read_loom writing output... [ 66%] api/generated/scanpy.read_mtx writing output... [ 66%] api/generated/scanpy.read_text writing output... [ 66%] api/generated/scanpy.read_umi_tools writing output... [ 67%] api/generated/scanpy.read_visium writing output... [ 67%] api/generated/scanpy.set_figure_params writing output... [ 68%] api/generated/scanpy.settings writing output... [ 68%] api/generated/scanpy.settings.override writing output... [ 68%] api/generated/scanpy.tl.dendrogram writing output... [ 69%] api/generated/scanpy.tl.diffmap writing output... [ 69%] api/generated/scanpy.tl.dpt writing output... [ 69%] api/generated/scanpy.tl.draw_graph writing output... [ 70%] api/generated/scanpy.tl.embedding_density writing output... [ 70%] api/generated/scanpy.tl.filter_rank_genes_groups writing output... [ 71%] api/generated/scanpy.tl.ingest writing output... [ 71%] api/generated/scanpy.tl.leiden writing output... [ 71%] api/generated/scanpy.tl.louvain writing output... [ 72%] api/generated/scanpy.tl.marker_gene_overlap writing output... [ 72%] api/generated/scanpy.tl.paga writing output... [ 72%] api/generated/scanpy.tl.rank_genes_groups writing output... [ 73%] api/generated/scanpy.tl.score_genes writing output... [ 73%] api/generated/scanpy.tl.score_genes_cell_cycle writing output... [ 74%] api/generated/scanpy.tl.sim writing output... [ 74%] api/generated/scanpy.tl.tsne writing output... [ 74%] api/generated/scanpy.tl.umap writing output... [ 75%] api/generated/scanpy.write writing output... [ 75%] api/get writing output... [ 75%] api/index writing output... [ 76%] api/io writing output... [ 76%] api/metrics writing output... [ 76%] api/plotting writing output... [ 77%] api/preprocessing writing output... [ 77%] api/queries writing output... [ 78%] api/settings writing output... [ 78%] api/tools writing output... [ 78%] basic_usage writing output... [ 79%] community writing output... [ 79%] contributors writing output... [ 79%] dev/ci writing output... [ 80%] dev/code writing output... [ 80%] dev/documentation writing output... [ 81%] dev/getting-set-up writing output... [ 81%] dev/index writing output... [ 81%] dev/release writing output... [ 82%] dev/testing writing output... [ 82%] dev/versioning writing output... [ 82%] external/exporting writing output... [ 83%] external/generated/scanpy.external.exporting.cellbrowser writing output... [ 83%] external/generated/scanpy.external.exporting.spring_project writing output... [ 84%] external/generated/scanpy.external.pl.phate writing output... [ 84%] external/generated/scanpy.external.pl.sam writing output... [ 84%] external/generated/scanpy.external.pl.trimap writing output... [ 85%] external/generated/scanpy.external.pl.wishbone_marker_trajectory writing output... [ 85%] external/generated/scanpy.external.pp.bbknn writing output... [ 85%] external/generated/scanpy.external.pp.hashsolo writing output... [ 86%] external/generated/scanpy.external.pp.magic writing output... [ 86%] external/generated/scanpy.external.pp.mnn_correct writing output... [ 87%] external/generated/scanpy.external.pp.scanorama_integrate writing output... [ 87%] external/generated/scanpy.external.tl.cyclone writing output... [ 87%] external/generated/scanpy.external.tl.harmony_timeseries writing output... [ 88%] external/generated/scanpy.external.tl.palantir writing output... [ 88%] external/generated/scanpy.external.tl.palantir_results writing output... [ 88%] external/generated/scanpy.external.tl.phate writing output... [ 89%] external/generated/scanpy.external.tl.phenograph writing output... [ 89%] external/generated/scanpy.external.tl.sam writing output... [ 90%] external/generated/scanpy.external.tl.sandbag writing output... [ 90%] external/generated/scanpy.external.tl.trimap writing output... [ 90%] external/generated/scanpy.external.tl.wishbone writing output... [ 91%] external/index writing output... [ 91%] external/plotting writing output... [ 91%] external/preprocessing writing output... [ 92%] external/tools writing output... [ 92%] how-to/cell-cycle writing output... [ 93%] how-to/index writing output... [ 93%] how-to/knn-transformers writing output... [ 93%] how-to/plotting-with-marsilea writing output... [ 94%] index writing output... [ 94%] installation writing output... [ 94%] references writing output... [ 95%] release-notes/index writing output... [ 95%] tutorials/basics/clustering writing output... [ 96%] tutorials/basics/clustering-2017 writing output... [ 96%] tutorials/basics/index writing output... [ 96%] tutorials/basics/integrating-data-using-ingest writing output... [ 97%] tutorials/experimental/dask writing output... [ 97%] tutorials/experimental/index writing output... [ 97%] tutorials/experimental/pearson_residuals writing output... [ 98%] tutorials/index writing output... [ 98%] tutorials/plotting/advanced writing output... [ 99%] tutorials/plotting/core writing output... [ 99%] tutorials/plotting/index writing output... [ 99%] tutorials/trajectories/index writing output... [100%] tutorials/trajectories/paga-paul15 writing output... [100%] usage-principles generating indices... genindex py-modindex done writing additional pages... search done copying images... [ 0%] _build/jupyter_execute/81b00b841d8c45b479ef4a0727fd19605fdd7045412275f97265a3134cc4aa7a.png copying images... [ 1%] _build/jupyter_execute/349337720df0497658a7dfa02d5346d99cf4a8223b4e3592d386147225b299af.png copying images... [ 1%] _build/jupyter_execute/fd30adf06630b8c67eb0f6324b7a7cd09eee983bcf80c9a640bd9be0aa3b2390.png copying images... [ 2%] _build/jupyter_execute/0a34e75145a87e329e15b69af4ec2f811fbe86ed2c2e7c036a64326b30783265.png copying images... [ 2%] _build/jupyter_execute/1e6c6a3219fdf7a9f848d8ddacd309079af84ce9adba003f1bf1b63327110cd2.png copying images... [ 3%] _build/jupyter_execute/a08fc270ea69befd908a23e5eb2c40e0c739e9f1f56cf790a6114be742dd540a.png copying images... [ 3%] _build/jupyter_execute/2e1dfb12c62ba9034712d2d22b25a13178da2255a8af28fbe407757fc599ff47.png copying images... [ 4%] _build/jupyter_execute/571560db43b86fc6eb0e1de51c5070f175025067629d1c79b91001f6ef39755d.png copying images... [ 4%] _build/jupyter_execute/e9895c1fe129dab4d4a6de99bf0abc338a9f0701633dd7350e7bbf16d82c2ca2.png copying images... [ 5%] _build/jupyter_execute/899924541d5cd23e1d823a15f57a1c398854fb21d9bb2b186d7844a633d8361c.png copying images... [ 5%] _build/jupyter_execute/e24a985978a0f903d1ed3530586e5e4376316a78276510ab596127b72bb3b6cf.png copying images... [ 6%] _build/jupyter_execute/104a8b92438633b381635ac07ab19db85dc14a82da82860e243825bce6d4902a.png copying images... [ 6%] _build/jupyter_execute/f88d9f09acb25cf5394ffb62dd38b56cc1a612c02248efbf372dbf9450f2229d.png copying images... [ 6%] _build/jupyter_execute/edeca8ea57e2a28d6294bce6c8bf4d1d96c0c591ed4e6f9b71da24921e2c6c48.png copying images... [ 7%] _build/jupyter_execute/786e31ffe683d10d06791285a6bb683f014b505652ff686a37acc499d8eb477a.png copying images... [ 7%] _build/jupyter_execute/e554a8079eadb56d832a21864fc4ec24eb17e011786e6a0b87ab16e86f71e5a7.png copying images... [ 8%] _build/jupyter_execute/be8ee60a85ec84fc8dbbf7fef09f5511b7d35b49f60f033cd900f5589e1a9419.png copying images... [ 8%] _build/jupyter_execute/96732ada4f884a888336fb50df57f77e5ddcff289bd7679444a3c111bb89ae60.png copying images... [ 9%] _build/jupyter_execute/4b0516f0ffc772d9fe5db0ebf07de0a38ebad165dd3e99f85c1056984d8f069f.png copying images... [ 9%] _build/jupyter_execute/86c78b84272adc5d0823dca7922dad0ee375882e8275d3de94831107871bda15.png copying images... [ 10%] _build/jupyter_execute/6a2c0193f7424c172d17e88ad8f0a30889a4eec665f664bb8873c87c785f7419.png copying images... [ 10%] _build/jupyter_execute/71ec195a767885e626d7a3ead43d2d10c8bb08fc06f9098b505baee1b3bf0454.png copying images... [ 11%] _build/jupyter_execute/145f7edc2e439fe066dcfc309872254dd335f8a550da694e98288f11aeeb1b23.png copying images... [ 11%] _build/jupyter_execute/b0a08fc250491381cc5293e8f00c642088e238fe8e5b115e633d6ef9b41251e3.png copying images... [ 11%] _build/jupyter_execute/de8c176008e44647c279c140221bf0c907539b94ca88c02169f4dfd883e05d7c.png copying images... [ 12%] _build/jupyter_execute/5364f5bd7a994b81d55d3d34d670a5c34a32e79254d83dbce9fa72a7c7275885.png copying images... [ 12%] _build/jupyter_execute/d4814b40169a9af329729127e3321d3d8e1b9ff71f3dcf5f3313c14a7fc85147.png copying images... [ 13%] _build/jupyter_execute/debdc9ffc351e5348fa43a462032eb46692980c9c1ef9d0857f8587b9a1d7c96.png copying images... [ 13%] _build/jupyter_execute/2bfd5962cecb2dcdaa53f375dc3588894180a6beef3b7af63e68778733563639.png copying images... [ 14%] _build/jupyter_execute/221914fd3030ad3db63557eaf0d874a12d9de8a29dc1c3e673b4eee5659478b6.png copying images... [ 14%] _build/jupyter_execute/57d7f4305c95465099f4d97ed757f1e4ecaf12f7123e1d1e88f988e3b64c2072.png copying images... [ 15%] _build/jupyter_execute/9c35ecdb0589b0c06f511e2d2718bb36885018cbd94eef2c9c3f45de88e96b8e.png copying images... [ 15%] _build/jupyter_execute/739ac5c7a5dbfc51a9baacdcc2de446daf2666d86bb856882b72871ffe8a61fe.png copying images... [ 16%] _build/jupyter_execute/66613dc878324e56a2b7bcca2617b3796504075e317632a137d523d7309e5f8e.png copying images... [ 16%] _build/jupyter_execute/9b36f17db0315df16e253045e21e6eb76fcaf8c3a42f715aa49492c5f5970e6b.png copying images... [ 17%] _build/jupyter_execute/bc35d937c4234bfa66ee7a55221a313931e66dc3bb70d378b14fddc941edc1ea.png copying images... [ 17%] _build/jupyter_execute/994e63306f6ae4dc6783242e14563bb0bf7bdea127cadc196a637409dccb6464.png copying images... [ 17%] _build/jupyter_execute/0027a98d970f62a1eaaf157b1f5260da0ced266e3462d7f565bff0f6d00da000.png copying images... [ 18%] _build/jupyter_execute/f406a45688952e3256a3e788a01c00d0734c9bb44b5b043ae23df876238ee92d.png copying images... [ 18%] _build/jupyter_execute/16839f2562f8325feb3b3215dd9d01c8d51f7e371f60c9a5305433f6c81a144f.png copying images... [ 19%] _build/jupyter_execute/32de2dfa77c81768a4aba025838bad650e1365a463b28614caa401fa3e51e820.png copying images... [ 19%] _build/jupyter_execute/83d0b6cf9916d2346f6e824d0af737a6db9ea3eca8f5807b632a1ea624678033.png copying images... [ 20%] _build/jupyter_execute/fe0b650013b855d70330e923bfa3c52230d01f3992ac623054340c2d46698b83.png copying images... [ 20%] _build/jupyter_execute/e556ec2727e2131ef2b5475ceb2404a77a0ee368a0e6e67f69edc98d5bd30688.png copying images... [ 21%] _build/jupyter_execute/6b89f3e5a692a163730b9321087254dfc8bdc7342fa428273c44cc593d80926d.png copying images... [ 21%] _build/jupyter_execute/c305b7f9c00a8003bd6668015e4ca4cfac40f83878b157bbb62a20db1f5828c3.png copying images... [ 22%] _build/jupyter_execute/f75a9b46835965cc0d0c0f642b469583f5779fee33d1bc9f2b6ae2eec6712093.png copying images... [ 22%] _build/jupyter_execute/6f078569c99b4504cc6a55558cb90e1be0272f945052aacae058da1e98f7c5e6.png copying images... [ 22%] _build/jupyter_execute/6c00e0d49638dd9272dc09bac544041a2bb56a3df041f20b2b83855fa3cef06b.png copying images... [ 23%] _build/jupyter_execute/7701a86fcc5ca2f0009cf1d1cb9e37fcc2e2413bb31f98842d79fff6e1741fea.png copying images... [ 23%] _build/jupyter_execute/a2bf062cf303a5437e6cbce68563fc20ff621851ede35a6ff50e48626e880a36.png copying images... [ 24%] _build/jupyter_execute/d490c4c0bdbe9d7254c40fdcd1145fae54eb08e1dadf72b8b6ec11bdc2d2c89d.png copying images... [ 24%] _build/jupyter_execute/9be661f838e442e966261cfeda4d9cec95c17fbabe978dc057e53ac34cdee769.png copying images... [ 25%] _build/jupyter_execute/8fb246eac48eb221d2175a853880b9d706aa6664a14a1dc206d3b5d231a8fa92.png copying images... [ 25%] _build/jupyter_execute/56fd11183c1365ab02ec05fa9fa8453b5b0127b1ac2cf35141716609b02c73b7.png copying images... [ 26%] _build/jupyter_execute/78f3c014b336739d14f8cb8605008de724221b440bf4acc8c5fef554b8b78e8a.png copying images... [ 26%] _build/jupyter_execute/d644c0752e4ffab51e32c7328cacd8c2a8e3765a15469ff8b8dcaf720b01279d.png copying images... [ 27%] _build/jupyter_execute/564a3cbbc177057082eed185dee6dab9b783b41d3d64f2670a0e1ab358a0b6ee.png copying images... [ 27%] _build/jupyter_execute/6f2a2df292136e5dfb0473129b5c657d14edae0648e8212c79bd8a0929524daf.png copying images... [ 28%] _build/jupyter_execute/e12e7c672419e2192ebb2d09008a46320e539bf32e03e339f14c49d9c3552bf7.png copying images... [ 28%] _build/jupyter_execute/2c4331d372afea0151cfabd2654a03148af13318a432c381e8461ab6837cc1ae.png copying images... [ 28%] _build/jupyter_execute/7715255d4b5b4f8a5b5e7d0e1bcfa57e9da802aca29e6d9d81ed4dd30a48de3b.png copying images... [ 29%] _build/jupyter_execute/f0602d6b63ee269058f809abd30c4b4a204c0fdbd8e07df762d09e21239cc6a8.png copying images... [ 29%] _build/jupyter_execute/1e414e3b0611de68003683bdbfe7db7bde386d7a27130da881de880bd2840b5c.png copying images... [ 30%] _build/jupyter_execute/b361d915316bac61bdb00cffd2130b156b57cf445da207eea3c3e2312350b315.png copying images... [ 30%] _build/jupyter_execute/3e52ec58327596116953baa0513313a66b424554dd3f8a9f99b32a4659d368b7.png copying images... [ 31%] _build/jupyter_execute/75b483f18e6ff0687b8c9ccca0b28a193113a2cc5d555b40cd209187fe3b07e9.png copying images... [ 31%] _build/jupyter_execute/291f0c419b57fd3b8c9627b52f196fe3f241eb6f4d99668a59f8caac4339e194.png copying images... [ 32%] _build/jupyter_execute/5096d22c4b13ffc5dd48a96fbfb5d743d6cfd492b14e90b4e9aeedd1bc1d52f2.png copying images... [ 32%] _build/jupyter_execute/d29b5805e234d51a527c372b5c159194a066b7bdf76b6d0a73ef6e4d9d81a642.png copying images... [ 33%] _build/jupyter_execute/3f5e370f665eaa1bcfa8760157ef25ef7cd0aafff2b51e84be5cffc3fdb285c6.png copying images... [ 33%] _build/jupyter_execute/174b2bc6c71a1b4535a75ba0d7c4f90e04d7e71aa0a34e6acc67dcca3a0cdf46.png copying images... [ 33%] _static/img/ci_plot-view_tests-tab.png copying images... [ 34%] _static/img/ci_plot-view_select-test.png copying images... [ 34%] _static/img/ci_plot-view_attachment-tab.png copying images... [ 35%] _build/jupyter_execute/1d57a6a6f897c88b6acfc435bbfeb70798036d973008ed199b9b93305844c407.png copying images... [ 35%] _build/jupyter_execute/9201238033dc3d71525ffa4c3fd342931493cbc4154f10dad379a148746ccc9b.png copying images... [ 36%] _build/jupyter_execute/ad8d8a4b869e02ab2b2ca1c0cddab9f8150214bfc27e6036a49ab5d854f5983c.png copying images... [ 36%] _build/jupyter_execute/ba1422e2b60f77f4c59fc07a3c5ba6e7f359b149f5b44d7efe832e736794d28e.png copying images... [ 37%] _build/jupyter_execute/2ad8c5624f6b1b9c504a9523579d15ea2f93a9fd5b609091b38786f953fe046b.png copying images... [ 37%] _build/jupyter_execute/da883131a1fe9eb22a8c860e07c36a34e00e64e4442b006d9dde552fc2a40ead.png copying images... [ 38%] _build/jupyter_execute/d81354fd0bdf8a72378abcefbc182d8285486fa17d8bd53f0c1f47b6cd1d28c4.png copying images... [ 38%] _build/jupyter_execute/2d213968ea3f453f2cae74ae49e17f1fec45a53a476ae046b14010f283eda1a7.png copying images... [ 39%] _build/jupyter_execute/4d8511ed85ad86dbf378823408503c528a42a79cd98b0e04f7be0f949decd72d.png copying images... [ 39%] _build/jupyter_execute/4391834d507f58697345693f7e02b03afbb9057c3fe0d8386df4a8596d54803d.png copying images... [ 39%] _build/jupyter_execute/e1ed4633b95cd6bec57e431a9b5349d46a96ac78dd24940d173cd3fca0428694.png copying images... [ 40%] _build/jupyter_execute/a8fd5ce09328052fe68df76c87130f355b9a63a46d81cbfd679a2c87cb6ab4e7.png copying images... [ 40%] _build/jupyter_execute/28915039aa4b875685c8d73a7139b94924f2a96e9041916eaeb5d593c3bace11.png copying images... [ 41%] _build/jupyter_execute/2369cb7f97a8853b39251e0ca2ccae217e8613cbea0bf8c599d13adfed54622b.png copying images... [ 41%] _build/jupyter_execute/3385e74bc3cd67483b2cc40687bbe1089c590fd399799f887c24323ea25ea637.png copying images... [ 42%] _build/jupyter_execute/83a982f840b154da4420735c806689e16b150ad10ab64372e4ad9c0404390dd3.png copying images... [ 42%] _build/jupyter_execute/9a168f2d7a68905521ea3fb1ef5a0ac2a22d65e6a5e7c3796a55da1c24c28cb1.png copying images... [ 43%] _build/jupyter_execute/bd436a0a79afac682ff8132b32d4c90d3f74738d57e07f5743a03a55d9f82f68.png copying images... [ 43%] _build/jupyter_execute/12e4e27cf02e408effd640d9a5846b20c0b4ea4856511e9af58f5743897aaf38.png copying images... [ 44%] _build/jupyter_execute/e77d6bf9cd6e938808b2d57ffd8840f0d1aa27233c819a4f8f7b9fdd1d6a44cb.png copying images... [ 44%] _build/jupyter_execute/610d17bf258b0cc0d840713ebac7867cf292c626df2e807ebd78b459a03ebd28.png copying images... [ 44%] _build/jupyter_execute/08cb70daba840353bbf8529bf9f27d6121451a8200114c5b77f581df4bbf1a7b.png copying images... [ 45%] _build/jupyter_execute/2b92963adeb5c28502e023b24967f509deb537d668944e8bec22585c1e66e341.png copying images... [ 45%] _build/jupyter_execute/7c615842aa3a955f46581c1333bbb91b74a2fb9d38b7f18966a67a39cb1ce0f2.png copying images... [ 46%] _build/jupyter_execute/17e024239d09ec7c14e90bdb43ea70d7959aab70f7e5d3d2f1620a8f96b77809.png copying images... [ 46%] _build/jupyter_execute/e103233bd60eaaf71b1bee1293d49a4732a3e96a1e206df311d8166de065a188.png copying images... [ 47%] _build/jupyter_execute/d016caf498b3b59f81afddca30abfa1354fc0d904eaa8c69776bf7c4e305996e.png copying images... [ 47%] _build/jupyter_execute/7ab7710568efacc3fcbcc8db7885b30e22db6ad7378ff0066a5bba5f361e065b.png copying images... [ 48%] _build/jupyter_execute/8107930e37d0eafac40456afc53660e627a7e8aff939fdad1739e6c92b339ca1.png copying images... [ 48%] _build/jupyter_execute/fe4652b5bd85c01a706bcc93db6c339dd350de04d627e4ef5fca03de302e6645.png copying images... [ 49%] _build/jupyter_execute/2790ff5a1d746af5c3cddd2b9f6a01dffc82af62fa724a41dba40310b072dadb.png copying images... [ 49%] _build/jupyter_execute/1c3c62cdb30781ddde75b5168f150794c33e30a2eac387a07c59109d806a8af1.png copying images... [ 50%] _build/jupyter_execute/ce00e90fb7bec4e416b07a495c303c0bb48c5e3322abe38320b4f98e4c7bf8c7.png copying images... [ 50%] _build/jupyter_execute/b33128be615a2b323623ecc32c332bab41abbe66c9e4d92e29b14f7e2a65c25f.png copying images... [ 50%] _build/jupyter_execute/a785da9a2a7b016091062159786f39353ea020780d58f478c874cd068037a82f.png copying images... [ 51%] _build/jupyter_execute/6922a7ae96be672bcf25f5ae2b5461a6edce80dc0ae0c8b2545ab7a2b6cdf33b.png copying images... [ 51%] _build/jupyter_execute/7a7d1bfab01e7b0068e7ee926964efeb8d89ffd1cd1b845768be6a7d08e230d2.png copying images... [ 52%] _build/jupyter_execute/e1f3cb4f01fdc24afcbd9ed1b8e820fc53a57b919830e78473855a6706b6ca8d.png copying images... [ 52%] _build/jupyter_execute/4632938fb4db7519939461a858c1030d618b13b23a2d3c2ed4da00637d2764d9.png copying images... [ 53%] _build/jupyter_execute/e2b6fba2faaec41ee9da18283a730844ba9e2eab5a876d3e7c8bb2811df11c01.png copying images... [ 53%] _build/jupyter_execute/88aa4fcc109c878a374a7361bbf99b87b1c3ee5ad41957c3c695ade45960c104.png copying images... [ 54%] _build/jupyter_execute/70675aebfc80dcc9fc70fb92aa56f1262c94fc1f42438391d3f5b29d971e2106.png copying images... [ 54%] _build/jupyter_execute/3a9d72ea573f04a7eb5ee2f1ef2ba2927e434ab65fad265b993a0350053f34db.png copying images... [ 55%] _build/jupyter_execute/d2237124534fa2abfee97367a26620a9ff3898e6f0091608f6e5c06b9562c509.png copying images... [ 55%] _build/jupyter_execute/b70775c7fa5fbbb119b9ce5cd9c829177e17a29336ff12221903431ddbdb1d89.png copying images... [ 56%] _build/jupyter_execute/9309793bba6f25f718659e6ad9c686807b635ecf2fad7aae7c45cbef5ebe8170.png copying images... [ 56%] _build/jupyter_execute/019de1cdde7388e76e22ab5f4c813b4a2513c977f75ff179e148db6c183dbe61.png copying images... [ 56%] _build/jupyter_execute/b3514cbca07c9d355f66075ace5d4a16aacb62f6147dcd62a736f1e937938bbd.png copying images... [ 57%] _build/jupyter_execute/d4527a4e03bbd6fe4dd09c91d02efc2faf580783935ae9bb5a222db257521af8.png copying images... [ 57%] _build/jupyter_execute/6c8974cc011958acd47098c3a1a932191a7876764f737b820d16390a5ec783ac.png copying images... [ 58%] _build/jupyter_execute/30aa821349148a81487ab563d4a6a75e3c0e020dca4fb21b0139509cfceea398.png copying images... [ 58%] _build/jupyter_execute/3f2faaf30df23cf5c7dc5a27dc4d9e4de270fa4e9c4e5e26fbec40d1c0c387ce.png copying images... [ 59%] _build/jupyter_execute/e99df2c4982238793f5b4ac08047e40a7678573d6271fca7f7745ec296d115d9.png copying images... [ 59%] _build/jupyter_execute/d98c6dde98a2b75c80d393a309920062f038c5c38183705b573c8e3b538a38b9.png copying images... [ 60%] _build/jupyter_execute/61fa512d676d7e19397cd18d4333e7429601886e60f2d54178db1bcdb8e89880.png copying images... [ 60%] _build/jupyter_execute/7a6bd5a47fad48feef0b93724055e620e7500410149d6bca969c6b72f9857b6c.png copying images... [ 61%] _build/jupyter_execute/b9b0f6d973000a37268783e706bfbb973a9817010756dfd5fb4652496a2a8fb9.png copying images... [ 61%] _build/jupyter_execute/628660e3a52a692ea4efaddc5db8b60a1a10880a63a27602a8e82350aaff529a.png copying images... [ 61%] _build/jupyter_execute/fa0c98ce178a6f4397cff03e594908df66ade84306568b7660e14258413e837c.png copying images... [ 62%] _build/jupyter_execute/7280e7628c2d51572ba50bdeb1600d6b8579ff7c9fab4536e4a730b1904a789a.png copying images... [ 62%] _build/jupyter_execute/7892b8f497b868bf4353f873b5762e96e73c1fa06356dbf9e971f51c5e41aa37.png copying images... [ 63%] _build/jupyter_execute/13cc6c1d53e9a3aba72799cd93759ce396bc0cf762f3b46d5a762e2e276cd168.png copying images... [ 63%] _build/jupyter_execute/5f159fa54af4fc9b8f206c572e1b24b1f1eb24f3711032a9892df784cc5bdd7c.png copying images... [ 64%] _build/jupyter_execute/2eba1ec7ea236ae4f0ec8644785ccb3e4c08e44a3615eb1f0fcecbf277c408ae.png copying images... [ 64%] _build/jupyter_execute/67a8f588f5e935db5d190240996d7ef24c757b99131454c54c9a4463823244a5.png copying images... [ 65%] _build/jupyter_execute/915d74a745633da1ae5a4b91ea8bde5ace438f0cb3c103f3908c86e8166b46b1.png copying images... [ 65%] _build/jupyter_execute/2e949f6382ce68273faebe569154569a3ee12f69ebcd948c449e0354db3c3858.png copying images... [ 66%] _build/jupyter_execute/c4c7363df186dd1e25bb52b3ab60a88f27e65c5fd273d15d0e8e90d084b61a10.png copying images... [ 66%] _build/jupyter_execute/58a1e8c7549f5784c7d394c45d782825e39f1bdf074e3fdded8f85138303dbb8.png copying images... [ 67%] _build/jupyter_execute/f70cfa87abeee08705f1c0f68850c7f473f43cd828bd61d505236881b3929ea3.png copying images... [ 67%] _build/jupyter_execute/18bc84a5f8b79b26336676391d299a04a557a748cf1d07ed08e6e8cac7da4c96.png copying images... [ 67%] _build/jupyter_execute/db7abd6c2ccafd0838aad46c2bc2b048630dbb12171d5517102e5c05ff61195e.png copying images... [ 68%] _build/jupyter_execute/dfecea44c594db8a640293ba3b83b768f0f8fffb11feb06bb02a9db87ac88f07.png copying images... [ 68%] _build/jupyter_execute/dd9bd20407057e3f381a408e020551eab4a8158f49ffb9a4a5df3182d2245762.png copying images... [ 69%] _build/jupyter_execute/5894ed27c5482d0a22c852ad7ec122674a5403866dfc7b981dc53aaa358cd43c.png copying images... [ 69%] _build/jupyter_execute/9dde4846823e894d0bd646d737d64babb11955d44121dd294a676ecda2030ff7.png copying images... [ 70%] _build/jupyter_execute/56b1242b1fc93eb876458f16b792cfc8f378a7ecc1fd970d8a885833f3d7a134.png copying images... [ 70%] _build/jupyter_execute/75e95ac30061d0a6c4b5bbf3d3e5a9680b19ff08269fe2d8ea59ab10a023914e.png copying images... [ 71%] _build/jupyter_execute/71c776827198f5562510afe4c17873f7d10a2a35357ffe4aeaa128a78e788e1b.png copying images... [ 71%] _build/jupyter_execute/2d65107bba327ff05ed6987cc4c2777b641bed01c1ba09b6cc252a8e67c11998.png copying images... [ 72%] _build/jupyter_execute/656a59ad999749dafe447f6f02f9dc776d629197c94870a322466e09d20cb963.png copying images... [ 72%] _build/jupyter_execute/1e16be2728eeb5c9ab9542cc63fb3644e3b7c76f944de373115f046e2bddaa41.png copying images... [ 72%] _build/jupyter_execute/00e09d35a6edfcfa22e4469241715ce73a888cecd411514d94cd40d382f41e22.png copying images... [ 73%] _build/jupyter_execute/fec4e153d5cfd92a83fcba1cc62c2cdec87e8e91e1cb6f6b083ba8bf0f20f406.png copying images... [ 73%] _build/jupyter_execute/5a26fa44dcc471d706f3f7ecf801d3cf31743edbb836a393073e937ab85c7237.png copying images... [ 74%] _build/jupyter_execute/a7ed97e5192d909da6c3aef055bd93d31530c357a5110bf8219524f59aea1f47.png copying images... [ 74%] _build/jupyter_execute/114213c032705aeaf87f170cedba7f54024e21f20b59eff12c40067b3eff9d64.png copying images... [ 75%] _build/jupyter_execute/4b80a8ebb2fe694a361810d5829ad423339dec1272a186549a7f918f37259dd9.png copying images... [ 75%] _build/jupyter_execute/0f9a0935c010d0ca3f3e91c8fa02275b0be7c9ee8e544f273cbb72a6a0ce3350.png copying images... [ 76%] _build/jupyter_execute/03cce8ccfd5513f7ddc46190831f275b68395b19629c77570c13b7bb2ef5c0fd.png copying images... [ 76%] _build/jupyter_execute/95d4d301cb8d8f1010e6cd414b366f4226bcaa19ee061e88e0366e862ceca920.png copying images... [ 77%] _build/jupyter_execute/d5a3a68c99b881daa67c137c3d7bc76e191396f0a10909e3c86a00a4a5c3075c.png copying images... [ 77%] _build/jupyter_execute/fc25f73c02ceb1211cb72c585ad3dc7b21852f9c79f8a4477e41a704f851dbaf.png copying images... [ 78%] _build/jupyter_execute/f8a3a5f206cfdbc8fb57787377fb9f7ed9aee4755e69529878a36325eb9d9d3e.png copying images... [ 78%] _build/jupyter_execute/014721e47639c9d7f9c1d1a707959e3c7d87bee55dab814b24034ef26bee0cd8.png copying images... [ 78%] _build/jupyter_execute/82bf8185351514bbacde2d71cdbed19bd39ad9914092251bd40b07b1cc9ec0dc.png copying images... [ 79%] _build/jupyter_execute/47e219415022be69ebab4ddc0dc565d07df0d0e7ec71e622d328381286b0cdb3.png copying images... [ 79%] _build/jupyter_execute/bc2843555a0c778a2bc285fea5f772e8357d4f62eff7531e77a08e1c58094456.png copying images... [ 80%] _build/jupyter_execute/3a82d437cedadd52481ef022d5d5ac673e0870db60f66a000e7c06be9804b29d.png copying images... [ 80%] _build/jupyter_execute/a04173d282b7225af891853648454277c62aa658e3ed12b0e5a82cbdb2bc1bbf.png copying images... [ 81%] _build/jupyter_execute/c1e530b06deed8e1a2861304d545d88ceaa563443748219fc5782a11bfed8bab.png copying images... [ 81%] _build/jupyter_execute/2c9701ef266c8b3b9490dcb11623e4e2a3d69eaadb9f187953a8c0613a65ad00.png copying images... [ 82%] _build/jupyter_execute/d4f91a929016b982fdee738f747f0a8d1809c43e7e3d33245259adb7b1338791.png copying images... [ 82%] _build/jupyter_execute/b083f58cdecea3e188f5448696676033caad5295288a66e6200fe35079cd4cec.png copying images... [ 83%] _build/jupyter_execute/ab8ceac0ade73d69c35dae952929be9a16a21b7e5a9612e76511dcf341274cad.png copying images... [ 83%] _build/jupyter_execute/d9dcabc0cdd72d9908378b6689153e8b23c803c4078439c92b6aeb3e47787a58.png copying images... [ 83%] _build/jupyter_execute/08940b0dd5b929575cafae1e9d952d7177831ff7796a50edc2331e78b7ec073d.png copying images... [ 84%] _build/jupyter_execute/352f3ecd06ce5d90c523472f90e001df88d69becc556dba6dfd4aaaceea7e1f4.png copying images... [ 84%] _build/jupyter_execute/4d4980d62f791299b4db8748e42969abcf258c24a8e16b6dbc4c4f0b6f3c0954.png copying images... [ 85%] _build/jupyter_execute/6fc7410a8fe298e3f12b23877016321dc26fc5084064a189722cb82abb675c57.png copying images... [ 85%] _build/jupyter_execute/fc2449724f50fc3a4891f902f64112fc8d709eb0c11b3ea02648dfba0b8b49cb.png copying images... [ 86%] _build/jupyter_execute/2991fe558766f086411c6f1949c4c664c819a0ed608a34f7d3f878fb2a8bd46d.png copying images... [ 86%] _build/jupyter_execute/dd2fab22e25749d072c93ec385a1f448cf3fb7665eb2f992c9515ebdea1d4e70.png copying images... [ 87%] _build/jupyter_execute/2fdf057d113584ecc12239fb66397e9636b946d24fd9f6250b8e189a3c2dd238.png copying images... [ 87%] _build/jupyter_execute/bcf01e7a13a626a9d44a9f87b1a2c719f829981b46ec34b7f6ec6942e411ec64.png copying images... [ 88%] _build/jupyter_execute/4e39081732f70423300980f2b389aa5ae21497dc3f9446681e22f5a8a1525a6f.png copying images... [ 88%] _build/jupyter_execute/50b2b99a1a055abb06df268721d9be07613f992127cda844f616625219955568.png copying images... [ 89%] _build/jupyter_execute/92c8c115b1c591c74b8cb6e9d0835a859d6707b376d57f5b4f946258c9fdd8a4.png copying images... [ 89%] _build/jupyter_execute/c8a97f882cf8e155013d4ce88b30b12db459333f31fee35eb80d12633c02cddd.png copying images... [ 89%] _build/jupyter_execute/1653ef8b3d91e89e509984dd8cc5d19145350beaedaaab86a3a6c07672a28ef6.png copying images... [ 90%] _build/jupyter_execute/052f07fe780438b12d496b3ddaed3f958cc22f5a321991ae7ae593c773a35b76.png copying images... [ 90%] _build/jupyter_execute/e679f7ec42621cd951b12ed129b4f6474d24b5043fcb2fecdc96479a77531681.png copying images... [ 91%] _build/jupyter_execute/93488e44a5f2084884177480f5d1f8f1dbe87f53b44d9f1cc7058b983ff35938.png copying images... [ 91%] _build/jupyter_execute/f7e0871712a60e23b35c9f3379edb644d0dfeb0fd817a7e126b69d519253307f.png copying images... [ 92%] _build/jupyter_execute/72ca059296ecfe466026a5012c4c135420684573ae6e42aabc2968efb1290002.png copying images... [ 92%] _build/jupyter_execute/2a280bd3e22958f78430cfd4c41d5d37b44469e45a82ac05f5ccbca717b17457.png copying images... [ 93%] _build/jupyter_execute/daa55f3a8d5cc51906bb0897a81840e0c18cc86a174bf3eb891139934c50140d.png copying images... [ 93%] _build/jupyter_execute/f9429a2e1aaf6d889692fb40258efd524f12209e521b2b03f95b222f00c9e6df.png copying images... [ 94%] _build/jupyter_execute/5cfbe9eb92b9a937a933a0a604a872e7914012b0a7d2008e62bf8363a6cd5b42.png copying images... [ 94%] _build/jupyter_execute/600e370a6717ab2f4fea7b390eb08c45b8a20a5e3d0ad61a09a06adaed6e81d4.png copying images... [ 94%] _build/jupyter_execute/4b1be5ff87b37ad710d192a2dd9b53793c01f155b84f1d13932229b4583f7a37.png copying images... [ 95%] _build/jupyter_execute/c018c4b6b1363e6601efbaa0dc27c3f9e12cdddfeb15d75739291ddf554fa91e.png copying images... [ 95%] _static/img/tutorials/paga_planaria.png copying images... [ 96%] _build/jupyter_execute/b29e2eca5649a24042512f543f420cc021b77b8b9412c5bf77e1529588f06125.png copying images... [ 96%] _build/jupyter_execute/effe244049eb70377b606638583e2122c66538497cc7b1509820624883ea8580.png copying images... [ 97%] _build/jupyter_execute/199cd4d8abf199025931fd9fd2a043006cf2499cdd39ec71938a70db7ca91073.png copying images... [ 97%] _build/jupyter_execute/8f933a8f5774c68d14c62f9eaba449929338793be23ab1fc2b74fd6d3abff70b.png copying images... [ 98%] _build/jupyter_execute/2592ae333c0e7528751820f8406144b1f4aaf8eadee0dd37578ddbfb4b80ec08.png copying images... [ 98%] _build/jupyter_execute/44ce029c56c32532a6decdf808dd4e4f6b4e41dfad3597791df4a2763b9188cb.png copying images... [ 99%] _build/jupyter_execute/43f8eabe0205c95dc1674637d23c1a4912c9de0f0b874fb8fda2d9e61377a492.png copying images... [ 99%] _build/jupyter_execute/8d249fd99ddebeb2f583b36f78d8b745ef118be493cdc158ab0b18ee904fb8aa.png copying images... [100%] _build/jupyter_execute/6c3b6c2fef8ccfbbaa0b16b5baa60d3ce29c14b5d1703c87f6cea468813577a5.png copying images... [100%] _build/jupyter_execute/86278d709cf8712744109ad897a4c314d2ce612cf45f807bd702a3786a0d9d68.png dumping search index in English (code: en)... done dumping object inventory... done build finished with problems, 2 warnings (with warnings treated as errors).