Read the Docs build information
Build id: 3976317
Project: icb-scanpy
Version: 4081
Commit: 108c5deed2afdc2c2bb975475f8c4ef4f157bf37
Date: 2026-04-30T15:31:13.705307Z
State: finished
Success: True


[rtd-command-info] start-time: 2026-04-30T15:32:58.998118Z, end-time: 2026-04-30T15:33:00.032321Z, duration: 1, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2026-04-30T15:33:00.148610Z, end-time: 2026-04-30T15:33:00.737833Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/4081/head:external-4081
From https://github.com/scverse/scanpy
 * [new ref]         refs/pull/4081/head -> external-4081

[rtd-command-info] start-time: 2026-04-30T15:33:01.497198Z, end-time: 2026-04-30T15:33:01.567898Z, duration: 0, exit-code: 0
git checkout --force 108c5deed2afdc2c2bb975475f8c4ef4f157bf37
Note: switching to '108c5deed2afdc2c2bb975475f8c4ef4f157bf37'.

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 <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 108c5de fix individual settings docs

[rtd-command-info] start-time: 2026-04-30T15:33:01.767140Z, end-time: 2026-04-30T15:33:01.813801Z, 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
        - mv docs/_build $READTHEDOCS_OUTPUT

[rtd-command-info] start-time: 2026-04-30T15:33:02.010934Z, end-time: 2026-04-30T15:33:02.077613Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2026-04-30T15:33:02.176131Z, end-time: 2026-04-30T15:33:24.142753Z, duration: 21, 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/4081/notebooks'...
Submodule path 'notebooks': checked out '33dcb2d93b4686f313019f52705d5c752b37fc4e'

[rtd-command-info] start-time: 2026-04-30T15:33:24.229444Z, end-time: 2026-04-30T15:33:29.679156Z, duration: 5, 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: 2026-04-30T15:33:34.438515Z, end-time: 2026-04-30T15:33:34.493576Z, duration: 0, exit-code: 0
asdf global python 3.13.9


[rtd-command-info] start-time: 2026-04-30T15:33:34.890952Z, end-time: 2026-04-30T15:33:35.982482Z, duration: 1, exit-code: 0
asdf plugin add uv
updating plugin repository...From https://github.com/asdf-vm/asdf-plugins
   8e311ee..c0369a1  master     -> origin/master
 * [new branch]      dependabot/github_actions/actions/checkout-6 -> origin/dependabot/github_actions/actions/checkout-6
 * [new branch]      dependabot/github_actions/amannn/action-semantic-pull-request-6.1.1 -> origin/dependabot/github_actions/amannn/action-semantic-pull-request-6.1.1
 * [new branch]      dependabot/github_actions/asdf-vm/actions-4 -> origin/dependabot/github_actions/asdf-vm/actions-4
HEAD is now at c0369a1 feat: add yasm plugin (#1087)

[rtd-command-info] start-time: 2026-04-30T15:33:36.072312Z, end-time: 2026-04-30T15:33:37.207430Z, duration: 1, exit-code: 0
asdf install uv latest
redirect url: https://github.com/astral-sh/uv/releases/tag/0.11.8
* Downloading uv release 0.11.8...
uv 0.11.8 installation was successful!

[rtd-command-info] start-time: 2026-04-30T15:33:37.290501Z, end-time: 2026-04-30T15:33:37.411795Z, duration: 0, exit-code: 0
asdf global uv latest
redirect url: https://github.com/astral-sh/uv/releases/tag/0.11.8

[rtd-command-info] start-time: 2026-04-30T15:33:37.576778Z, end-time: 2026-04-30T15:33:43.058331Z, duration: 5, exit-code: 0
( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true
Downloading virtualenv (7.2MiB)
Downloading pygments (1.2MiB)
Downloading cryptography (4.5MiB)
Downloading uv (23.7MiB)
 Downloaded virtualenv
 Downloaded cryptography
 Downloaded uv
 Downloaded pygments
Installed 42 packages in 24ms
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/4081/docs/release-notes/4055.feat.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/release-notes/3953.feat.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/release-notes/4052.breaking.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/release-notes/4010.chore.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/release-notes/3983.feat.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/release-notes/4039.breaking.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/release-notes/4036.perf.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/release-notes/4079.docs.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/release-notes/3999.feat.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/release-notes/4017.feat.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/release-notes/4062.perf.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/release-notes/3984.breaking.md
Done!

[rtd-command-info] start-time: 2026-04-30T15:33:43.148200Z, end-time: 2026-04-30T15:36:51.179662Z, duration: 188, exit-code: 0
uvx hatch run docs:build
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
checking bibtex cache... out of date
parsing bibtex file /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/references.bib... parsed 81 entries
myst v5.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'html_admonition', 'colon_fence', 'amsmath', 'deflist', 'dollarmath', 'html_image'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, 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='off', execution_cache_path='', execution_excludepatterns=(), execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=True, render_plugin='default', remove_code_source=False, remove_code_outputs=False, scroll_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='remove', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/_build/.jupyter_cache
loading intersphinx inventory 'anndata' from https://anndata.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'bbknn' from https://bbknn.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'cuml' from https://docs.rapids.ai/api/cuml/stable/objects.inv ...
loading intersphinx inventory 'cycler' from https://matplotlib.org/cycler/objects.inv ...
loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable/objects.inv ...
loading intersphinx inventory 'dask_ml' from https://ml.dask.org/objects.inv ...
loading intersphinx inventory 'decoupler' from https://decoupler.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'fast_array_utils' from https://icb-fast-array-utils.readthedocs-hosted.com/en/stable/objects.inv ...
loading intersphinx inventory 'h5py' from https://docs.h5py.org/en/stable/objects.inv ...
loading intersphinx inventory 'zarr' from https://zarr.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'ipython' from https://ipython.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'igraph' from https://python.igraph.org/en/stable/api/objects.inv ...
loading intersphinx inventory 'leidenalg' from https://leidenalg.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'louvain' from https://louvain-igraph.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'matplotlib' from https://matplotlib.org/stable/objects.inv ...
loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv ...
loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ...
loading intersphinx inventory 'pandas' from https://pandas.pydata.org/pandas-docs/stable/objects.inv ...
loading intersphinx inventory 'pydeseq2' from https://pydeseq2.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'pynndescent' from https://pynndescent.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'pytest' from https://docs.pytest.org/en/latest/objects.inv ...
loading intersphinx inventory 'rapids_singlecell' from https://rapids-singlecell.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ...
loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv ...
loading intersphinx inventory '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/4081/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/scanpy.pl.correlation_matrix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/scanpy.pl.embedding_density.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.tl.umap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.write.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.Preset.pca.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.Preset.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.Preset.scale.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.Preset.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.Verbosity.debug.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.Verbosity.error.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.Verbosity.hint.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.Verbosity.info.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.Verbosity.level.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.Verbosity.warning.rst
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 53 source files that are out of date
updating environment: [new config] 264 added, 0 changed, 0 removed
/home/docs/.asdf/installs/python/3.13.9/lib/python3.13/importlib/__init__.py:88: ZarrUserWarning: pytest not installed, skipping test suite
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/home/docs/.asdf/installs/python/3.13.9/lib/python3.13/importlib/__init__.py:88: ZarrUserWarning: pytest not installed, skipping test suite
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/home/docs/.asdf/installs/python/3.13.9/lib/python3.13/importlib/__init__.py:88: ZarrUserWarning: pytest not installed, skipping test suite
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<string>:3: UserWarning: In previous versions of scanpy, calling tsne with `n_jobs` > 1 would use MulticoreTSNE. Now this uses the scikit-learn version of TSNE by default. If you’d like the old behaviour (which is deprecated), pass `use_fast_tsne=True`. Note, MulticoreTSNE is not actually faster anymore.
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4081/docs/generated/scanpy.pp.pca.rst: document is referenced in multiple toctrees: ['api/preprocessing', 'api/tools'], selecting: api/tools <- generated/scanpy.pp.pca
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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 succeeded.

The HTML pages are in docs/_build/html.

[rtd-command-info] start-time: 2026-04-30T15:36:51.352705Z, end-time: 2026-04-30T15:36:51.398653Z, duration: 0, exit-code: 0
mv docs/_build $READTHEDOCS_OUTPUT