Read the Docs build information
Build id: 3833096
Project: icb-scanpy
Version: latest
Commit: beff1e98ad9b6f01f1e4f7b151038b69653f0ba7
Date: 2026-03-16T07:41:45.765880Z
State: finished
Success: False


[rtd-command-info] start-time: 2026-03-16T07:41:46.619529Z, end-time: 2026-03-16T07:41:47.509116Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2026-03-16T07:41:47.621854Z, end-time: 2026-03-16T07:41:49.756122Z, duration: 2, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50
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      -> 1.10.0
 * [new tag]           1.10.0.dev0 -> 1.10.0.dev0
 * [new tag]           1.10.0rc1   -> 1.10.0rc1
 * [new tag]           1.10.0rc2   -> 1.10.0rc2
 * [new tag]           1.10.1      -> 1.10.1
 * [new tag]           1.10.2      -> 1.10.2
 * [new tag]           1.10.3      -> 1.10.3
 * [new tag]           1.10.4      -> 1.10.4
 * [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]           1.11.1      -> 1.11.1
 * [new tag]           1.11.2      -> 1.11.2
 * [new tag]           1.11.3      -> 1.11.3
 * [new tag]           1.11.4      -> 1.11.4
 * [new tag]           1.11.5      -> 1.11.5
 * [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]           1.4.4.post1 -> 1.4.4.post1
 * [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]           1.6.1       -> 1.6.1
 * [new tag]           1.7.0       -> 1.7.0
 * [new tag]           1.7.0rc1    -> 1.7.0rc1
 * [new tag]           1.7.1       -> 1.7.1
 * [new tag]           1.7.2       -> 1.7.2
 * [new tag]           1.8.0       -> 1.8.0
 * [new tag]           1.8.0.a0    -> 1.8.0.a0
 * [new tag]           1.8.0.dev0  -> 1.8.0.dev0
 * [new tag]           1.8.1       -> 1.8.1
 * [new tag]           1.8.2       -> 1.8.2
 * [new tag]           1.9.0       -> 1.9.0
 * [new tag]           1.9.0.dev0  -> 1.9.0.dev0
 * [new tag]           1.9.1       -> 1.9.1
 * [new tag]           1.9.2       -> 1.9.2
 * [new tag]           1.9.3       -> 1.9.3
 * [new tag]           1.9.4       -> 1.9.4
 * [new tag]           1.9.5       -> 1.9.5
 * [new tag]           1.9.6       -> 1.9.6
 * [new tag]           1.9.7       -> 1.9.7
 * [new tag]           1.9.8       -> 1.9.8
 * [new tag]           docs        -> docs

[rtd-command-info] start-time: 2026-03-16T07:41:50.403360Z, end-time: 2026-03-16T07:41:50.443350Z, 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 "--with=virtualenv<21" hatch run towncrier build --keep || true
    build:
      html:
        - uvx "--with=virtualenv<21" hatch run docs:build
        - mv docs/_build $READTHEDOCS_OUTPUT

[rtd-command-info] start-time: 2026-03-16T07:41:50.580467Z, end-time: 2026-03-16T07:41:50.641977Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2026-03-16T07:41:50.736522Z, end-time: 2026-03-16T07:42:09.303005Z, duration: 18, exit-code: 0
git submodule update --init --force --
Submodule 'notebooks' (https://github.com/scverse/scanpy-tutorials/) registered for path 'notebooks'
Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/notebooks'...
Submodule path 'notebooks': checked out '33dcb2d93b4686f313019f52705d5c752b37fc4e'

[rtd-command-info] start-time: 2026-03-16T07:42:09.384215Z, end-time: 2026-03-16T07:42:11.564611Z, duration: 2, exit-code: 0
git fetch --unshallow || true


[rtd-command-info] start-time: 2026-03-16T07:42:16.243430Z, end-time: 2026-03-16T07:42:16.296510Z, duration: 0, exit-code: 0
asdf global python 3.13.3


[rtd-command-info] start-time: 2026-03-16T07:42:16.627998Z, end-time: 2026-03-16T07:42:17.685443Z, 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: 2026-03-16T07:42:17.766617Z, end-time: 2026-03-16T07:42:18.904088Z, duration: 1, exit-code: 0
asdf install uv latest
redirect url: https://github.com/astral-sh/uv/releases/tag/0.10.10
* Downloading uv release 0.10.10...
uv 0.10.10 installation was successful!

[rtd-command-info] start-time: 2026-03-16T07:42:18.985521Z, end-time: 2026-03-16T07:42:19.097864Z, duration: 0, exit-code: 0
asdf global uv latest
redirect url: https://github.com/astral-sh/uv/releases/tag/0.10.10

[rtd-command-info] start-time: 2026-03-16T07:42:19.256597Z, end-time: 2026-03-16T07:42:25.440233Z, duration: 6, exit-code: 0
( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx "--with=virtualenv<21" hatch run towncrier build --keep || true
Downloading pygments (1.2MiB)
Downloading cryptography (4.3MiB)
Downloading uv (22.4MiB)
Downloading virtualenv (5.6MiB)
 Downloaded virtualenv
 Downloaded cryptography
 Downloaded uv
 Downloaded pygments
Installed 41 packages in 21ms
Creating environment: default
Installing project in development mode
Checking dependencies
Syncing dependencies
Loading template...
Finding news fragments...
Rendering news fragments...
Writing to newsfile...
Staging newsfile...
Keeping the following files:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/3980.fix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/3994.fix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/3984.chore.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/3999.feat.md
Done!

[rtd-command-info] start-time: 2026-03-16T07:42:25.518810Z, end-time: 2026-03-16T07:46:09.886906Z, duration: 224, exit-code: 1
uvx "--with=virtualenv<21" 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/latest/docs/references.bib... parsed 80 entries
myst v5.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'dollarmath', 'amsmath', 'deflist', 'colon_fence', 'html_admonition', 'html_image'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
myst-nb v1.4.0.dev: 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/latest/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 '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 ...
WARNING: failed to reach any of the inventories with the following issues:
intersphinx inventory 'https://pandas.pydata.org/pandas-docs/stable/objects.inv' not fetchable due to <class 'requests.exceptions.HTTPError'>: 404 Client Error: Not Found for url: https://pandas.pydata.org/pandas-docs/stable/objects.inv
loading intersphinx inventory 'seaborn' from https://seaborn.pydata.org/objects.inv ...
loading intersphinx inventory 'session_info2' from https://session-info2.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'squidpy' from https://squidpy.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'sklearn' from https://scikit-learn.org/stable/objects.inv ...
[autosummary] generating autosummary for: api/classes.md, api/datasets.md, api/deprecated.md, api/experimental.md, api/get.md, api/index.md, api/io.md, api/metrics.md, api/plotting.md, api/preprocessing.md, ..., tutorials/experimental/dask.ipynb, tutorials/experimental/index.md, tutorials/experimental/pearson_residuals.ipynb, tutorials/index.md, tutorials/plotting/advanced.ipynb, tutorials/plotting/core.ipynb, tutorials/plotting/index.md, tutorials/trajectories/index.md, tutorials/trajectories/paga-paul15.ipynb, usage-principles.md
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.correlation_matrix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.embedding_density.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.umap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.write.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.settings.figdir.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.settings.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.settings.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.settings.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.settings.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.settings.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.settings.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.settings.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.settings.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.settings.writedir.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] 276 added, 0 changed, 0 removed
/home/docs/.asdf/installs/python/3.13.3/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/3.13.3/lib/python3.13/importlib/__init__.py:88: ZarrUserWarning: pytest not installed, skipping test suite
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/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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dumping search index in English (code: en)... done
dumping object inventory... done
build finished with problems, 67 warnings (with warnings treated as errors).