Read the Docs build information Build id: 3885813 Project: icb-scanpy Version: 4025 Commit: c7eaeccab443465eb59ae25e782f34fc7c338593 Date: 2026-03-31T22:42:30.609142Z State: finished Success: True [rtd-command-info] start-time: 2026-03-31T22:42:31.389470Z, end-time: 2026-03-31T22:42:32.358411Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2026-03-31T22:42:32.448661Z, end-time: 2026-03-31T22:42:33.523234Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/4025/head:external-4025 From https://github.com/scverse/scanpy * [new ref] refs/pull/4025/head -> external-4025 * [new tag] 1.12.0 -> 1.12.0 [rtd-command-info] start-time: 2026-03-31T22:42:34.329344Z, end-time: 2026-03-31T22:42:34.496906Z, duration: 0, exit-code: 0 git checkout --force c7eaeccab443465eb59ae25e782f34fc7c338593 Note: switching to 'c7eaeccab443465eb59ae25e782f34fc7c338593'. 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 c7eaecc docs(plotting): add inline plot examples to highest_expr_genes and highly_variable_genes [rtd-command-info] start-time: 2026-03-31T22:42:34.574658Z, end-time: 2026-03-31T22:42:34.614181Z, 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: 2026-03-31T22:42:34.736782Z, end-time: 2026-03-31T22:42:34.814078Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2026-03-31T22:42:34.891706Z, end-time: 2026-03-31T22:42:58.803180Z, duration: 23, 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/4025/notebooks'... Submodule path 'notebooks': checked out '33dcb2d93b4686f313019f52705d5c752b37fc4e' [rtd-command-info] start-time: 2026-03-31T22:42:58.884923Z, end-time: 2026-03-31T22:43:03.591065Z, 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] 1.12.0rc1 -> 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: 2026-03-31T22:43:08.580334Z, end-time: 2026-03-31T22:43:08.639028Z, duration: 0, exit-code: 0 asdf global python 3.13.3 [rtd-command-info] start-time: 2026-03-31T22:43:09.001242Z, end-time: 2026-03-31T22:43:10.266759Z, 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: 2026-03-31T22:43:10.361767Z, end-time: 2026-03-31T22:43:11.566856Z, duration: 1, exit-code: 0 asdf install uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.11.2 * Downloading uv release 0.11.2... uv 0.11.2 installation was successful! [rtd-command-info] start-time: 2026-03-31T22:43:11.648123Z, end-time: 2026-03-31T22:43:11.766926Z, duration: 0, exit-code: 0 asdf global uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.11.2 [rtd-command-info] start-time: 2026-03-31T22:43:11.908393Z, end-time: 2026-03-31T22:43:18.600424Z, duration: 6, exit-code: 0 ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true Downloading virtualenv (5.6MiB) Downloading cryptography (4.3MiB) Downloading uv (23.4MiB) Downloading pygments (1.2MiB) Downloaded virtualenv Downloaded uv Downloaded cryptography 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/4025/docs/release-notes/3980.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/release-notes/4015.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/release-notes/3994.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/release-notes/3984.chore.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/release-notes/4010.chore.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/release-notes/4011.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/release-notes/3983.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/release-notes/3999.feat.md Done! [rtd-command-info] start-time: 2026-03-31T22:43:18.686854Z, end-time: 2026-03-31T22:47:05.971762Z, duration: 227, 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/4025/docs/references.bib... parsed 80 entries myst v5.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'html_admonition', 'html_image', 'deflist', 'dollarmath', 'amsmath', 'colon_fence'}, 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/4025/docs/_build/.jupyter_cache loading intersphinx inventory 'bbknn' from https://bbknn.readthedocs.io/en/latest/objects.inv ... loading intersphinx inventory 'anndata' from https://anndata.readthedocs.io/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://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 ... 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/4025/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/scanpy.pl.correlation_matrix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/scanpy.pl.embedding_density.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.tl.umap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.write.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.settings.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.settings.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.settings.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.settings.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.settings.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.settings.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.settings.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.settings.preset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/docs/generated/scanpy.settings.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4025/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] 281 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 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 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... [ 2%] 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... [ 5%] 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... [ 6%] 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... [ 7%] api/generated/classes/scanpy.pl.DotPlot.legend reading sources... [ 8%] api/generated/classes/scanpy.pl.DotPlot.style reading sources... [ 8%] api/generated/classes/scanpy.pl.MatrixPlot 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... [ 9%] 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... [ 10%] api/generated/classes/scanpy.pl.MatrixPlot.style reading sources... [ 11%] api/generated/classes/scanpy.pl.StackedViolin reading sources... [ 11%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP reading sources... [ 11%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE reading sources... [ 12%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT reading sources... [ 12%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_DENSITY_NORM reading sources... [ 12%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER reading sources... [ 13%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER reading sources... [ 13%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE reading sources... [ 14%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH reading sources... [ 14%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING reading sources... [ 14%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS reading sources... [ 15%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING reading sources... [ 15%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE reading sources... [ 15%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX reading sources... [ 16%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT reading sources... [ 16%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM reading sources... [ 16%] api/generated/classes/scanpy.pl.StackedViolin.style reading sources... [ 17%] api/generated/scanpy.pl.correlation_matrix reading sources... [ 17%] api/generated/scanpy.pl.diffmap reading sources... [ 17%] api/generated/scanpy.pl.dpt_groups_pseudotime reading sources... [ 18%] api/generated/scanpy.pl.dpt_timeseries reading sources... [ 18%] api/generated/scanpy.pl.draw_graph WARNING: Package 'fa2-modified' is not installed, falling back to layout 'fr'.To use the faster and better ForceAtlas2 layout, install package 'fa2-modified' (`pip install fa2-modified`). reading sources... [ 19%] api/generated/scanpy.pl.embedding reading sources... [ 19%] api/generated/scanpy.pl.embedding_density reading sources... [ 19%] api/generated/scanpy.pl.highest_expr_genes 0%| | 0.00/23.5M [00:00:3: UserWarning: Some cells have zero counts :1: UserWarning: Some cells have zero counts reading sources... [ 20%] api/generated/scanpy.pl.highly_variable_genes reading sources... [ 20%] api/generated/scanpy.pl.paga reading sources... [ 20%] api/generated/scanpy.pl.paga_compare reading sources... [ 21%] api/generated/scanpy.pl.paga_path reading sources... [ 21%] api/generated/scanpy.pl.pca reading sources... [ 21%] api/generated/scanpy.pl.pca_loadings reading sources... [ 22%] api/generated/scanpy.pl.pca_overview reading sources... [ 22%] api/generated/scanpy.pl.pca_variance_ratio reading sources... [ 22%] api/generated/scanpy.pl.rank_genes_groups reading sources... [ 23%] api/generated/scanpy.pl.rank_genes_groups_dotplot WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different. categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc. var_group_labels: T-cell, B-cell, myeloid reading sources... [ 23%] api/generated/scanpy.pl.rank_genes_groups_heatmap WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Gene labels are not shown when more than 50 genes are visualized. To show gene labels set `show_gene_labels=True` reading sources... [ 23%] api/generated/scanpy.pl.rank_genes_groups_matrixplot WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different. categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc. var_group_labels: T-cell, B-cell, myeloid reading sources... [ 24%] api/generated/scanpy.pl.rank_genes_groups_stacked_violin reading sources... [ 24%] api/generated/scanpy.pl.rank_genes_groups_tracksplot WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. reading sources... [ 25%] api/generated/scanpy.pl.rank_genes_groups_violin reading sources... [ 25%] api/generated/scanpy.pl.scrublet_score_distribution reading sources... [ 25%] api/generated/scanpy.pl.sim reading sources... [ 26%] api/generated/scanpy.pl.spatial reading sources... [ 26%] api/generated/scanpy.pl.tsne reading sources... [ 26%] api/generated/scanpy.pl.umap reading sources... [ 27%] api/generated/scanpy.pp.combat reading sources... [ 27%] api/generated/scanpy.pp.neighbors reading sources... [ 27%] api/generated/scanpy.pp.recipe_seurat reading sources... [ 28%] api/generated/scanpy.pp.recipe_weinreb17 reading sources... [ 28%] api/generated/scanpy.pp.recipe_zheng17 reading sources... [ 28%] api/generated/scanpy.pp.scrublet reading sources... [ 29%] api/generated/scanpy.pp.scrublet_simulate_doublets reading sources... [ 29%] api/get reading sources... [ 30%] api/index reading sources... [ 30%] api/io reading sources... [ 30%] api/metrics reading sources... [ 31%] api/plotting reading sources... [ 31%] api/preprocessing reading sources... [ 31%] api/queries reading sources... [ 32%] api/settings reading sources... [ 32%] api/tools reading sources... [ 32%] basic_usage reading sources... [ 33%] community reading sources... [ 33%] contributors reading sources... [ 33%] dev/ci reading sources... [ 34%] dev/code reading sources... [ 34%] dev/documentation reading sources... [ 35%] dev/getting-set-up reading sources... [ 35%] dev/index reading sources... [ 35%] dev/release reading sources... [ 36%] dev/testing reading sources... [ 36%] dev/versioning reading sources... [ 36%] ecosystem reading sources... [ 37%] external/exporting reading sources... [ 37%] external/generated/scanpy.external.tl.cyclone reading sources... [ 37%] external/generated/scanpy.external.tl.harmony_timeseries reading sources... [ 38%] external/generated/scanpy.external.tl.palantir reading sources... [ 38%] external/generated/scanpy.external.tl.palantir_results reading sources... [ 38%] external/generated/scanpy.external.tl.phate reading sources... [ 39%] external/generated/scanpy.external.tl.phenograph reading sources... [ 39%] external/generated/scanpy.external.tl.sam reading sources... [ 40%] external/generated/scanpy.external.tl.sandbag reading sources... [ 40%] external/generated/scanpy.external.tl.trimap reading sources... [ 40%] external/generated/scanpy.external.tl.wishbone reading sources... [ 41%] external/index reading sources... [ 41%] external/plotting reading sources... [ 41%] external/preprocessing reading sources... [ 42%] external/tools reading sources... [ 42%] generated/scanpy.Neighbors reading sources... [ 42%] generated/scanpy.Neighbors.compute_eigen reading sources... [ 43%] generated/scanpy.Neighbors.compute_neighbors reading sources... [ 43%] generated/scanpy.Neighbors.compute_transitions reading sources... [ 43%] generated/scanpy.Neighbors.connectivities reading sources... [ 44%] generated/scanpy.Neighbors.distances reading sources... [ 44%] generated/scanpy.Neighbors.distances_dpt reading sources... [ 44%] generated/scanpy.Neighbors.eigen_basis reading sources... [ 45%] generated/scanpy.Neighbors.eigen_values reading sources... [ 45%] generated/scanpy.Neighbors.rp_forest reading sources... [ 46%] generated/scanpy.Neighbors.to_igraph reading sources... [ 46%] generated/scanpy.Neighbors.transitions reading sources... [ 46%] generated/scanpy.Neighbors.transitions_sym reading sources... [ 47%] generated/scanpy.Preset reading sources... [ 47%] generated/scanpy.Preset.highly_variable_genes reading sources... [ 47%] generated/scanpy.Preset.leiden reading sources... [ 48%] generated/scanpy.Preset.override reading sources... [ 48%] generated/scanpy.Preset.pca reading sources... [ 48%] generated/scanpy.Preset.rank_genes_groups reading sources... [ 49%] generated/scanpy.Preset.scale reading sources... [ 49%] generated/scanpy.Preset.score_genes reading sources... [ 49%] generated/scanpy.Verbosity reading sources... [ 50%] generated/scanpy.Verbosity.debug reading sources... [ 50%] generated/scanpy.Verbosity.error reading sources... [ 51%] generated/scanpy.Verbosity.hint reading sources... [ 51%] generated/scanpy.Verbosity.info reading sources... [ 51%] generated/scanpy.Verbosity.level reading sources... [ 52%] generated/scanpy.Verbosity.override reading sources... [ 52%] generated/scanpy.Verbosity.warning reading sources... [ 52%] generated/scanpy.datasets.blobs reading sources... [ 53%] generated/scanpy.datasets.ebi_expression_atlas reading sources... [ 53%] generated/scanpy.datasets.krumsiek11 reading sources... [ 53%] generated/scanpy.datasets.moignard15 reading sources... [ 54%] generated/scanpy.datasets.paul15 reading sources... [ 54%] generated/scanpy.datasets.pbmc3k reading sources... [ 54%] generated/scanpy.datasets.pbmc3k_processed reading sources... [ 55%] generated/scanpy.datasets.pbmc68k_reduced reading sources... [ 55%] generated/scanpy.datasets.toggleswitch reading sources... [ 56%] generated/scanpy.datasets.visium_sge reading sources... [ 56%] generated/scanpy.experimental.pp.highly_variable_genes reading sources... [ 56%] generated/scanpy.experimental.pp.normalize_pearson_residuals reading sources... [ 57%] generated/scanpy.experimental.pp.normalize_pearson_residuals_pca reading sources... [ 57%] generated/scanpy.experimental.pp.recipe_pearson_residuals reading sources... [ 57%] generated/scanpy.external.exporting.cellbrowser reading sources... [ 58%] generated/scanpy.external.exporting.spring_project reading sources... [ 58%] generated/scanpy.external.pl.phate reading sources... [ 58%] generated/scanpy.external.pl.sam reading sources... [ 59%] generated/scanpy.external.pl.trimap reading sources... [ 59%] generated/scanpy.external.pl.wishbone_marker_trajectory reading sources... [ 59%] generated/scanpy.external.pp.bbknn reading sources... [ 60%] generated/scanpy.external.pp.harmony_integrate reading sources... [ 60%] generated/scanpy.external.pp.hashsolo reading sources... [ 60%] generated/scanpy.external.pp.magic reading sources... [ 61%] generated/scanpy.external.pp.mnn_correct reading sources... [ 61%] generated/scanpy.external.pp.scanorama_integrate reading sources... [ 62%] generated/scanpy.get.aggregate reading sources... [ 62%] generated/scanpy.get.obs_df reading sources... [ 62%] generated/scanpy.get.rank_genes_groups_df reading sources... [ 63%] generated/scanpy.get.var_df reading sources... [ 63%] generated/scanpy.logging.print_header reading sources... [ 63%] generated/scanpy.logging.print_versions reading sources... [ 64%] generated/scanpy.metrics.confusion_matrix reading sources... [ 64%] generated/scanpy.metrics.gearys_c reading sources... [ 64%] generated/scanpy.metrics.modularity reading sources... [ 65%] generated/scanpy.metrics.morans_i reading sources... [ 65%] generated/scanpy.pl.clustermap /home/docs/.local/share/hatch/env/virtual/scanpy/wmnd6JyS/docs/lib/python3.13/site-packages/anndata/_core/anndata.py:1796: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`. utils.warn_names_duplicates("obs") reading sources... [ 65%] generated/scanpy.pl.dendrogram reading sources... [ 66%] generated/scanpy.pl.dotplot WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different. categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc. var_group_labels: T-cell, B-cell, myeloid reading sources... [ 66%] generated/scanpy.pl.heatmap reading sources... [ 67%] generated/scanpy.pl.matrixplot WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different. categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc. var_group_labels: T-cell, B-cell, myeloid reading sources... [ 67%] generated/scanpy.pl.ranking reading sources... [ 67%] generated/scanpy.pl.scatter reading sources... [ 68%] generated/scanpy.pl.stacked_violin WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different. categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc. var_group_labels: T-cell, B-cell, myeloid reading sources... [ 68%] generated/scanpy.pl.tracksplot WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently. WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different. categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc. var_group_labels: T-cell, B-cell, myeloid reading sources... [ 68%] generated/scanpy.pl.violin reading sources... [ 69%] generated/scanpy.pp.calculate_qc_metrics 0%| | 0.00/5.58M [00:00