[maltekuehl]

Release 0.10.1. Release notes: docs/source/release-notes/0.10.1.md.

Bug fixes

• Cluster colors match the colormap. so.plot.cluster_image, save_cluster_image, cluster_legend, cluster_selection, save_cluster_selection, som_clusters and the colorbars of cluster_scatter and connectivity_graph now show each cluster in the color with the same index in the colormap. Before, the colormap was scaled to the range of labels present in each image, so images that lacked the highest cluster labels, or that contained unassigned pixels, showed clusters in the colors of other clusters. Colormap names and continuous colormaps, e.g., colormap="flag" for segmentation masks with many labels, are still spread from label 0 to the highest label.
• Unassigned pixels are supported. Pixels without a nearest SOM node, i.e., all-zero pixels with the cosine metric and constant pixels with the correlation metric, are labelled -1 by so.dimension.som().label since 0.10.0. They are now handled throughout:
  • Cluster plots show them transparent (black in cluster_selection), and cluster_location does not show them as a cluster.
  • so.spatial.vicinity_composition counts them neither as a cluster nor as a neighbor, and its permutation test keeps them in place.
  • so.spatial.autocorrelation does not analyse them as a cluster, and so.spatial.local_heteroskedasticity assigns them to no cluster.
  • so.spatial.local_autocorrelation, which operates on the label values, raises a ValueError for them.
• Integer labels of any type are accepted. vicinity_composition, autocorrelation and local_autocorrelation rejected the int32 labels returned by so.dimension.som().label since 0.10.0. Invalid clustered images now raise a TypeError or ValueError instead of an AssertionError.

Docs

Reruns the full_example, scverse, segment and spatial tutorials with 0.10.x.

Testing

• ruff, ruff format, mypy -p spatiomic, bandit: clean
• CPU suite: 230 passed
• New test/plot/test_cluster_image.py checks the exact colors drawn and saved, including unassigned pixels, missing labels and continuous colormaps; spatial tests check that results with unassigned pixels equal those with an extra cluster that is then dropped.
• Docs build cleanly.
• The mypy pre-commit hook now runs in the project environment (uv run mypy); before, it used whichever mypy was on the PATH.

🤖 Generated with Claude Code

[codecov-commenter]

Codecov Report

❌ Patch coverage is 72.00000% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.94%. Comparing base (877cf4f) to head (810bd6e).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
spatiomic/spatial/_local_heteroskedasticity.py	16.66%	5 Missing ⚠️
spatiomic/spatial/_local_autocorrelation.py	33.33%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #29      +/-   ##
==========================================
+ Coverage   78.73%   78.94%   +0.21%     
==========================================
  Files          54       55       +1     
  Lines        1876     1890      +14     
==========================================
+ Hits         1477     1492      +15     
+ Misses        399      398       -1     

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