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Fix instance_key dtype check rejecting object vs str string ids - #1270
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Since 65dc73e the check in `validate_table_in_spatialdata` raised whenever the dtypes differed and either side was string-like. With pandas>=3 the index of shapes read from parquet is `str`, while anndata reads string columns of zarr v2 stores as `object`, so valid datasets (e.g. the mouse_liver sandbox dataset) failed to load. Only raise for a string vs non-string mismatch. Add a network regression test on the real `cells` dataset, annotating `cell_boundaries` via the `cell_id` column. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
LucaMarconato
enabled auto-merge (squash)
October 8, 2026 22:59
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #1270 +/- ##
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+ Coverage 91.40% 91.42% +0.01%
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Files 53 53
Lines 8381 8381
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+ Hits 7661 7662 +1
+ Misses 720 719 -1
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Since 65dc73e the check in
validate_table_in_spatialdataraised whenever the dtypes differed and either side was string-like. With pandas>=3 the index of shapes read from parquet isstr, while anndata reads string columns asobject, so valid datasets (e.g. the mouse_liver sandbox dataset) failed to load. Only raise for a string vs non-string mismatch.Add a network regression test on the real
cellsdataset, annotatingcell_boundariesvia thecell_idcolumn.