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The refactored version of calculate_nearest_neighbor resolved the index mismatch by reindexing the result DataFrame before storing it in adata.obsm. This ensures the final DataFrame will have exactly the same row labels (and order) as adata.obs_names, which Anndata requires for storing in .obsm.

@fangliu117 fangliu117 merged commit 8f5cb05 into dev Jan 22, 2025
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