feat: Spatial Conservation Metrics for scib-metrics

src/scib_metrics/__init__.py

@@ -16,6 +16,13 @@
     silhouette_batch,
     silhouette_label,
     bras,
+    spatial_mrre,
+    spatial_knn_overlap,
+    spatial_distance_correlation,
+    spatial_morans_i,
+    spatial_niche_knn_overlap,
+    spatial_pas,
+    spatial_chaos,
 )
 from ._settings import settings
 
@@ -35,6 +42,13 @@
     "kbet",
     "kbet_per_label",
     "graph_connectivity",
+    "spatial_mrre",
+    "spatial_knn_overlap",
+    "spatial_distance_correlation",
+    "spatial_morans_i",
+    "spatial_niche_knn_overlap",
+    "spatial_pas",
+    "spatial_chaos",
     "settings",
 ]
 

src/scib_metrics/benchmark/__init__.py

@@ -1,3 +1,19 @@
-from ._core import BatchCorrection, Benchmarker, BioConservation
+from ._core import (
+    BatchCorrection,
+    Benchmarker,
+    BioConservation,
+    CoordinatePreservation,
+    DomainBoundary,
+    NichePreservation,
+    SpatialConservation,
+)
 
-__all__ = ["Benchmarker", "BioConservation", "BatchCorrection"]
+__all__ = [
+    "Benchmarker",
+    "BioConservation",
+    "BatchCorrection",
+    "CoordinatePreservation",
+    "NichePreservation",
+    "DomainBoundary",
+    "SpatialConservation",  # backward-compat alias for CoordinatePreservation
+]

src/scib_metrics/metrics/__init__.py

@@ -5,6 +5,15 @@
 from ._nmi_ari import nmi_ari_cluster_labels_kmeans, nmi_ari_cluster_labels_leiden
 from ._pcr_comparison import pcr_comparison
 from ._silhouette import bras, silhouette_batch, silhouette_label
+from ._spatial import (
+    spatial_chaos,
+    spatial_distance_correlation,
+    spatial_knn_overlap,
+    spatial_morans_i,
+    spatial_mrre,
+    spatial_niche_knn_overlap,
+    spatial_pas,
+)
 
 __all__ = [
     "isolated_labels",
@@ -20,4 +29,11 @@
     "kbet",
     "kbet_per_label",
     "graph_connectivity",
+    "spatial_mrre",
+    "spatial_knn_overlap",
+    "spatial_distance_correlation",
+    "spatial_morans_i",
+    "spatial_niche_knn_overlap",
+    "spatial_pas",
+    "spatial_chaos",
 ]