Initial framework of the niche refactor

hatch.toml

@@ -13,6 +13,10 @@ scripts.download = "python ./.scripts/ci/download_data.py {args}"
 
 [envs.hatch-test]
 dependency-groups = ["test"]
+# to pass spatialleiden-using tests in test_niche.py
+features = [
+  "leiden"
+]
 extra-dependencies = ["diff-cover"]
 matrix = [
   { deps = ["stable"], python = ["3.12", "3.13", "3.14"] },

src/squidpy/gr/__init__.py

@@ -20,7 +20,22 @@
     interaction_matrix,
     nhood_enrichment,
 )
-from squidpy.gr._niche import calculate_niche
+from squidpy.gr._niche import (
+    CellcharterEmbedder,
+    GMMClusterer,
+    LeidenClusterer,
+    MaskPostprocessor,
+    MinNicheSizePostprocessor,
+    NhoodProfileEmbedder,
+    RenamePostprocessor,
+    UtagEmbedder,
+    calculate_niche,
+    calculate_niche_cellcharter,
+    calculate_niche_custom,
+    calculate_niche_neighborhood,
+    calculate_niche_spatialleiden,
+    calculate_niche_utag,
+)
 from squidpy.gr._ppatterns import co_occurrence, spatial_autocorr
 from squidpy.gr._ripley import ripley
 from squidpy.gr._sepal import sepal
@@ -38,11 +53,24 @@
     "spatial_neighbors_radius",
     "spatial_neighbors_delaunay",
     "spatial_neighbors_grid",
+    "calculate_niche",
+    "calculate_niche_neighborhood",
+    "calculate_niche_utag",
+    "calculate_niche_cellcharter",
+    "calculate_niche_spatialleiden",
+    "calculate_niche_custom",
+    "NhoodProfileEmbedder",
+    "UtagEmbedder",
+    "CellcharterEmbedder",
+    "LeidenClusterer",
+    "GMMClusterer",
+    "MinNicheSizePostprocessor",
+    "MaskPostprocessor",
+    "RenamePostprocessor",
     "ligrec",
     "centrality_scores",
     "interaction_matrix",
     "nhood_enrichment",
-    "calculate_niche",
     "co_occurrence",
     "spatial_autocorr",
     "ripley",