Fix Python 3.13 failures in neighborhood enrichment and AnnData test fixture

src/cellcharter/gr/_nhood.py

@@ -140,9 +140,10 @@ def _nhood_enrichment(
 
     enrichment = np.log2(observed / expected) if log_fold_change else observed - expected
     if only_inter:
-        np.fill_diagonal(observed.values, np.nan)
-        np.fill_diagonal(expected.values, np.nan)
-        np.fill_diagonal(enrichment.values, np.nan)
+        diagonal_mask = np.eye(len(observed), dtype=bool)
+        observed = observed.mask(diagonal_mask, np.nan)
+        expected = expected.mask(diagonal_mask, np.nan)
+        enrichment = enrichment.mask(diagonal_mask, np.nan)
 
     result = {"enrichment": enrichment}
 

tests/conftest.py

@@ -44,8 +44,8 @@ def _download_codex(path: Path) -> None:
 
 @pytest.fixture()
 def non_visium_adata() -> ad.AnnData:
-    non_visium_coords = np.array([[1, 0], [3, 0], [5, 6], [0, 4]])
-    adata = ad.AnnData(X=non_visium_coords, dtype=int)
+    non_visium_coords = np.array([[1, 0], [3, 0], [5, 6], [0, 4]], dtype=int)
+    adata = ad.AnnData(X=non_visium_coords)
     adata.obsm[Key.obsm.spatial] = non_visium_coords
     return adata
 

tests/graph/test_nhood_local.py

@@ -0,0 +1,28 @@
+import numpy as np
+import pandas as pd
+import scipy.sparse as sps
+from anndata import AnnData
+from squidpy._constants._pkg_constants import Key
+
+import cellcharter as cc
+
+
+def test_nhood_enrichment_only_inter_sets_diagonal_to_nan():
+    adata = AnnData(X=np.ones((4, 2)))
+    adata.obs["cluster"] = pd.Categorical(["0", "0", "1", "1"])
+    adata.obsp[Key.obsp.spatial_conn()] = sps.csr_matrix(
+        np.array(
+            [
+                [0, 1, 1, 0],
+                [1, 0, 1, 1],
+                [1, 1, 0, 1],
+                [0, 1, 1, 0],
+            ]
+        )
+    )
+
+    result = cc.gr.nhood_enrichment(adata, cluster_key="cluster", only_inter=True, observed_expected=True, copy=True)
+
+    assert np.all(np.isnan(np.diag(result["observed"])))
+    assert np.all(np.isnan(np.diag(result["expected"])))
+    assert np.all(np.isnan(np.diag(result["enrichment"])))