fix test

YosefLab · Dec 28, 2023 · 578e5c1 · 578e5c1
1 parent 78aaca2
commit 578e5c1
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/tests/test_metrics.py b/tests/test_metrics.py
@@ -73,7 +73,10 @@ def test_lisi_knn():
     harmonypy_lisi_res = harmonypy_lisi(
         X, pd.DataFrame(labels, columns=["labels"]), label_colnames=["labels"], perplexity=10
     )[:, 0]
-    np.testing.assert_allclose(lisi_res, harmonypy_lisi_res)
+    # Slight numerical differences arise due to how self edges are handled. With approximate nearest
+    # neighbors methods, there is no guarantee that the self edge is the first edge. To accomodate this,
+    # we mask out self edges internally in lisi computation which causes slight numerical differences.
+    np.testing.assert_allclose(lisi_res, harmonypy_lisi_res, rtol=5e-5, atol=5e-5)
 
 
 def test_ilisi_clisi_knn():