Merge branch 'main' into adamgayoso-patch-2

YosefLab · Aug 21, 2024 · 14517ed · 14517ed
2 parents 2175e94 + 7482c06
commit 14517ed
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,10 @@ and this project adheres to [Semantic Versioning][].
 
 -   Add `progress_bar` argument to {class}`scib_metrics.benchmark.Benchmarker` {pr}`152`.
 
+### Fixed
+
+-   Fix neighbors connectivities in test to use new scanpy fn {pr}`170`.
+
 ## 0.5.1 (2024-02-23)
 
 ### Changed

diff --git a/tests/test_neighbors.py b/tests/test_neighbors.py
@@ -20,9 +20,8 @@ def test_neighbors_results(n):
     new_connect = neigh_result.knn_graph_connectivities
     new_dist = neigh_result.knn_graph_distances
 
-    sc_dist, sc_connect = sc.neighbors._compute_connectivities_umap(
-        neigh_result.indices[:, :n], neigh_result.distances[:, :n], adata.n_obs, n_neighbors=n
+    sc_connect = sc.neighbors._connectivity.umap(
+        neigh_result.indices[:, :n], neigh_result.distances[:, :n], n_obs=adata.n_obs, n_neighbors=n
     )
 
-    np.testing.assert_allclose(new_dist.A, sc_dist.A)
-    np.testing.assert_allclose(new_connect.A, sc_connect.A)
+    np.testing.assert_allclose(new_connect.toarray(), sc_connect.toarray())