Fix kmeans test instability (#172)

* Fix kmeans test instability * Update test_neighbors.py * Update test_metrics.py * Update CHANGELOG.md
YosefLab · Aug 21, 2024 · a04c58f · a04c58f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning][].
 ### Fixed
 
 -   Fix neighbors connectivities in test to use new scanpy fn {pr}`170`.
+-   Fix Kmeans test {pr}`172`.
 
 ## 0.5.1 (2024-02-23)
 

diff --git a/tests/test_metrics.py b/tests/test_metrics.py
@@ -133,9 +133,10 @@ def test_isolated_labels():
 
 
 def test_kmeans():
-    centers = [[1, 1], [-1, -1], [1, -1]]
+    centers = np.array([[1, 1], [-1, -1], [1, -1]]) * 2
     len(centers)
-    X, labels_true = make_blobs(n_samples=3000, centers=centers, cluster_std=0.7)
+    X, labels_true = make_blobs(n_samples=3000, centers=centers, cluster_std=0.7, random_state=42)
+
     kmeans = scib_metrics.utils.KMeans(n_clusters=3)
     kmeans.fit(X)
     assert kmeans.labels_.shape == (X.shape[0],)

diff --git a/tests/test_neighbors.py b/tests/test_neighbors.py
@@ -18,7 +18,6 @@ def test_neighbors_results(n):
     neigh_result = pynndescent(adata.obsm[embedding_keys[0]], n_neighbors=n)
     neigh_result = neigh_result.subset_neighbors(n=n)
     new_connect = neigh_result.knn_graph_connectivities
-    new_dist = neigh_result.knn_graph_distances
 
     sc_connect = sc.neighbors._connectivity.umap(
         neigh_result.indices[:, :n], neigh_result.distances[:, :n], n_obs=adata.n_obs, n_neighbors=n