Fix tests

tests/conftest.py

@@ -1,27 +1,27 @@
+import anndata as ad
 import numpy as np
 import pytest
 import scanpy as sc
-from anndata import AnnData
 from squidpy._constants._pkg_constants import Key
 
 _adata = sc.read("tests/_data/test_data.h5ad")
 _adata.raw = _adata.copy()
 
 
 @pytest.fixture()
-def non_visium_adata() -> AnnData:
+def non_visium_adata() -> ad.AnnData:
     non_visium_coords = np.array([[1, 0], [3, 0], [5, 6], [0, 4]])
-    adata = AnnData(X=non_visium_coords, dtype=int)
+    adata = ad.AnnData(X=non_visium_coords, dtype=int)
     adata.obsm[Key.obsm.spatial] = non_visium_coords
     return adata
 
 
 @pytest.fixture()
-def adata() -> AnnData:
+def adata() -> ad.AnnData:
     return _adata.copy()
 
 
 @pytest.fixture()
-def codex_adata() -> AnnData:
-    adata = sc.read("tests/_data/codex_adata.h5ad")
+def codex_adata() -> ad.AnnData:
+    adata = ad.read_h5ad("tests/_data/codex_adata.h5ad")
     return adata

tests/graph/test_build.py

@@ -25,8 +25,8 @@ def test_remove_long_links(self, non_visium_adata: AnnData):
         sq.gr.spatial_neighbors(non_visium_adata, coord_type="generic", delaunay=True)
         cc.gr.remove_long_links(non_visium_adata, distance_percentile=50)
 
-        spatial_graph = non_visium_adata.obsp[Key.obsp.spatial_conn()].A
-        spatial_dist = non_visium_adata.obsp[Key.obsp.spatial_dist()].A
+        spatial_graph = non_visium_adata.obsp[Key.obsp.spatial_conn()].toarray()
+        spatial_dist = non_visium_adata.obsp[Key.obsp.spatial_dist()].toarray()
 
         np.testing.assert_array_equal(spatial_graph, correct_graph_perc)
         np.testing.assert_allclose(spatial_dist, correct_dist_perc)
@@ -47,8 +47,8 @@ def test_mixed_clusters(self, non_visium_adata: AnnData):
 
         cc.gr.remove_intra_cluster_links(non_visium_adata, cluster_key="cluster")
 
-        trimmed_conns = non_visium_adata.obsp[Key.obsp.spatial_conn()].A
-        trimmed_dists = non_visium_adata.obsp[Key.obsp.spatial_dist()].A
+        trimmed_conns = non_visium_adata.obsp[Key.obsp.spatial_conn()].toarray()
+        trimmed_dists = non_visium_adata.obsp[Key.obsp.spatial_dist()].toarray()
 
         np.testing.assert_array_equal(trimmed_conns, correct_conns)
         np.testing.assert_allclose(trimmed_dists, correct_dists)
@@ -67,8 +67,8 @@ def test_same_clusters(self, non_visium_adata: AnnData):
 
         cc.gr.remove_intra_cluster_links(non_visium_adata, cluster_key="cluster")
 
-        trimmed_conns = non_visium_adata.obsp[Key.obsp.spatial_conn()].A
-        trimmed_dists = non_visium_adata.obsp[Key.obsp.spatial_dist()].A
+        trimmed_conns = non_visium_adata.obsp[Key.obsp.spatial_conn()].toarray()
+        trimmed_dists = non_visium_adata.obsp[Key.obsp.spatial_dist()].toarray()
 
         np.testing.assert_array_equal(trimmed_conns, correct_conns)
         np.testing.assert_allclose(trimmed_dists, correct_dists)
@@ -88,11 +88,11 @@ def test_different_clusters(self, non_visium_adata: AnnData):
 
         cc.gr.remove_intra_cluster_links(non_visium_adata, cluster_key="cluster")
 
-        trimmed_conns = non_visium_adata.obsp[Key.obsp.spatial_conn()].A
-        trimmed_dists = non_visium_adata.obsp[Key.obsp.spatial_dist()].A
+        trimmed_conns = non_visium_adata.obsp[Key.obsp.spatial_conn()].toarray()
+        trimmed_dists = non_visium_adata.obsp[Key.obsp.spatial_dist()].toarray()
 
-        np.testing.assert_array_equal(trimmed_conns, correct_conns.A)
-        np.testing.assert_allclose(trimmed_dists, correct_dists.A)
+        np.testing.assert_array_equal(trimmed_conns, correct_conns.toarray())
+        np.testing.assert_allclose(trimmed_dists, correct_dists.toarray())
 
     def test_copy(self, non_visium_adata: AnnData):
         non_visium_adata.obsp[Key.obsp.spatial_conn()] = sps.csr_matrix(
@@ -108,11 +108,11 @@ def test_copy(self, non_visium_adata: AnnData):
 
         cc.gr.remove_intra_cluster_links(non_visium_adata, cluster_key="cluster", copy=True)
 
-        trimmed_conns = non_visium_adata.obsp[Key.obsp.spatial_conn()].A
-        trimmed_dists = non_visium_adata.obsp[Key.obsp.spatial_dist()].A
+        trimmed_conns = non_visium_adata.obsp[Key.obsp.spatial_conn()].toarray()
+        trimmed_dists = non_visium_adata.obsp[Key.obsp.spatial_dist()].toarray()
 
-        np.testing.assert_array_equal(trimmed_conns, correct_conns.A)
-        np.testing.assert_allclose(trimmed_dists, correct_dists.A)
+        np.testing.assert_array_equal(trimmed_conns, correct_conns.toarray())
+        np.testing.assert_allclose(trimmed_dists, correct_dists.toarray())
 
 
 class TestConnectedComponents: