update tests

tests/ann2data/test_ann2data_by_category.py

@@ -11,10 +11,17 @@ def test_sample_case_ann2data_basic():
     # so that the resulting splits number of edges will be the same
     # as the sum of the number of edges in each cluster
     func_args = {"radius": 4.0, "coord_type": "generic"}
-    coordinates[:25, 0] += 100
+    cell_type = ["a"] * 20 + ["b"] * 20 + ["c"] * 5 + ["d"] * 5
+    image_id = list("xy" * 20) + ["z"] * 10
+    # make clusters for each cell type
+    for i, ct in enumerate(set(cell_type)):
+        idx = np.where(np.array(cell_type) == ct)[0]
+        coordinates[idx, 0] += 100 * i
+        coordinates[idx, 1] += 100 * i
+
     adata_gt = ad.AnnData(
         np.random.rand(50, 2),
-        obs={"cell_type": ["a"] * 20 + ["b"] * 20 + ["c"] * 5 + ["d"] * 5, "image_id": list("xy" * 20) + ["z"] * 10},
+        obs={"cell_type": cell_type, "image_id": image_id},
         obsm={"spatial_init": coordinates},
     )
     a2d = ann2data.Ann2DataByCategory(
@@ -55,11 +62,13 @@ def test_sample_case_ann2data_basic():
     assert torch.allclose(torch.cat([d.x for d in datas]), torch.from_numpy(big_adata.X).to(torch.float))
     assert sum([d.edge_index.shape[1] for d in datas]) == big_adata.uns["edge_index"].shape[1]
     adatas = list(iterables.ToCategoryIterator(category="cell_type")(big_adata))
-    assert np.allclose(
-        np.array(adatas[0].obsp["graph_distances"].todense()),
-        np.array(big_adata.obsp["graph_distances"][0:25, 0:25].todense()),
-    )
-    assert np.allclose(
-        np.array(adatas[1].obsp["graph_distances"].todense()),
-        np.array(big_adata.obsp["graph_distances"][25:, 25:].todense()),
-    )
+    assert len(adatas) == 4
+    # this line is the for loop version of the last two assertions
+
+    for a in adatas:
+        ct = a.obs["cell_type"].values[0]
+        ct_idx = np.where(np.array(cell_type) == ct)[0]
+        np.allclose(
+            a.obsp["graph_distances"].todense(),
+            big_adata.obsp["graph_distances"][ct_idx, :][:, ct_idx].todense(),
+        )

tests/transforms/test_add_edge_index.py

@@ -62,7 +62,7 @@ def test_add_edge_index():
     tf = transforms.AddEdgeIndex(
         spatial_key="spatial_init",
         key_added="pred",
-        func_args={"radius": median_dist, "n_neighs": 4},
+        func_args={"radius": median_dist, "n_neighs": 4, "coord_type": "generic"},
         edge_index_key="edge_index",
         edge_weight_key="edge_weight",
         gets_connectivities=False, # gets distances