[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

tests/graph/test_niche.py

@@ -26,9 +26,7 @@
 
 def test_niche_calc_nhood(adata_seqfish: AnnData):
     """Check whether niche calculation using neighborhood profile approach works as intended."""
-    spatial_neighbors(
-        adata_seqfish, coord_type="generic", delaunay=False, n_neighs=N_NEIGHBORS
-    )
+    spatial_neighbors(adata_seqfish, coord_type="generic", delaunay=False, n_neighs=N_NEIGHBORS)
     calculate_niche(
         adata_seqfish,
         groups=GROUPS,
@@ -50,12 +48,8 @@ def test_niche_calc_nhood(adata_seqfish: AnnData):
     matrix = adata_seqfish.obsp[SPATIAL_CONNECTIVITIES_KEY].tocoo()
 
     # get obs x category matrix where each column is the absolute/relative frequency of a category in the neighborhood
-    rel_nhood_profile = _calculate_neighborhood_profile(
-        adata_seqfish, groups=GROUPS, matrix=matrix, abs_nhood=False
-    )
-    abs_nhood_profile = _calculate_neighborhood_profile(
-        adata_seqfish, groups=GROUPS, matrix=matrix, abs_nhood=True
-    )
+    rel_nhood_profile = _calculate_neighborhood_profile(adata_seqfish, groups=GROUPS, matrix=matrix, abs_nhood=False)
+    abs_nhood_profile = _calculate_neighborhood_profile(adata_seqfish, groups=GROUPS, matrix=matrix, abs_nhood=True)
     # assert shape obs x groups
     assert rel_nhood_profile.shape == (
         adata_seqfish.n_obs,
@@ -71,12 +65,8 @@ def test_niche_calc_nhood(adata_seqfish: AnnData):
 
 def test_niche_calc_utag(adata_seqfish: AnnData):
     """Check whether niche calculation using UTAG approach works as intended."""
-    spatial_neighbors(
-        adata_seqfish, coord_type="generic", delaunay=False, n_neighs=N_NEIGHBORS
-    )
-    calculate_niche(
-        adata_seqfish, flavor="utag", n_neighbors=N_NEIGHBORS, resolutions=[0.1, 1.0]
-    )
+    spatial_neighbors(adata_seqfish, coord_type="generic", delaunay=False, n_neighs=N_NEIGHBORS)
+    calculate_niche(adata_seqfish, flavor="utag", n_neighbors=N_NEIGHBORS, resolutions=[0.1, 1.0])
 
     niches = adata_seqfish.obs["utag_niche_res=1.0"]
     niches_low_res = adata_seqfish.obs["utag_niche_res=0.1"]
@@ -112,12 +102,8 @@ def test_niche_calc_utag(adata_seqfish: AnnData):
 def test_niche_calc_cellcharter(adata_seqfish: AnnData):
     """Check whether niche calculation using CellCharter approach works as intended."""
 
-    spatial_neighbors(
-        adata_seqfish, coord_type="generic", delaunay=False, n_neighs=N_NEIGHBORS
-    )
-    calculate_niche(
-        adata_seqfish, groups=GROUPS, flavor="cellcharter", distance=3, n_components=5
-    )
+    spatial_neighbors(adata_seqfish, coord_type="generic", delaunay=False, n_neighs=N_NEIGHBORS)
+    calculate_niche(adata_seqfish, groups=GROUPS, flavor="cellcharter", distance=3, n_components=5)
     niches = adata_seqfish.obs["cellcharter_niche"]
 
     assert niches.nunique() == 5
@@ -148,12 +134,8 @@ def test_niche_calc_cellcharter(adata_seqfish: AnnData):
 
 class TestNiches(PlotTester, metaclass=PlotTesterMeta):
     def test_plot_utag_niche(self, adata_seqfish: AnnData):
-        spatial_neighbors(
-            adata_seqfish, coord_type="generic", delaunay=False, n_neighs=N_NEIGHBORS
-        )
-        calculate_niche(
-            adata_seqfish, flavor="utag", n_neighbors=N_NEIGHBORS, resolutions=0.5
-        )
+        spatial_neighbors(adata_seqfish, coord_type="generic", delaunay=False, n_neighs=N_NEIGHBORS)
+        calculate_niche(adata_seqfish, flavor="utag", n_neighbors=N_NEIGHBORS, resolutions=0.5)
 
         sq.pl.spatial_scatter(
             adata_seqfish,
@@ -162,9 +144,7 @@ def test_plot_utag_niche(self, adata_seqfish: AnnData):
         )
 
     def test_plot_neighborhood_niche(self, adata_seqfish: AnnData):
-        spatial_neighbors(
-            adata_seqfish, coord_type="generic", delaunay=False, n_neighs=N_NEIGHBORS
-        )
+        spatial_neighbors(adata_seqfish, coord_type="generic", delaunay=False, n_neighs=N_NEIGHBORS)
 
         calculate_niche(
             adata_seqfish,
@@ -182,9 +162,7 @@ def test_plot_neighborhood_niche(self, adata_seqfish: AnnData):
         )
 
     def test_plot_cellcharter_niche(self, adata_seqfish: AnnData):
-        spatial_neighbors(
-            adata_seqfish, coord_type="generic", delaunay=False, n_neighs=N_NEIGHBORS
-        )
+        spatial_neighbors(adata_seqfish, coord_type="generic", delaunay=False, n_neighs=N_NEIGHBORS)
         calculate_niche(
             adata_seqfish,
             groups=GROUPS,