update tests

tests/d2_graph_test.py

@@ -33,13 +33,11 @@ class TestD2Graph(unittest.TestCase):
             else:
                 self.assertEqual(1, len(d2.index[dmer]))
 
-
     def test_linear_d2_construction(self):
         for d in range(1, 10):
             size = 2 * d + 3
             index_k = 2 * d - 1
 
-
             G = gm.generate_d_graph_chain(size, d)
             d2 = D2Graph(G)
             d2.construct_from_barcodes(index_size=index_k, verbose=False)
@@ -49,7 +47,7 @@ class TestD2Graph(unittest.TestCase):
             self.assertEqual(awaited_d_num, len(d2.all_d_graphs))
 
             # Test index
-            awaited_index_size = comb(2*d+1, index_k) + (size - (2*d+1)) * comb(2*d, index_k-1)
+            awaited_index_size = comb(2 * d + 1, index_k) + (size - (2 * d + 1)) * comb(2 * d, index_k - 1)
             if len(d2.index) != awaited_index_size:
                 dmers = [list(x) for x in d2.index]
                 dmers = [str(x) for x in dmers if len(x) != len(frozenset(x))]
@@ -59,15 +57,15 @@ class TestD2Graph(unittest.TestCase):
             # Test connectivity
             # Center node names
             c1 = d
-            c2 = d+1
-            c3 = d+2
+            c2 = d + 1
+            c3 = d + 2
             # Connectivity matrix
             awaited_distances = {
-                c1:{c2:2, c3:4},
-                c2:{c1:2, c3:2},
-                c3:{c1:4, c2:2}
+                c1: {c2: 2, c3: 4},
+                c2: {c1: 2, c3: 2},
+                c3: {c1: 4, c2: 2}
             }
-            
+
             for x, y, data in d2.edges(data=True):
                 dg1 = d2.node_by_idx[x]
                 dg2 = d2.node_by_idx[y]
@@ -81,11 +79,10 @@ class TestD2Graph(unittest.TestCase):
 
             #     for idx2, dist in neighbors.items():
             #         dg2 = d2.node_by_idx[idx2]
-                    
+
             #         awaited_dist = awaited_distances[dg1.center][dg2.center]
             #         self.assertEqual(dist, awaited_dist)
 
-
     def test_reloading(self):
         # Parameters
         d = 3