Merge origin

tests/loaders/test_ctc.py

@@ -65,6 +65,7 @@ def test_ctc_single_nodes():
     # This should raise an error if there are no times for single nodes
     TrackingGraph(G)
 
+
 def test_ctc_with_gap_closing():
     data = [
         {"Cell_ID": 1, "Start": 0, "End": 1, "Parent_ID": 0},
@@ -81,6 +82,7 @@ def test_ctc_with_gap_closing():
     assert G.has_edge("1_1", "3_3")
     assert G.has_edge("2_1", "4_6")
 
+
 def test_load_data():
     test_dir = os.path.abspath(__file__)
     data_dir = os.path.abspath(

tests/test_utils.py

@@ -153,11 +153,11 @@ def get_division_graphs():
 def get_gap_close_graphs():
     """
     G1
-                                      3_5 -- 3_6 -- -- -- 5_10                   
+                                      3_5 -- 3_6 -- -- -- 5_10
     1_0 -- 1_1 -- -- -- 2_3 -- 2_4 -<
                                       4_5 -- 4_6
     G2
-                                      2_5 -- 2_6 -- -- -- 4_10                   
+                                      2_5 -- 2_6 -- -- -- 4_10
     1_0 -- 1_1 -- 1_2 -- 1_3 -- 1_4 -<
                                       3_5 -- 3_6
     """
@@ -201,10 +201,21 @@ def get_gap_close_graphs():
     nx.set_node_attributes(G2, attrs)
 
     # G1, G2 mapper
-    mapper = [("1_0", "1_0"), ("1_1", "1_1"), ("2_3", "1_3"), ("2_4", "1_4"), ("3_5", "2_5"), ("3_6", "2_6"), ("5_10", "4_10"), ("4_5", "3_5"), ("4_6", "3_6")]
+    mapper = [
+        ("1_0", "1_0"),
+        ("1_1", "1_1"),
+        ("2_3", "1_3"),
+        ("2_4", "1_4"),
+        ("3_5", "2_5"),
+        ("3_6", "2_6"),
+        ("5_10", "4_10"),
+        ("4_5", "3_5"),
+        ("4_6", "3_6"),
+    ]
 
     return G1, G2, mapper
 
+
 def get_division_gap_close_graphs():
     """
     G1
@@ -248,6 +259,13 @@ def get_division_gap_close_graphs():
         attrs[node] = {"t": int(node[-1:]), "x": 0, "y": 0}
     nx.set_node_attributes(G2, attrs)
 
-    mapper = [("1_0", "1_0"), ("1_1", "1_1"), ("2_3", "2_3"), ("2_4", "2_4"), ("3_2", "3_2"), ("3_4", "4_4")]
+    mapper = [
+        ("1_0", "1_0"),
+        ("1_1", "1_1"),
+        ("2_3", "2_3"),
+        ("2_4", "2_4"),
+        ("3_2", "3_2"),
+        ("3_4", "4_4"),
+    ]
 
-    return G1, G2, mapper
+    return G1, G2, mapper

tests/track_errors/test_divisions.py

@@ -11,7 +11,7 @@
     _get_succ_by_t,
 )
 
-from tests.test_utils import get_division_graphs, get_division_gap_close_graphs
+from tests.test_utils import get_division_gap_close_graphs, get_division_graphs
 
 
 @pytest.fixture
@@ -221,28 +221,29 @@ def test_evaluate_division_events():
 
     assert np.all([isinstance(k, int) for k in results.keys()])
 
+
 def test_gap_close_divisions():
     g_gt, g_pred, mapper = get_division_gap_close_graphs()
     matched_data = Matched(TrackingGraph(g_gt), TrackingGraph(g_pred), mapper)
     _classify_divisions(matched_data)
 
     # missing gap close div edge so FN DIV
-    assert g_gt.nodes['1_1'][NodeAttr.FN_DIV]
-    
+    assert g_gt.nodes["1_1"][NodeAttr.FN_DIV]
+
     # fix division, assert it's identified correctly
-    g_pred.remove_node('2_2')
-    g_pred.add_edge('1_1', '2_3')
+    g_pred.remove_node("2_2")
+    g_pred.add_edge("1_1", "2_3")
     # mapper doesn't need to change as removed node was always missing
     matched_data = Matched(TrackingGraph(g_gt), TrackingGraph(g_pred), mapper)
     _classify_divisions(matched_data)
-    assert g_gt.nodes['1_1'][NodeAttr.TP_DIV]
-    assert g_gt.nodes['1_1'][NodeAttr.TP_DIV]
+    assert g_gt.nodes["1_1"][NodeAttr.TP_DIV]
+    assert g_gt.nodes["1_1"][NodeAttr.TP_DIV]
 
     g_gt, g_pred, mapper = get_division_gap_close_graphs()
     # remove gt division
-    g_gt.remove_edge('1_1', '2_3')
-    g_gt.remove_edge('1_1', '3_2')
+    g_gt.remove_edge("1_1", "2_3")
+    g_gt.remove_edge("1_1", "3_2")
     matched_data = Matched(TrackingGraph(g_gt), TrackingGraph(g_pred), mapper)
     _classify_divisions(matched_data)
     # assert fp division classified correctly
-    assert g_pred.nodes['1_1'][NodeAttr.FP_DIV]
+    assert g_pred.nodes["1_1"][NodeAttr.FP_DIV]