bugfix on graph manipulation for merging and test to verify it

deconvolution/graph_manipulator.py

@@ -34,14 +34,15 @@ def merge_nodes(G, node1, node2):
     new_node = f"{node1}_{node2}" if node1 < node2 else f"{node2}_{node1}"
     G.add_node(new_node)
 
-    # Add the edges from previous nodes
+    # List the edges to add
+    neighbors = []
     for edge in G.edges(node1):
         neighbor = edge[0] if edge[0] != node1 else edge[1]
 
         if neighbor == node2:
             continue
 
-        G.add_edge(neighbor, new_node)
+        neighbors.append(neighbor)
 
     for edge in G.edges(node2):
         neighbor = edge[0] if edge[0] != node2 else edge[1]
@@ -49,6 +50,13 @@ def merge_nodes(G, node1, node2):
         if neighbor == node1:
             continue
 
+        neighbors.append(neighbor)
+
+    # De-replicate neighbors
+    neighbors = set(neighbors)
+
+    # Add neighbors
+    for neighbor in neighbors:
         G.add_edge(neighbor, new_node)
 
     # Remove previous nodes from the graph

tests/graph_manipulation_test.py

 import unittest
 
-from d_graph import Dgraph
+import graph_manipulator as gm
 
 
 
 class TestGraphManipulation(unittest.TestCase):
 
-    def test_dg_to_list(self):
-        center, h1, h2, G = unit_d_graph
-        dg = Dgraph(center)
-        dg.put_halves(h1, h2, G)
-        lst = dg.to_ordered_lists()
-
-        self.assertEquals([['A0'], ['A1'], ['A2'], ['C'], ['B2'], ['B1'], ['B0']], lst)
-
+    def test_generate_d_graph_chain(self):
+        for size in range(10, 100, 10):
+            for d in range(1, 4):
+                G = gm.generate_d_graph_chain(size, d)
+                
+                # Test the size
+                self.assertEquals(len(G.nodes()), size)
+                # Test arities
+                for idx in range(d):
+                    self.assertEquals(len(G.edges(idx)), d+idx)
+                    self.assertEquals(len(G.edges(size-idx-1)), d+idx)
+                for idx in range(d, size-d):
+                    self.assertEquals(len(G.edges(idx)), d*2)
+
+
+
+    def test_merging_node(self):
+        size = 15
+        d = 3
+        G = gm.generate_d_graph_chain(size, d)
+
+        for gap in range(1, d+1):
+            H = G.copy()
+            gm.merge_nodes(H, d+1, d+gap+1)
+
+            self.assertEquals(len(H.nodes()), size-1)
+
+            g_nodes = list(G.nodes())
+            for node in H.nodes():
+                if node in g_nodes:
+                    g_neighbors = list(G.neighbors(node))
+                    h_neighbors = list(H.neighbors(node))
+                    if (d+1) in g_neighbors and (d+gap+1) in g_neighbors:
+                        self.assertEquals(len(g_neighbors), len(h_neighbors)+1)
+                    else:
+                        self.assertEquals(len(g_neighbors), len(list(h_neighbors)))
+                else:
+                    cumulative_neighbors = set(list(G.neighbors(d+1)) + list(G.neighbors(d+gap+1)))
+                    h_neighbors = H.neighbors(f"{d+1}_{d+gap+1}")
+                    self.assertEquals(len(cumulative_neighbors)-2, len(list(h_neighbors)))