updated mcf code

README.md

@@ -8,6 +8,18 @@ More details of the algorithm can be found in:
 Chris S Magnano, Anthony Gitter.
 *npj Systems Biology and Applications*, 7:12, 2021.
 
+## Edge Handling
+The code is designed to process both undirected and directed edges, prioritizing directed edges in scenarios where an equivalent undirected edge exists and selecting higher edge weights in the case of duplicate edges.
+
+## Input Format Example
+The input should be formatted as follows, with columns for node1, node2, rank, and direction:
+```
+A       B       0.9     U
+B       A       0.1     D
+...
+```
+In this format, "U" represents an undirected edge, and "D" represents a directed edge.
+
 ## Dependencies
 
 Google's [OR-Tools library](https://developers.google.com/optimization/flow/mincostflow) is required to run this script. 
@@ -32,3 +44,8 @@ Python 3 is required to run this script
 >  --output         Prefix for all output files. 
 >
 >  --capacity       The amount of flow which can pass through a single edge. 
+
+## Testing
+`python test_minCostFlow.py`
+
+The code executes two sets of graph series, namely the 'graph series' and the 'test series' The graphs series of graphs are used to check the code's correctness. Except for internal tiebreaking by the solver, each result is deterministic. The tests series of graphs are used to verify whether the code is executing appropriately depending on distinct edge cases. The expected results for both series can be found in graphs/correct_outputs.txt for the graph series and tests/correct_outputs.txt for the test series.

minCostFlow.py

@@ -53,7 +53,7 @@ def construct_digraph(edges_file, cap):
 
             if d == "D":
                 if edge in directed_dict:
-                    if w > directed_dict[edge]:
+                    if w < directed_dict[edge]:
                         directed_dict[edge] = w
                 elif sorted_edge in undirected_dict:
                     del undirected_dict[sorted_edge]
@@ -65,13 +65,13 @@ def construct_digraph(edges_file, cap):
                 if edge not in directed_dict and sorted_edge not in directed_dict and sorted_edge not in undirected_dict:
                     undirected_dict[sorted_edge] = w
                 elif sorted_edge in undirected_dict:
-                    if w > undirected_dict[sorted_edge]:
+                    if w < undirected_dict[sorted_edge]:
                         undirected_dict[sorted_edge] = w
             else:
                 raise ValueError (f"Cannot add edge: d = {d}")
 
-    # print("undirected_dict: ", undirected_dict)
-    # print("directed_dict: ", directed_dict)
+    print("undirected_dict: ", undirected_dict)
+    print("directed_dict: ", directed_dict)
     # go through and add the edges from directed_dict and undirected_dict to G
     for key, value in directed_dict.items():
         G.add_arc_with_capacity_and_unit_cost(idDict[key[0]],idDict[key[1]], default_capacity, int(value))

test_minCostFlow.py

@@ -5,7 +5,7 @@
 command = "python"
 script = "minCostFlow.py"
 
-print("testing code functionality")
+print("TEST SERIES")
 for i in range (1,8):
 
     print("test: ",i)
@@ -21,7 +21,7 @@
     subprocess.run(cmd)
 
 
-print("\ntesting code correctness")
+print("\nGRAPHS SERIES")
 for i in range (1,14):
     print("graph: ",i)
     args = [

tests/correct_outputs.txt

@@ -8,24 +8,28 @@ B	C	D
 test2: check if higher edge weight is selected for the same directed edge from the input
 Output:
 A	B	D
-B	D	D
+B	C	D
 
 test3: If a directed edge is present in the input and an undirected edge from that edge already exists, the directed edge is prioritized and added to directed_dict and the undirected edge is deleted from undirected_dict.
-A	C	D
-C	D	D
+Output:
+B   C   D
+A   B   D
 
 test4: check if unique undirected edges are added to undirected_dict 
-A	B	D
-B	D	D
+Output:
+A	B	U
+B	C	U
 
 test5: check that an undirected edge is not added if a directed edge of that edge already exists
-A	B	U
-B	D	U
+Output:
+A	B	D
+B	C	D
 
 test6: check if higher edge weight is selected for the same undirected edge from the input
+Output:
 A	B	U
-B	D	U
+B	C	U
 
 test7: check that code still runs and outputs an error message with an empty edges.txt
-A	B	U
-B	D	U
+Output:
+N/A

tests/test2/edges.txt

@@ -1,4 +1,4 @@
 A   B   0.2	D
 B   C   0.2	D
-A   B   0.1	D
-B   C   0.3	D
+A   B   0.9	D
+B   C   0.1	D

tests/test5/edges.txt

@@ -1,6 +1,5 @@
 A   B   0.1	D
 A   B   0.1	U
 B   A   0.1	U
-B   A   0.1	D
 B   C   0.1	D
 B   C   0.1	U

tests/test6/edges.txt

@@ -1,4 +1,4 @@
 A   B   0.2	U
 B   C   0.2	U
-A   B   0.1	U
-B   C   0.3	U
+A   B   0.9	U
+B   C   0.1	U