Merge pull request #22 from saibalmars/nk_fix

Networkit fix: update to support the nk's new neighbor iterator

Author: saibalmars

GraphRicciCurvature/OllivierRicci.py

@@ -72,11 +72,11 @@ def _get_single_node_neighbors_distributions(node, direction="successors"):
     """
     if _Gk.isDirected():
         if direction == "predecessors":
-            neighbors = _Gk.inNeighbors(node)
+            neighbors = list(_Gk.iterInNeighbors(node))
         else:  # successors
-            neighbors = _Gk.neighbors(node)
+            neighbors = list(_Gk.iterNeighbors(node))
     else:
-        neighbors = _Gk.neighbors(node)
+        neighbors = list(_Gk.iterNeighbors(node))
 
     # Get sum of distributions from x's all neighbors
     heap_weight_node_pair = []
@@ -93,10 +93,11 @@ def _get_single_node_neighbors_distributions(node, direction="successors"):
 
     nbr_edge_weight_sum = sum([x[0] for x in heap_weight_node_pair])
 
-    if len(neighbors) == 0:
+    if not neighbors:
         # No neighbor, all mass stay at node
         return [1], [node]
-    elif nbr_edge_weight_sum > EPSILON:
+
+    if nbr_edge_weight_sum > EPSILON:
         # Sum need to be not too small to prevent divided by zero
         distributions = [(1.0 - _alpha) * w / nbr_edge_weight_sum for w, _ in heap_weight_node_pair]
     else:
@@ -283,10 +284,10 @@ def _average_transportation_distance(source, target):
 
     t0 = time.time()
     if _Gk.isDirected():
-        source_nbr = _Gk.inNeighbors(source)
+        source_nbr = list(_Gk.iterInNeighbors(source))
     else:
-        source_nbr = _Gk.neighbors(source)
-    target_nbr = _Gk.neighbors(target)
+        source_nbr = list(_Gk.iterNeighbors(source))
+    target_nbr = list(_Gk.iterNeighbors(target))
 
     share = (1.0 - _alpha) / (len(source_nbr) * len(target_nbr))
     cost_nbr = 0

GraphRicciCurvature/__init__.py

@@ -1,3 +1,3 @@
-__version__ = "0.5.2"
+__version__ = "0.5.2.1"
 __author__ = "Chien-Chun Ni"
 __email__ = "saibalmars@gmail.com"

example.py

@@ -20,7 +20,7 @@
 # -----------------------------------------------
 print("\n-Construct a directed graph example")
 Gd = nx.DiGraph()
-Gd.add_edges_from([(1, 2), (2, 3), (3, 4), (2, 4), (4, 2)])
+Gd.add_edges_from([(0, 1), (1, 2), (2, 3), (1, 3), (3, 1)])
 
 print("\n===== Compute the Ollivier-Ricci curvature of the given directed graph Gd =====")
 orc_directed = OllivierRicci(Gd)

setup.py

@@ -8,7 +8,7 @@
 
 setuptools.setup(
     name="GraphRicciCurvature",
-    version="0.5.2",
+    version="0.5.2.1",
     author="Chien-Chun Ni",
     author_email="saibalmars@gmail.com",
     description="Compute discrete Ricci curvatures and Ricci flow on NetworkX graphs.",

test/test_OllivierRicci.py

@@ -29,6 +29,40 @@ def test_compute_ricci_curvature():
     npt.assert_array_almost_equal(rc, ans)
 
 
+def test_compute_ricci_curvature_directed():
+    Gd = nx.DiGraph()
+    Gd.add_edges_from([(0, 1), (1, 2), (2, 3), (1, 3), (3, 1)])
+    orc = OllivierRicci(Gd, method="OTD", alpha=0.5)
+    Gout = orc.compute_ricci_curvature()
+    rc = list(nx.get_edge_attributes(Gout, "ricciCurvature").values())
+    ans = [-0.49999999999999956,
+           -3.842615114990622e-11,
+           0.49999999996158007,
+           0.49999999992677135,
+           0.7499999999364129]
+
+    npt.assert_array_almost_equal(rc, ans)
+
+
+def test_compute_ricci_curvature_ATD():
+    G = nx.karate_club_graph()
+    orc = OllivierRicci(G, alpha=0.5, method="ATD", verbose="INFO")
+    orc.compute_ricci_curvature()
+    Gout = orc.compute_ricci_curvature()
+    rc = list(nx.get_edge_attributes(Gout, "ricciCurvature").values())
+    ans = [-0.343750, -0.437500, -0.265625, -0.250000, -0.390625, -0.390625, -0.195312, -0.443750, -0.250000,
+           0.000000, -0.140625, -0.287500, -0.109375, -0.291667, -0.109375, -0.640625, -0.311111, -0.175926,
+           -0.083333, -0.166667, 0.000000, -0.166667, 0.000000, -0.333333, -0.241667, -0.137500, -0.220000,
+           -0.125000, -0.160000, -0.400000, -0.200000, -0.479167, 0.020833, 0.041667, -0.100000, -0.041667,
+           0.055556, -0.062500, -0.041667, 0.000000, 0.000000, -0.075000, -0.275000, -0.300000, -0.176471,
+           -0.464706, 0.000000, -0.073529, 0.000000, -0.073529, 0.000000, -0.073529, -0.421569, 0.000000,
+           -0.073529, 0.000000, -0.073529, -0.200000, -0.200000, -0.125000, -0.291667, -0.335294, -0.055556,
+           -0.208333, -0.194444, -0.194444, 0.062500, -0.176471, -0.375000, -0.166667, -0.245098, -0.197917,
+           -0.227941, -0.250000, -0.294118, -0.430556, -0.455882, -0.355392]
+
+    npt.assert_array_almost_equal(rc, ans)
+
+
 def test_compute_ricci_flow():
     G = nx.karate_club_graph()
     orc = OllivierRicci(G, method="OTD", alpha=0.5)