fix bug "AttributeError("'Graph' object has no attribute 'node'",)" for new version of NetworkX.

gklearn/kernels/__init__.py

@@ -9,3 +9,4 @@ __date__ = "November 2018"
 
 from gklearn.kernels.graph_kernel import GraphKernel
 from gklearn.kernels.structural_sp import StructuralSP
+from gklearn.kernels.shortest_path import ShortestPath

gklearn/kernels/graph_kernel.py

@@ -44,7 +44,7 @@ class GraphKernel(object):
 			
 		elif len(graphs) == 2:
 			if self.is_graph(graphs[0]) and self.is_graph(graphs[1]):
-				kernel = self.__compute_single_kernel(graphs[0], graphs[1])
+				kernel = self.__compute_single_kernel(graphs[0].copy(), graphs[1].copy())
 				return kernel, self._run_time
 			elif self.is_graph(graphs[0]) and isinstance(graphs[1], list):
 				g1 = graphs[0].copy()

gklearn/kernels/treeletKernel.py

@@ -308,7 +308,7 @@ def get_canonkeys(G, node_label, edge_label, labeled, is_directed):
         for i in range(1, 6): # for i in range(1, 6):
             treelet = []
             for pattern in patterns[str(i)]:
-                canonlist = list(chain.from_iterable((G.node[node][node_label], \
+                canonlist = list(chain.from_iterable((G.nodes[node][node_label], \
                     G[node][pattern[idx+1]][edge_label]) for idx, node in enumerate(pattern[:-1])))
                 canonlist.append(G.node[pattern[-1]][node_label])
                 canonkey_t = canonlist if canonlist < canonlist[::-1] else canonlist[::-1]

gklearn/kernels/untilHPathKernel.py

@@ -637,7 +637,7 @@ def paths2labelseqs(plist, G, ds_attrs, node_label, edge_label):
                             (G.node[node][node_label],
                              G[node][path[idx + 1]][edge_label])
                             for idx, node in enumerate(path[:-1]))) +
-                    [G.node[path[-1]][node_label]]) for path in plist
+                    [G.nodes[path[-1]][node_label]]) for path in plist
             ]
             # path_strs = []
             # for path in all_paths:

gklearn/preimage/median_preimage_generator.py

@@ -704,7 +704,7 @@ class MedianPreimageGenerator(PreimageGenerator):
 			
 			
 # 	def __clean_graph(self, G, node_labels=[], edge_labels=[], node_attrs=[], edge_attrs=[]):
-	def __clean_graph(self, G):
+	def __clean_graph(self, G): # @todo: this may not be needed when datafile is updated.
 		"""
 		Cleans node and edge labels and attributes of the given graph.
 		"""

gklearn/utils/utils.py

@@ -134,7 +134,7 @@ def untotterTransformation(G, node_label, edge_label):
 	gt.add_nodes_from(G.nodes(data=True))
 	for edge in G.edges():
 		gt.add_node(edge)
-		gt.node[edge].update({node_label: G.node[edge[1]][node_label]})
+		gt.nodes[edge].update({node_label: G.node[edge[1]][node_label]})
 		gt.add_edge(edge[0], edge)
 		gt.edges[edge[0], edge].update({
 			edge_label: