Improve large graph performance, fix typo, remove spurious file.

pygraphml/__init__.py

@@ -5,7 +5,7 @@
 from __future__ import absolute_import
 from __future__ import print_function
 
-from .attribute import Attribute
+from .attribute import Attribute, EdgeAttribute, NodeAttribute
 from .item import Item
 from .point import Point
 from .node import Node

pygraphml/attribute.py

@@ -10,7 +10,7 @@ class Attribute:
     """
     """
 
-    def __init__(self, name, value, type = "string"):
+    def __init__(self, name, value, type="string"):
         """
         """
 
@@ -26,3 +26,27 @@ def __str__(self):
         s += "%s : %s" % (self.name, str(self.value))
         return s
 
+    def for_str(self):
+        return NotImplemented
+
+
+class EdgeAttribute(Attribute):
+    """
+    """
+
+    def __init__(self, name, value, type, forStr):
+        Attribute.__init__(self, name, value, type)
+
+    def for_str(self):
+        return "edge"
+
+
+class NodeAttribute(Attribute):
+    """
+    """
+
+    def __init__(self, name, value, type, forStr):
+        Attribute.__init__(self, name, value, type)
+
+    def for_str(self):
+        return "node"

pygraphml/edge.py

@@ -7,12 +7,14 @@
 
 
 from . import Item
+from . import EdgeAttribute
+
 
 class Edge(Item):
     """
     """
 
-    def __init__(self, node1, node2, directed = False):
+    def __init__(self, node1, node2, directed=False):
         """
         """
 
@@ -50,7 +52,6 @@ def child(self):
 
         return self.node2
 
-
     def directed(self):
         """
         """
@@ -63,3 +64,7 @@ def set_directed(self, dir):
 
         self._directed = dir
 
+    def set_attribute(self, name, value):
+        """
+        """
+        self.attr[name] = EdgeAttribute(name, value, type)

pygraphml/graph.py

@@ -23,8 +23,8 @@ def __init__(self, name=""):
 
         self.name = name
 
-        self._nodes = []
-        self._edges = []
+        self._nodes = set()
+        self._edges = set()
         self._root = None
         self.directed = True
 
@@ -124,7 +124,7 @@ def add_node(self, label="", id=None):
 
         n = Node(id)
         n['label'] = label
-        self._nodes.append(n)
+        self._nodes.add(n)
 
         return n
 
@@ -133,12 +133,14 @@ def add_edge(self, n1, n2, directed=False):
         """
 
         if n1 not in self._nodes:
-            raise Test("fff")
+            print(n1)
+            raise Test("n1 has not been added")
         if n2 not in self._nodes:
-            raise Test("fff")
+            print(n2)
+            raise Test("n2 has not been added")
 
         e = Edge(n1, n2, directed)
-        self._edges.append(e)
+        self._edges.add(e)
 
         return e
 
@@ -192,7 +194,7 @@ def set_root_by_attribute(self, value, attribute='label'):
                 self.set_root(n)
                 return n
 
-    def get_attributs(self):
+    def get_attributes(self):
         """
         """
 

pygraphml/graphml_parser.py

@@ -12,6 +12,7 @@
 from . import Node
 from . import Edge
 
+
 class GraphMLParser:
     """
     """
@@ -30,11 +31,12 @@ def write(self, graph, fname=None):
         doc.appendChild(root)
 
         # Add attributs
-        for a in graph.get_attributs():
+        for a in graph.get_attributes():
             attr_node = doc.createElement('key')
             attr_node.setAttribute('id', a.name)
             attr_node.setAttribute('attr.name', a.name)
             attr_node.setAttribute('attr.type', a.type)
+            attr_node.setAttribute('for', a.for_str())
             root.appendChild(attr_node)
 
         graph_node = doc.createElement('graph')
@@ -65,7 +67,8 @@ def write(self, graph, fname=None):
             edge.setAttribute('source', e.node1['label'])
             edge.setAttribute('target', e.node2['label'])
             if e.directed() != graph.directed:
-                edge.setAttribute('directed', 'true' if e.directed() else 'false')
+                edge.setAttribute(
+                    'directed', 'true' if e.directed() else 'false')
             for a in e.attributes():
                 if e != 'label':
                     data = doc.createElement('data')
@@ -85,7 +88,7 @@ def parse(self, fname):
         """
 
         g = None
-        with open( fname, 'r' ) as f:
+        with open(fname, 'r') as f:
             dom = minidom.parse(f)
             root = dom.getElementsByTagName("graphml")[0]
             graph = root.getElementsByTagName("graph")[0]
@@ -131,5 +134,3 @@ def parse(self, fname):
     g = parser.parse('test.graphml')
 
     g.show(True)
-
-

pygraphml/item.py

@@ -8,6 +8,7 @@
 
 from . import Attribute
 
+
 class Item(object):
     """
     """
@@ -37,17 +38,16 @@ def __str__(self):
 
         return s
 
-    def __setitem__(self, name, value):
+    def set_attribute(self, name, value):
         """
         """
+        return NotImplemented
 
-        self.attr[name] = Attribute(name, value)
-
-    def __getitem__(self, name):
+    def set_attribute(self, name, value, type):
         """
         """
 
-        return self.attr[name].value
+        self.attr[name] = Attribute(name, value, type)
 
     def attributes(self):
         """

pygraphml/node.py

@@ -7,6 +7,8 @@
 
 
 from . import Item
+from . import NodeAttribute
+
 
 class Node(Item):
     """
@@ -26,7 +28,6 @@ def edges(self, ):
 
         return self._edges
 
-
     def children(self):
         """
         """
@@ -49,3 +50,7 @@ def parent(self):
 
         return parent
 
+    def set_attribute(self, name, value, type):
+        """
+        """
+        self.attr[name] = NodeAttribute(name, value, type)