Fix possible circular reference with property maps

Use weakrefs to keep track of known property maps in graphs, and owner
graphs in property maps to avoid circular references, which may lead to
memory leaks.

This also fixes a vertex removal bug.

src/graph_tool/core.py

@@ -40,7 +40,7 @@ import io # sets up libcore io routines
 
 import os, os.path, re, struct, fcntl, termios, gzip, bz2, string,\
        textwrap, time, signal, traceback, shutil, time, math, inspect, \
-       functools, types
+       functools, types, weakref
 from StringIO import StringIO
 from decorators import _wraps, _require, _attrs, _handle_exceptions, _limit_args
 
@@ -130,16 +130,22 @@ class PropertyMap(object):
     """Property Map class"""
     def __init__(self, pmap, g, key_type, key_trans = None):
         self.__map = pmap
-        self.__g = g
+        self.__g = weakref.ref(g)
         self.__key_type = key_type
         self.__key_trans = key_trans if key_trans != None else lambda k: k
         self.__register_map()
 
     def __register_map(self):
-        self.__g._Graph__known_properties.append((self.key_type(), self.__map))
+        if self.__g() == None:
+            return
+        self.__g()._Graph__known_properties.append((self.key_type(),
+                                                    weakref.ref(self.__map)))
     def __unregister_map(self):
-        i = self.__g._Graph__known_properties.index((self.key_type(), self.__map))
-        del self.__g._Graph__known_properties[i]
+        if self.__g() == None:
+            return
+        i = self.__g()._Graph__known_properties.index((self.key_type(),
+                                                       weakref.ref(self.__map)))
+        del self.__g()._Graph__known_properties[i]
 
     def __del__(self):
         self.__unregister_map()
@@ -152,7 +158,7 @@ class PropertyMap(object):
 
     def get_graph(self):
         """Get the graph to which the map refers"""
-        return self.__g
+        return self.__g()
 
     def key_type(self):
         """The key type of the map. Either 'g', 'v' or 'e'"""
@@ -241,6 +247,11 @@ class Graph(object):
                 self.__stashed_filter_state[0]["edge_filter"] = (new_filt,
                                                                  e_rev)
             self.pop_filter()
+        # internal index maps
+        self.__vertex_index = \
+                 PropertyMap(libcore.get_vertex_index(self.__graph), self, "v")
+        self.__edge_index = \
+                 PropertyMap(libcore.get_edge_index(self.__graph), self, "e")
 
     @_handle_exceptions
     def copy(self):
@@ -277,8 +288,9 @@ class Graph(object):
         k = vertex.in_degree() + vertex.out_degree()
         index = self.vertex_index[vertex]
         for pmap in self.__known_properties:
-            if pmap[0] == "v":
-                self.__graph.ShiftVertexProperty(pmap[1].get_map(), index)
+            if pmap[0] == "v" and pmap[1]() != None and \
+                   pmap[1]() != self.__vertex_index._PropertyMap__map:
+                self.__graph.ShiftVertexProperty(pmap[1]().get_map(), index)
         self.__graph.RemoveVertex(vertex)
 
     @_handle_exceptions
@@ -389,11 +401,11 @@ class Graph(object):
     # index properties
 
     def _get_vertex_index(self):
-        return PropertyMap(libcore.get_vertex_index(self.__graph), self, "v")
+        return self.__vertex_index
     vertex_index = property(_get_vertex_index, doc="Vertex index map")
 
     def _get_edge_index(self):
-        return PropertyMap(libcore.get_edge_index(self.__graph), self, "v")
+        return self.__edge_index
     edge_index = property(_get_edge_index, doc="Edge index map")
 
     # Property map creation