Properly remove in- and out-edges when vertex is removed

The edge index housekeeping was not performed on edges which were
deleted due to vertex removal.

src/graph/graph_wrap.hh

@@ -158,27 +158,6 @@ degree(typename graph_traits<GraphWrap<Graph> >::vertex_descriptor u,
     return degree(u, g._g);
 }
 
-template <class Graph>
-inline typename graph_traits<GraphWrap<Graph> >::vertex_descriptor
-add_vertex(GraphWrap<Graph>& g)
-{
-    return add_vertex(g._g);
-}
-
-template <class Graph>
-inline void clear_vertex(typename graph_traits<GraphWrap<Graph> >::vertex_descriptor u,
-                         GraphWrap<Graph>& g)
-{
-    clear_vertex(u, g._g);
-}
-
-template <class Graph>
-inline void remove_vertex(typename graph_traits<GraphWrap<Graph> >::vertex_descriptor u,
-                          GraphWrap<Graph>& g)
-{
-    remove_vertex(u, g._g);
-}
-
 template <class Graph>
 inline std::pair<typename graph_traits<GraphWrap<Graph> >::edge_descriptor, bool>
 add_edge(typename graph_traits<GraphWrap<Graph> >::vertex_descriptor u,
@@ -215,6 +194,41 @@ inline void remove_edge(typename graph_traits<GraphWrap<Graph> >::vertex_descrip
 }
 
 
+template <class Graph>
+inline typename graph_traits<GraphWrap<Graph> >::vertex_descriptor
+add_vertex(GraphWrap<Graph>& g)
+{
+    return add_vertex(g._g);
+}
+
+template <class Graph>
+inline void clear_vertex(typename graph_traits<GraphWrap<Graph> >::vertex_descriptor u,
+                         GraphWrap<Graph>& g)
+{
+    typedef GraphWrap<Graph> graph_t;
+    vector<typename graph_traits<graph_t>::edge_descriptor> del_es;
+    typename graph_traits<graph_t>::out_edge_iterator e, e_end;
+    for (tie(e,e_end) == out_edges(u, g); e != e_end; ++e)
+        del_es.push_back(*e);
+    if (is_directed::apply<graph_t>::type::value)
+    {
+        typename in_edge_iteratorS<graph_t>::type e, e_end;
+        for (tie(e,e_end) == in_edge_iteratorS<graph_t>::get_edges(u, g);
+             e != e_end; ++e)
+            del_es.push_back(*e);
+    }
+    for (size_t i = 0; i < del_es.size(); ++i)
+        remove_edge(del_es[i], g);
+}
+
+template <class Graph>
+inline void remove_vertex(typename graph_traits<GraphWrap<Graph> >::vertex_descriptor u,
+                          GraphWrap<Graph>& g)
+{
+    clear_vertex(u, g);
+    remove_vertex(u, g._g);
+}
+
 template <class Graph, class Predicate>
 inline void
 remove_out_edge_if(typename graph_traits<GraphWrap<Graph> >::vertex_descriptor u,

src/graph_tool/core.py

@@ -318,6 +318,7 @@ class Graph(object):
             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.clear_vertex(vertex)
         self.__graph.RemoveVertex(vertex)
 
     @_handle_exceptions
@@ -330,6 +331,15 @@ class Graph(object):
             if predicate(v):
                 self.remove_vertex(v)
 
+    @_handle_exceptions
+    def clear_vertex(self, vertex):
+        """Removes all in and out-edges from the given vertex."""
+        del_es = []
+        for e in vertex.all_edges():
+            del_es.append(e)
+        for e in del_es:
+            self.remove_edge(e)
+
     @_handle_exceptions
     def add_edge(self, source, target):
         """Add a new edge from 'source' to 'target' to the graph, and return