Re-include graph rewiring code in the new scheme

This also creates the misc sub-module. This may be re-organized in the
future.

configure.ac

@@ -251,6 +251,7 @@ src/graph/generation/Makefile
 src/graph/stats/Makefile
 src/graph/clustering/Makefile
 src/graph/util/Makefile
+src/graph/misc/Makefile
 src/graph_tool/Makefile
 ])
 

src/graph/Makefile.am

 ## Process this file with automake to produce Makefile.in
 
-SUBDIRS = generation correlations stats clustering util
+SUBDIRS = generation correlations stats clustering util misc
 
 AM_CPPFLAGS =\
     -I$(srcdir)/.. \

src/graph/misc/Makefile.am

+## Process this file with automake to produce Makefile.in
+
+AM_CPPFLAGS =\
+    -I$(srcdir) -I$(srcdir)/.. \
+    -I$(srcdir)/../boost-workaround \
+    -DHAVE_CONFIG_H
+
+AM_CFLAGS=$(AM_CXXFLAGS)
+
+libgraph_tool_miscdir = $(pythondir)/graph_tool/misc
+
+libgraph_tool_misc_LTLIBRARIES = libgraph_tool_misc.la
+
+libgraph_tool_misc_la_includedir = $(pythondir)/graph_tool/include
+
+libgraph_tool_misc_la_SOURCES = \
+    graph_rewiring.cc \
+    graph_misc.cc
+
+libgraph_tool_misc_la_include_HEADERS = \
+    graph_rewiring.hh
+
+libgraph_tool_misc_la_LIBADD = \
+    $(PYTHON_LDFLAGS) \
+    $(BOOST_LDFLAGS) \
+    $(OPENMP_LDFLAGS) \
+    -lboost_python \
+    -lboost_iostreams \
+    -lexpat
+
+# needed for typeinfo objects to work across DSO boundaries.
+# see http://gcc.gnu.org/faq.html#dso
+libgraph_tool_misc_la_LDFLAGS = \
+    -module \
+    -avoid-version \
+    -export-dynamic \
+    -no-undefined \
+    -Wl,-E

src/graph/misc/graph_misc.cc

+// graph-tool -- a general graph modification and manipulation thingy
+//
+// Copyright (C) 2007  Tiago de Paula Peixoto <tiago@forked.de>
+//
+// This program is free software; you can redistribute it and/or
+// modify it under the terms of the GNU General Public License
+// as published by the Free Software Foundation; either version 3
+// of the License, or (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+#include <boost/python.hpp>
+#include "graph.hh"
+
+using namespace boost;
+using namespace boost::python;
+using namespace graph_tool;
+
+void random_rewire(GraphInterface& gi, string strat, bool self_loops,
+                   bool parallel_edges, size_t seed);
+
+BOOST_PYTHON_MODULE(libgraph_tool_misc)
+{
+    def("random_rewire", &random_rewire);
+}

src/graph/misc/graph_rewiring.cc

@@ -19,29 +19,33 @@
 
 #include "graph.hh"
 #include "graph_filtering.hh"
+
+#include <boost/random.hpp>
+typedef boost::mt19937 rng_t;
+
 #include "graph_rewiring.hh"
 
 using namespace graph_tool;
 using namespace boost;
 using namespace boost::lambda;
 
-void GraphInterface::RandomRewire(string strat, bool self_loops,
-                                  bool parallel_edges, size_t seed)
+void random_rewire(GraphInterface& gi, string strat, bool self_loops,
+                   bool parallel_edges, size_t seed)
 {
-    bool reversed = GetReversed();
-    SetReversed(false);
+    rng_t rng(seed);
 
+    GraphInterface::edge_index_map_t edge_index =
+        any_cast<GraphInterface::edge_index_map_t>(gi.GetEdgeIndex());
     if (strat == "uncorrelated")
-        run_action<detail::never_reversed>()
-            (*this, bind<void>(graph_rewire<RandomRewireStrategy>(),
-                               _1, _edge_index, seed, self_loops,
-                               parallel_edges))();
+        run_action<graph_tool::detail::never_reversed>()
+            (gi, bind<void>(graph_rewire<RandomRewireStrategy>(),
+                            _1, edge_index, ref(rng), self_loops,
+                            parallel_edges))();
     else if (strat == "correlated")
-        run_action<detail::never_reversed>()
-            (*this, bind<void>(graph_rewire<CorrelatedRewireStrategy>(),
-                               _1, _edge_index, seed, self_loops,
-                               parallel_edges))();
+        run_action<graph_tool::detail::never_reversed>()
+            (gi, bind<void>(graph_rewire<CorrelatedRewireStrategy>(),
+                            _1, edge_index, ref(rng), self_loops,
+                            parallel_edges))();
     else
         throw GraphException("invalid random rewire stategy: " + strat);
-    SetReversed(reversed);
 }

src/graph/misc/graph_rewiring.hh

@@ -30,8 +30,6 @@ namespace graph_tool
 using namespace std;
 using namespace boost;
 
-typedef boost::mt19937 rng_t;
-
 // this will get the source of an edge for directed graphs and the target for
 // undirected graphs, i.e. "the source of an in-edge"
 struct source_in
@@ -231,14 +229,13 @@ template <template <class Graph, class EdgeIndexMap> class RewireStrategy>
 struct graph_rewire
 {
     template <class Graph, class EdgeIndexMap>
-    void operator()(Graph* gp, EdgeIndexMap edge_index, size_t seed,
+    void operator()(Graph* gp, EdgeIndexMap edge_index, rng_t& rng,
                     bool self_loops, bool parallel_edges) const
     {
         typedef typename graph_traits<Graph>::vertex_descriptor vertex_t;
         typedef typename graph_traits<Graph>::edge_descriptor edge_t;
 
         Graph& g = *gp;
-        rng_t rng(static_cast<rng_t::result_type>(seed));
 
         if (!self_loops)
         {

src/graph_tool/Makefile.am

@@ -44,3 +44,7 @@ graph_tool_drawdir = $(pythondir)/graph_tool/draw
 graph_tool_util_PYTHON = \
     util/__init__.py
 graph_tool_utildir = $(pythondir)/graph_tool/util
+
+graph_tool_misc_PYTHON = \
+    misc/__init__.py
+graph_tool_miscdir = $(pythondir)/graph_tool/misc

src/graph_tool/all.py

@@ -41,5 +41,7 @@ from graph_tool.clustering import *
 import graph_tool.clustering
 from graph_tool.run_action import *
 graph_tool.run_action
+from graph_tool.misc import *
+import graph_tool.misc
 from graph_tool.util import *
 import graph_tool.util

src/graph_tool/misc/__init__.py

+#! /usr/bin/env python
+# graph_tool.py -- a general graph manipulation python module
+#
+# Copyright (C) 2007 Tiago de Paula Peixoto <tiago@forked.de>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+import sys
+# RTLD_GLOBAL needs to be set in dlopen() if we want typeinfo and friends to
+# work properly across DSO boundaries. See http://gcc.gnu.org/faq.html#dso
+
+# The "except" is because the dl module raises a system error on ia64 and x86_64
+# systems because "int" and addresses are different sizes.
+try:
+    from dl import RTLD_LAZY, RTLD_NOW, RTLD_GLOBAL
+except ImportError:
+    RTLD_LAZY = 1
+    RTLD_NOW = 2
+    RTLD_GLOBAL = 256
+_orig_dlopen_flags = sys.getdlopenflags()
+
+sys.setdlopenflags(RTLD_LAZY|RTLD_GLOBAL)
+import libgraph_tool_misc
+sys.setdlopenflags(_orig_dlopen_flags) # reset it to normal case to avoid
+                                       # unnecessary symbol collision
+import random, sys
+__all__ = ["random_rewire"]
+
+def random_rewire(g, strat="uncorrelated", self_loops = False,
+                  parallel_edges = False, seed = 0):
+    if seed != 0:
+        seed = random.randint(0, sys.maxint)
+    if g.is_reversed():
+        was_reversed = True
+    else:
+        was_reversed = False
+    g.set_reversed(False)
+    libgraph_tool_misc.random_rewire(g._Graph__graph, strat, self_loops,
+                                     parallel_edges, seed)
+    if was_reversed:
+        g.set_reversed(True)