Port to c++11

configure.ac

@@ -53,7 +53,10 @@ AC_ARG_ENABLE([debug], [AS_HELP_STRING([--enable-debug],[compile debug informati
 	[AC_MSG_RESULT(no)]
         )
 
-dnl set template depth and hidden visibility
+dnl enable c++11
+[CXXFLAGS="${CXXFLAGS} -std=gnu++11"]
+
+dnl set template depth
 [CXXFLAGS="${CXXFLAGS} -ftemplate-depth-150"]
 
 dnl disable deprecation warning, to silence some harmless BGL-related warnings

src/boost-workaround/boost/graph/graphml.hpp

@@ -328,8 +328,8 @@ std::string print_value(dynamic_property_map& pmap, Descriptor v)
 {
     std::string val;
     boost::any oval = pmap.get(v);
-    mpl::for_each<ValueTypes>(bind<void>(get_string(), ref(oval),
-                                         ref(val), _1));
+    mpl::for_each<ValueTypes>(boost::bind<void>(get_string(), boost::ref(oval),
+                                                boost::ref(val), _1));
     return val;
 }
 

src/boost-workaround/boost/graph/isomorphism.hpp

@@ -144,12 +144,12 @@ namespace boost {
           std::vector<invar1_value> invar1_array;
           BGL_FORALL_VERTICES_T(v, G1, Graph1)
             invar1_array.push_back(invariant1(v));
-          sort(invar1_array);
+          std::sort(invar1_array.begin(), invar1_array.end());
         
           std::vector<invar2_value> invar2_array;
           BGL_FORALL_VERTICES_T(v, G2, Graph2)
             invar2_array.push_back(invariant2(v));
-          sort(invar2_array);
+          std::sort(invar2_array.begin(), invar2_array.end());
           if (! equal(invar1_array, invar2_array))
             return false;
         }
@@ -161,7 +161,8 @@ namespace boost {
           std::vector<size_type> multiplicity(max_invariant, 0);
           BGL_FORALL_VERTICES_T(v, G1, Graph1)
             ++multiplicity.at(invariant1(v));
-          sort(V_mult, compare_multiplicity(invariant1, &multiplicity[0]));
+          std::sort(V_mult.begin(), V_mult.end(),
+                    compare_multiplicity(invariant1, &multiplicity[0]));
         }
         
         std::vector<default_color_type> color_vec(num_vertices(G1));
@@ -193,7 +194,7 @@ namespace boost {
         for (vertex_iter v = dfs_vertices.begin(); v != dfs_vertices.end(); ++v)
           dfs_num[*v] = n++;
         
-        sort(ordered_edges, edge_cmp(G1, dfs_num));
+        std::sort(ordered_edges.begin(), ordered_edges.end(), edge_cmp(G1, dfs_num));
         
     
         int dfs_num_k = -1;

src/graph/Makefile.am

@@ -57,7 +57,6 @@ libgraph_tool_core_la_include_HEADERS = \
     random.hh \
     str_repr.hh \
     shared_map.hh \
-    tr1_include.hh \
     transform_iterator.hh
 
 libgraph_tool_core_la_workarounddir = $(MOD_DIR)/include/boost-workaround/boost/graph/

src/graph/centrality/graph_betweenness.cc

@@ -36,8 +36,8 @@ void normalize_betweenness(const Graph& g,
 {
     double vfactor = (n > 2) ? 1.0/((n-1)*(n-2)) : 1.0;
     double efactor = (n > 1) ? 1.0/(n*(n-1)) : 1.0;
-    if (is_convertible<typename graph_traits<Graph>::directed_category,
-                       undirected_tag>::value)
+    if (std::is_convertible<typename graph_traits<Graph>::directed_category,
+                            undirected_tag>::value)
     {
         vfactor *= 2;
         efactor *= 2;
@@ -63,6 +63,7 @@ void normalize_betweenness(const Graph& g,
 
 struct get_betweenness
 {
+    typedef void result_type;
     template <class Graph, class EdgeBetweenness, class VertexBetweenness>
     void operator()(Graph& g,
                     GraphInterface::vertex_index_map_t index_map,
@@ -90,6 +91,7 @@ struct get_betweenness
 
 struct get_weighted_betweenness
 {
+    typedef void result_type;
     template <class Graph, class EdgeBetweenness, class VertexBetweenness,
               class VertexIndexMap>
         void operator()(Graph& g, VertexIndexMap vertex_index,
@@ -137,10 +139,11 @@ void betweenness(GraphInterface& g, boost::any weight,
     if (!weight.empty())
     {
         run_action<>()
-            (g, bind<void>
-             (get_weighted_betweenness(), _1, g.GetVertexIndex(),
-              _2, _3, weight, normalize,
-              g.GetNumberOfVertices(), g.GetMaxEdgeIndex()),
+            (g, std::bind<>(get_weighted_betweenness(),
+                            std::placeholders::_1, g.GetVertexIndex(),
+                            std::placeholders::_2,
+                            std::placeholders::_3, weight, normalize,
+                            g.GetNumberOfVertices(), g.GetMaxEdgeIndex()),
              edge_floating_properties(),
              vertex_floating_properties())
             (edge_betweenness, vertex_betweenness);
@@ -148,8 +151,10 @@ void betweenness(GraphInterface& g, boost::any weight,
     else
     {
         run_action<>()
-            (g, bind<void>(get_betweenness(), _1, g.GetVertexIndex(), _2,
-                           _3, normalize, g.GetNumberOfVertices()),
+            (g, std::bind<void>(get_betweenness(), std::placeholders::_1,
+                                g.GetVertexIndex(), std::placeholders::_2,
+                                std::placeholders::_3, normalize,
+                                g.GetNumberOfVertices()),
              edge_floating_properties(),
              vertex_floating_properties())
             (edge_betweenness, vertex_betweenness);
@@ -171,8 +176,8 @@ double central_point(GraphInterface& g,
 {
     double c = 0.0;
     run_action<graph_tool::detail::never_reversed>()
-        (g, bind<void>(get_central_point_dominance(), _1,
-                       _2, ref(c)),
+        (g, std::bind<>(get_central_point_dominance(), std::placeholders::_1,
+                        std::placeholders::_2, std::ref(c)),
          vertex_scalar_properties()) (vertex_betweenness);
     return c;
 }

src/graph/centrality/graph_closeness.cc

@@ -22,8 +22,9 @@
 
 #include "graph_closeness.hh"
 
+#include <functional>
+
 using namespace std;
-using namespace boost;
 using namespace graph_tool;
 
 void do_get_closeness(GraphInterface& gi, boost::any weight,
@@ -32,17 +33,17 @@ void do_get_closeness(GraphInterface& gi, boost::any weight,
     if (weight.empty())
     {
         run_action<>()(gi,
-                       bind<void>(get_closeness(), _1,
-                                  gi.GetVertexIndex(), no_weightS(),
-                                  _2, harmonic, norm),
+                       std::bind(get_closeness(), placeholders::_1,
+                                 gi.GetVertexIndex(), no_weightS(),
+                                 placeholders::_2, harmonic, norm),
                        writable_vertex_scalar_properties())(closeness);
     }
     else
     {
         run_action<>()(gi,
-                       bind<void>(get_closeness(), _1,
-                                  gi.GetVertexIndex(), _2,
-                                  _3, harmonic, norm),
+                       std::bind(get_closeness(), placeholders::_1,
+                                 gi.GetVertexIndex(), placeholders::_2,
+                                 placeholders::_3, harmonic, norm),
                        edge_scalar_properties(),
                        writable_vertex_scalar_properties())(weight, closeness);
     }
@@ -50,5 +51,5 @@ void do_get_closeness(GraphInterface& gi, boost::any weight,
 
 void export_closeness()
 {
-    python::def("closeness", &do_get_closeness);
+    boost::python::def("closeness", &do_get_closeness);
 }

src/graph/centrality/graph_closeness.hh

@@ -31,14 +31,13 @@
 namespace graph_tool
 {
 using namespace std;
-using namespace boost;
 
 struct no_weightS {};
 
 template <class Map>
 struct get_val_type
 {
-    typedef typename property_traits<Map>::value_type type;
+    typedef typename boost::property_traits<Map>::value_type type;
 };
 
 template <>
@@ -49,16 +48,17 @@ struct get_val_type<no_weightS>
 
 struct get_closeness
 {
-
+    typedef void result_type;
     template <class Graph, class VertexIndex, class WeightMap, class Closeness>
     void operator()(const Graph& g, VertexIndex vertex_index, WeightMap weights,
                     Closeness closeness, bool harmonic, bool norm)
         const
     {
+        using namespace boost;
         typedef typename graph_traits<Graph>::vertex_descriptor vertex_t;
 
         // select get_vertex_dists based on the existence of weights
-        typedef typename mpl::if_<is_same<WeightMap, no_weightS>,
+        typedef typename mpl::if_<std::is_same<WeightMap, no_weightS>,
                                   get_dists_bfs,
                                   get_dists_djk>::type get_vertex_dists_t;
 
@@ -113,7 +113,7 @@ struct get_closeness
          }
     }
 
-    class component_djk_visitor: public dijkstra_visitor<>
+    class component_djk_visitor: public boost::dijkstra_visitor<>
     {
     public:
         //component_visitor() { }
@@ -139,6 +139,7 @@ struct get_closeness
                         DistanceMap dist_map, WeightMap weights,
                         size_t& comp_size) const
         {
+            using namespace boost;
             component_djk_visitor vis(comp_size);
             dijkstra_shortest_paths(g, s, vertex_index_map(vertex_index).
                                     weight_map(weights).distance_map(dist_map).visitor(vis));
@@ -146,7 +147,7 @@ struct get_closeness
     };
 
     template <class DistMap>
-    class component_bfs_visitor: public bfs_visitor<>
+    class component_bfs_visitor: public boost::bfs_visitor<>
     {
     public:
         //component_visitor() { }
@@ -179,9 +180,10 @@ struct get_closeness
         void operator()(const Graph& g, Vertex s, VertexIndex vertex_index,
                         DistanceMap dist_map, no_weightS, size_t& comp_size) const
         {
+            using namespace boost;
             typedef typename graph_traits<Graph>::vertex_descriptor vertex_t;
-            typedef tr1::unordered_map<vertex_t,default_color_type,
-                                       DescriptorHash<VertexIndex> > cmap_t;
+            typedef unordered_map<vertex_t,default_color_type,
+                                  DescriptorHash<VertexIndex> > cmap_t;
             cmap_t cmap(0, DescriptorHash<VertexIndex>(vertex_index));
             InitializedPropertyMap<cmap_t>
                 color_map(cmap, color_traits<default_color_type>::white());

src/graph/centrality/graph_eigentrust.cc

@@ -24,7 +24,6 @@
 #include "graph_eigentrust.hh"
 
 using namespace std;
-using namespace boost;
 using namespace graph_tool;
 
 size_t eigentrust(GraphInterface& g, boost::any c, boost::any t,
@@ -38,10 +37,9 @@ size_t eigentrust(GraphInterface& g, boost::any c, boost::any t,
 
     size_t iter = 0;
     run_action<>()
-        (g, bind<void>
-         (get_eigentrust(),
-          _1, g.GetVertexIndex(), g.GetEdgeIndex(), _2,
-          _3, epslon, max_iter, ref(iter)),
+        (g, bind(get_eigentrust(),
+                 _1, g.GetVertexIndex(), g.GetEdgeIndex(), _2,
+                 _3, epslon, max_iter, ref(iter)),
          writable_edge_scalar_properties(),
          vertex_floating_properties())(c,t);
     return iter;

src/graph/centrality/graph_eigentrust.hh

@@ -25,16 +25,17 @@
 namespace graph_tool
 {
 using namespace std;
-using namespace boost;
 
 struct get_eigentrust
 {
+    typedef void result_type;
     template <class Graph, class VertexIndex, class EdgeIndex, class TrustMap,
               class InferredTrustMap>
     void operator()(Graph& g, VertexIndex vertex_index,
                     EdgeIndex edge_index, TrustMap c, InferredTrustMap t,
                     double epslon, size_t max_iter, size_t& iter) const
     {
+        using namespace boost;
         typedef typename property_traits<TrustMap>::value_type c_type;
         typedef typename property_traits<InferredTrustMap>::value_type t_type;
 

src/graph/centrality/graph_eigenvector.cc

@@ -17,14 +17,11 @@
 
 #include "graph_filtering.hh"
 
-#include <boost/python.hpp>
-
 #include "graph.hh"
 #include "graph_selectors.hh"
 #include "graph_eigenvector.hh"
 
 using namespace std;
-using namespace boost;
 using namespace graph_tool;
 
 long double eigenvector(GraphInterface& g, boost::any w, boost::any c,
@@ -37,7 +34,7 @@ long double eigenvector(GraphInterface& g, boost::any w, boost::any c,
                              " value type");
 
     typedef ConstantPropertyMap<int, GraphInterface::edge_t> weight_map_t;
-    typedef mpl::push_back<writable_edge_scalar_properties, weight_map_t>::type
+    typedef boost::mpl::push_back<writable_edge_scalar_properties, weight_map_t>::type
         weight_props_t;
 
     if(w.empty())
@@ -45,14 +42,16 @@ long double eigenvector(GraphInterface& g, boost::any w, boost::any c,
 
     long double eig = 0;
     run_action<>()
-        (g, bind<void>
-         (get_eigenvector(), _1, g.GetVertexIndex(), _2,
-          _3, epsilon, max_iter, ref(eig)),
+        (g, std::bind(get_eigenvector(), placeholders::_1, g.GetVertexIndex(),
+                      placeholders::_2, placeholders::_3, epsilon, max_iter,
+                      std::ref(eig)),
          weight_props_t(),
          vertex_floating_properties())(w, c);
     return eig;
 }
 
+#include <boost/python.hpp>
+
 void export_eigenvector()
 {
     using namespace boost::python;

src/graph/centrality/graph_eigenvector.hh

@@ -22,8 +22,16 @@
 #include "graph_filtering.hh"
 #include "graph_util.hh"
 
+#ifndef __clang__
 #include <ext/numeric>
 using __gnu_cxx::power;
+#else
+template <class Value>
+Value power(Value value, int n)
+{
+    return pow(value, n);
+}
+#endif
 
 namespace graph_tool
 {

src/graph/centrality/graph_hits.cc

@@ -60,7 +60,7 @@ long double hits(GraphInterface& g, boost::any w, boost::any x, boost::any y,
                              " value type");
 
     typedef ConstantPropertyMap<int, GraphInterface::edge_t> weight_map_t;
-    typedef mpl::push_back<writable_edge_scalar_properties, weight_map_t>::type
+    typedef boost::mpl::push_back<writable_edge_scalar_properties, weight_map_t>::type
         weight_props_t;
 
     if(w.empty())
@@ -68,9 +68,9 @@ long double hits(GraphInterface& g, boost::any w, boost::any x, boost::any y,
 
     long double eig = 0;
     run_action<>()
-        (g, bind<void>
-         (get_hits_dispatch(), _1, g.GetVertexIndex(), _2,
-          _3, y, epsilon, max_iter, ref(eig)),
+        (g, std::bind(get_hits_dispatch(), placeholders::_1, g.GetVertexIndex(),
+                      placeholders::_2,  placeholders::_3, y, epsilon, max_iter,
+                      std::ref(eig)),
          weight_props_t(),
          vertex_floating_properties())(w, x);
     return eig;

src/graph/centrality/graph_hits.hh

@@ -22,8 +22,16 @@
 #include "graph_filtering.hh"
 #include "graph_util.hh"
 
+#ifndef __clang__
 #include <ext/numeric>
 using __gnu_cxx::power;
+#else
+template <class Value>
+Value power(Value value, int n)
+{
+    return pow(value, n);
+}
+#endif
 
 namespace graph_tool
 {

src/graph/centrality/graph_katz.cc

@@ -40,22 +40,22 @@ void katz(GraphInterface& g, boost::any w, boost::any c, boost::any beta,
                              " value type");
 
     typedef ConstantPropertyMap<double, GraphInterface::edge_t> weight_map_t;
-    typedef mpl::push_back<writable_edge_scalar_properties, weight_map_t>::type
+    typedef boost::mpl::push_back<writable_edge_scalar_properties, weight_map_t>::type
         weight_props_t;
 
     if(w.empty())
         w = weight_map_t(1.);
 
     typedef ConstantPropertyMap<double, GraphInterface::vertex_t> beta_map_t;
-    typedef mpl::push_back<vertex_floating_properties, beta_map_t>::type
+    typedef boost::mpl::push_back<vertex_floating_properties, beta_map_t>::type
         beta_props_t;
 
     if(beta.empty())
         beta = beta_map_t(1.);
 
-    run_action<>()(g, bind<void>
-                   (get_katz(), _1, g.GetVertexIndex(), _2,
-                    _3, _4, alpha, epsilon, max_iter),
+    run_action<>()(g, std::bind(get_katz(), placeholders::_1, g.GetVertexIndex(),
+                                placeholders::_2, placeholders::_3,
+                                placeholders::_4, alpha, epsilon, max_iter),
                    weight_props_t(),
                    vertex_floating_properties(),
                    beta_props_t())(w, c, beta);

src/graph/centrality/graph_katz.hh

@@ -22,8 +22,16 @@
 #include "graph_filtering.hh"
 #include "graph_util.hh"
 
+#ifndef __clang__
 #include <ext/numeric>
 using __gnu_cxx::power;
+#else
+template <class Value>
+Value power(Value value, int n)
+{
+    return pow(value, n);
+}
+#endif
 
 namespace graph_tool
 {

src/graph/centrality/graph_pagerank.cc

@@ -38,14 +38,14 @@ size_t pagerank(GraphInterface& g, boost::any rank, boost::any pers,
         throw ValueException("personalization vertex property must have a scalar value type");
 
     typedef ConstantPropertyMap<double, GraphInterface::vertex_t> pers_map_t;
-    typedef mpl::push_back<vertex_scalar_properties, pers_map_t>::type
+    typedef boost::mpl::push_back<vertex_scalar_properties, pers_map_t>::type
         pers_props_t;
 
     if(pers.empty())
         pers = pers_map_t(1.0 / g.GetNumberOfVertices());
 
     typedef ConstantPropertyMap<double, GraphInterface::edge_t> weight_map_t;
-    typedef mpl::push_back<edge_scalar_properties, weight_map_t>::type
+    typedef boost::mpl::push_back<edge_scalar_properties, weight_map_t>::type
         weight_props_t;
 
     if (!weight.empty() && !belongs<edge_scalar_properties>()(weight))
@@ -56,9 +56,10 @@ size_t pagerank(GraphInterface& g, boost::any rank, boost::any pers,
 
     size_t iter;
     run_action<>()
-        (g, bind<void>(get_pagerank(),
-                       _1, g.GetVertexIndex(), _2, _3, _4, d,
-                       epsilon, max_iter, ref(iter)),
+        (g, std::bind(get_pagerank(),
+                      placeholders::_1, g.GetVertexIndex(), placeholders::_2,
+                      placeholders::_3, placeholders::_4, d,
+                      epsilon, max_iter, std::ref(iter)),
          vertex_floating_properties(),
          pers_props_t(), weight_props_t())(rank, pers, weight);
     return iter;

src/graph/clustering/graph_clustering.cc

@@ -31,15 +31,16 @@ using namespace std;
 using namespace boost;
 using namespace graph_tool;
 
-python::tuple global_clustering(GraphInterface& g)
+boost::python::tuple global_clustering(GraphInterface& g)
 {
     double c, c_err;
     bool directed = g.GetDirected();
     g.SetDirected(false);
     run_action<graph_tool::detail::never_directed>()
-        (g, bind<void>(get_global_clustering(), _1, ref(c), ref(c_err)))();
+        (g, std::bind(get_global_clustering(), std::placeholders::_1,
+                      std::ref(c), std::ref(c_err)))();
     g.SetDirected(directed);
-    return python::make_tuple(c, c_err);
+    return boost::python::make_tuple(c, c_err);
 }
 
 void local_clustering(GraphInterface& g, boost::any prop)
@@ -47,17 +48,19 @@ void local_clustering(GraphInterface& g, boost::any prop)
     bool directed = g.GetDirected();
     g.SetDirected(false);
     run_action<graph_tool::detail::never_directed>()
-        (g, bind<void>(set_clustering_to_property(), _1, _2),
+        (g, std::bind(set_clustering_to_property(),
+                      std::placeholders::_1,
+                      std::placeholders::_2),
          writable_vertex_scalar_properties())(prop);
     g.SetDirected(directed);
 }
 
 using namespace boost::python;
 
-void extended_clustering(GraphInterface& g, python::list props);
-void get_motifs(GraphInterface& g, size_t k, python::list subgraph_list,
-                python::list hist, python::list pvmaps, bool collect_vmaps,
-                python::list p, bool comp_iso, bool fill_list, rng_t& rng);
+void extended_clustering(GraphInterface& g, boost::python::list props);
+void get_motifs(GraphInterface& g, size_t k, boost::python::list subgraph_list,
+                boost::python::list hist, boost::python::list pvmaps, bool collect_vmaps,
+                boost::python::list p, bool comp_iso, bool fill_list, rng_t& rng);
 
 BOOST_PYTHON_MODULE(libgraph_tool_clustering)
 {

src/graph/clustering/graph_clustering.hh

@@ -20,16 +20,23 @@
 
 #include "config.h"
 
-#include "tr1_include.hh"
-#include TR1_HEADER(unordered_set)
+#include <unordered_set>
 #include <boost/mpl/if.hpp>
 
 #ifdef HAVE_SPARSEHASH
 #include <dense_hash_set>
 #endif
 
+#ifndef __clang__
 #include <ext/numeric>
 using __gnu_cxx::power;
+#else
+template <class Value>
+Value power(Value value, int n)
+{
+    return pow(value, n);
+}
+#endif
 
 namespace graph_tool
 {
@@ -37,6 +44,8 @@ using namespace boost;
 
 #ifdef HAVE_SPARSEHASH
 using google::dense_hash_set;
+#else
+using std::unordered_set;
 #endif
 
 // calculates the number of triangles to which v belongs
@@ -162,10 +171,10 @@ struct set_clustering_to_property
     struct get_undirected_graph
     {
         typedef typename mpl::if_
-            < is_convertible<typename graph_traits<Graph>::directed_category,
-                             directed_tag>,
-              const UndirectedAdaptor<Graph>,
-              const Graph& >::type type;
+           <std::is_convertible<typename graph_traits<Graph>::directed_category,
+                                directed_tag>,
+            const UndirectedAdaptor<Graph>,
+            const Graph& >::type type;
     };
 };
 

src/graph/clustering/graph_extended_clustering.cc

@@ -35,9 +35,9 @@ struct prop_vector
     boost::any operator()(const vector<boost::any>& props, size_t size) const
     {
         boost::any prop_vec;
-        mpl::for_each<PropertySequence>
-            (bind<void>(get_prop_vector(), _1, ref(props), ref(prop_vec),
-                        size));
+        boost::mpl::for_each<PropertySequence>
+            (std::bind(get_prop_vector(), placeholders::_1, std::ref(props),
+                       std::ref(prop_vec), size));
         return prop_vec;
     }
 
@@ -74,11 +74,11 @@ struct get_property_vector_type
     };
 };
 
-void extended_clustering(GraphInterface& g, python::list props)
+void extended_clustering(GraphInterface& g, boost::python::list props)
 {
-    vector<any> cmaps(python::len(props));
+    vector<any> cmaps(boost::python::len(props));
     for (size_t i = 0; i < cmaps.size(); ++i)
-        cmaps[i] = python::extract<boost::any>(props[i])();
+        cmaps[i] = boost::python::extract<boost::any>(props[i])();
 
     boost::any vprop =
         prop_vector<writable_vertex_scalar_properties>()
@@ -87,14 +87,13 @@ void extended_clustering(GraphInterface& g, python::list props)
         throw ValueException("all vertex properties must be of the same"
                              " floating point type");
 
-    typedef mpl::transform<writable_vertex_scalar_properties,