genmodel 0.0.27 → 0.0.28

data/ext/Genmodel/GraphTools.cpp

@@ -0,0 +1,211 @@
+//
+//  GraphTools.cpp
+//  
+//
+//  Created by Mathieu Bouchard on 2014-03-21.
+//
+//
+
+#include <GraphTools.h>
+#include <lemon/list_graph.h>
+#include <stdlib.h>
+#include <time.h>
+
+# define n_id nodeFromId
+# define e_id edgeFromId
+
+vector<vector<size_t> > GmGraph::GetCliqueCover()
+{
+    size_t n = countNodes(g);
+    size_t e = countEdges(g);
+    vector<vector<size_t> > out;
+
+    vector<bool> done(e,false);
+    size_t curr_e = 0;
+    size_t added = 0;
+    while(true)
+    {
+        while(curr_e < e && done[curr_e])
+            ++curr_e;
+        
+        if(curr_e == e)
+            break;
+        done[curr_e] = true;
+        added++;
+        //printf("curr_e = %ld (added = %ld)\n", curr_e, added);
+        
+        vector<bool> node_in(n,false);
+        vector<size_t> node_depth(n,0);
+        
+        vector<size_t> clique;
+        size_t curr_n = g.id(g.u(g.e_id(curr_e)));
+        size_t next_n = g.id(g.v(g.e_id(curr_e)));
+        
+        //ve.push_back(e);
+        
+        clique.push_back(curr_n);
+        node_in[curr_n] = true;
+        
+        vector<size_t> dc = in(curr_n);
+        for(size_t i = 0; i < dc.size(); i++)
+            ++(node_depth[dc[i]]);
+        size_t depth = 1;
+        
+        while(next_n != -1 && depth < e*e)
+        {
+            //printf("1-Add %ld (depth %ld)\n", next_n, depth);
+
+            clique.push_back(next_n);
+            node_in[next_n] = true;
+            vector<size_t> de = ie(next_n);
+            depth++;
+            curr_n = next_n;
+            next_n = -1;
+            size_t next_nn = -1;
+            for(size_t i = 0; i < de.size(); i++)
+            {
+                size_t nn = (g.id(g.u(g.e_id(de[i]))) == curr_n ?  g.id(g.v(g.e_id(de[i]))) : g.id(g.u(g.e_id(de[i]))));
+                size_t onn = (g.id(g.u(g.e_id(de[i]))) == curr_n ?  g.id(g.u(g.e_id(de[i]))) : g.id(g.v(g.e_id(de[i]))));
+                ++(node_depth[nn]);
+                if(node_in[nn] && !done[de[i]])
+                {
+                    done[de[i]] = true;
+                    added++;
+                    //printf("\t2-From %ld : Add edge %ld (depth %ld) [added = %ld] d=%ld --> %ld (other = %ld)\n", curr_n, de[i], depth, added, de.size(), nn, onn);
+                }
+                if(node_depth[nn] == depth && next_n == -1 && !done[de[i]] && !node_in[nn])
+                {
+                    next_n = nn;
+                    done[de[i]] = true;
+                    added++;
+                    //printf("\t3-Add edge %ld (depth %ld) [added = %ld]\n", de[i], depth, added);
+                }
+                else if(node_depth[nn] == depth && next_n == -1 && !node_in[nn])
+                {
+                    next_nn = nn;
+                }
+            }
+            if (next_n == -1)
+                next_n = next_nn;
+        }
+        if (depth == e*e)
+            throw string("GmGraph::GetCliqueCover : Max depth reached");
+        out.push_back(clique);
+        if(added >= e)
+            break;
+    }
+    if(added < e)
+        throw string("GmGraph::GetCliqueCover : The graph was not covered by clique.");
+    //printf("Finish %ld!\n", added);
+    
+    return out;
+}
+
+vector<size_t> GmGraph::ie(size_t i)
+{
+    vector<size_t> out(di(i));
+    size_t ii = 0;
+    for (ListGraph::IncEdgeIt _e(g, g.n_id(i)); _e != INVALID; ++_e, ++ii)
+        out[ii] = (g.id(_e)-g.id(_e)%2)/2;
+    return out;
+}
+
+BitVector GmGraph::ie2bv(size_t i)
+{
+    BitVector out(countEdges(g)*2);
+    for (ListGraph::IncEdgeIt _e(g, g.n_id(i)); _e != INVALID; ++_e)
+        out.set((g.id(_e)-g.id(_e)%2)/2, true);
+    return out;
+}
+
+vector<size_t> GmGraph::in(size_t i)
+{
+    vector<size_t> out(di(i));
+    size_t ii = 0;
+    for (ListGraph::IncEdgeIt _e(g, g.n_id(i)); _e != INVALID; ++_e, ++ii)
+        out[ii] = (g.id(g.u(_e)) == i ?  g.id(g.v(_e)) : g.id(g.u(_e)));
+    return out;
+}
+
+BitVector GmGraph::in2bv(size_t i)
+{
+    BitVector out(countNodes(g));
+    for (ListGraph::IncEdgeIt _e(g, g.n_id(i)); _e != INVALID; ++_e)
+        (g.id(g.u(_e)) == i ?  out.set(g.id(g.v(_e)),true) : out.set(g.id(g.u(_e)),true));
+    return out;
+}
+
+
+size_t GmGraph::n()
+{
+    return countNodes(g);
+}
+
+size_t GmGraph::e()
+{
+    return countEdges(g);
+}
+
+size_t GmGraph::di(size_t i)
+{
+    return countIncEdges(g, g.n_id(i));
+}
+
+size_t GmGraph::AddNode()
+{
+    return g.id(g.addNode());
+}
+
+size_t GmGraph::AddEdge(size_t i, size_t j)
+{
+    return g.id(g.addEdge(g.n_id(i), g.n_id(j)));
+}
+
+size_t GmGraph::u(size_t i)
+{
+    return g.id(g.u(g.e_id(i)));
+}
+size_t GmGraph::v(size_t i)
+{
+    return g.id(g.v(g.e_id(i)));
+}
+
+void GmGraph::EraseNode(size_t i)
+{
+    g.erase(g.n_id(i));
+}
+
+void GmGraph::EraseEdge(size_t i)
+{
+    g.erase(g.e_id(i));
+}
+
+void GmGraph::ChangeU(size_t i, size_t j)
+{
+    g.changeU(g.e_id(i),g.n_id(j));
+}
+
+void GmGraph::ChangeV(size_t i, size_t j)
+{
+    g.changeV(g.e_id(i),g.n_id(j));
+}
+
+void GmGraph::Contract(size_t i, size_t j, bool r)
+{
+    g.contract(g.n_id(i), g.n_id(j), r);
+}
+
+void GmGraph::Clear()
+{
+    g.clear();
+}
+
+void GmGraph::ReserveNode(size_t n)
+{
+     g.reserveNode(n);
+}
+
+void GmGraph::ReserveEdge(size_t m)
+{
+    g.reserveEdge(2 * m);
+}

data/ext/Genmodel/GraphTools.h

@@ -0,0 +1,49 @@
+//
+//  GraphTools.h
+//  
+//
+//  Created by Mathieu Bouchard on 2014-03-21.
+//
+//
+
+#ifndef _GraphTools_h
+#define _GraphTools_h
+
+#include <lemon/concepts/graph.h>
+#include <lemon/list_graph.h>
+#include "BitVector.h"
+
+using namespace lemon;
+using namespace std;
+
+class GmGraph
+{
+public:
+    GmGraph() {}
+    ~GmGraph() {}
+    size_t AddNode();
+    size_t AddEdge(size_t i, size_t j);
+    void EraseNode(size_t i);
+    void EraseEdge(size_t i);
+    void ChangeU(size_t i, size_t j);
+    void ChangeV(size_t i, size_t j);
+    size_t u(size_t i);
+    size_t v(size_t i);
+    void Contract(size_t i, size_t j, bool r = true);
+    void Clear();
+    void ReserveNode(size_t n);
+    void ReserveEdge(size_t m);
+    size_t n();
+    size_t e();
+    size_t di(size_t i);
+    vector<size_t> ie(size_t i);
+    vector<size_t> in(size_t i);
+    BitVector ie2bv(size_t i);
+    BitVector in2bv(size_t i);
+    
+    vector<vector<size_t> > GetCliqueCover();
+    
+    ListGraph g;
+};
+
+#endif

data/ext/Genmodel/extconf.rb

@@ -68,16 +68,16 @@ if is_darwin
     end
     
     #path = "/usr/local/Cellar/cbc/2.8.6/include/coin/"+sep+"/usr/local/Cellar/cgl/0.58.3/include/coin/"
-    cbc_path = "/usr/local/Cellar/cbc/"
-    cbc_file = "/include/coin/OsiClpSolverInterface.hpp"
-    puts "Looking for OsiClpSolverInterface.hpp in "+cbc_path+"/*"
+    search_path = "/usr/local/Cellar/cbc/"
+    search_file = "/include/coin/OsiClpSolverInterface.hpp"
+    puts "Looking for OsiClpSolverInterface.hpp in "+search_path+"/*"
     file_exist = nil
-    Find.find(cbc_path) do |path|
+    Find.find(search_path) do |path|
         if (FileTest.directory?(path))
-            puts path+cbc_file
+            puts path+search_file
             temp_name = (path).gsub(/\/usr\/local\/Cellar\/cbc\//,'')
             count = temp_name.count('/')
-            if ((count == 0) && (File.exist?(path+cbc_file)))
+            if ((count == 0) && (File.exist?(path+search_file)))
                 file_exist = "-I#{path}/include/coin"
                 break
             end
@@ -91,6 +91,30 @@ if is_darwin
         is_osi = false
     end
     
+    search_path = "/usr/local/Cellar/lemon-graph/"
+    search_file = "/include/lemon/core.h"
+    puts "Looking for lemon/core.h in "+search_path+"/*"
+    file_exist = nil
+    Find.find(search_path) do |path|
+        if (FileTest.directory?(path))
+            puts path+search_file
+            temp_name = (path).gsub(/\/usr\/local\/Cellar\/lemon-graph\//,'')
+            count = temp_name.count('/')
+            if ((count == 0) && (File.exist?(path+search_file)))
+                file_exist = "-I#{path}/include"
+                break
+            end
+        end
+    end
+    if(is_osi && file_exist != nil)
+        $INCFLAGS << " " << file_exist.quote
+        puts "found"
+    else
+        puts "not found"
+        is_osi = false
+    end
+    
+    
     path = "/usr/lib:/usr/local/lib/"
     puts "Looking for Clp (function main) in "+path
     if(is_osi && find_library("Clp",nil,path))
@@ -145,6 +169,15 @@ if is_darwin
         #is_osi = false
     end
     
+    path = "/usr/lib:/usr/local/lib/"
+    puts "Looking for libemon.dylib (function main) in "+path
+    if(is_osi && find_library("emon",nil,path))
+        puts "found"
+        else
+        puts "not found"
+        is_osi = false
+    end
+    
 elsif is_linux
     # path = Dir.home+"/ibm/ILOG/CPLEX_Studio126/cplex/include:/opt/ibm/ILOG/CPLEX_Studio126/cplex/include"
     path = "/opt/ibm/ILOG/CPLEX_Studio126/cplex/include"
@@ -245,6 +278,6 @@ if(is_osi)
     $defs.push("-DOSI_MODULE")
 end
 
-
+#swig -ruby -o ext/GenModelGem/Genmodel.cpp -c++ src/Genmodel.i
 
 create_makefile (extension_name)

data/lib/Genmodel.rb

@@ -1,5 +1,5 @@
 module Genmodel
-    GENMODEL_VERSION = "0.0.27"
+    
 end
 
 require "Genmodel/Genmodel"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: genmodel
 version: !ruby/object:Gem::Version
-  version: 0.0.27
+  version: 0.0.28
 platform: ruby
 authors:
 - Mathieu Bouchard
@@ -17,6 +17,8 @@ extensions:
 - ext/Genmodel/extconf.rb
 extra_rdoc_files: []
 files:
+- ext/Genmodel/BitVector.cpp
+- ext/Genmodel/BitVector.h
 - ext/Genmodel/GenModel.h
 - ext/Genmodel/GenModelBase.cpp
 - ext/Genmodel/GenModelCplex.cpp
@@ -26,6 +28,8 @@ files:
 - ext/Genmodel/GenModelOsiInterface.cpp
 - ext/Genmodel/GenModelOsiInterface.h
 - ext/Genmodel/Genmodel.cpp
+- ext/Genmodel/GraphTools.cpp
+- ext/Genmodel/GraphTools.h
 - ext/Genmodel/ProblemReaderOsi.cpp
 - ext/Genmodel/ProblemReaderOsi.h
 - ext/Genmodel/extconf.rb