igraph 0.9.1 → 0.9.5

data/Rakefile.rb

@@ -3,7 +3,7 @@ require 'hoe'
 $LOAD_PATH.unshift("./ext")
 
 class IGraph
-  VERSION = "0.9.1"
+  VERSION = "0.9.5"
 end
 
 begin 
@@ -14,7 +14,7 @@ end
 hoe = Hoe.new("igraph",IGraph::VERSION) do |p|
   
   p.author = "Alex Gutteridge"
-  p.email = "alexg@kuicr.kyoto-u.ac.jp"
+  p.email = "ag357@cam.ac.uk"
   p.url = "http://igraph.rubyforge.org/"
   
   p.description = p.paragraphs_of("README.txt",1..3)[0]

data/ext/cIGraph.c

@@ -546,7 +546,7 @@ void Init_igraph(){
   rb_include_module(cIGraph, cIGraph_community);
   
   rb_define_method(cIGraph_community, "modularity",   cIGraph_modularity,   1); /* in cIGraph_community.c */
-  rb_define_method(cIGraph_community, "community_to_membership", cIGraph_community_to_membership, 2);  /* in cIGraph_community.c */
+  rb_define_method(cIGraph_community, "community_to_membership", cIGraph_community_to_membership, 3);  /* in cIGraph_community.c */
   rb_define_method(cIGraph_community, "community_spinglass", cIGraph_community_spinglass, 8);  /* in cIGraph_community.c */
   rb_define_method(cIGraph_community, "community_spinglass_single", cIGraph_community_spinglass_single, 5);  /* in cIGraph_community.c */
   rb_define_method(cIGraph_community, "community_leading_eigenvector", cIGraph_community_leading_eigenvector, 1);  /* in cIGraph_community.c */      
@@ -556,7 +556,7 @@ void Init_igraph(){
   rb_define_method(cIGraph_community, "community_eb_get_merges", cIGraph_community_eb_get_merges, 1);  /* in cIGraph_community.c */  
   rb_define_method(cIGraph_community, "community_fastgreedy", cIGraph_community_fastgreedy, 0);  /* in cIGraph_community.c */  
 
-  rb_define_const(cIGraph, "VERSION", rb_str_new2("0.9.1"));
+  rb_define_const(cIGraph, "VERSION", rb_str_new2("0.9.5"));
 
   rb_define_const(cIGraph, "EDGEORDER_ID",   INT2NUM(1));
   rb_define_const(cIGraph, "EDGEORDER_FROM", INT2NUM(2));
@@ -624,7 +624,7 @@ void Init_igraph(){
   rb_define_method(cIGraphMatrix, "ncol", cIGraph_matrix_ncol, 0); /* in cIGraph_matrix.c */
   rb_define_method(cIGraphMatrix, "max",  cIGraph_matrix_max,  0); /* in cIGraph_matrix.c */
 
-  rb_define_method(cIGraphMatrix, "*", cIGraph_matrix_multiply, 1); /* in cIGraph_matrix.c */
+  rb_define_method(cIGraphMatrix, "*", cIGraph_matrix_scale, 1); /* in cIGraph_matrix.c */
 
   rb_define_method(cIGraphMatrix, "to_a", cIGraph_matrix_toa, 0); /* in cIGraph_matrix.c */
 

data/ext/cIGraph.h

@@ -287,7 +287,7 @@ VALUE cIGraph_cohesion(VALUE self);
 //Community
 VALUE cIGraph_modularity                         (VALUE self, VALUE groups);
 VALUE cIGraph_community_to_membership            (VALUE self, VALUE merge, 
-						  VALUE steps);
+						  VALUE steps, VALUE nodes);
 VALUE cIGraph_community_spinglass                (VALUE self, VALUE weights, 
 						  VALUE spins, 
 						  VALUE parupdate,
@@ -390,7 +390,7 @@ VALUE cIGraph_matrix_nrow(VALUE self);
 VALUE cIGraph_matrix_ncol(VALUE self);
 VALUE cIGraph_matrix_max (VALUE self);
 
-VALUE cIGraph_matrix_multiply(VALUE self, VALUE x);
+VALUE cIGraph_matrix_scale(VALUE self, VALUE x);
 
 VALUE cIGraph_matrix_toa(VALUE self);
 

data/ext/cIGraph_centrality.c

@@ -161,8 +161,8 @@ VALUE cIGraph_pagerank(VALUE self, VALUE vs, VALUE directed, VALUE niter, VALUE
   //create vertex selector from the vecotr of ids
   igraph_vs_vector(&vids,&vidv);
 
-  igraph_pagerank(graph,&res,vids,dir,
-		  NUM2INT(niter),NUM2DBL(eps),NUM2DBL(damping));
+  igraph_pagerank_old(graph,&res,vids,dir,
+		  NUM2INT(niter),NUM2DBL(eps),NUM2DBL(damping),0);
 
   for(i=0;i<igraph_vector_size(&res);i++){
     rb_ary_push(pagerank,rb_float_new(VECTOR(res)[i]));

data/ext/cIGraph_community.c

@@ -34,7 +34,7 @@ VALUE cIGraph_modularity(VALUE self, VALUE groups){
     }
   }
 
-  igraph_modularity(graph,&membership,&value);
+  igraph_modularity(graph,&membership,&value,NULL);
   
   igraph_vector_destroy(&membership);
 
@@ -53,7 +53,7 @@ VALUE cIGraph_modularity(VALUE self, VALUE groups){
  *
  */
 
-VALUE cIGraph_community_to_membership(VALUE self, VALUE merge, VALUE steps){
+VALUE cIGraph_community_to_membership(VALUE self, VALUE merge, VALUE steps, VALUE nodes){
 
   igraph_t *graph;
   igraph_matrix_t *merges;
@@ -69,7 +69,7 @@ VALUE cIGraph_community_to_membership(VALUE self, VALUE merge, VALUE steps){
 
   igraph_vector_init(&membership,0);
 
-  igraph_community_to_membership(graph,merges,NUM2INT(steps),&membership,NULL);
+  igraph_community_to_membership(merges,NUM2INT(nodes),NUM2INT(steps),&membership,NULL);
 
   max_groupid = 0;
   for(i=0;i<igraph_vector_size(&membership);i++){
@@ -253,6 +253,9 @@ VALUE cIGraph_community_leading_eigenvector(VALUE self, VALUE steps){
 
   igraph_vector_t membership;
   igraph_matrix_t *merges = malloc(sizeof(igraph_matrix_t));
+  
+igraph_arpack_options_t arpack_opt;
+igraph_arpack_options_init(&arpack_opt);
 
   int i,groupid,max_groupid;
 
@@ -264,7 +267,7 @@ VALUE cIGraph_community_leading_eigenvector(VALUE self, VALUE steps){
   igraph_vector_init(&membership,0);
 
   igraph_community_leading_eigenvector(graph,merges,&membership,
-				       NUM2INT(steps));
+				       NUM2INT(steps),&arpack_opt);
 
   max_groupid = 0;
   for(i=0;i<igraph_vector_size(&membership);i++){
@@ -316,6 +319,9 @@ VALUE cIGraph_community_leading_eigenvector_naive(VALUE self, VALUE steps){
   igraph_vector_t membership;
   igraph_matrix_t *merges = malloc(sizeof(igraph_matrix_t));
 
+igraph_arpack_options_t arpack_opt;
+igraph_arpack_options_init(&arpack_opt);
+
   int i,groupid,max_groupid;
 
   VALUE groups, group, res;
@@ -326,7 +332,7 @@ VALUE cIGraph_community_leading_eigenvector_naive(VALUE self, VALUE steps){
   igraph_vector_init(&membership,0);
 
   igraph_community_leading_eigenvector_naive(graph,merges,&membership,
-					     NUM2INT(steps));
+					     NUM2INT(steps), &arpack_opt);
 
   max_groupid = 0;
   for(i=0;i<igraph_vector_size(&membership);i++){
@@ -380,6 +386,9 @@ VALUE cIGraph_community_leading_eigenvector_step(VALUE self, VALUE membership, V
 
   int i,j,groupid,max_groupid,vid;
 
+igraph_arpack_options_t arpack_opt;
+igraph_arpack_options_init(&arpack_opt);
+
   VALUE groups, group, res, eigenvector_a, obj;
 
   Data_Get_Struct(self, igraph_t, graph);
@@ -402,7 +411,7 @@ VALUE cIGraph_community_leading_eigenvector_step(VALUE self, VALUE membership, V
 
   igraph_community_leading_eigenvector_step(graph,&membership_vec,
 					    NUM2INT(community),
-					    &split,&eigenvector,&eigenvalue);
+					    &split,&eigenvector,&eigenvalue,&arpack_opt,NULL);
 
   max_groupid = 0;
   for(i=0;i<igraph_vector_size(&membership_vec);i++){
@@ -634,7 +643,7 @@ VALUE cIGraph_community_fastgreedy(VALUE self){
   igraph_matrix_init(merges,0,0);
   igraph_vector_init(&modularity,0);
 
-  igraph_community_fastgreedy(graph,
+  igraph_community_fastgreedy(graph,NULL,
 			      merges,&modularity);
 
   modularity_a = rb_ary_new();

data/ext/cIGraph_generators_random.c

@@ -26,7 +26,7 @@ VALUE cIGraph_grg_game(VALUE self, VALUE nodes, VALUE radius, VALUE torus){
 
   igraph_destroy(graph);
   igraph_grg_game(graph, NUM2INT(nodes), NUM2DBL(radius), 
-		  torus == Qtrue ? 1: 0);
+		  torus == Qtrue ? 1: 0, NULL, NULL);
 
   return new_graph;
 

data/ext/cIGraph_isomorphism.c

@@ -21,7 +21,7 @@ VALUE cIGraph_isomorphic(VALUE self, VALUE g){
   Data_Get_Struct(self, igraph_t, graph);
   Data_Get_Struct(g,    igraph_t, graph2);
 
-  IGRAPH_CHECK(igraph_isomorphic(graph,graph2,&res));
+  igraph_isomorphic(graph,graph2,&res);
 
   return res == 0 ? Qfalse : Qtrue;
 
@@ -46,7 +46,7 @@ VALUE cIGraph_isomorphic_vf2(VALUE self, VALUE g){
   Data_Get_Struct(self, igraph_t, graph);
   Data_Get_Struct(g,    igraph_t, graph2);
 
-  IGRAPH_CHECK(igraph_isomorphic_vf2(graph,graph2,&res));
+  IGRAPH_CHECK(igraph_isomorphic_vf2(graph,graph2,&res,NULL,NULL));
 
   return res == 0 ? Qfalse : Qtrue;
 
@@ -72,7 +72,7 @@ VALUE cIGraph_isomorphic_vf2(VALUE self, VALUE g){
  */
 VALUE cIGraph_isoclass(VALUE self){
 
-  int res = 0;
+  igraph_integer_t res = 0;
   igraph_t *graph;
 
   Data_Get_Struct(self, igraph_t, graph);
@@ -92,7 +92,7 @@ VALUE cIGraph_isoclass(VALUE self){
  */
 VALUE cIGraph_isoclass_subgraph(VALUE self, VALUE vs){
 
-  int res = 0;
+  igraph_integer_t res = 0;
   igraph_t *graph;
   igraph_vector_t vidv;
 

data/ext/cIGraph_layout.c

@@ -70,7 +70,7 @@ VALUE cIGraph_layout_fruchterman_reingold(VALUE self,
 				     NUM2DBL(area),
 				     NUM2DBL(coolexp),
 				     NUM2DBL(repulserad),
-				     use_seed == Qtrue ? 1: 0);
+				     use_seed == Qtrue ? 1: 0, NULL);
 
   return Data_Wrap_Struct(cIGraphMatrix, 0, cIGraph_matrix_free, res);
 
@@ -103,7 +103,7 @@ VALUE cIGraph_layout_kamada_kawai(VALUE self,
 			     NUM2DBL(sigma),
 			     NUM2DBL(initemp),
 			     NUM2DBL(coolexp),
-			     NUM2DBL(kkconst));
+			     NUM2DBL(kkconst),0);
 
   return Data_Wrap_Struct(cIGraphMatrix, 0, cIGraph_matrix_free, res);
 

data/ext/cIGraph_layout3d.c

@@ -79,7 +79,7 @@ VALUE cIGraph_layout_fruchterman_reingold_3d(VALUE self,
 					NUM2DBL(volume),
 					NUM2DBL(coolexp),
 					NUM2DBL(repulserad),
-					1);
+					1, NULL);
 
   return Data_Wrap_Struct(cIGraphMatrix, 0, cIGraph_matrix_free, res);
 
@@ -112,7 +112,7 @@ VALUE cIGraph_layout_kamada_kawai_3d(VALUE self,
 				NUM2DBL(sigma),
 				NUM2DBL(initemp),
 				NUM2DBL(coolexp),
-				NUM2DBL(kkconst));
+				NUM2DBL(kkconst),0);
 
   return Data_Wrap_Struct(cIGraphMatrix, 0, cIGraph_matrix_free, res);
 

data/ext/cIGraph_matrix.c

@@ -191,11 +191,11 @@ VALUE cIGraph_matrix_max(VALUE self){
 }
 
 /* call-seq:
- *   matrix * matrix -> IGraphMatrix
+ *   matrix * num -> IGraphMatrix
  *
  * Multiples two IGraphMatrix objects together
  */
-VALUE cIGraph_matrix_multiply(VALUE self, VALUE x){
+VALUE cIGraph_matrix_scale(VALUE self, VALUE x){
 
   igraph_matrix_t *m;
   igraph_matrix_t *n = malloc(sizeof(igraph_matrix_t));
@@ -204,7 +204,7 @@ VALUE cIGraph_matrix_multiply(VALUE self, VALUE x){
   Data_Get_Struct(self, igraph_matrix_t, m);
 
   igraph_matrix_copy(n,m);
-  igraph_matrix_multiply(n, NUM2DBL(x));
+  igraph_matrix_scale(n, NUM2DBL(x));
 
   nobj = Data_Wrap_Struct(cIGraphMatrix, 0, cIGraph_matrix_free, n);
 

data/test/tc_centrality.rb

@@ -16,7 +16,7 @@ class TestGraph < Test::Unit::TestCase
   end    
   def test_pagerank
     g = IGraph.new(['A','B','C','D','E','B','F','B'],true)
-    assert_equal 67, (g.pagerank(['B'],true,100,0.01,0.8)[0] * 100).to_i
+    assert_equal 48, (g.pagerank(['B'],true,100,0.01,0.8)[0] * 100).to_i
   end 
   def test_constraint
     g = IGraph.new(['A','B','C','D'],true)

data/test/tc_cliques.rb

@@ -8,7 +8,7 @@ class TestGraph < Test::Unit::TestCase
    end
    def test_largest_cliques
      g = IGraph.new(['A','B','C','D','A','E','B','E'],false)
-     assert_equal [['A','B','E','B','E']], g.largest_cliques()
+     assert_equal [['A','B','E']], g.largest_cliques()
    end
    def test_maximal_cliques
      g = IGraph.new(['A','B','C','D','A','E','B','E'],false)

data/test/tc_community.rb

@@ -31,15 +31,15 @@ class TestGraph < Test::Unit::TestCase
       g.community_leading_eigenvector_step([['A','B','C','D','E','F']],0)
     assert_equal [['A','B','C'],['D','E','F']], groups
     assert split
-    assert_in_delta 0.433, eigenvec[0], 0.001
-    assert_in_delta 2.100, eigenval,    0.001
+    assert_in_delta 0.433, eigenvec[0], 0.02
+    assert_in_delta 1.730, eigenval,    0.02
 
   end
 
   def test_random_walk
     g = IGraph.new(['A','B','B','C','A','C','C','D','D','E','E','F','D','F'],false)
     merges,modularity = g.community_walktrap([],10)
-    groups = g.community_to_membership(merges,4)
+    groups = g.community_to_membership(merges,4,6)
     assert_equal [['A','B','C'],['D','E','F']], groups.sort
     assert_in_delta 0.19, modularity[3], 0.1
   end
@@ -48,14 +48,14 @@ class TestGraph < Test::Unit::TestCase
 
     g = IGraph.new(['A','B','B','C','A','C','C','D','D','E','E','F','D','F'],false)
     merges,result,edge_betw,bridges = g.community_edge_betweenness(false)    
-    groups = g.community_to_membership(merges,4)
+    groups = g.community_to_membership(merges,4,6)
     assert_equal [['A','B','C'],['D','E','F']], groups.sort
     assert_equal 3, result[0]
     assert_equal 9, edge_betw[0]
     assert_equal 7, bridges[0]
 
     merges,bridges = g.community_eb_get_merges(result)
-    groups = g.community_to_membership(merges,4)
+    groups = g.community_to_membership(merges,4,6)
     assert_equal [['A','B','C'],['D','E','F']], groups.sort
     assert_equal 7, bridges[0]    
     
@@ -64,7 +64,7 @@ class TestGraph < Test::Unit::TestCase
   def test_fastgreedy
     g = IGraph.new(['A','B','B','C','A','C','C','D','D','E','E','F','D','F'],false)
     merges,mod = g.community_fastgreedy
-    groups = g.community_to_membership(merges,4)
+    groups = g.community_to_membership(merges,4,6)
     assert_equal [['A','B','C'],['D','E','F']], groups.sort
     assert_in_delta 0.19, mod[3], 0.1
   end

data/test/tc_file_read_write.rb

@@ -167,7 +167,11 @@ class TestGraph < Test::Unit::TestCase
        return
     end
     g = nil
+    err = StringIO.open('','w')
+    $stderr = err
     g = IGraph::FileRead.read_graph_graphml(StringIO.new(Graphml),0)
+    assert_equal "warning: unknown attribute key in GraphML file, ignoring attribute\n", err.string.sub(/.*?:\d+: /,'')
+    $stderr = STDERR
     assert_instance_of IGraph, g
     assert_equal '2006-11-12', g.attributes['date']
     h = g.dup

metadata

@@ -1,33 +1,28 @@
 --- !ruby/object:Gem::Specification 
-rubygems_version: 0.9.4
-specification_version: 1
 name: igraph
 version: !ruby/object:Gem::Version 
-  version: 0.9.1
-date: 2007-11-20 00:00:00 +09:00
-summary: IGraph is a Ruby extension for interfacing with the C igraph library (http://cneurocvs.rmki.kfki.hu/igraph/). igraph is a library for creating and manipulating graphs with a particular emphasis on network analysis functions.
-require_paths: 
-- test
-email: alexg@kuicr.kyoto-u.ac.jp
-homepage: http://igraph.rubyforge.org/
-rubyforge_project: igraph
-description: IGraph is a Ruby extension for interfacing with the C igraph library (http://cneurocvs.rmki.kfki.hu/igraph/). igraph is a library for creating and manipulating graphs with a particular emphasis on network analysis functions.
-autorequire: 
-default_executable: 
-bindir: bin
-has_rdoc: true
-required_ruby_version: !ruby/object:Gem::Version::Requirement 
-  requirements: 
-  - - ">"
-    - !ruby/object:Gem::Version 
-      version: 0.0.0
-  version: 
+  version: 0.9.5
 platform: ruby
-signing_key: 
-cert_chain: 
-post_install_message: 
 authors: 
 - Alex Gutteridge
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2008-04-25 00:00:00 +01:00
+default_executable: 
+dependencies: []
+
+description: IGraph is a Ruby extension for interfacing with the C igraph library (http://cneurocvs.rmki.kfki.hu/igraph/). igraph is a library for creating and manipulating graphs with a particular emphasis on network analysis functions.
+email: ag357@cam.ac.uk
+executables: []
+
+extensions: 
+- ext/extconf.rb
+extra_rdoc_files: 
+- README.txt
+- History.txt
+- License.txt
 files: 
 - History.txt
 - License.txt
@@ -110,23 +105,35 @@ files:
 - test/tc_transitivity.rb
 - test/tc_vertex_neighbourhood.rb
 - test/test_all.rb
-test_files: 
-- test/test_all.rb
+has_rdoc: true
+homepage: http://igraph.rubyforge.org/
+post_install_message: 
 rdoc_options: 
 - --exclude
 - test/*
 - --main
 - README.txt
 - --inline-source
-extra_rdoc_files: 
-- README.txt
-- History.txt
-- License.txt
-executables: []
-
-extensions: 
-- ext/extconf.rb
+require_paths: 
+- test
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
 requirements: []
 
-dependencies: []
-
+rubyforge_project: igraph
+rubygems_version: 1.1.0
+signing_key: 
+specification_version: 2
+summary: IGraph is a Ruby extension for interfacing with the C igraph library (http://cneurocvs.rmki.kfki.hu/igraph/). igraph is a library for creating and manipulating graphs with a particular emphasis on network analysis functions.
+test_files: 
+- test/test_all.rb