git-svn-id: http://igraph.rubyforge.org/svn/trunk@28 71f48855-0bbf-4aa5-930d-4df415e86613

ext/cIGraph.c

@@ -244,6 +244,8 @@ void Init_igraph(){
   rb_define_alias (cIGraph, "neighborhood", "neighbourhood");
   rb_define_alias (cIGraph, "neighborhood_graphs", "neighbourhood_graphs");
 
+  rb_define_method(cIGraph, "subcomponent", cIGraph_subcomponent, 2); /* in cIGraph_components.c */
+
   rb_define_method(cIGraph, "topological_sorting", cIGraph_topological_sorting, 1); /* in cIGraph_topological_sort.c */
 
   rb_define_singleton_method(cIGraph, "read_graph_edgelist", cIGraph_read_graph_edgelist, 2); /* in cIGraph_file.c */

ext/cIGraph_attribute_handler.c

@@ -181,12 +181,12 @@ int cIGraph_attribute_add_vertices(igraph_t *graph, long int nv, igraph_vector_p
   VALUE values;
 
   if(attr){
-    if(((igraph_i_attribute_record_t*)VECTOR(*attr)[0])->type == IGRAPH_ATTRIBUTE_PY_OBJECT){
+    if(igraph_vector_ptr_size(attr) > 0 && ((igraph_i_attribute_record_t*)VECTOR(*attr)[0])->type == IGRAPH_ATTRIBUTE_PY_OBJECT){
 
       values = (VALUE)((igraph_i_attribute_record_t*)VECTOR(*attr)[0])->value;
       Check_Type(values, T_ARRAY);
       for(i=0;i<RARRAY(values)->len;i++){
-	rb_ary_push(vertex_array, RARRAY(values)->ptr[i]);
+      rb_ary_push(vertex_array, RARRAY(values)->ptr[i]);
       }
       //Otherwise read each attriute into hashes and use those
     } else {
@@ -196,6 +196,12 @@ int cIGraph_attribute_add_vertices(igraph_t *graph, long int nv, igraph_vector_p
 	igraph_i_attribute_record_t *attr_rec;
 	char *s;
 	record = rb_hash_new();
+
+	//For when no attributes are given
+	if(igraph_vector_ptr_size(attr) == 0){
+	  record = INT2NUM(i+1);
+	}
+	
 	for (j=0; j<igraph_vector_ptr_size(attr); j++) {
 	  VALUE key;
 	  VALUE value;

ext/cIGraph_components.c

@@ -0,0 +1,37 @@
+#include "igraph.h"
+#include "ruby.h"
+#include "cIGraph.h"
+
+/* call-seq:
+ *   graph.subcomponent(v,mode) -> Array
+ *
+ * Returns an Array of vertices that are in the same component as the vertex v.
+ * mode defines the type of the component for directed graphs, possible 
+ * values: IGraph::OUT: the set of vertices reachable from the vertex, 
+ * IGraph::IN the set of vertices from which the vertex is reachable, 
+ * IGraph::ALL 	the graph is considered as an undirected graph. Note that 
+ * this is not the same as the union of the previous two. 
+ */
+VALUE cIgraph_subcomponent(VALUE self, VALUE v, VALUE mode){
+
+  igraph_t *graph;
+  igraph_neimode_t pmode = NUM2INT(mode);
+  igraph_vector_t neis;
+  int i;
+  VALUE component = rb_ary_new();
+
+  igraph_vector_init_int(&neis,0);
+
+  Data_Get_Struct(self, igraph_t, graph);
+
+  igraph_subcomponent(graph, &neis, cIGraph_get_vertex_id(self,from), pmode);
+
+  for(i=0;i<igraph_vector_size(&neis);i++){
+    rb_ary_push(component,cIGraph_get_vertex_object(self,VECTOR(neis)[i]));
+  }
+
+  igraph_vector_destroy(&neis);
+
+  return component;  
+
+}

ext/cIGraph_file.c

@@ -0,0 +1,176 @@
+#include "igraph.h"
+#include "ruby.h"
+#include "cIGraph.h"
+
+/* call-seq:
+ *   IGraph.read_graph_edgelist(file,mode) -> IGraph
+ *
+ *  Reads an edge list from a File (or any IO) and creates a graph.
+ *
+ * This format is simply a series of even number integers separated by
+ * whitespace. The one edge (ie. two integers) per line format is thus not 
+ * required (but recommended for readability). Edges of directed graphs are 
+ * assumed to be in from, to order. 
+ */
+VALUE cIGraph_read_graph_edgelist(VALUE self, VALUE file, VALUE directed){
+
+  VALUE string;
+  FILE *stream;
+  VALUE new_graph;
+  VALUE v_ary;
+  igraph_t *graph;
+  igraph_bool_t directed_b = 0;
+
+  igraph_vs_t vs;
+  igraph_vit_t vit;
+
+  int vid;
+
+  if(directed)
+    directed_b = 1;
+
+  new_graph = cIGraph_alloc(cIGraph);
+  Data_Get_Struct(new_graph, igraph_t, graph);
+
+  string = rb_funcall(file, rb_intern("read"), 0);
+  stream = fmemopen(RSTRING(string)->ptr,RSTRING(string)->len, "r");
+
+  igraph_read_graph_edgelist(graph, stream, 0, directed_b);
+
+  fclose(stream);
+
+  igraph_vs_all(&vs);
+  igraph_vit_create(graph, vs, &vit);
+
+  v_ary =  ((VALUE*)graph->attr)[0];
+
+  while (!IGRAPH_VIT_END(vit)) {
+    vid = IGRAPH_VIT_GET(vit);
+    rb_ary_push(v_ary,INT2NUM(vid));
+    IGRAPH_VIT_NEXT(vit);
+  }
+  
+  igraph_vit_destroy(&vit);
+  igraph_vs_destroy(&vs);
+
+  return new_graph;
+
+}
+
+/* call-seq:
+ *   graph.write_graph_edgelist(file) -> Integer
+ *
+ *  Writes an edge list to an IO
+ *
+ * This format is simply a series of even number integers separated by
+ * whitespace. The one edge (ie. two integers) per line format is thus not 
+ * required (but recommended for readability). Edges of directed graphs are 
+ * assumed to be in from, to order. 
+ */
+VALUE cIGraph_write_graph_edgelist(VALUE self, VALUE file){
+
+  char *buf;
+  size_t size;
+  FILE *stream;
+  igraph_t *graph;
+  int e;
+
+  Data_Get_Struct(self, igraph_t, graph);
+
+  stream = open_memstream(&buf,&size);
+  e = igraph_write_graph_edgelist(graph, stream);
+  fflush(stream);
+
+  rb_funcall(file, rb_intern("write"), 1, rb_str_new(buf,size));
+
+  fclose(stream);
+
+  return e;
+
+}
+
+VALUE cIGraph_read_graph_graphml(VALUE self, VALUE file, VALUE index){
+
+  VALUE string;
+  FILE *stream;
+  VALUE new_graph;
+  igraph_t *graph;
+
+  new_graph = cIGraph_alloc(cIGraph);
+  Data_Get_Struct(new_graph, igraph_t, graph);
+
+  string = rb_funcall(file, rb_intern("read"), 0);
+  stream = fmemopen(RSTRING(string)->ptr,RSTRING(string)->len, "r");
+
+  igraph_read_graph_graphml(graph, stream, NUM2INT(index));
+
+  fclose(stream);
+
+  return new_graph;  
+
+}
+
+VALUE cIGraph_write_graph_graphml(VALUE self, VALUE file){
+
+  char *buf;
+  size_t size;
+  FILE *stream;
+  igraph_t *graph;
+  int e;
+
+  Data_Get_Struct(self, igraph_t, graph);
+
+  stream = open_memstream(&buf,&size);
+  e = igraph_write_graph_graphml(graph, stream);
+  fflush(stream);
+
+  rb_funcall(file, rb_intern("write"), 1, rb_str_new(buf,size));
+
+  fclose(stream);
+
+  return e;
+
+}
+
+VALUE cIGraph_read_graph_pajek(VALUE self, VALUE file){
+
+  VALUE string;
+  FILE *stream;
+  VALUE new_graph;
+  igraph_t *graph;
+
+  new_graph = cIGraph_alloc(cIGraph);
+  Data_Get_Struct(new_graph, igraph_t, graph);
+
+  string = rb_funcall(file, rb_intern("read"), 0);
+  stream = fmemopen(RSTRING(string)->ptr,RSTRING(string)->len, "r");
+
+  igraph_read_graph_pajek(graph, stream);
+
+  fclose(stream);
+
+  return new_graph;  
+
+}
+
+VALUE cIGraph_write_graph_pajek(VALUE self, VALUE file){
+
+  char *buf;
+  size_t size;
+  FILE *stream;
+  igraph_t *graph;
+  int e;
+
+  Data_Get_Struct(self, igraph_t, graph);
+
+  stream = open_memstream(&buf,&size);
+  e = igraph_write_graph_pajek(graph, stream);
+  fflush(stream);
+
+  rb_funcall(file, rb_intern("write"), 1, rb_str_new(buf,size));
+
+  fclose(stream);
+
+  return e;
+
+}

ext/cIGraph_layout.c

@@ -0,0 +1,62 @@
+#include "igraph.h"
+#include "ruby.h"
+#include "cIGraph.h"
+
+/* call-seq:
+ *   graph.layout_random -> IGraphMatrix
+ * 
+ * Returns a random layout
+ */
+VALUE cIGraph_layout_random(VALUE self){
+
+  igraph_t *graph;
+  igraph_matrix_t *res = malloc(sizeof(igraph_matrix_t));
+
+  Data_Get_Struct(self, igraph_t, graph);
+ 
+  igraph_matrix_init(res,0,0);
+  igraph_layout_random(graph,res);
+
+  return Data_Wrap_Struct(cIGraphMatrix, 0, cIGraph_matrix_free, res);
+
+}
+
+VALUE cIGraph_layout_circle(VALUE self){
+
+  igraph_t *graph;
+  igraph_matrix_t *res = malloc(sizeof(igraph_matrix_t));
+
+  Data_Get_Struct(self, igraph_t, graph);
+ 
+  igraph_matrix_init(res,0,0);
+  igraph_layout_circle(graph,res);
+
+  return Data_Wrap_Struct(cIGraphMatrix, 0, cIGraph_matrix_free, res);
+
+}
+
+VALUE cIGraph_layout_fruchterman_reingold(VALUE self,
+					  VALUE niter,
+					  VALUE maxdelta,
+					  VALUE area,
+					  VALUE coolexp,
+					  VALUE repulserad,
+					  VALUE use_seed){
+
+  igraph_t *graph;
+  igraph_matrix_t *res = malloc(sizeof(igraph_matrix_t));
+
+  Data_Get_Struct(self, igraph_t, graph);
+ 
+  igraph_matrix_init(res,0,0);
+  igraph_layout_fruchterman_reingold(graph,res,
+				     NUM2INT(niter),
+				     NUM2DBL(maxdelta),
+				     NUM2DBL(area),
+				     NUM2DBL(coolexp),
+				     NUM2DBL(repulserad),
+				     use_seed == Qtrue ? 1: 0);
+
+  return Data_Wrap_Struct(cIGraphMatrix, 0, cIGraph_matrix_free, res);
+
+}

ext/cIGraph_matrix.c

@@ -0,0 +1,199 @@
+#include "igraph.h"
+#include "ruby.h"
+#include "cIGraph.h"
+
+//Classes
+VALUE cIGraphMatrix;
+
+void cIGraph_matrix_free(void *p){
+  igraph_matrix_destroy(p);
+}
+
+VALUE cIGraph_matrix_alloc(VALUE klass){
+
+  igraph_matrix_t *m = malloc(sizeof(igraph_matrix_t));
+  VALUE obj;
+
+  igraph_matrix_init(m, 0, 0);
+
+  obj = Data_Wrap_Struct(klass, 0, cIGraph_matrix_free, m);
+
+  return obj;
+  
+}
+
+/* Document-method: initialize_copy
+ *
+ * Internal method for copying IGraph objects.
+ */
+VALUE cIGraph_matrix_init_copy(VALUE copy, VALUE orig){
+
+  igraph_matrix_t *orig_m;
+  igraph_matrix_t *copy_m;
+
+  if (copy == orig)
+    return copy;
+
+  if(TYPE(orig) != T_DATA || RDATA(orig)->dfree != (RUBY_DATA_FUNC)cIGraph_free){
+    rb_raise(rb_eTypeError, "Wrong argument type.");
+  }
+  
+  Data_Get_Struct(copy, igraph_matrix_t, copy_m); 
+  Data_Get_Struct(orig, igraph_matrix_t, orig_m);
+
+  igraph_matrix_copy(copy_m,orig_m);
+
+  return copy;
+
+}
+
+/* call-seq:
+ *   IGraphMatrix[[x,y,...],...] -> IGraphMatrix
+ *
+ *   IGraphMatrix[[1,2],[3,4]]
+ *
+ * Creates a graph with four vertices. Vertex 1 is connected to vertex 2.
+ * Vertex 3 is connected to vertex 4.
+ */
+
+VALUE cIGraph_matrix_initialize(int argc, VALUE *argv, VALUE self){
+
+  igraph_matrix_t *m;
+  VALUE rows;
+  int nrows;
+  int ncols;
+  int i;
+  int j;
+
+  rb_scan_args(argc,argv,"0*", &rows);
+
+  Data_Get_Struct(self, igraph_matrix_t, m);
+
+  nrows = RARRAY(rows)->len;
+  ncols = RARRAY(RARRAY(rows)->ptr[0])->len;
+
+  igraph_matrix_resize(m, nrows, ncols);
+
+  //Loop through rows
+  for (i=0; i<nrows; i++) {
+    for (j=0; j<ncols; j++){
+      MATRIX(*m,i,j) = NUM2DBL(RARRAY(RARRAY(rows)->ptr[i])->ptr[j]);
+    }
+  }
+
+  return self;
+
+}
+
+VALUE cIGraph_matrix_get(VALUE self, VALUE i, VALUE j){
+
+  igraph_matrix_t *m;
+
+  Data_Get_Struct(self, igraph_matrix_t, m);
+  return rb_float_new(MATRIX(*m,NUM2INT(i),NUM2INT(j)));
+
+}
+
+VALUE cIGraph_matrix_set(VALUE self, VALUE i, VALUE j, VALUE x){
+
+  igraph_matrix_t *m;
+
+  Data_Get_Struct(self, igraph_matrix_t, m);
+  MATRIX(*m,NUM2INT(i),NUM2INT(j)) = NUM2DBL(x);
+  return x;
+
+}
+
+VALUE cIGraph_matrix_each(VALUE self){
+
+  igraph_matrix_t *m;
+  int i;
+  int j;
+
+  Data_Get_Struct(self, igraph_matrix_t, m);
+  
+  for(i=0;i < m->nrow;i++){
+    for(j=0;j < m->ncol;j++){
+      rb_yield(rb_float_new(MATRIX(*m,i,j)));
+    }
+  }
+
+  return Qnil;
+
+}
+
+VALUE cIGraph_matrix_size(VALUE self){
+
+  igraph_matrix_t *m;
+
+  Data_Get_Struct(self, igraph_matrix_t, m);
+  return LONG2FIX(igraph_matrix_size(m));
+
+}
+
+VALUE cIGraph_matrix_nrow(VALUE self){
+
+  igraph_matrix_t *m;
+
+  Data_Get_Struct(self, igraph_matrix_t, m);
+  return LONG2FIX(igraph_matrix_nrow(m));
+
+}
+
+VALUE cIGraph_matrix_ncol(VALUE self){
+
+  igraph_matrix_t *m;
+
+  Data_Get_Struct(self, igraph_matrix_t, m);
+  return LONG2FIX(igraph_matrix_ncol(m));
+
+}
+
+VALUE cIGraph_matrix_max(VALUE self){
+
+  igraph_matrix_t *m;
+
+  Data_Get_Struct(self, igraph_matrix_t, m);
+  return rb_float_new(igraph_matrix_max(m));
+
+}
+
+VALUE cIGraph_matrix_multiply(VALUE self, VALUE x){
+
+  igraph_matrix_t *m;
+  igraph_matrix_t *n = malloc(sizeof(igraph_matrix_t));
+  VALUE nobj;
+
+  Data_Get_Struct(self, igraph_matrix_t, m);
+
+  igraph_matrix_copy(n,m);
+  igraph_matrix_multiply(n, NUM2DBL(x));
+
+  nobj = Data_Wrap_Struct(cIGraphMatrix, 0, cIGraph_matrix_free, n);
+
+  return nobj;
+
+}
+
+VALUE cIGraph_matrix_toa(VALUE self){
+
+  igraph_matrix_t *m;
+  int i;
+  int j;
+  VALUE a = rb_ary_new();
+  VALUE row;
+
+  Data_Get_Struct(self, igraph_matrix_t, m);
+
+  for(i=0;i < m->nrow;i++){
+    row = rb_ary_new();
+    for(j=0;j < m->ncol;j++){
+      rb_ary_push(row,rb_float_new(MATRIX(*m,i,j)));
+    }
+    rb_ary_push(a,row);
+  }
+
+  return a;
+
+}
+  

ext/cIGraph_topological_sort.c

@@ -0,0 +1,43 @@
+#include "igraph.h"
+#include "ruby.h"
+#include "cIGraph.h"
+
+/* call-seq:
+ *   graph.topological_sorting(mode) -> Array
+ *
+ * Calculate a possible topological sorting of the graph. A topological 
+ * sorting of a directed acyclic graph is a linear ordering of its nodes 
+ * where each node comes before all nodes to which it has edges. Every DAG 
+ * has at least one topological sort, and may have many. This function 
+ * returns a possible topological sort among them. If the graph is not 
+ * acyclic (it has at least one cycle), a partial topological sort is 
+ * returned and a warning is issued. mode specifies how to use the direction 
+ * of the edges. For IGRAPH_OUT, the sorting order ensures that each node 
+ * comes before all nodes to which it has edges, so nodes with no incoming 
+ * edges go first. For IGRAPH_IN, it is quite the opposite: each node comes 
+ * before all nodes from which it receives edges. Nodes with no outgoing 
+ * edges go first. 
+ */
+VALUE cIGraph_topological_sorting(VALUE self, VALUE mode){
+
+  igraph_t *graph;
+  igraph_vector_t res;
+  igraph_neimode_t pmode = NUM2INT(mode);
+  VALUE result = rb_ary_new();
+  int i;
+
+  igraph_vector_init_int(&res,0);  
+
+  Data_Get_Struct(self, igraph_t, graph);
+
+  igraph_topological_sorting(graph, &res, pmode);
+
+  for(i=0;i<igraph_vector_size(&res);i++){
+    rb_ary_push(result,cIGraph_get_vertex_object(self,VECTOR(res)[i]));
+  }
+
+  igraph_vector_destroy(&res);
+
+  return result;
+
+}

test/tc_components.rb

@@ -0,0 +1,54 @@
+require 'test/unit'
+require 'igraph'
+
+class TestGraph < Test::Unit::TestCase
+   def test_graph_size
+    assert_equal 4, IGraph.new([1,2,3,4],true).vcount
+    assert_equal 2, IGraph.new([1,2,3,4],true).ecount
+  end
+
+  def test_eid_get_edge
+    assert_nothing_raised do 
+      IGraph.new(['A','B','C','D'],true).get_eid('A','B')
+    end
+    graph = IGraph.new(['A','B','C','D'],true)
+    eid1  = graph.get_eid('A','B')
+    eid2  = graph.get_eid('C','D') 
+    assert_equal ['A','B'], graph.edge(eid1)
+    assert_equal ['C','D'], graph.edge(eid2);
+    assert_not_equal eid1,eid2
+  end
+
+  def test_neighbours
+    assert_nothing_raised do
+      IGraph.new(['A','B','C','D'],true).neighbors('A',IGraph::ALL)
+    end
+    graph = IGraph.new(['A','B','C','D'],true)
+    assert_equal ['B'], graph.neighbors('A',IGraph::ALL)
+    assert_equal ['D'], graph.neighbors('C',IGraph::ALL)    
+  end
+
+  def test_adjacent
+    assert_nothing_raised do
+      IGraph.new(['A','B','C','D'],true).adjacent('A',IGraph::ALL)
+    end
+    graph = IGraph.new(['A','B','C','D'],true)
+    eid1  = graph.get_eid('A','B')
+    eid2  = graph.adjacent('A',IGraph::ALL)[0]
+    assert_equal eid1, eid2
+  end
+
+  def test_directed
+    assert IGraph.new(['A','B','C','D'],true).is_directed?
+    assert !(IGraph.new(['A','B','C','D'],false).is_directed?)
+  end
+
+  def test_degree
+    graph = IGraph.new(['A','B','C','D'],true)
+    assert_equal [1],  graph.degree(['A'],    IGraph::ALL,true)
+    assert_equal [1,1],graph.degree(['A','B'],IGraph::ALL,true)
+    assert_raises IGraphError do 
+      graph.degree('A',IGraph::ALL,true)
+    end
+  end
+end

test/tc_copy.rb

@@ -0,0 +1,13 @@
+require 'test/unit'
+require 'igraph'
+
+class TestGraph < Test::Unit::TestCase
+  def test_copy
+    g = IGraph.new(['A','B','C','D'],true,[1,2]);
+    h = g.dup
+    assert g.vcount == h.vcount
+    assert g['A','B'] == h['A','B']
+    h['A','B'] = g['A','B'] + 1
+    assert g['A','B'] != h['A','B']
+  end
+end

test/tc_debug.rb

@@ -0,0 +1,10 @@
+require 'test/unit'
+require 'igraph'
+
+class TestGraph < Test::Unit::TestCase
+  def test_adj
+    graph = IGraph.new(['A','B','C','D'],true)
+    assert_equal ['B'], graph.adjacent_vertices('A',IGraph::ALL)
+  end
+end
+ 

test/tc_file_read_write.rb

@@ -0,0 +1,161 @@
+require 'test/unit'
+require 'igraph'
+require 'stringio'
+
+class TestGraph < Test::Unit::TestCase
+  def test_edgelist_read
+    g = nil
+    assert_nothing_raised{
+      g = IGraph.read_graph_edgelist(StringIO.new("0 1 2 3"),true)
+    }
+    assert_instance_of IGraph, g
+    assert_equal 4, g.vcount
+    assert g.are_connected?(0,1)
+  end
+
+  def test_edgelist_write
+    g = IGraph.new([0,1,2,3])
+    s = StringIO.new("")
+    str = g.write_graph_edgelist(s)
+    s.rewind
+    assert_equal "0 1\n2 3\n", s.read
+  end
+
+  def test_graphml_read
+    g = nil
+    g = IGraph.read_graph_graphml(StringIO.new(Graphml),0)
+    assert_instance_of IGraph, g
+    assert_equal '2006-11-12', g.attributes['date']
+    h = g.dup
+    assert_equal g.to_a,h.to_a
+    assert_equal g.attributes['date'], h.attributes['date']
+  end
+
+  def test_graphml_write
+    g = IGraph.new([{'id'=>0,'name'=>'a','type' => 4.0},
+                    {'id'=>1,'name'=>'b','type' => 5},
+                    {'id'=>2,'type' => 6},
+                    {'id'=>3,'name'=>'d'}],
+                   true,
+                   [{'eid'=>'e1'},
+                    {'eid'=>'e2'}])
+    g.attributes['date'] = 'Friday'
+    s = StringIO.new("")
+    str = g.write_graph_graphml(s)
+    s.rewind
+    assert_equal Graphml_out, s.read
+  end
+
+  def test_pajek_read_write
+    g = nil
+    g = IGraph.read_graph_pajek(StringIO.new(Pajek),0)
+    assert_instance_of IGraph, g
+    assert_equal 4, g.vcount
+    assert_equal 1, g[4,1]['weight']
+    h = g.dup
+    s = StringIO.new('')
+    h.write_graph_pajek(s)
+    s.rewind
+    str = s.read
+    str.gsub!(/\r/,'')
+    assert_equal Pajek, str
+  end
+
+  Graphml = %q{<?xml version="1.0" encoding="UTF-8"?>
+<!-- This file was written by the JAVA GraphML Library.-->
+<graphml xmlns="http://graphml.graphdrawing.org/xmlns"  xmlns:xsi="http://www.w3
+.org/2001/XMLSchema-instance"
+xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdr
+awing.org/xmlns/1.0/graphml.xsd">
+  <key id="d0" for="node" attr.name="color" attr.type="string">yellow</key>
+  <key id="d1" for="edge" attr.name="weight" attr.type="double"/>
+  <key id="d2" for="graph" attr.name="date" attr.type="string"></key>
+  <graph id="G" edgedefault="undirected">
+    <data key="d2">2006-11-12</data>
+    <node id="n0">
+      <data key="d0">green</data>
+      <data key="d3">incorrect</data>
+      <!-- incorrect attribute key, should issue a warning -->
+    </node>
+    <node id="n1"/>
+    <node id="n2">
+      <data key="d0">blue</data>
+    </node>
+    <node id="n3">
+      <data key="d0">red</data>
+    </node>
+    <node id="n4"/>
+    <node id="n5">
+      <data key="d0">turquoise</data>
+    </node>
+    <edge id="e0" source="n0" target="n2">
+      <data key="d1">1.0</data>
+    </edge>
+    <edge id="e1" source="n0" target="n1">
+      <data key="d1">1.0</data>
+    </edge>
+    <edge id="e2" source="n1" target="n3">
+      <data key="d1">2.0</data>
+    </edge>
+    <edge id="e3" source="n3" target="n2"/>
+    <edge id="e4" source="n2" target="n4"/>
+    <edge id="e5" source="n3" target="n5"/>
+    <edge id="e6" source="n5" target="n4">
+      <data key="d1">1.1</data>
+    </edge>
+  </graph>
+</graphml>
+}
+
+
+  Graphml_out = %q{<?xml version="1.0" encoding="UTF-8"?>
+<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
+         http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
+<!-- Created by igraph -->
+  <key id="date" for="graph" attr.name="date" attr.type="string"/>
+  <key id="name" for="node" attr.name="name" attr.type="string"/>
+  <key id="type" for="node" attr.name="type" attr.type="double"/>
+  <key id="id" for="node" attr.name="id" attr.type="double"/>
+  <key id="eid" for="edge" attr.name="eid" attr.type="string"/>
+  <graph id="G" edgedefault="directed">
+    <data key="date">Friday</data>
+    <node id="n0">
+      <data key="name">a</data>
+      <data key="type">4</data>
+      <data key="id">0</data>
+    </node>
+    <node id="n1">
+      <data key="name">b</data>
+      <data key="type">5</data>
+      <data key="id">1</data>
+    </node>
+    <node id="n2">
+      <data key="name"></data>
+      <data key="type">6</data>
+      <data key="id">2</data>
+    </node>
+    <node id="n3">
+      <data key="name">d</data>
+      <data key="id">3</data>
+    </node>
+    <edge source="n0" target="n1">
+      <data key="eid">e1</data>
+    </edge>
+    <edge source="n2" target="n3">
+      <data key="eid">e2</data>
+    </edge>
+  </graph>
+</graphml>
+}
+
+  Pajek = %q{*Vertices 4
+*Edges
+4 1 1
+1 2 4
+1 3 2
+2 3 2
+}
+
+end

test/tc_layout.rb

@@ -0,0 +1,26 @@
+require 'test/unit'
+require 'igraph'
+
+class TestGraph < Test::Unit::TestCase
+  def test_random
+    g = IGraph.new([1,2,3,4],true)
+    l = g.layout_random
+    assert_instance_of IGraphMatrix, l
+    assert_equal g.vcount, l.nrow
+    assert_equal 2,        l.ncol
+  end
+  def test_circle
+    g = IGraph.new([1,2,3,4],true)
+    l = g.layout_circle
+    assert_instance_of IGraphMatrix, l
+    assert_equal g.vcount, l.nrow
+    assert_equal 2,        l.ncol
+  end
+  def test_fruchterman_reingold
+    g = IGraph.new([1,2,3,4],true)
+    l = g.layout_fruchterman_reingold(10,1,1,2,1,false)
+    assert_instance_of IGraphMatrix, l
+    assert_equal g.vcount, l.nrow
+    assert_equal 2,        l.ncol
+  end
+end

test/tc_matrix.rb

@@ -0,0 +1,32 @@
+require 'test/unit'
+require 'igraph'
+
+class TestGraph < Test::Unit::TestCase
+  def test_matrix
+    m = IGraphMatrix.new([1,2],[3,4])
+    assert_equal 1, m[0,0]
+    assert_equal 3, m[1,0]
+  end
+  def test_set
+    m = IGraphMatrix.new([1,2],[3,4])
+    m[0,0] = 6
+    assert_equal 6, m[0,0]
+  end
+  def test_prop
+    m = IGraphMatrix.new([1,2],[3,4])
+    assert_equal 4, m.size
+    assert_equal 2, m.nrow
+    assert_equal 2, m.ncol
+    assert_equal 4, m.max
+  end
+  def test_op
+    m = IGraphMatrix.new([1,2],[3,4])
+    n = m * 2
+    assert_equal 1, m[0,0]
+    assert_equal 2, n[0,0]
+  end
+  def test_to_a
+    m = IGraphMatrix.new([1,2],[3,4])
+    assert_equal [[1,2],[3,4]], m.to_a
+  end
+end

test/tc_topological_sort.rb

@@ -0,0 +1,10 @@
+require 'test/unit'
+require 'igraph'
+
+class TestGraph < Test::Unit::TestCase
+  def test_top_sort
+    g = IGraph.new([1,2,2,3,3,4])
+    assert_equal [1,2,3,4], g.topological_sorting(IGraph::OUT)
+  end
+  
+end