Ticket #5793: cliquer-3.patch

deleted file sage/ext/cliquer.pxd

@@ -1 @@
-cdef extern from "cliquer/graph.h":
-    struct graph_t:
-       pass
-
-cdef extern from "cliquer/cliquer.h":
-    struct clique_options:
-       pass
-
-
-cdef extern from "cliquer/reorder.h":
-     cdef int *reorder_by_greedy_coloring(graph_t *g, bool weighted)
-     cdef int *reorder_by_degree(graph_t *g, bool weighted)
-
-cdef extern from "cliquer/cliquer.h":
-     bool clique_print_time(intlevel, int i, int n, int max, double cputime, double realtime, clique_options *opts)
-
-
-cdef extern from "cliquer/cl.h":
-     cdef int sage_clique_max(graph_t *g, int ** list)
-     cdef int sage_all_clique_max(graph_t *g, int ** list)
-     cdef int sage_clique_number(graph_t *g)
-     cdef void parse_input(char *str,graph_t *g)
-
-cdef extern from "cliquer/graph.h":
-     cdef graph_t * graph_new(int n)
-

new file sage/graphs/cliquer.pxd

@@ +1 @@
+cdef extern from "cliquer/graph.h":
+    struct graph_t:
+       pass
+
+cdef extern from "cliquer/cliquer.h":
+    struct clique_options:
+       pass
+
+
+cdef extern from "cliquer/reorder.h":
+     cdef int *reorder_by_greedy_coloring(graph_t *g, bool weighted)
+     cdef int *reorder_by_degree(graph_t *g, bool weighted)
+
+cdef extern from "cliquer/cliquer.h":
+     bool clique_print_time(intlevel, int i, int n, int max, double cputime, double realtime, clique_options *opts)
+
+
+cdef extern from "cliquer/cl.h":
+     cdef int sage_clique_max(graph_t *g, int ** list)
+     cdef int sage_all_clique_max(graph_t *g, int ** list)
+     cdef int sage_clique_number(graph_t *g)
+     cdef void parse_input(char *str,graph_t *g)
+
+cdef extern from "cliquer/graph.h":
+     cdef graph_t * graph_new(int n)
+

sage/graphs/cliquer.pyx

@@ -1 @@
-include '../ext/cliquer.pxd'
-
-# computes the maximum clique of a graph and return the list of its members
-
 def max_clique(graph):
+    """
+    Returns the vertex set of a maximum complete subgraph.
+    
+    Currently only implemented for undirected graphs. Use
+    to_undirected to convert a digraph to an undirected graph.
+    
+    EXAMPLES::
+    
+    sage: C=graphs.PetersenGraph()
+    sage: max_clique(C)
+    [7, 9]
+    """
     cdef graph_t *g
     g=graph_new(graph.order())
     buf="p edges %d %d" %(graph.order(),graph.size())
@@ -10 +18 @@
 
     for e in graph.edge_iterator():
           (u,v,w)=e
-          buf=' e %d %d' %(u,v)
+          buf=' e %d %d' %(u+1,v+1)
           parse_input(buf,g)
 
-
     cdef int* list
     cdef int size
     size=sage_clique_max(g, &list)
@@ -27 +34 @@
 # computes all the maximum clique of a graph and return its list
 
 def all_max_clique(graph):
+    """
+    Returns the vertex sets of *ALL* the maximum complete subgraphs.
+    
+    Currently only implemented for undirected graphs. Use
+    to_undirected to convert a digraph to an undirected graph.
+    
+    EXAMPLES::
+    
+    sage: C=graphs.PetersenGraph()
+    sage: all_max_clique(C)
+    [[2, 7], [7, 9], [6, 8], [6, 9], [0, 4], [4, 9], [5, 7], [0, 5], [5, 8], [3, 4], [2, 3], [3, 8], [1, 6], [0, 1], [1, 2]]
+    """
     cdef graph_t *g
     g=graph_new(graph.order())
     buf="p edges %d %d" %(graph.order(),graph.size())
@@ -34 +53 @@
 
     for e in graph.edge_iterator():
           (u,v,w)=e
-          buf=' e %d %d' %(u,v)
+          buf=' e %d %d' %(u+1,v+1)
           parse_input(buf,g)
 
     cdef int* list
@@ -55 +74 @@
 #computes the clique number of a graph 
 
 def clique_number(graph):
+    """
+    Returns the size of the largest clique of the graph (clique
+    number). 
+    
+    Currently only implemented for undirected graphs. Use
+    to_undirected to convert a digraph to an undirected graph.
+    
+    EXAMPLES::
+    
+    sage: C = Graph('DJ{')
+    sage: clique_number(C)
+    4
+    sage: G = Graph({0:[1,2,3], 1:[2], 3:[0,1]})
+    sage: G.show(figsize=[2,2])
+    sage: clique_number(G)
+    3
+    """
     cdef graph_t *g
     g=graph_new(graph.order())
     buf="p edges %d %d" %(graph.order(),graph.size())
@@ -62 +98 @@
 
     for e in graph.edge_iterator():
           (u,v,w)=e
-          buf=' e %d %d' %(u,v)
+          buf=' e %d %d' %(u+1,v+1)
           parse_input(buf,g)
     return sage_clique_number(g)
+
+
+
+

sage/graphs/graph.py

@@ -9238 +9238 @@
         from bipartite_graph import BipartiteGraph
         return BipartiteGraph(networkx.cliques.make_clique_bipartite(self.networkx_graph(copy=False), **kwds))
 
-    def clique_number(self,algorithm="cliquer"):
+
+    def clique_number(self,algorithm="cliquer",cliques=None):
         """
         Returns the size of the largest clique of the graph (clique
         number). By default, the Cliquer algorithm is used 
         ( algorithm="cliquer" ) but you can also chose the networkx
         algorithm instead ( algorithm="networkx" )
+
+        The parameter 'cliques' is an optional list of cliques that can be input if already computed.
+        ONLY USED BY NetworkX !!!
         
         Currently only implemented for undirected graphs. Use
         to_undirected to convert a digraph to an undirected graph.
@@ -9263 +9267 @@
             return clique_number(self)        
         elif algorithm=="networkx":
             import networkx.cliques
-            return networkx.cliques.graph_clique_number(self.networkx_graph(copy=False))
+            return networkx.cliques.graph_clique_number(self.networkx_graph(copy=False),cliques)
         else:
             raise NotImplementedError("Only 'networkx' and 'cliquer' are supported.")
 
+
     def maximum_clique(self):
         """
         Returns the vertex set of a maximum complete subgraph.
@@ -9277 +9282 @@
         EXAMPLES::
         
         sage: C=graphs.PetersenGraph()
-        sage: C.maximum_cliq()
-        C.maximum_clique   C.maximum_cliques  
         sage: C.maximum_clique()
-        [7, 9]
+        [6, 8]
         """
         from sage.graphs.cliquer import max_clique
         return max_clique(self)
@@ -9313 +9316 @@
         
         sage: C=graphs.PetersenGraph()
         sage: C.maximum_cliques()
-        
-        [[2, 7],
-        [7, 9],
-        [6, 8],
-        [6, 9],
-        [0, 4],
-        [4, 9],
-        [5, 7],
-        [0, 5],
-        [5, 8],
-        [3, 4],
-        [2, 3],
-        [3, 8],
-        [1, 6],
-        [0, 1],
-        [1, 2]]
+        [[1, 6], [6, 8], [5, 7], [5, 8], [3, 8], [4, 6], [4, 7], [2, 3], [1, 2], [2, 7], [0, 5], [0, 1]]
         """
 
         from sage.graphs.cliquer import all_max_clique