New algorithm for Max Clique in Graph class using Cython

[nathanncohen]

This depends on #6355.

CC: @rlmill

Component: graph theory

Author: Nathann Cohen

Reviewer: Robert Miller, Minh Van Nguyen

Merged: Sage 4.1.1.rc1

Issue created by migration from https://trac.sagemath.org/ticket/5793

[sagetrac-mabshoff]

comment:1

Hi,

the patch as is will not go into Sage since you are putting the sources for cliquer-1.2 into the Sage library tree where they do not belong.

I have not looked at the cython interface, but my guess would be that we need to change cliquer-1.2 to create a library. Please split the cython interface work (the code you wrote minus the cliquer-1.2 source code) and the cliquer-1.2.spkg work. The Cython code should remain here while spkg should go to #5669.

Cheers,

Michael

[nathanncohen]

comment:2

A new patch using the SPKG you can find at :
#6355

[rlmill]

comment:4

Duplication of #6355.

[jasongrout]

comment:5

To get this going again, here are some specific suggestions for patch 12427.patch and the associated spkg:

• copy the header files to somewhere in $SAGE_LOCAL/include (maybe $SAGE_LOCAL/include/cliquer/*.h

• Make a cliquer.pxd file that declares the necessary functions and structs from the header files. Make sure that you are only doing cdef externs from the header files, not the .c files like the patch is currently doing. Don't include the path; just do cdef extern from "cliquer/graph.h": since the header is in the include path. This cliquer.pxd file can go into sage/graphs.

• Make a cliquer.pyx in sage/graphs that contains the definitions of max_clique, all_max_clique, and clique_number. Document and add doctests to these functions.

• Delete the lines

from sage.graphs.graph import Graph 
#from distutils.core import setup 
#from distutils.extension import Extension 
from Cython.Distutils import build_ext 

• In module_list.py, add a libraries = ['cliquer'] option (see the surrounding declarations for examples of this).

• Compile the cliquer sources into a shared library, named libcliquer.so, using the instructions in the HowTo William posted. Place this shared library into $SAGE_LOCAL/lib.

• In the graphs.py, I don't think you need to do from sage.graphs.cliquer import clique_number. Since the module will be in that directory, I think it would be sufficient to do from cliquer import clique_number.