Update is_chordal to return certificates

[Nathann Cohen]

This patch lets is_chordal return a certificate when asked to do so. The former algorithm is kept, and several lines are added to collect the certificate on the way and return it.

Nathann

[Robert Miller]

You should define what a "perfect elimination order" and a "hole" are in the documentation.

sage -t -long ./sage/graphs/generic_graph.py
**********************************************************************
File "/home/rlmill/sage-4.6/devel/sage-main/sage/graphs/generic_graph.py", line 8758:
    sage: (_, peo) = g.is_chordal(certificate = True)
Exception raised:
    Traceback (most recent call last):
      File "/home/rlmill/sage-4.6/local/bin/ncadoctest.py", line 1231, in run_one_test
        self.run_one_example(test, example, filename, compileflags)
      File "/home/rlmill/sage-4.6/local/bin/sagedoctest.py", line 38, in run_one_example
        OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags)
      File "/home/rlmill/sage-4.6/local/bin/ncadoctest.py", line 1172, in run_one_example
        compileflags, 1) in test.globs
      File "<doctest __main__.example_135[7]>", line 1, in <module>
        (_, peo) = g.is_chordal(certificate = True)###line 8758:
    sage: (_, peo) = g.is_chordal(certificate = True)
      File "/home/rlmill/sage-4.6/local/lib/python/site-packages/sage/graphs/generic_graph.py", line 8854, in is_chordal
        return True, peo_copy
    NameError: global name 'peo_copy' is not defined
**********************************************************************
File "/home/rlmill/sage-4.6/devel/sage-main/sage/graphs/generic_graph.py", line 8759:
    sage: for v in peo:
          if not g.subgraph(g.neighbors(v)).is_clique():
               print "This should never happen !"
          g.delete_vertex(v)
Exception raised:
    Traceback (most recent call last):
      File "/home/rlmill/sage-4.6/local/bin/ncadoctest.py", line 1231, in run_one_test
        self.run_one_example(test, example, filename, compileflags)
      File "/home/rlmill/sage-4.6/local/bin/sagedoctest.py", line 38, in run_one_example
        OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags)
      File "/home/rlmill/sage-4.6/local/bin/ncadoctest.py", line 1172, in run_one_example
        compileflags, 1) in test.globs
      File "<doctest __main__.example_135[8]>", line 1, in <module>
        for v in peo:###line 8759:
    sage: for v in peo:
    NameError: name 'peo' is not defined
**********************************************************************

[Nathann Cohen]

Hello ! I added a short definition of what a hole is (a cycle of length at least 4), and replaced peo_copy by peo (sorry for that O_o).

What about my Such an ordering is called a Perfect Elimination Order ? Would you like something more formal instead ?

Nathann

[Robert Miller]

Replying to ncohen:

What about my Such an ordering is called a Perfect Elimination Order ? Would you like something more formal instead ?

I'm not sure whether this is enough. Imagine a user who knows what the definition of chordal is, but not much else. You still want the documentation for this function to make sense to that user. Granted, it is not Sage's job to educate people about all of mathematics, but it certainly should be able to make clear what the input and output of each function is. Perhaps in this case it could do a better job of informing the user of what it is returning.

As long as you say what an elimination order is, then I think that's enough, but right now it is an undefined term.

[Nathann Cohen]

What about this one, then ?

It was a good idea to explain it... I quite liked writing it :-)

Nathann

[Robert Miller]

Much better! :)