[SciPy-dev] [announce] scikits.sparse v0.1, wrapper for CHOLMOD (and hopefully more)

Robert Cimrman cimrman3@ntc.zcu...
Tue Dec 15 16:23:44 CST 2009

Quoting Nathaniel Smith <njs@pobox.com>:

> As mentioned previously[0], I've written a scipy.sparse-compatible
> wrapper for the CHOLMOD sparse Cholesky routines. I considered making
> it 'scikits.cholmod' (cf. scikits.umfpack), but creating a new scikit
> every time someone needs a sparse linear algebra routine seems like it
> will become very silly very quickly, so instead I hereby declare the
> existence of 'scikits.sparse' as a home for all such routines. (Of
> course, it currently only contains scikits.sparse.cholmod).
> Manual:
>   http://packages.python.org/scikits.sparse/
> Source:
>   hg clone https://scikits-sparse.googlecode.com/hg/ scikits.sparse
> Homepage:
>   http://code.google.com/p/scikits-sparse
> Bug tracker:
>   http://code.google.com/p/scikits-sparse/issues/list
> Mailing list:
>   scikits-sparse-discuss@lists.vorpus.org
>   http://lists.vorpus.org/cgi-bin/mailman/listinfo/scikits-sparse-discuss
> I would have sucked scikits.umfpack in, except that it uses SWIG,
> which I don't understand and am not really inspired to learn, at least
> for a v0.1 release. Also, there appear to still be some sort of
> complicated entanglements with scipy.sparse (e.g. in at least part of
> the test suite). Anyone feeling inspired? It's not a very complicated
> interface; just rewrapping it might be as easy as anything else.

It would be great to have all the suitesparse in one scikit, thanks
for working in that direction.

Concerning the test entanglement - all direct umfpack references
should be removed from scipy, the tests should live in the scikit
IMHO. It's just my lack of time it's not done yet. As for wrappers,
they just translate the numpy array arguments to the C arrays that
umfpack expects - I guess it's the same you do with cython, so it
should be easy to adapt. The umfpack scikit also uses a simple reuse
mechanisms for the partial solution objects (symbolic, numeric, the LU
factors etc.) - it would be great if this could be preserved. I cannot
assist you right now by code as I am out of town this week, but I will
gladly help with the conversion later.

As for the wrapper licence, the umfpack scikit has been BSD, but I
guess GPL is ok too, especially if the underlying library is GPL. Do
you have a strong opinion on this?


> SuiteSparseQR would also be a natural fit, since it uses the (already
> wrapped) CHOLMOD matrix interfaces.
> [0] http://mail.scipy.org/pipermail/scipy-dev/2009-November/013244.html
> Share and enjoy,
> -- Nathaniel

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