[SciPy-dev] Inclusion of cython code in scipy

Anne Archibald peridot.faceted@gmail....
Wed Apr 23 19:22:54 CDT 2008


My goodness, I had no intention of touching off such a discussion.

On 23/04/2008, Nathan Bell <wnbell@gmail.com> wrote:

> I don't see how writing Cython is easier than writing C/C++/Fortran.
>  Clearly if you only know Python, then Cython is an easier language to
>  learn.  However, I doubt the Cython abstraction is so complete that
>  one can avoid learning C.

Here's a concrete example.

I recently wrote code to do Lagrange polynomial interpolation using
barycentric interpolation (based on Berrut and Trefethen 2004). It's
relatively simple code, but it accomplishes a delicate numerical task.

I wrote the initial version in python, along with a test suite. It
works fine, and is quite stable numerically. But the whole point of
interpolation is that it be fast to evaluate, so I thought about how
to make it run faster. Since cython was an active topic on the list
these days, I thought I'd give it a try, in spite of never having
looked into it before.

Simply running cython on the file required me to rewrite a couple of
in-place operations, but the nearly unmodified file ran fine with no
speedups. Annotating the evaluation routine and rewriting the loops
took maybe an hour, and got me a fourfold speedup. Annotating the
whole class took another couple of hours (remember I'd never done this
before), and got me a significant speedup in the construction (my
tests report a twenty-fold improvement but I don't much believe that
number).

Writing cython to do this is easier than writing C to do this. You do
not need to know C to do this.

There are a number of shortcomings in cython - dealing with numpy
arrays could be made vastly easier by one minor change (make A[i]
become (<double*>(A.data))[i*A.strides[0]] when A is an ndarray and i
is an integer), and documentation is currently sparse, but having
tried writing C code to interface with python, I'll take this. I'll
even take it over writing raw C. It would also be extremely
straightforward to turn it back into python if cython were suddenly
wiped from the face of the planet.

Whether we want to allow it into scipy is a different question, but I
thought a specific example would help focus the discussion. Thus find
attached polyint.py, cpolyint.pyx, and test_cpolyint.py.

Anne
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