[SciPy-dev] Cython, f2py and GSoC

David Huard david.huard@gmail....
Thu Mar 26 09:01:44 CDT 2009


On Wed, Mar 25, 2009 at 6:23 PM, Dag Sverre Seljebotn <
dagss@student.matnat.uio.no> wrote:

> This is in preparation for a GSoC project application; Kurt Smith has
> approached me about doing a project on Fortran integration in Cython
> with myself as mentor.
>
> Although we started out with a Fortran/Cython perspective, we think
> that this potentially affects the SciPy community and f2py as well.
>
> The main issues:
>  1) f2py doesn't work that well for Cython, as it requires Python
> packing/unpacking of arguments. A more direct call approach is needed.
>  2) f2py and Cython has a certain overlap in their implementation (both
> generate Python extension modules), and need to tackle many of the same
> issues both now and especially in the future
>
> Could we solve this so that in getting Fortran/Cython integration, we
> also set up a development path for further development of f2py with
> Cython as a backend?
>
> Below is a scetch of our current plan to give you an idea. More full
> specifications etc. will come later and we can have any discussions then.
>
>  1) Add a Cython syntax and API for passing acquired PEP-3118
> buffers/NumPy arrays to external C functions (i.e. as a struct with the
> necesarry information (pointer, shape, strides)). This simply means
> defining a syntax for passing information that Cython already has to an
> external C function.
>
>  2) Create a new tool which uses the parser part of f2py (with any
> necesarry improvements) but adds a different backend which generates a C
> interface to the given Fortran module, along with a Cython pxd file for
> it. (Adding a C .h file target, to get "f2c" functionality, would be
> trivial.)
>
> This will be done using the Fortran 2003 C bindings. So a .f90 file is
> generated which compiles to a C interface to the library. Array
> parameters will be passed as the PEP-3118-like structs we define in 1),
> and so the functions will be callable directly with e.g. NumPy arrays
> from Cython. Copy-in/out might be necesarry for Fortran to be able to
> work with the arrays, if so this will happen in the Fortran wrapper
> generated by this new tool.
>

Do you plan to write a modified copy of the entire subroutine or just a
wrapper subroutine accepting C types, which then calls the original function
?


>
>  3) One could then add a feature to Cython to automatically export
> external functions as Python functions so that one doesn't have to write
> wrapper stubs. This should bring the functionality to a level comparable
> to current f2py.
>

This would be really nice.

>
> Now, how does the SciPy community see this project?
>
>  1) Is there a potential for a joint Cython/SciPy project on
> Fortran/Python integration here? I could do the main mentoring work, but
> support of the idea etc. is important too.
>

I think this is a great project. I really wish I could interface fortran and
python more closely. Many new features of f90 are not supported by f2py, so
I am ending up writing python code that I already wrote in f90.


>
>  2) Any co-mentors perhaps on the f2py parser side? Improvements might
> be needed there.
>
>  3) Would you prefer us to a) rip/fork the parser out of f2py and stay
> within the Cython project, or b) work on f2py upstream to add another
> backend? Or something else?
>

> --
> Dag Sverre
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> Scipy-dev@scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
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