[BioPython] Migrating from Numerical Python to numpy

[Peter]

On Sat, Sep 20, 2008 at 4:02 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Dear all,
>
> As you probably are well aware, Biopython releases to date have used
> the now obsolete Numeric python library.  This is no longer being
> maintained and has been superseded by the numpy library.  See
> http://www.scipy.org/History_of_SciPy for more about details on the
> history of numerical python.  Biopython 1.48 should be the last
> Numeric only release of Biopython - we have already started moving to
> numpy in CVS.
>
> Supporting both Numeric and numpy ought to be fairly straightforward
> for the pure python modules in Biopython. However, we also have C code
> which must interact with Numeric/numpy, and trying to support both
> would be harder.
>
> Would anyone be inconvenienced if the next release of Biopython
> supported numpy ONLY (dropping support for Numeric)?  If so please
> speak up now - either here or on the development mailing list.
> Otherwise, a simple switch from Numeric to numpy will probably be the
> most straightforward migration plan.

No one has objected, and a simple switch from Numeric to numpy is
underway in CVS.  The next release of Biopython will suport numpy only
(dropping support for Numeric).

As an aside, from my own testing Biopython CVS looks happy with numpy
1.0, 1.1 and the just released 1.2 (although if we have missed any
deprecation warnings please let us know).

For preparing Windows installers for Biopython, it might be helpful to
know what version of numpy most Windows users (will) have installed
(this is important due to numpy C API changes between versions).

Thanks,

Peter