[Biopython-dev] Numeric/numpy

[Michiel de Hoon]

OK, I'll send your message to the biopython mailing list.

--Michiel.


--- On Fri, 9/19/08, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> From: Peter Cock <p.j.a.cock at googlemail.com>
> Subject: Re: [Biopython-dev] Numeric/numpy
> To: mjldehoon at yahoo.com
> Cc: "BioPython-Dev Mailing List" <biopython-dev at lists.open-bio.org>
> Date: Friday, September 19, 2008, 11:42 AM
> Michiel wrote:
> >Peter wrote:
> >> I was assuming dual support for both numpy or
> Numeric for the next
> >> release based on code like this:
> >>
> >> try:
> >>     from Numeric import x, y, z
> >> except ImportError:
> >>     from numpy.oldnumeric import x, y, z
> >
> > This is the easy part. Keep in mind though that the
> "from numpy.oldnumeric import x, y, z" approach is
> only a temporary solution; at some point, the oldnumeric
> wrapper will disappear from numpy.
> 
> Yes, if/when the oldnumeric wrapper goes away we'll
> have more work to
> do.  Something to worry about later.
> 
> >> where I assumed the C code would have been decided
> at
> >> compile time.
> >
> > This is the complicated part; it's not just
> replacing one #include with another. We'd have to use a
> bunch of #ifdefs to separate the old code from the new code.
> >
> > Anyway I was planning to go through the Numerical
> Python - dependent code to see if any other
> > changes are needed. If anybody wants to be able to use
> the old Numerical Python, please let
> > yourself be heard; otherwise I suggest we go directly
> to NumPy.
> >
> > --Michiel
> 
> That suits me - how about we post something like this on
> the main
> discussion list then?:
> 
> 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 maintained and has been superseded by the numpy library.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
> straight forward
> 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.
> 
> Thank you,
> 
> ...