[BioPython] Migrating from Numerical Python to numpy

[Michiel de Hoon]

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maintained and has been superseded by the numpy library.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.

Thank you,

--Mihiel.