[Biopython-dev] Numpy conversion

Peter biopython at maubp.freeserve.co.uk
Wed Oct 1 08:36:38 UTC 2008

On Wed, Oct 1, 2008 at 1:24 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Bio.kNN is the only module that imports Bio.distance. Bio.distance is
> written in Python, but it also imports a C version of Bio.distance if it
> is available. From the comments in the code, I gather that the
> purpose of the C-version is to get fast distance calculations without
> using Numeric / NumPy. However, Bio.kNN itself uses Numeric /
> NumPy, which defeats the purpose of the C-version of Bio.distance.
> I would therefore like to propose to add a NumPy-aware version of
> the code in Bio.distance to Bio.kNN, and to deprecate Bio.distance.
> Any objections?

If Bio.kNN is the only usage of Bio.distance, then that sounds very
sensible.  However, there is a small chance that someone out there is
using Bio.distance (perhaps because it doesn't use Numeric/NumPy).  As
a courtesy, we could ask on the main mailing list if anyone is using
it before its deprecation, but otherwise I have no objections.


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