[BioPython] numpy migration for Bio.PDB.Vector

[Peter]

On Mon, Sep 22, 2008 at 3:56 PM, Christian Meesters
<meesters at uni-mainz.de> wrote:
>
>>
>> It seems Thomas has been a little too busy lately to spend much time
>> on Biopython.  Could you file an enhancement bug on bugzilla for this,
>> and then upload your code as an attachment?
>
> Done. Only that I didn't find how to attach files. So I simply pasted
> the code Feel free to use or drop anything.
>
> Christian

Thanks for that.  I did wonder if I should be more explicit - its a
two step process, file the bug, then add the attachment.  Odd, I
agree.

As to the code, I've only skimmed over it.  One thing that caught my
eye is you are using scipy, which we currently do not want to
introduce as a Biopython dependency.

Also, by the nature of your code (using the new numpy API, not
numpy.oldnumeric), making this kind of change will have to wait until
we have agreed to completely drop support for Numeric.  There is a
thread proposing a simple transition from Numeric only (Biopython 1.48
or older) to numpy only (Biopython 1.49 onwards), but a transition
period supporting both could be possible (but would probably be more
work!).  If you have any views on this migration, please voice them
(ideally on that thread).

Thanks,

Peter