[BioPython] NumPy changes ready to check in

[Brad Chapman]

Hi Peter;

> Wow - welcome back!

Thanks. Glad to be able to help; great to see you around.

> Its certainly the C/C++ bits that make life complicated.
> 
> Have you looked at the patch on Bug 2251 at all?
> http://bugzilla.open-bio.org/show_bug.cgi?id=2251

I did; sorry, forgot to mention that in my last e-mail. I wasn't
exactly sure why this wasn't checked in then as the thread dies a
bit. It was a great help for getting started.

I think the idea there is good, but might be a little more
complicated than needed. My thoughts were that we need to manage a
transition to NumPy rather than support both Numeric and NumPy
concurrently. Numeric hasn't been updated since 2005 and the
compatibility modules for transitioning seem solid, so most people
should have moved by now or need some encouragement to do so. We are
probably being more annoying to up to date users by keeping Numeric
support.

The way it is implemented in my recent changes are that Numeric users will
not get broken builds, but will rather not get the C extensions
compiled unless they have NumPy. So the users who absolutely need to
install NumPy are those still using Numeric and using the C/C++
extensions.

> Michiel and I had chatted about doing one more release with Numeric
> only - there are a few things I'd like to try and get in first like
> ambiguous translation (Bug 2530) but perhaps we should just do
> Biopython 1.48 pretty much as is.
> http://bugzilla.open-bio.org/show_bug.cgi?id=2530
> 
> I'm happy to try and put together the release this week - but will
> need a hand for the windows builds.
> 
> If that pans out, then we could start the Numeric to numpy transition in CVS.

That sounds fine to me. Once the new release is out I can check
things in and we can find out if there are any issues.

Brad
-- 
Brad Chapman
Codon Devices 
http://www.codondevices.com