[Biopython-dev] Properties in Bio.Application interface?

[Peter]

On Wed, Apr 29, 2009 at 11:25 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> I've filed Bug 2822 for these enhancements to the Bio.Application
> based command line objects,
> http://bugzilla.open-bio.org/show_bug.cgi?id=2822

I think I learnt some more about python in the process, which may be a
sign that the code I've come up with is too complicated, but Bug 2822
now has a patch to support both keyword arguments and properties in
the Bio.Application style command line wrappers.  This will require
minor changes to the __init__ method of any command line sub-class
(demonstrated using Bio.Emboss.Applications only thus far).  I can
envision a simpler approach to this code by defining the properties
explicitly in each subclass, but that would mean a lot of boring/risky
refactoring (or a clever script to do it for us).

There are examples using the new code in the bug comments.  Apart from
preferring this API, the other big difference is the properties
provide built in help.

I'll be away for the next four days so I (probably) won't be able to
reply to any comments or questions till Monday.

Peter