[Bioperl-l] Bio module using Moose

[Chris Fields]

On Jun 17, 2010, at 8:46 AM, Emmanuel Quevillon wrote:

> On 06/17/2010 03:12 PM, Chris Fields wrote:
>> Emmanuel,
>> 
>> I don't think we could do this for direct inclusion within BioPerl core, due to the heavy load of dependencies Moose carries on top of the ones we already have.  But you have two possible options:
>> 
>> 1) I have started a separate project on github that is a full Moose-based BioPerl, which may evolve into a BioPerl 2.0 at some point:
>> 
>> http://github.com/cjfields/biome
>> 
> 
> Hi Chris,
> 
> Yep I've seen it already from one of your email on the Moose list :)
> I can try plug my modules to your project, however my code might be
> not as evolved as yours, so it could need some improvements and
> tuning to run faster and better.
> 
>> This will eventually move into the bioperl github account, and is probably a better fit.  Not sure what version of Perl you are using, though (we just changed the required version to 5.12, but that could be dropped to 5.10).  
>> 
>> 2) Release it on CPAN on it's own, listing BioPerl as a dependency.  That frees you up to do whatever you want with the code. 
>> 
> 
> Well I don't really know. Let me think about it (between github and
> CPAN), I'll also need to read and understand carefully your biome
> project. Moreover, as already said in my previous emails, I am not
> very ease with Moose right now....
> 
> Anyway what I can do it to change my code to better fit with actual
> implementation of BioPerl 1.6 and send it to the team for later
> integration?
> I can also send you my Moosified version to have a look?
> 
> Let me know
> 
> Regards
> 
> Emmanuel

If the code works, wouldn't be much work to get it into Biome.  Essentially you would change 'use Moose' to 'use Biome' and 'use Moose::Role' to 'use Biome::Role'.  Tests and such are pretty straightforward.  If needed you can wrap BioPerl objects.

Let me know.

chris