[Bioperl-l] GSoC/BioPerl Reorganization Project

[Dave Messina]

First of all, welcome Sheena! Awesome that you'll be working on this.

2) The Bio::Root modules are probably the true core modules and are the most
> stable with regards to changes, so those could be moved to something like
> BioPerl-Core.  Beyond that, what are the proposed splits?  (we've discussed
> this on-list before, but it's appropriate to bring this up again)
>

I believe the last version of the proposed splits is here:
http://www.bioperl.org/wiki/Proposed_BioPerl_changes

Looking at it now, it seems like the "pieces" are a little too big. For
example, I think maybe Bio::Tools::* should be separate from core.



> 3) How do we want to handle versioning?  We can't (and probably shouldn't)
> release everything on a synchronized versioning scheme (via
> Bio::Root::Version, for instance), that'll quickly fall apart.  Personally I
> can foresee each split-off dist having it's own version, with the BioPerl
> network of modules being in effect it's own mini-CPAN.
>

I think each sub-dist should have its own version.



> 5) Related to versioning, in my opinion we should maybe aim on eventually
> calling this BioPerl v2.0 and starting with a simpler X.Y versioning scheme.
>  Lincoln has already done something like this with Bio::Graphics, which was
> originally part of BioPerl but split off prior to v 1.6.0.
>

Yep.




> 6) In some cases I can see particularly thorny problems, such as circular
> dependencies.  I can think of a few ways to address that (creating a simple
> lightweight Bio::Species class as a fallback if Bio::Tree code isn't
> present, for instance), but any additional thoughts on this would be
> helpful.
>

One way to look into this would be to use Class::Inspector to check
dependencies. Or see Rob's find_mod_deps.pl in /maintenance. But more to the
point, yes, once the circularities are identified, there should be graceful,
well-defined behavior that breaks the circularity requirement.



> 7) Do we want to set up something like 'git submodule' for the devs to pull
> down all BioPerl-relevant code?


I don't know enough about the implications of this to comment.




>  On Apr 27, 2011, at 12:17 AM, Sheena Scroggins wrote:
> > I look forward to collaborating with many of you on the reorganization
> (hint
> > hint)!
>
> Yes! Definitely don't hesitate to call for help on the list. Once you get
going and have some specific tasks laid out, that'll make it easier for
people to jump in on them.



Dave