[Bioperl-l] Bioperl partitioning (was Re: SVN and ...Re: Perltidy)

Sendu Bala bix at sendu.me.uk
Tue Jun 19 15:13:39 EDT 2007

Steve Chervitz wrote:
> Valid points, Sendu. I wonder if there might be a best-of-both-worlds
> approach here.

You haven't convinced me, but I'd go along with the majority decision if 
best-of-both-worlds was picked.

> DB, Graphics, Search+SearchIO, Tools.

I will, however, say that DB interleaves into too many core modules. It 
should stay in core. Tools? Its hardly touched anyway, so I don't see 
the value of taking it out, what with Bio::Tools::Run already being its 
own package. Most Bioperl users probably get Bioperl just to do 
something Blast related, so all Blast stuff really ought to stay in core.

Graphics is an obvious choice and I agree. Updated frequently, and has 
its own release needs. It also has some of the trickier dependencies, so 
would make installing core simpler.

I can imagine plucking Search+SearchIO out, and its something that needs 
regular updating. Another good candidate.

> Perhaps it would be worth experimenting with such an approach so we
> can judge it based on actual experience. We could identify one
> functional sub part and segregate it out, do a release cycle or two,
> along with a sub part release, and decide if this makes things easier
> or harder, for devs as well as users.

Well, we already have the run package. Its a split-off subpart that gets 
updated. The only 'experiment' left to do is finding it its own pumpkin.

More information about the Bioperl-l mailing list