[Bioperl-l] Splits again

David Messina dmessina at wustl.edu
Thu Jun 28 18:13:48 EDT 2007

Coming late to this party, I'm replying to snippets from multiple  

> [Chris]
> what we do about deprecated modules which linger
> about on CPAN

> [Sendu]
> Delete them from CPAN seems appropriate.

I coulda sworn this was frowned upon, but a recent thread suggests  
it's totally kosher.


> [Sendu]
> So, regardless of anything else can we all agree that per-module test
> scripts are a good idea and should be worked on?

I agree.

> [Sendu]
> people don't have to
> 'install' Bioperl, they can still just uncompress the archive (or  
> check
> out the package from svn) and point their PERL5LIB to the root dir of
> the package.

Could you elaborate a bit on how this works? How is XS code that  
needs compiling handled? Or the scripts directory? I would love to be  
able to do this.

> [Sendu]
> For that reason I very much like the idea of folding the current
> split-out packages (run, network etc.) back into the core package so
> everything is one place. Folding them back in should obviously wait
> until everything is in place and working with core already.

 From an organizational standpoint, I'm concerned that with ~900  
modules in core right now, adding all of the additional stuff from  
the split-out packages would make for a daunting directory.

But as you said, this is way down the road, so this proposal doesn't  
bear on the other, closer-to-now issues on the table.

> [Chris]
> Okay.  Maybe it's worth doing on a branch  as a test run when 1.5.3
> is ready to go.  We'll still need to get thoughts on this from other
> core devs out there, and it prob. should until everybody is
> comfortable with the idea.

If we go forward with the CPAN split plan, I like the idea of having  
a trial. We can foresee some of the issues that such a change may  
bring, and yet still more no doubt wait for us once we do it.


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