[Bioperl-l] Splits again

Sendu Bala bix at sendu.me.uk
Thu Jun 28 15:19:35 EDT 2007


Chris Fields wrote:
> On Jun 28, 2007, at 11:03 AM, Sendu Bala wrote:
> Here's a question: how do we plan on handling uploading bioperl  
> updates to CPAN via PAUSE?  Do we want to run every single module  
> through one pumpkin?  Or do we want to have a core dev group PAUSE  
> account?  I can see, for instance, removing everything EUtilities- 
> related and submitting it independently using my own PAUSE account,  
> but it would be nice to have it under an umbrella 'bioperl-devs'  
> account instead.

All Bioperl modules (except the Bundle!) are owned by BIOPERLML on 
PAUSE. Its a little akward since PAUSE is uploader-centric, but see my 
notes at http://www.bioperl.org/wiki/Making_a_BioPerl_release

And certainly, everything that wants to consider itself part of Bioperl 
(and gain the benefit of lots of devs looking after it) should certainly 
  have BIOPERLML as the primary owner.


> I think so, but the feasibility issue is critical.  Do we want cvs/ 
> svn to be divided up into 900 subdirectories (one for each module),  
> or do we want to have a similar directory structure as we have now,  
> but with each module in it's own directory?  Or leave everything as  
> is and generate Build.PL on-the-fly (prob. least feasible)?

Very definitely the latter. The key benefit of my approach is that the 
organisation stays as is and that a snapshot of the repository remains a 
single directory of modules in Bio so that 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.

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.


My proposal obviously wasn't very clear. As far as all other devs are 
concerned, nothing changes at all (except for lots of new improved test 
scripts). The pumpkin will, however, be able to say:

./Build dist

Right now that generates the distribution archives (in different 
compression formats) - one big archive containing everything.
My proposal is simply that instead it generates lots of archives, one 
archive per module. It will also generate some Bundles and whatever else 
might be needed.

I don't envisage any major difficulties in achieving this. The 
'feasibility' issue I was going to look into was strictly regarding 
doing all the new test scripts.


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