[Bioperl-l] Splits again

Chris Fields cjfields at uiuc.edu
Thu Jun 28 16:29:09 EDT 2007

On Jun 28, 2007, at 2:19 PM, Sendu Bala wrote:

> 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.

Alrighty then.

>> 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.

Okay, makes sense.

> 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.

I agree, but that's up to Brian, Hilmar, and the others who donated  
the packages (or at least a consensus of core devs).  One thing at a  

> 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.

We'll need to define which tests and data goes with each module and  
so on.

> 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.

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.


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