[Bioperl-l] Test overhaul complete

Sendu Bala bix at sendu.me.uk
Wed Jun 27 17:05:50 EDT 2007


Sendu Bala wrote:
> Nathan S. Haigh wrote:
>> It seems (to me at least) that Bioperl modules could/should? be released
>> as individual modules and that "bioperl" would really constitute a
>> "bundle" of all these modules - in terms of CPAN anyway. Am I correct in
>> this thinking? The Bio::ASN1::EntrezGene could simply require a
>> particular module rather than the whole of bioperl - might get out of
>> the circular dependency theoretically!?
> 
> No, it wouldn't.
[snip]
> You only avoid circularity by choosing not to install everything in one 
> go.

Errr... I take that back. Since CPAN bundles install things in a certain 
order, you just have to make sure that everything Bio::ASN1::EntrezGene 
needs is installed first, then Bio::ASN1::EntrezGene, then 
Bio::SeqIO::entrezgene.

But the main problem with this approach is that maintenance, 
global-style code improvements and releases become a nightmare. I could, 
perhaps, imagine a scenario where the repository stayed as-is (one 
monolithic collection), but the dist action of Build.PL could be altered 
to generate a release package per module instead of one big release 
package of all modules, as is currently the case.

Is there much value in doing that? Does anyone want me to look into the 
feasibility of such a thing?


More information about the Bioperl-l mailing list