[Bioperl-l] Test overhaul complete

Nathan S. Haigh n.haigh at sheffield.ac.uk
Wed Jun 27 17:25:53 EDT 2007


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Sendu Bala wrote:
> 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?


I think the value would be in other external modules being able to use
bioperl modules with more ease (not sure how many modules have, or
currently depend on bioperl) as they would depend on a single module,
rather than the whole package. However, how would the dependencies of
each module be handled? I'm clearly thinking aloud, but....Maybe this
would tease apart "cliques" of modules that are interdependent? and
could in themselves be shipped as bundles e.g. Bio::Graphics and have a
"master" bioperl bundle that installa all the bioperl modules.
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