[Bioperl-l] bioperl reorganization

Scott Cain cain.cshl at gmail.com
Sat Jul 18 08:23:50 EDT 2009 

Hi All,

I don't want to wade in too deeply, but I like the idea of splitting  
things up.  I think the Bio::Graphics split has gone well and has made  
life easier in GBrowse world.  I could see Bio::DB::SeqFeature and  
Bio::DB::GFF being split and either being kept together or going there  
separate ways (though I have a nagging suspicion that SeqFeature code  
depends on GFF code in a few places, so it may make sense to just keep  
them together.

And Chris, if it makes you feel any better, I don't think anything  
you've done or not done has held up GBrowse2.

Scott


On Jul 17, 2009, at 11:14 PM, Chris Fields wrote:

> My 2c...
>
> On Jul 17, 2009, at 12:01 PM, Jason Stajich wrote:
>
>> Will try to weigh in more, a little bit of stream of consciousness  
>> to let you know I'm thinking about it.  Tough summer to focus much  
>> on this.
>
> Yes, for me as well.  That will change soon (approx two weeks) ;>
>
>> It's too bad we are apparently the laughing stock of Perl gurus,  
>> but it would be great to see how to modernize aspects of the  
>> development.
>>
>> I'm curious how it will work that we'll have dozens of separate  
>> distros that we'll have a hard time keeping track of what directory  
>> things are in? Will there have to be a master list of what version  
>> and what modules are in what distro now?
>
> I don't think we're a laughingstock as much as we haven't had the  
> time to dedicate towards this (and much of this occurred at a point  
> early on, with that whole 'Cathedral and Bazaar' esr-based thingy).   
> BTW,, those same gurus shouldn't speak: perl core is just as bad and  
> riddled with worse bugs, though rgs and co. wouldn't admit it.
>
> In fact, base.pm itself has a nasty one; I'm surprised no one in the  
> bioperl community has noticed it yet (it's listed as a bug on RT I  
> think):
>
> pyrimidine1:biomoose cjfields$ perl -MBio::SeqIO -e 'print  
> $Bio::SeqIO::VERSION."\n"'
> 1.0069
> pyrimidine1:biomoose cjfields$ perl -MBio::SeqIO -e 'print  
> $Bio::Root::IO::VERSION."\n"'
> -1, set by base.pm
>
> Imported modules do not have VERSION set correctly when it is  
> exported.  This hasn't become an issue in bioperl yet (it's really  
> an edge case), but several devs have run into this. And really, why  
> set VERSION to a string like '-1, set by base.pm'?
>
> Anyway, re: versioning, the way I think about it, if we have a small  
> very stable core with version X, and a focused very stable module  
> group with version Y, other distributions would have a separate  
> version and require subgroup version Y (which would in turn require  
> core version X).  CPAN would take care of it.  This isn't much  
> different than what occurs everyday on CPAN anyway (Jay's Catalyst,  
> Moose and MooseX, and so on).  In fact, several Moose-requiring  
> distributions don't require the latest Moose.
>
>> When I do a SVN (or git) checkout do I need to checkout each of  
>> these in its own directory?  Or will there be a master packaging  
>> script that makes the necessary zip files for CPAN submission?
>
> Not sure; that would be up to us I suppose.  I think it would be  
> easier to maintain and release if they were separate or packaged up  
> as Jay suggests.
>
>> If they are in separate directories are we organizing by conceptual  
>> topic (phylogenetics, alignment, database search) or by namespace  
>> of the modules?
>
> By topic, retaining namespaces.  We have a basic Bio::* directory  
> structure already in place for various generic terms (Tools, DB,  
> etc), so I see this crossing simple namespaces very easily.  And as  
> I pointed out to Robert, several of those could possibly go together.
>
>> Do all the 'database' modules live together - probably not  - so do  
>> we name bioperl-db-remote bioperl-db-local-index, bioperl-db-local- 
>> sql, etc?  really bioperl-db is somewhat focused on sequences and  
>> features, but what about things that integrate multiple data types  
>> - like biosql?
>
> I don't see bioperl-db (BioSQL) being split up.  I think it's too  
> intrinsically linked and cohesive (it's almost a separate core unto  
> itself), so it would be counterproductive to do so.
>
> Maybe have bioperl-db become bioperl-biosql.  Web-based = bioperl- 
> remotedb.  Local = bioperl-localdb. OBDA = bioperl-obda.
>
>> If they are in separate directories, what about all the test data  
>> that might be shared, is this replicated among all the sub- 
>> directories - how do we do a good job keeping that up to date,  
>> could we have a test-data distro instead with symlinks within SVN?
>
> We have to see how much is actually shared and proceed from there.   
> I would like to eventually resurrect the idea of a separate biodata  
> repo that we could just ftp the data from as needed.  That would cut  
> down on the package size quite a bit, but I'm not sure how feasible  
> that is from the testing point of view (would we have to skip all  
> tests if there were no network access)?
>
>> For some other obvious modules that can be split off and self- 
>> contained, each of these could be a package.  I would estimate more  
>> than 20 packages depending on how Bio::Tools are carved up.
>> - I think Bio::DB::SeqFeature needs to be split off for sure this  
>> is a nice logical peeling off.  Could be another test case since it  
>> is a Gbrowse dependancy
>> -  Bio::DB::GFF as well for the same reasons.
>
> Completely agree (and I think Lincoln would like this as well).
>
>> -  Bio::PopGen - self contained for the most part, but depends on  
>> Bio::Tree and Bio::Align objects
>
> Could list those as a required dependency.
>
>> -  Bio::Variation
>> -  Bio::Map and Bio::MapIO
>> -  Bio::Cluster and Bio::ClusterIO
>> -  Bio::Assembly
>> - Bio::Coordinate
>>
>> My nightmare is that we're going to have to manage a lot of 'use XX  
>> 1.01' enforcing version requiring when dealing with the  
>> dependancies on the interface classes and having to keep these all  
>> up to date?  The version was implicit when they are all part of the  
>> same big distro.
>
> Right.  But it also becomes a maintenance problem when serious bugs  
> in one module impede the needed release of others to CPAN.
>
>> Also the splits need not only include one namespace if need be I  
>> guess but we have generally grouped things by namespace.
>>
>> What do you want to do about the bioperl-run.  Do we make a set of  
>> parallel splits from all of these?  I think at the outset we need  
>> to coordinate the applications supported here in some sort of loose  
>> ontology - the namespaces were not consistently applied so we have  
>> some alignment tools in different directories, etc.  So the  
>> namespace sort of classifies them but it could be better.  One of  
>> the challenges of multiple developers without a totally shared  
>> vision on how it should be done.
>
> We could split bp-run and Tools, pairing the wrappers with the  
> relevant parsers modules.  Not sure if this can be done with  
> SearchIO as well but it could be tested to see how feasible that  
> would be.
>
>> I'm not convinced that the Bio::Graphics splitoff has been painless  
>> so we should take stock of how that is working.
>
> Really?  Lincoln has made several fixes lately on CPAN, so I thought  
> everything was going well.  If anything I would think the lack of  
> additional 1.6.x bioperl releases has probably held Gbrowse 2.0 up  
> more due to Bio::DB::SeqFeature (my fault, but as you know life and  
> job take precedence sometimes).
>
>> It seems like this split off would be a way to better streamline  
>> things in bioperl so that modern versions of bioperl might be able  
>> to better interface with things like Ensembl again too.
>>
>> How much of this effort is worth triaging on the current code  
>> versus the efforts we want to make on a cleaner, simpler bioperl  
>> system that appears to scare so many users (and potential  
>> developers) off.
>
> I say triage away on a branch, but we need to indicate which ones to  
> whittle out first.  The reason I believe we went for a larger split  
> initially (as indicated on the wiki page) was to push something  
> forward and not get too bogged down in the details.  But we may as  
> well go full throttle and do this right away.
>
>> Okay I rambled, hope that was helpful.
>>
>> -jason
>> --
>> Jason Stajich
>> jason at bioperl.org
>
> Very, very helpful.  Now I need a beer.
>
> chris
>
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Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

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