[Bioperl-l] split of Bio::Root from bioperl-live

[Fields, Christopher J]

I think the idea was sound in theory, but in practice in caused a number of problems with other tool chains that had incorrect dependencies.  

I had been getting fairly regular emails about this, primarily off-list, from developers with distributions not on CPAN or on github (not terribly uncommon in our field unfortunately) who would test against bioperl-live and have things break because they needed a Bio::Root installation, which wasn’t on CPAN (it was on github).  Also, I found a number of disributions, including a few GMOD tools, that had a Bio::Root::Root dependency listed to pull in BioPerl as a whole, but the *actual* direct dependency was a specific module or interface within Bioperl (say, Bio::DB::SeqFeature or Bio::SeqFeatureI).  

When the last release (1.7) was being worked on this became more and more apparent as a problem, because a new release with a separate Bio::Root distribution would break these distributions right off the bat, and to fix each of these would require updating all of them to have the correct dependencies.  It became enough of an impediment to an actual 1.7 release that we made a decision to roll this back:

https://github.com/bioperl/bioperl-live/issues/114

It was announced on the mail list here:

https://groups.google.com/d/msg/bioperl-l/fPYyLgN0w2E/GwItrwreAwAJ

I do think a stripped-down bioperl-live is a really good idea but it may be best pruning the leaves and not the root, as the vast majority of dependencies are for single modules that see infrequent use on the edges.  So beyond splitting out code that can be functionally independent like Bio::FeatureIO etc I could see having the less-used SeqIO modules with dependencies go either to independent modules on CPAN or to a catch-all ‘bioperl-extras’ or somesuch.

chris

On 8/31/17, 7:59 AM, "Bioperl-l on behalf of Carnë Draug" <bioperl-l-bounces+cjfields=illinois.edu at mailman.open-bio.org on behalf of carandraug+dev at gmail.com> wrote:

    Hi
    
    Over the years there's been the occasional split of bioperl modules as
    separate distributions.  On github, there's the remains of a Bio-Root
    which state they are deprecated.
    
    I have been doing some work in Debian package and the bio-root
    distribution would be useful.  There's some non bioperl projects that
    are only dependent on Bio::Root::* modules but because they are part
    of bioperl, that brings in a whole lot of dependencies.
    
    I could prepare a Bio-Root release and sync it with bioperl-live.  But
    I was wondering why the split of bio-root was deprecated in the first
    place.
    
    As a side note, the split of the rest of bioperl would also be useful,
    it's just that it's the split of bio-root that would be most useful
    for the packages I have been preparing now.
    
    Thank you
    Carnë
    
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