[Bioperl-l] Significant blocker for 1.6.1 : Nexml

[Mark A. Jensen]

Chris - 
I would like to vote for option #1, since working on Bio::Nexml with
Chase gave me the opp'y to patch Bio::Phylo some (including fixing
an old "fix" of mine), so (IMO) the CPAN version of Bio::Phylo 
would benefit too. Option #2 is ok, since Bio::Nexml has to be
essentially optional for the user anyway, dependent on whether
the user is willing to install Bio::Phylo, a fairly major commitment
 (nexml.t already skips if Bio::Phylo is unavailable); I think it's 
no problem if we make that dependency more stringent. We could
have nexml.t check the svn revision directly, rather than $VERSION,
as a kludge.
cheers MAJ 
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Tuesday, September 08, 2009 12:23 AM
Subject: [Bioperl-l] Significant blocker for 1.6.1 : Nexml


> All,
> 
> I'm running into a pretty significant blocker for 1.6.1 re: Chase's  
> Nexml code.  In particular, I have tried three versions of Bio::Phylo;  
> the default CPAN installation (1.6), the latest CPAN RC (1.7_RC9, not  
> installed by default), and the latest from Bio::Phylo svn:
> 
> https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/perl
> 
> At this moment only the Bio::Phylo code from svn is working with  
> BioPerl's Nexml modules.  From my local tests Bio::Phylo 1.6 appears  
> to be missing Bio::Phylo::Factory (all Nexml tests fail), whereas  
> 1.7_RC9 has some kind of versioning issue (again, all tests fail).   
> The problem: CPAN will always install 1.6 (the others are RC, so they  
> won't be installed unless the full path is used).  Even so, nothing on  
> CPAN even works; one must use the latest Bio::Phylo SVN code.
> 
> ATM I'm just not seeing how this can be released with 1.6.1 right now,  
> unless one of the following occurs:
> 
> 1) Rutger V. drops a quick non-RC release to CPAN,
> 2) check for the minimal working Bio::Phylo version and safely skip  
> any Nexml-related tests unless proper version is present (not easy  
> with a $VERSION like '1.7_RC9'),
> 3) push Nexml into it's own distribution (something we were planning  
> on anyway with a number of modules)
> 
> As for #3 above, I think it probably belongs in a larger bioperl-phylo  
> as Mark had previously proposed.  I'm open to just about any solution.
> 
> chris
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