[Bioperl-l] Significant blocker for 1.6.1 : Nexml

[Chris Fields]

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