[Bioperl-l] Significant blocker for 1.6.1 : Nexml

[Mark A. Jensen]

I agree with Hilmar-- I have no problem keeping it in the trunk for a while
longer, as I have an addition for dealing with arbitrary non-seq
data using the Population API sitting in bioperl-dev that's nearly
ready, but prob. not before cjf wants to get the release out.
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Hilmar Lapp" <hlapp at gmx.net>
Cc: "BioPerl List" <bioperl-l at lists.open-bio.org>; "Rutger A. Vos" 
<rutgeraldo at gmail.com>
Sent: Tuesday, September 08, 2009 9:15 AM
Subject: Re: [Bioperl-l] Significant blocker for 1.6.1 : Nexml


> On Sep 8, 2009, at 7:16 AM, Hilmar Lapp wrote:
>
>> I'd suspect that the latest Bio::Phylo changes have been due for  CPAN 
>> release anyway, so unless those are unstable that seems like  the easiest fix 
>> to me.
>
> My thought as well, just not sure how stable that code is right now. 
> Bio::Phylo has been in RC for a while now, correct?
>
>> If the Nexml code works against not yet stable updates to  Bio::Phylo, it 
>> shouldn't be in a BioPerl stable release, right?
>
> Right.  That should be sorted out first.
>
> I can wait a bit longer for Rutger to respond; there are a few other  odds and 
> ends that can been worked on in the meantime.  I would like  to get the alpha 
> out soon and 1.6.1 in the next week or so though.
>
> chris
>
>> -hilmar
>>
>> On Sep 8, 2009, at 12:23 AM, Chris Fields wrote:
>>
>>> 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
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
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