[Bioperl-l] Significant blocker for 1.6.1 : Nexml

[Chris Fields]

I don't see an update to Bio::Phylo on CPAN yet, so I'm assuming we  
will leave Nexml off the 1.6.1 alpha for now.  I'll likely be  
releasing it later today or tomorrow to CPAN.

chris

On Sep 8, 2009, at 10:43 AM, Chris Fields wrote:

> Mark
>
> We can hold it in trunk until the next point release or we start  
> splitting things off (whichever is first).
>
> I have a little more time, though, and I'm thinking it would be a  
> good idea to get the Nexml code into the wild (sooner than later)  
> for users to test out.  Let's see if Rutger responds.
>
> chris
>
> On Sep 8, 2009, at 9:39 AM, Mark A. Jensen wrote:
>
>> 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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