[Bioperl-l] Significant blocker for 1.6.1 : Nexml

[Chris Fields]

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 :
>>> ===========================================================
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l