[Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6 release agenda

[Hilmar Lapp]

Looks like a great structure!

(Sorry I can't help much at this time, so I'm resigning myself to  
cheering from the sidelines :)

	-hilmar

On Nov 27, 2008, at 12:05 PM, Dave Messina wrote:

> Chris et al,
> A few quick notes on the SeqIO test reorg I just committed:
>
> - each SeqIO driver now has its own .t file.
>
>
>
> - six modules have all tests skipped (except for use_ok) because  
> there isn't
> a sample input file against which to test. Those are:
>
> agave
> alf
> chadoxml
> chaos
> flybase_chadoxml
> strider
>
>
> - where possible, I renamed the sample file in data/ to be  
> test.<format>
> (e.g. test.fasta, test.embl). There were several already named this  
> way, and
> future refactoring will benefit from the consistency.
> - a few of the modules throw off some warnings (which don't cause  
> any test
> failures).
>
> An example is Bio::Location::Fuzzy, called by Bio::SeqIO::genbank,
> complaining about not finding valid fuzzy encodings.
>
> The modules throwing warnings are:
>
> SeqIO::chadoxml
> SeqIO::genbank (really Location::Fuzzy)
> SeqIO::phd
>
>
> I don't think it's serious.
>
>
> - I opted to organize all of the .t in a subdirectory, SeqIO. So it's
>
> t/SeqIO.t
> t/SeqIO/abi.t
> t/SeqIO/ace.t
> ...etc...
>
>
> Chris, I know you've been doing SearchIO_blast.t.
>
> I propose this alternative, hierarchical structure so that the t/  
> directory
> would be more manageable, but I will happily rename the SeqIO test  
> files to
> conform to your standard if you prefer.
>
>
> Dave
> _______________________________________________
> 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 :
===========================================================