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

[Chris Fields]

On Nov 27, 2008, at 11:05 AM, 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

Possible candidates to be moved out of core into a dev (unless we come  
up with some tests!).

> - 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.

I agree.

> - 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.

Still warrants some investigation, but I agree.  We can turn off  
warning if needed, but I would rather try to find what is triggering  
them (it's almost always something).

> - 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.

I like!  I'll change AlignIO and SearchIO over to this and work on  
cleaning up test file names.  We'll need to update the wiki accordingly.

> Dave

Thanks Dave!  Feel free to do more restructuring along these lines; we  
have the other IO's (Assembly, Resstriction, Tree, Feature, and a few  
others I think), and I could see collecting various modules into a  
collective structure, such as Ontology, Tools, Graphics, etc.  If you  
do just post a note here or on the wiki (I'll do likewise) so we don't  
work on the same thing.  Anyone else wanting to join in please let us  
know likewise.

chris