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

[Dave Messina]

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