[Bioperl-l] Thoughts on some test reorganization

Nathan S. Watson-Haigh nhaigh at sheffield.ac.uk
Sun Nov 16 17:57:19 EST 2008

Hi Chris,

I don't know if using Test::Class might be an option:

Anyway, just threw that out there to see if there were any thoughts on this.


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Monday, 17 November 2008 2:39 AM
To: BioPerl List
Subject: [Bioperl-l] Thoughts on some test reorganization


I'm still working on an overall plan for a 1.6 release and fixing some  
bugs.  In the meantime, for my sanity I'm planning on doing some test  
reorganization in subversion, starting with splitting up SearchIO.t  
(which has become very long and unwieldy) into separate format- 
specific test files.

This may be something to think about for other sets of modules as well  
which are plugin-able or parser-specific (SeqIO, AlignIO, Bio::Tools*,  
etc).  Though it will lead to quite a few more files, I think it will  
be easier in the long term to identify and fix format-specific bugs.   
It also may be helpful in the long term with splitting up bioperl into  
subdistributions, identifying holes in test coverage, deprecating  
unsupported modules, etc.

The details (of course subject to debate!):

1) Tests which are parser-specific will be moved to test files in the  
form SearchIO_*.t, where the '*' represents the specific parser being  
2) Tests for methods implemented in SearchIO.pm (such as  
_guess_format) will remain in SearchIO.t.
3) I'll also move other SearchIO-related tests (hmmer, the pull  
parsers) to their related SearchIO_* counterparts.
4) The utility method in SearchIO.t will probably be moved to  
Bio::Search::SearchUtils and imported in to prevent code dups.

Comments?  Thoughts?

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