[Bioperl-l] Thoughts on some test reorganization

Chris Fields cjfields at illinois.edu
Sun Nov 16 21:34:00 EST 2008


I would support adding support for Test::Class, but it isn't part of  
perl 5.6.1 or 5.8.x core.  So, would we need to add it as another  
dependency for testing (which, unless there is a workaround, appears  
to be 'yes')?

Speaking of older perl releases, I would like to get an idea of how  
many users are still using (over 8-yr old) perl 5.6.1.  I would really  
like to require 5.8 or above for bioperl 1.6.   perl 5.6.x stopped  
development many moons ago now, and 5.8.x is about to be 'end-of-lifed':



On Nov 16, 2008, at 4:57 PM, Nathan S. Watson-Haigh wrote:

> Hi Chris,
> I don't know if using Test::Class might be an option:
> http://safari.oreilly.com/0596100922/perltestingadn-CHP-8
> http://perlandmac.blogspot.com/2007/08/using-perl-testclass-to-organized-uni
> t.html
> http://search.cpan.org/dist/Test-Class/
> Anyway, just threw that out there to see if there were any thoughts  
> on this.
> Nath
> -----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
> All,
> 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
> tested.
> 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?
> chris
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