[Bioperl-l] Test overhaul complete

Sendu Bala bix at sendu.me.uk
Wed Jun 27 06:23:58 EDT 2007

Sendu Bala wrote:
> Sendu Bala wrote:
>> In considering updating all the test scripts to [... use] 
>> t/lib/BioperlTest.pm
> I'm now in the process of converting all test scripts.

And I've now completed that job (for bioperl-live at least), except for 
t/EUtilities.t since I know Chris is working on it.

In addition to converting to Test::More where necessary, I've also made 
all psuedo-TODO blocks real ones. Previously I had advised to use SKIP 
blocks instead since TODO blocks need a Test::Harness upgrade. However I 
think in the next release we ought to make such upgrading compulsory 
(which should be automatic when combined with compulsory usage of 
Module::Build and Test::More in turn: users simply have to update CPAN).

The conversion to BioperlTest directly led to the discovery and fixing 
of 6 minor bugs, so was certainly not without merit.

No user or developer needs to have BIOPERLDEBUG permanently set to true 
anymore. To run all tests you just have to answer yes to the BioDBGFF 
and networking questions of 'perl Build.PL'. With './Build test' you 
then get clean, easy-to-read output where it is obvious to see that we 
currently have these issues:

t/Sopma.t and t/BioGraphics.t still have fails that I mentioned in 
another thread.

t/protgraph.t, t/blast_pull.t, t/SearchIO.t, t/RestrictionIO.t, 
t/RNA_SearchIO.t, t/PopGen.t, t/Genewise.t, t/Assembly.t and 
t/Annotation.t all have TODO tests. If you know about those modules, now 
would be a great time to implement those TODOs!

Bio::SeqIO::entrezgene is still generating 'Pseudo-hashes are 
deprecated' warnings.

To debug a particular test you could say:
BIOPERLDEBUG=1 ./Build test --verbose --test_files t/Sopma.t

I've updated the HOWTO for writing test scripts:

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