[Bioperl-l] Test overhaul complete
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]
> 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
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
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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