[Bioperl-l] Test overhaul complete

Nathan S. Haigh n.haigh at sheffield.ac.uk
Wed Jun 27 14:44:16 EDT 2007

Sendu Bala wrote:
> 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.

Ah, that reminds me!

I recently tried to do an install of the cvs head (a week or two ago) on
a clean installation of Debian 4.0 (etch). During the installation, of
dependencies, Bio::ASN1::EntrezGene threw an error as it depends on
Bioperl. I seem to remember this circular dependency cropping up before
- am I correct - and can you remind me how this was "fixed"?


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