[Bioperl-l] Devel::Cover

Chris Fields cjfields at uiuc.edu
Thu Mar 8 09:50:45 EST 2007

On Mar 8, 2007, at 8:27 AM, Nathan Haigh wrote:
> Sendu Bala wrote:
>> ...
>> PS. Did you run this with BIOPERLDEBUG=1 ? I have t/RemoteBlast.t
>> hanging on me atm.
> Yep - ideally, those two columns should all be at 100%. Yes I ran it
> I didn't watch the output for any anomalies, although I did get a  
> couple
> of fails:
> Failed Test        Stat Wstat Total Fail  Failed  List of Failed
> ---------------------------------------------------------------------- 
> ---------
> t/HtSNP.t             2   512     7   14 200.00%  1-7
> t/alignUtilities.t  255 65280    35   42 120.00%  15-35

The alignUtilities.t flop is my fault; forgot to remove those when I  
changed bracket_strings to a SimpleAlign class method.  I committed a  
change to CVS and they should pass now.  I'll add those tests back to  
SimpleAlign when I can.  As for other work, I still have more work to  
do on the RNA_SearchIO tests since they're throwing warnings due to  
seqfeatures w/o sequences, but they should all pass.

The SNP tests pass on my end, but I really need to run a clean  
checkout and rerun tests.

> I've just added some JavaScript to allow the table to be sorted by any
> column - a bit easier to find those low % modules now 8-)  - I'm
> notifying the authors of Devel::Cover as it's nice feature if they
> include it in their code.
> I'll have a look at addressing some of the pod issues as and when I  
> get
> a bit of time.
> Nath

I like that!  You should talk to Jason, Mauricio, or Chris D. about  
adding this to the bioperl website with live updates (like PDOC or  
Deobfuscator).  It would be a valuable resource and give us close to  
real-time progress on what modules need work, etc.


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