[Bioperl-l] Devel::Cover

Nathan Haigh n.haigh at sheffield.ac.uk
Thu Mar 8 09:27:49 EST 2007

Sendu Bala wrote:
> Nathan Haigh wrote:
>> Find the Devel::Cover report for bioperl-live here:
>> http://www.bioinf.shef.ac.uk/public/bioperl-live/cover_db/coverage.html
> Thanks for that.
>> First things to note are:
>> 1) There appear to be quite a few modules without POD for all methods
>> (pod column).
>> 2) The test suite doesn't test all subs in the modules (sub column).
>> More rigorous code coverage would be achieved by ensuring tests were
>> designed to execute all statements (stmt column). Details of the other
>> columns can be found in Devel::Cover::Tutorial but essentially inform
>> how well all the different possible routes in condition statements are
>> covered by the tests.
>> Have fun!
> Really interesting, but fun? I'm actually kind of frightened by it ;)
> In some crazy dream I'd like to see the pod and sub columns at 100%
> for all modules in time for Bioperl 1.6. From a brief scan though it
> seems like an incredible amount of work would be needed.
> Doing the POD would be relatively easy. Does anyone feel inspired to
> take on that particular challenge I wonder?
> 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

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.

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