[Bioperl-l] Test coverage for BioPerl now available

Nathan S. Watson-Haigh nhaigh at sheffield.ac.uk
Sun Oct 5 22:39:54 EDT 2008

Firstly, thanks Mauricio for getting this set up....it should be really
useful for everyone and make adding tests so much easier by focusing
attention on problem areas! In fact, it could help users make the transition
from using Bioperl to contributing code by giving them an entry point into
understanding the modules. Increasing test coverage in a group of modules
would make a good student project!


You should find this page useful:

I use the following as a list of priorities for code coverage:
1) Get the "subroutine" metric to 100% - every subroutine should have at
least 1 test to check it's returning the correct value/object given at least
one set of arguments.
2) Get the "statement" metric as close to 100% as possible by providing
various inputs so that each statement is tested for BOTH the true and false
3) Work on the "branch" and "path" metrics if after performing the above 2,
these are still in low coverage. You'll find that performing the above
steps, will have a knock-on effect of increasing these coverage's at the
same time.

Testing never proves the absence of faults, it only shows their presence.

I think as a result of better test coverage, there will be a need to
formalise/discuss the intended behaviour of some modules, as well as the
choice over default values. Also, Don't forget to test for situations where
you expect a die/warn using Test::Exception and Test::Warn

I Think there needs to be some consolidation of Testing
practices/information etc on the wiki, especially in light of the test
coverage pages, with the above page linked to. In particular the following
pages have info about testing:


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Heikki
Sent: Wednesday, 1 October 2008 5:31 PM
To: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Test coverage for BioPerl now available


I have trouble understanding the values in different columns. Could you whip

together a wiki page that explains in plain English how to read them?


On Tuesday 30 September 2008 23:56:04 Mauricio Herrera Cuadra wrote:
> Hi all,
> Daily-updated test coverage reports are now available for those BioPerl
> packages which make use of the Build.PL mechanism (except bioperl-db):
> http://bioperl.org/test-coverage/bioperl-live/
> http://bioperl.org/test-coverage/bioperl-network/
> http://bioperl.org/test-coverage/bioperl-run/
> These reports will help us to know the current 'quality' of the code in
> SVN for most of the BioPerl modules. This idea was started by Nathan
> Haigh and Sendu a long time ago and it was my fault to not implement on
> time the necessary script to run the process on a daily basis, so
> apologies for that.
> There are still a few things to be done in order to have this working as
> it should:
> - Nathan, current Devel::Cover module from CPAN doesn't include the JS
> modifications to make table columns sortable. Do you know what happened
> to the code you contributed to the author for that?
> - Reports could be generated for the rest of the BioPerl packages as
> soon as they're migrated to the Build.PL infrastructure. Anyone up for
> that?
> - bioperl-db tests require BioSQL to be setup in the webserver machine,
> and the same goes for bioperl-run's tests with ALL of its dependencies.
> The bioperl.org site is co-hosted with all of the other OBF projects and
> that machine also takes care of other things (mailing lists, etc), so I
> would like your feedback on possible workarounds to not overload the
> server if we want to setup such test reports.
> Thanks & regards,
> Mauricio.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Senior Scientist    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________

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