[Bioperl-l] Test coverage for BioPerl now available

Jason Stajich jason at bioperl.org
Wed Oct 1 04:07:49 EDT 2008


Thanks for doing this Mauricio!  Great to have this resource and to  
follow up on the excellent efforts by Nathan and Sendu to get this  
ball rolling..

We have a couple of Virtual Hosts through Chris Dagdigian and  
BioTeam's donated resources that we can setup postgres and mysql  
instances for biosql and even Bio::DB::GFF & Bio::DB::SeqFeature  
testing. Let's see what Chris's plans are for the current VM instance  
- we have talked about also starting to port some of the websites to  
separate instances of the VM to spread the load a little bit more.

One idea that can follow out of doing this work is some sort of  
testable reference servers for some of the bio{*} tools to access some  
basic datasets and hosting.   Maybe with a simple Swissprot instance  
and a slice of a genbank division so that working gbrowse backend &  
biosql instances can be used for code testing and development purposes.

-jason
On Sep 30, 2008, at 2:56 PM, 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.
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Jason Stajich
jason at bioperl.org





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