[Bioperl-l] Test coverage for BioPerl now available

[Jason Stajich]

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