[Bioperl-l] Test coverage for BioPerl now available

Lincoln Stein lincoln.stein at gmail.com
Thu Oct 2 11:41:00 EDT 2008


Actually I have a family of kvm images with a host of gbrowse databases (of
various types, including Bio::DB::GFF and Bio::SeqFeature::Store) running in
it. I would be very happy to contribute this to the cause.

Lincoln

On Wed, Oct 1, 2008 at 9:36 AM, Chris Fields <cjfields at illinois.edu> wrote:

> Speaking of databases and testing, one thing I would add to the list is a
> test aggregation server of some sort (maybe using Smolder).  If a VM is set
> up for BioSQL/Gbrowse-related tests it might be worth adding this in when we
> have the tuits.
>
> chris
>
>
> On Oct 1, 2008, at 3:07 AM, Jason Stajich wrote:
>
> 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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>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Marie-Claude Hofmann
> College of Veterinary Medicine
> University of Illinois Urbana-Champaign
>
>
>
>
>
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-- 
Lincoln D. Stein

Ontario Institute for Cancer Research
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