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Heikki Lehvaslaiho | 1 Oct 09:31
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Re: Test coverage for BioPerl now available

Cool!

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?

  -Heikki

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?
>
(Continue reading)

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Jason Stajich | 1 Oct 10:07
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Re: Test coverage for BioPerl now available

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/
>
(Continue reading)

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Sendu Bala | 1 Oct 10:43
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Re: Test coverage for BioPerl now available

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/

Brilliant, thanks for doing this Mauricio.

> - 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?

Could you, in any case, put Nathan's version in the private module area 
of the user running Build.PL, just so we have it in the meantime?
Permalink | Reply | 3 comments |
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Dave Messina | 1 Oct 11:09
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Re: Test coverage for BioPerl now available

Great, Mauricio! This should be a big help in encouraging everyone to
contribute tests.

Thanks for taking the time to do this.

Dave
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Spiros Denaxas | 1 Oct 11:13
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Re: Test coverage for BioPerl now available

Awesome work Mauricio, thanks for taking the time to do this. im sure
it will greatly benefit us.

Spiros

On Tue, Sep 30, 2008 at 10:56 PM, Mauricio Herrera Cuadra
<mauricio <at> open-bio.org> 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?
(Continue reading)

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Chris Fields | 1 Oct 14:54
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Re: Test coverage for BioPerl now available

On Sep 30, 2008, at 4:56 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?

Beyond bioperl-db (which Jason mentioned a solution for) and bioperl-
(Continue reading)

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Chris Fields | 1 Oct 15:36
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Re: Test coverage for BioPerl now available

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.
_______________________________________________
Bioperl-l mailing list
Bioperl-l <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason <at> bioperl.org



_______________________________________________
Bioperl-l mailing list
Bioperl-l <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign




_______________________________________________
Bioperl-l mailing list
Bioperl-l <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
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George Hartzell | 1 Oct 18:33
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Re: Test coverage for BioPerl now available


Awesome!  Thanks for pushing this forward.

g.
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George Hartzell | 2 Oct 02:32
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dpalign, local for one sequence, global for the other?


I need to produce an alignment between a hunk of genomic sequence (in
the sense that it hasn't had introns edited out or anything) that's on
the order of a 1000 bases to a genome/chromosome/fragment of similar
genomic sequence.  In an ideal situation they'll be the same,
differences will come from variations in the sources (e.g. the hunk
might have been clipped out of genome revision X and the current
genome might be X+i, or the hunk might have come from a paper (who
knows where it came from...).  Nothing across species or across
evolutionary time or anything fun.  I'm happy to narrow the region of
the genome hunk down using some/an/... heuristic first to avoid
running dp against an entire chromosome.

I need the alignment to account for all of the bases in the hunk.  In
dynamic programming terms, if the hunk is along the vertical axis, the
path through the matrix would have to run from the top to the bottom
(or vice versa).  The projection of the path onto the
horizontal/genomic axis can start/end wherever.

I'd like to not write this [again] and was hoping to use the bio-ext
dpalign stuff.  I'm hopeful that "ENDSFREE" is just what I need, but
from the docs I'm not convinced that it is.  A more pessimistic
reading makes it sounds a lot like a local alignment.

Can anyone out there who's familiar with the dpalign code tell me
whether it can do what I need?  Out of the box?  With modifications?

g.
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Nathan S. Watson-Haigh | 2 Oct 07:07
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Re: Test coverage for BioPerl now available

Hi Sendu,

The JS modifications made it into Devel::Cover 0.62, so no need for my
modified Devel::Cover code now:
http://search.cpan.org/src/PJCJ/Devel-Cover-0.62/CHANGES

The latest version is now 0.64.

Nath

-----Original Message-----
From: Sendu Bala [mailto:bix <at> sendu.me.uk] 
Sent: Wednesday, 1 October 2008 6:43 PM
To: Mauricio Herrera Cuadra
Cc: bioperl-l; Nathan Haigh
Subject: Re: Test coverage for BioPerl now available

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/

Brilliant, thanks for doing this Mauricio.

> - 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?

Could you, in any case, put Nathan's version in the private module area 
of the user running Build.PL, just so we have it in the meantime?
Permalink | Reply | 2 comments |

Gmane