[Bioperl-l] Deprecate Pise modules? was: Need some bioperl-run tests

Chris Fields cjfields at illinois.edu
Sun Jan 11 21:13:10 UTC 2009


We'll probably deprecate the Pise modules (according to Catherine's  
response below) unless someone wants to take them over (the service  
has been discontinued).  This will (in effect) remove 285 modules from  

They won't be included in the 1.6 release since the tests won't pass,  
but it's possible the module may come in useful for setting up a  
bioperl API for mobyle.  Should we leave them in the bioperl-run main  
trunk or remove them?


Begin forwarded message:

> On Jan 11, 2009, at 11:57 AM, Catherine Letondal wrote:
>> Hi,
>> Le 10 janv. 09 à 23:01, Chris Fields a écrit :
>>> All,
>>> I have been updating bioperl-run tests in subversion to use  
>>> Bio::Root::Test.  I need devs and anyone interested to check out  
>>> the latest bioperl-run and run tests checking for failures.  I'll  
>>> start tracking errors.
>>> I have also noticed that Pise.t and AnalysisFactory_soap.t tests  
>>> are failing.  I have updated the tests so they run to completion,  
>>> but (if possible) I need some indication whether these web  
>>> services are still available and should be incldued in a BioPerl- 
>>> run 1.6 release.
>> No, they are no longer available - Pise server has been replaced by  
>> mobyle.pasteur.fr, which does not yet offer a bioperl API.  I had  
>> sent a message to the bioperl mailing-list a few monthes ago about  
>> this service being discontinued, but the message had been rejected.  
>> It is possible to change the default Pise server address - provided  
>> someone else is willing to offer these services. If not, you can  
>> either remove the test or better, remove the Pise modules.
>> Best,
>> 	Catherine Letondal
> Thanks for letting us know Catherine.  I'll forward your response to  
> the mail list to get everyone's response.
> I'll remove the Pise modules from the 1.6 branch when it's ready  
> (should be the next day or two).  We'll likely also remove it from  
> main trunk if no one wants to take it over.  The effort into  
> maintaining it would probably be better spent towards developing a  
> mobyle API if anyone's interested.
> chris

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