[Bioperl-l] How to handle bugs in bioperl 1.4 on CPAN?

Phillip San Miguel pmiguel at purdue.edu
Mon Jun 26 12:53:56 EDT 2006


Chris Fields wrote:
> ...
>   
>> However, when view as an issue related to the setting of a
>> policy for the whole project, then it makes sense to have a
>> policy saying for how long a stable release will be
>> supported, and when and in which case bugfixes that are committed
>> to and tested in the development branch (as it should be)
>> will get merged back to stable.
>>     
>
> In a project this large which relies on a lot of outside resources
> maintaining API and availability at all times, having a completely bug-free
> fix for any reasonable length of time is impossible.  As a small example,
> almost every time NCBI changes BLAST output, it breaks our text parsers, and
> though we recommend using the BLAST XML format parser (which is much more
> stable), almost everybody continues using text parsing and wants that fixed.
> Now, NCBI routinely changes their BLAST version about every 3-6 months w/o
> notification, so remote BLAST parsing can break at any time.  Fold into that
> any software changes that change output or API (PAML comes to mind).  Fold
> into that remote database changes (EBI interface to Swissprot).  Oh, let's
> not forget sequence format changes (recent SwissProt and GenBank changes).
> And, worst of all, we can't expect them to maintain API or output b/c
> they're updating based on user input/suggestions or bug fixes which require
> them to make changes.  What's 'stable' about that?
>
> It's very easy to say you want something and then not volunteer to do it; if
> you want something then put forth the time and effort to get it done.  Put
> your money where your mouth is (as they say in my home state).
>
> Again (for the third or fourth time now), putting together a release takes
> some time and effort.  I actually think it takes more effort than Hilmar
> suggests; either way, it requires someone to act as the leader (release
> pumpkin) to handle changes, and I don't see anybody stepping forward.
> Personally, if I have the time, maybe I'll handle an interim release, but
> I'm looking for a job starting in the fall as well as finishing up research
> for publication so that will take up almost all the time I have.  As Hilmar
> says, if you want to do it, fine.  Realize, though, many many changes have
> been made since 1.4 and many more will likely be made on the road to 1.6
>
>   
Hi Chris et al.,

    I was just reporting the situation from where I sit. I think this 
issue was important enough to bring to everyones attention. I've done so 
and I'm more than satisfied with the response. I hope my emails were not 
too abrasive.
    I've have now read the wiki about coordinating a release. You are 
right, that does sound hard. At least to me--I've never even used CVS, 
nor contributed a module to CPAN. I just don't see myself as being 
qualified to coordinate a 1.4.1 release. So since I'm not, for that 
reason, able to volunteer to do it myself, I'll withdraw my request for 
a new release to CPAN.
    That being said, I think Fernan's suggestion bears keeping in mind 
once 1.6 has been released and bug fixes are being committed. By that 
time, I hope I'll be savvy enough to help out in the process.
    Thanks for your attention,

Phillip SanMiguel
   


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