[Bioperl-l] RE: Bio::FeatureHolderI interface confusion (Hilmar Lapp)

Hilmar Lapp hlapp at gnf.org
Wed Jun 18 18:39:06 EDT 2003

On Tuesday, June 17, 2003, at 05:49  PM, Nathan ((Nat)) Goodman wrote:

> Hi Hilmar

Hi Nat, good to hear from you.

>> Interfaces in perl to me have nothing to do with compile time
>> whatever, they mostly provide for contracts
> The point that you're missing is that BioPerl classes break contracts
> regularly whenever the developer feels like it.

I'm going to repeat that people who run red lights don't necessarily 
mean you better remove all traffic lights.

I concur with Paul in that some traffic lights may be ill-positioned, 
and some implementations need to be disciplined.

>   Many interface classes are
> far too grand or too idiocyncratic to be usefully implemented by 
> subclasses
> except the first one that the original developer came up with.

No surprise. Once you get out of bed you're going to make mistakes. 
Let's identify and fix those.

>> state how much that's going to destroy backward compatibility
> Again, BioPerl breaks backward compatibility with great regularity.

I wasn't trying to say we cannot break backward compatibility. I was 
saying the possible impact in this regard should be assessed and 
weighed in.

We do go to some lengths to achieve backward compatibility whenever 
reasonably possible. I'd be glad if you could point out a few examples 
of where we appeared to have unnecessarily and regularly broken that.

>   The problem is that it's too easy for code to be added to the core 
> library.
> There should be a CPAN-like repository where new code lives until it 
> proves
> itself to be generally useful, and where old code can migrate when it 
> grows
> obsolete.

Good suggestion. Volunteers welcome :-)


> Best,
> Nat
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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