[Bioperl-l] Other object oddities

Hilmar Lapp hlapp at gmx.net
Tue May 5 08:31:41 EDT 2009

On May 4, 2009, at 3:01 PM, Mark A. Jensen wrote:

> Maybe this should be an element of
> the "Align refactor" that perhaps should be an overall
> "Seq refactor".

Possibly. Most importantly, it'd be great if someone would volunteer  
to summarize what's been said here so it won't get lost.

> Are you saying that the trunk is fair game for api additions
> for this issue?

There's been talk some (a long, actually) time ago about BioPerl 2.0  
that would start on a clean slate and not be bothered by backwards  
compatibility demands. That effort never really took off, but maybe  
this is also a good time to ask the question again whether it's better  
to introduce the API changes we desire in add/deprecate/remove cycles,  
or in a more radical fashion starting on a clean slate.

The obvious advantage of the former is that we get API improvements  
sooner, but making them is possibly more dreadful, discouraging, or  
not even doable due to compatibility constraints. The disadvantage of  
the latter is that it really needs a committed crew of people to see  
it through or otherwise all the nice changes die in some grand but  
half-finished 2.0 construction site. I think Chris also had plans to  
branch off a Perl6 version of BioPerl - maybe those could be the same  

I'm not trying to advocate one over the other here; rather, I'd like  
to help push on that front that is best able to capture the energy of  
volunteers, as that's what it takes in the end.


: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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