[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

Hilmar Lapp hlapp at gmx.net
Wed Dec 1 01:23:32 EST 2004

Sounds very reasonable Aaron, and thanks for your gentle herding 
efforts. :-)

For the bioperl developers, this will also mean that for the lifetime 
of the 1.5 branch, efforts should be made to merge fixes applied to the 
HEAD to the branch right afterwards.


On Monday, November 29, 2004, at 06:07  AM, Aaron J. Mackey wrote:

> Yep, OK, I hear you.  I really thought all this was going to be 
> contained to Bio::SeqFeature::Annotated, but I see now that with all 
> sorts of implementation happening in the interfaces (ugh!), this can't 
> happen.  Woe is me.
> Here's what I'm willing to do to keep Allen from pulling his hair out: 
> there have been very few changes on the development trunk since RC1 
> that aren't Annotated.pm-related; therefore, (if this makes sense to 
> everyone) I will branch 1.5.0 off of RC1 and merge only those patches 
> that are Annotated.pm-*unrelated* to the 1.5.0 branch.  I will then 
> tag the branch at RC2 (and similarly tag the HEAD, so that any later 
> merging can be done relative to those tags).  Make sense?
> Then, the rest of you (Allen, Hilmar, Steffen, etc) need to figure out 
> the cleanest path for 1.6.0, in which all things may change (with an 
> eye towards at least some backwards compatibility); my vote would be 
> that there remain some separation between "heavy" and "light" feature 
> types.  I don't expect/need my Bio::SeqFeature::Simple to implement 
> AnnotationCollection!
> Thanks again to everyone; let me know if the CVS plan above sounds 
> reasonable ...
> -Aaron
> On Nov 28, 2004, at 10:08 PM, Hilmar Lapp wrote:
>> I'm not saying this change of direction may be a show-stopper for any 
>> dependent package like bioperl-db. All I'm suggesting is let's be 
>> clear that this *is* a change of direction for a core interface, and 
>> let's give it some time to phase it in and to iron out wrinkles, both 
>> on the end of bioperl itself as well as the end of people who write 
>> software against bioperl. Let's give it some time to see how it 
>> works, and how it works under stress, before letting it lose on the 
>> general public who just wanted to get some bugfixes on the 1.4.0 
>> release or some additional parsers.
> --
> Aaron J. Mackey, Ph.D.
> Dept. of Biology, Goddard 212
> University of Pennsylvania       email:  amackey at pcbi.upenn.edu
> 415 S. University Avenue         office: 215-898-1205
> Philadelphia, PA  19104-6017     fax:    215-746-6697
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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