[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
brian_osborne at cognia.com
Wed Dec 1 07:57:56 EST 2004
t/Biblio.t is one.
It tests Bio/Biblio/IO/medlinexml.pm, which uses XML::Parser, which uses
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Nathan Haigh
Sent: Wednesday, December 01, 2004 7:21 AM
To: 'Hilmar Lapp'
Subject: RE: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
Which BioPerl test(s) should determine if expat is working correctly?
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Hilmar Lapp
> Sent: 01 December 2004 06:24
> To: Aaron J. Mackey
> Cc: Allen Day; Bioperl
> Subject: Re: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
> 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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