[Bioperl-l] Re: Towards a 0.7 release

Ewan Birney birney@ebi.ac.uk
Fri, 10 Nov 2000 09:51:59 +0000 (GMT)

On Fri, 10 Nov 2000, Hilmar Lapp wrote:

Thanks Hilmar for the post - for people not in the know, I have been
hassling Hilmar to lead us towards 0.7 branching for a while - Hilmar has
finally given in ;)

Considering hilmar's valiant effort for the 0.6.2 release I feel he is
ideal to lead us to the 0.7 series...

> Since the 0.6.x series of BioPerl releases was branched off the main trunk
> people have contributed a considerable number of new modules that implement
> new functionality, and some of the existing modules were enhanced
> substantially.

BPLite (Ian korf) and the new AlignIO stuff from Peter and Hilmar's Gene
Structure code are 3 of the goodies waiting for us in 0.7. Much fun it
will be as well...

> It is high time to incorporate all this code into a release that people who
> have to rely on a stable version can use and play with. I guess that we can
> agree that the next BioPerl release shall be the first of a 0.7 series, and
> shall be branched off the main trunk. I didn't refuse to coordinate this
> release, so I'll try to get it on track, provided I get the help I need.

I am ready to help over here, and will be encouraging the Ensembl
group/Hinxton crowd to get stuck in.

> In order to keep the whole process on track with reasonable efforts, I like
> to propose the following: we define the goals we think this release should
> meet, and once these are defined, we stick to them and postpone anything
> else (new modules, additional restructuring, etc) to the next release
> series. This means that everyone who has a concern about the next release
> should speak up *now*. I give a starter below, and I hope that people add
> whatever you consider important, and please comment on the points left open
> for discussion.

I agree completely with Hilmar. I think it is important to be strict about
this. One of my failures on the 0.6 series of releases was accepting too 
many late additions to the codebase.

One thing to help us here is to have a concerted effort to improve the
test suite of bioperl. This gives us better automatic backward
compatibility/stability ...

> Issues/Objectives of the next BioPerl 0.7 release:

> 1) Timeline: While in principle the final timeline could be extended as far
> as January, given the new functionality covering technology frequently used
> by people I think a sooner release is preferable. So, if it should get out
> of the door by this year, Dec 11th is a reasonable timeline, because
> anything later is not much different from next year. This would imply a
> code freeze for the nascent branch on Dec 4th in terms of new code, meaning
> that once we start to branch the only changes will be bug-fixes. This would
> give us 4 weeks to implement everything we think is missing, see below.

Ok. I'm happy with this.

> 2) Bugs: Ideally, 0.7 starts bug-free. In reality, probably most of us feel
> unable to provide maintenance for the Blast.pm module, so a lot of those
> may remain unfixed. As was mentioned earlier, documentation bugs are
> serious and shall all be fixed.

I think we need someone committed to lead the documentation effort. 
**PLEASE** this is where many people who have used bioperl can contribute.
This will really impress me if someone volunteers to really lead the
documentation effort as we head up towards the 0.7 branch

  Don't ask what bioperl can do for you - ask what you can do for Bioperl!

> 3) Cross-compatibility:
> Ewan brought to my attention that the divisions of the bio* projects should
> interoperate smoothly through the BioCORBA layer, and that this needs to be
> ensured. Given the 0.2.0 BioCORBA proposal, the question now also is
> whether the 0.7 release shall be compliant with the latest BioCORBA
> version, and whether it is sensible to believe that this can be
> accomplished in due time.

It is more than just the Biocorba stuff. We have 3 major packages
coordinating with Bioperl

     - Biocorba (biocorba client/server)
     - Bioperl-gui 
     - Ensembl

My feeling is that these packages need to at least give a "no show
stopper" ok before we branch to 0.7. I am happy to do this for Ensembl.
I hope Jason can step up for biocorba and David/Mark for bioperl-gui

Biocorba has bigger implications however than the other 2 as for biocorba
it really has to have a small mismatch with bioperl, meaning generally
we have to make sure that bioperl adapts to be able to handle biocorba.

The big thing here is sequence feature/ sequence feature locations along
with the dreaded (and annoying) fuzziness.. 

> 4) Architecture
> What is the trend we wish codecore to go? Usage of Bio::Root::* modules,
> suggested StreamIO and NetIO classes. 

We need to debate these. I want to see Bio::Root::Object die (sorry
steve!) but I doubt we can do that officially in this release. This is
open to debate of course.

> 5) Functionality
> Some modules are pending, which needs to be fixd (e.g. SeqFeatureProducer).
> Some modules we agreed to modify in order to inherit off a particular base
> class (e.g., HHMER parser).

Indeed. I think we have

   BPLite upgrade to match Ian's latest release
   HMMER to come into the new Analysis framework

?? other stuff?

> Points 4 and 5 are certainly poorly stated, but it is very late for me, and
> I tried to finish before sleep takes full control of me.
> Please comment, and let us get it off the ground.
> 	Hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                                email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
> -----------------------------------------------------------------

Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420