[Bioperl-l] Towards a 0.7 release

Osborne, Brian Brian.Osborne@osip.com
Fri, 10 Nov 2000 15:50:31 -0000

To the group,

I would propose 6) Outline needs for documentation, then begin to assign
writers to specific sections or areas. 

I say this because I would be happy to work on documentation, if I only knew
what the intention of the documentation is. For example, I consider good
documentation to be rich in example code, whereas another user might
consider a structured description of the architecture or the formalisms,
POD-like, to be important. Perhaps both are important.

There's been some mention of acquiring/hiring a documentor, because this is
a large task. I cannot handle a large task myself but I could contribute to
the documentation in a specified way, specified both stylistically and by

Thanks again,

Brian O.

Brian Osborne, Information Technology
OSI Pharmaceuticals
777 Old Saw Mill River Rd.
Tarrytown NY 10591
TEL 914 467 6291
FAX 914 345 3565

-----Original Message-----
From: Hilmar Lapp [mailto:hlapp@gmx.net]
Sent: Friday, November 10, 2000 4:34 AM
To: Bioperl
Cc: Ewan Birney
Subject: [Bioperl-l] Towards a 0.7 release

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

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.

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.

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

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 Lapp                                email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
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