[Bioperl-l] Towards a 0.7 release

Jason Stajich jason@chg.mc.duke.edu
Fri, 10 Nov 2000 13:13:25 -0500 (EST)

Brian - 
This is a really necessary direction.  We have a diverse collection of
modules and scripts that are really useful for those who understand them,
but baffling otherwise.  I'd like to see a way for us to automatically
generate the pod-doc on the website from the code.  But then I think a
simple, clean set of documentation on Wiki site would be incredible
useful.  It needs to be a set of explainations that are accessible to
novice programmers and bioinforamtics newbies so that when they are faced
with a problem they can see how bioperl is easy to use.  

I will start some outlines on the bioperl wiki which can serve as your
starting point.  I think some simple scenarios:
- converting sequence formats
- downloading seqs from remote dbs using Bio::DB::GenBank
- parsing blastreports 

would be a good place to start.

Apparently there is something wrong with Wiki right now, so we'll have to
discuss the appropriate venue for this documentation to be entered.


On Fri, 10 Nov 2000, Osborne, Brian wrote:

> 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
> module.
> Thanks again,
> Brian O.
> Brian Osborne, Information Technology
> OSI Pharmaceuticals
> 777 Old Saw Mill River Rd.
> Tarrytown NY 10591
> brian.osborne@osip.com
> 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
> substantially.
> 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
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                                email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
> -----------------------------------------------------------------
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Jason Stajich
(919)684-1806 (office) 
(919)684-2275 (fax) 
Center for Human Genetics - Duke University Medical Center