[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.
-Jason
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
jason@chg.mc.duke.edu
http://galton.mc.duke.edu/~jason/
(919)684-1806 (office)
(919)684-2275 (fax)
Center for Human Genetics - Duke University Medical Center
http://wwwchg.mc.duke.edu/