Bioperl-dev

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What is it?

bioperl-dev is not a package as such, but a repository for new BioPerl code that is exploratory or experimental.

There is generally enough developer momentum behind the underlying concepts that, once the developer is satisfied with the state of the code, development will move to the Core or other distribution package.

On the other hand, if insurmountable difficulties ensue, or a better solution is found, a bioperl-dev module can die a quiet and dignified death.

Motivation

bioperl-dev exists to provide space for projects with legs whose code (and particularly, whose API) is still unstable. The idea is to buffer the core and the other "production" packages against instability and unfinished and/or unmaintainable code. However, because bioperl-dev code is intentionally made available to larger BioPerl community through the usual outlets, it can benefit from (brave) user testing, bug reports, patches and dev mods in the same way the production packages do.

Lively and interesting discussions on bioperl-l have debated the pros and cons of the existence of bioperl-dev, compared to more determined branching and merging to trunk.

Now Playing on The Dev

(as of 19:16, 12 January 2010 (UTC))

Facility for guessing the source Database of a given acc no. (chmille4)
Support for arbritary genotype data within NeXML I/O (maj)
XML read-write support for Bio::DB::HIV (maj)
Slim SeqFeatures (jason)

bioperl-dev Alumni

Modules Author Destination Port Date DevTag
Bio::Search::Tiling maj Core 01 Jun 2009 tiling-port-to-core-060109
Bio::NexmlIO, Bio::*IO::nexml chmille4 Core 17 Aug 2009 nexml-port-to-core-081609
bioperl-mode maj Core 16 Sep 2009 bioperl-mode-port-to-core-091609
blastplus facilities maj Run 19 Dec 2009 blastplus-port-to-run-121909
entrez websvc facilities maj Run 12 Jan 2010 soapeu-to-run-011210

bioperl-dev README

$Id: README 15617 2009-03-28 05:14:23Z maj $

o Version

 This is bioperl-dev version 1.6.9, a developer release.

o Description 
 
 bioperl-dev contains experimental modules intended to expand the
 Bioperl envelope. New ideas for future point and stable releases
 are being explored here. Interested users are encouraged to 
 give these a try, keeping in mind the following points:

 o the modules here will likely depend on the current HEAD 
   revision of Bioperl (bioperl-live/trunk); a release version 
   may not suffice;

 o documentation is likely to be spotty at best;
 
 o the code should be considered unsupported, though a polite email
   to the dev is likely to elicit a positive response; 

 o the code should not be considered "production quality"; when this
   level is reached, bioperl-dev modules will graduate to the 
   core or the appropriate specialty package.

 See the Changes file for more information about what is contained in
 here.

o Installation

 See the accompanying INSTALL file for details on installing
 bioperl-dev

o Feedback

Write down any problems or praise and send them to 
bioperl-l@bioperl.org  ;-)
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