[BioRuby] biogem and options

[Toshiaki Katayama]

Raoul,

http://twitter.com/#!/ilpuccio/status/24766316493672448
> @tktym could you point me to some example of what you mena, please?
> "provide a recommended template for rdoc, require lines, and class def"

In my example plugin,

  https://github.com/ktym/bioruby-hello/blob/master/lib/bio-hello.rb

I used a style something similar with the BioRuby core library
which is described in 

  https://github.com/bioruby/bioruby/blob/master/README_DEV.rdoc

but I'm not sure what is the best practice for plugin.
It might be better to include the documentation in the README file instead.

In ether case, what in my mind is to auto-generate a plugin description
from those embedded description for the "plugin showcase" which will be
available somewhere on the bioruby.org site in the future.

For that purpose, we may also want to have some flags indicating:

* status of the plugin (stable, usable, buggy, just started etc.)
* the plugin will override the BioRuby core or just provide new features harmlessly
* pre-requirements (especially, other than gems)

etc. etc.

Here's a material for further discussion (example template):

#
# = Bio::XXX - BioRuby plugin for XXX
#
# Copyright::  Copyright (C) 2001, 2003-2005 Bio R. Hacker <brh at example.org>,
# Copyright::  Copyright (C) 2006 Chem R. Hacker <crh at example.org>
# License::    The Ruby License
# Site:        http://github.com/user/bioruby-xxx
#
# == Description
#
# This plugin provides an interface for the XXX database.
#
# == Usage
#
# Lorem ipsum dolor sit amet, consectetur adipisicing elit, ....
#
# == Effects (Overrides?)
#
# * Modify the behavior of Bio::Sequence::NA#translate destructively
# * Add methods to the Bio::DB class
#
# == Depends (Requirements?)
#
# * External MySQL database system
# * RubyGem package 'foobar'
#
# == References
#
# * Hoge F. et al., The XXX database, Nucleic. Acid. Res. 123:100--123 (2030)
# * http://hoge.db/
#

# Do we need these two lines in every BioRuby plugin?
require 'rubygems'
require 'bio'

# Do we allow classes defined outside of the 'Bio' namespace?
module Bio
  class XXX
    # :
  end # XXX
end # Bio


Thanks,
Toshiaki

On 2011/01/11, at 15:38, Pjotr Prins wrote:

> Super!
> 
> On Mon, Jan 10, 2011 at 11:06:48PM +0100, Raoul Bonnal wrote:
>> Hi all,
>> I have updated the github repo with some requests from Pjotr.
>> Now is possible to create bin, db and test/data directory if needed from the command line 
>> 
>> biogem --with-bin --with-bd --with-test-data youprojectname
>> 
>> NOTE 1: older 'data' directory is now 'db' more compliant with rails. Why ? data cames from R packages but we are used to store database or look for databases in db directory.
>> NOTE 2: README updated.
>> 
>> about rspec and cucumber jeweler already has those options.
>> 
>> type 'biogem -h' and you'll get the help.
>> 
>> This gem is not yet available on rubygems I need to implement the templates requested from Toshiaki and Pjotr.
>> 
>> I'm refactoring the code so there are some variations in the original tree.
>> 
>> I "hope", by the end of the week, to provide templates files too.
>> 
>> --
>> R.J.P.B.
>> 
>> 
>> 
>> 
>> 
>> _______________________________________________
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