[BioRuby-cvs] bioruby README.DEV,1.10,1.11

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv31131

Modified Files:
	README.DEV 
Log Message:
* fix of the code template


Index: README.DEV
===================================================================
RCS file: /home/repository/bioruby/bioruby/README.DEV,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** README.DEV	11 May 2006 10:53:25 -0000	1.10
--- README.DEV	19 Sep 2006 05:39:05 -0000	1.11
***************
*** 1,6 ****
! $Id$
  
! Copyright (C):: 2005, 2006 Toshiaki Katayama <k at bioruby.org>
! Copyright (C):: 2006       Jan Aerts <jan.aerts at bbsrc.ac.uk>
  
  = HOW TO CONTRIBUTE TO THE BIORUBY PROJECT?
--- 1,8 ----
! = README.DEV
  
! Copyright::  Copyright (C) 2005, 2006 Toshiaki Katayama <k at bioruby.org>
! Copyright::  Copyright (C) 2006       Jan Aerts <jan.aerts at bbsrc.ac.uk>
! 
!   $Id$
  
  = HOW TO CONTRIBUTE TO THE BIORUBY PROJECT?
***************
*** 71,89 ****
  
  The header should be formatted as follows:
    #
    # = bio/db/hoge.rb - Hoge database parser classes
    #
!   # Copyright (C):: 2001, 2003-2005   Bio R. Hacker <brh at example.org>,
!   # Copyright (C):: 2006              Chem R. Hacker <crh at example.org>
    #
!   # License::     Ruby's
    #
!   # $Id$
    #
!   # = Description
    #
    # This file contains classes that implement an interface to the Hoge database.
    #
!   # = References
    #
    # * Hoge F. et al., The Hoge database, Nucleic. Acid. Res. 123:100--123 (2030)
--- 73,92 ----
  
  The header should be formatted as follows:
+ 
    #
    # = bio/db/hoge.rb - Hoge database parser classes
    #
!   # 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::    Ruby's
    #
!   # $ I d: $
    #
!   # == Description
    #
    # This file contains classes that implement an interface to the Hoge database.
    #
!   # == References
    #
    # * Hoge F. et al., The Hoge database, Nucleic. Acid. Res. 123:100--123 (2030)
***************
*** 91,98 ****
    #
  
! In the above sample, the
!   $Id$
! will be automatically changed into something like
    $Id$
  when commiting to the CVS repository for the first time.
  
--- 94,114 ----
    #
  
!   require 'foo'
! 
!   module Bio
! 
!     autoload :Bar, 'bio/bar'
! 
!   class Hoge
!     :
!   end  # Hoge
! 
!   end  # Bio
! 
! In the above sample, the '$ I d : $' (without spaces) will be automatically
! changed into something like
! 
    $Id$
+ 
  when commiting to the CVS repository for the first time.
  
***************
*** 102,106 ****
  following example (from lib/bio/sequence.rb):
  
!   # = DESCRIPTION
    # Bio::Sequence objects represent annotated sequences in bioruby.
    # A Bio::Sequence object is a wrapper around the actual sequence, 
--- 118,123 ----
  following example (from lib/bio/sequence.rb):
  
!   # == Description
!   #
    # Bio::Sequence objects represent annotated sequences in bioruby.
    # A Bio::Sequence object is a wrapper around the actual sequence, 
***************
*** 111,115 ****
    # these methods are not documented specifically for Bio::Sequence).
    #
!   # = USAGE
    #   require 'bio'
    #   
--- 128,133 ----
    # these methods are not documented specifically for Bio::Sequence).
    #
!   # == Usage
!   # 
    #   require 'bio'
    #   
***************
*** 168,173 ****
--- 186,194 ----
  example too much, try to provide any input data directly into the usage example,
  instead of refering to ARGV or ARGF for input.
+ 
    dna = Bio::Sequence.auto('atgcatgcATGCATGCAAAA')
+ 
  Otherwise, describe the input shortly, for example:
+ 
    # input should be string consisting of nucleotides
    dna = Bio::Sequence.auto(ARGF.read)
***************
*** 178,181 ****
--- 199,203 ----
  be listed, as well as the type of thing that is returned by the method. The
  format of this information is as follows:
+ 
    # ---
    # *Arguments*:
***************
*** 189,193 ****
--- 211,217 ----
  
  Don't use
+ 
    $stderr.puts "WARNING"
+ 
  in your code. Instead, try to avoid printing error messages. For fatal errors,
  use +raise+ with an appropriate message.
***************
*** 198,202 ****
  you meant to do with each method.  The test code is useful to make
  maintenance easy and ensure stability. The use of
!  if __FILE__ == $0
  is deprecated.
  
--- 222,228 ----
  you meant to do with each method.  The test code is useful to make
  maintenance easy and ensure stability. The use of
! 
!   if __FILE__ == $0
! 
  is deprecated.
  
***************
*** 204,209 ****
  
  To quicken the initial load time we have replaced most of 'require' to 
! 'autoload'
! since BioRuby version 0.7.  During this change, we have found
  some tips:
  
--- 230,234 ----
  
  To quicken the initial load time we have replaced most of 'require' to 
! 'autoload' since BioRuby version 0.7.  During this change, we have found
  some tips: