[BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.1,1.2

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/doc
In directory pub.open-bio.org:/tmp/cvs-serv15902/doc

Modified Files:
	Changes-0.7.rd 
Log Message:
* added notes on important changes, new features and descriptions on changes.


Index: Changes-0.7.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Changes-0.7.rd,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Changes-0.7.rd	23 Sep 2005 14:01:54 -0000	1.1
--- Changes-0.7.rd	26 Sep 2005 07:27:19 -0000	1.2
***************
*** 1,7 ****
! = Incompatible changes from BioRuby 0.6
  
! == Bio::Sequence
  
  * Bio::Sequence::NA#gc_percent returns integer instead of float
! * Bio::Sequence::NA#gc (alias to gc_percent) is removed
  
--- 1,63 ----
! = Incompatible and important changes since the BioRuby 0.6.4 release
  
! A lot of changes have been made to the BioRuby after the version 0.6.4
! is released.
! 
! --- Ruby 1.6 series are no longer supported.
! 
! We use autoload functionality and many other libraries bundled in
! Ruby 1.8.2 (such as SOAP, open-uri, pp etc.) by default.
! 
! --- BioRuby will be loaded about 30 times faster than before.
! 
! As we changed to use autoload instead of require, time required
! to start up the BioRuby library made surprisingly faster.
! 
! Other changes (including exciting BioRuby shell etc.) made in this release
! is described in this file.
! 
! == New features
! 
! --- BioRuby shell
! 
! Command line user interface for the BioRuby is included.
! You can invoke the shell by
! 
!   % bioruby
! 
! --- UnitTest
! 
! Test::Unit now covers wide range of the BioRuby library.
! You can run them by
! 
!   % ruby test/runner.rb
! 
! or
! 
!   % ruby install.rb config
!   % ruby install.rb setup
!   % ruby install.rb test
! 
! during the installation procedure.
! 
! --- Documents
! 
! README, README.DEV, doc/Tutorial.rd, doc/Tutorial.rd.ja etc. are updated
! or newly added.
! 
! == Incompatible changes
! 
! --- Bio::Sequence
  
  * Bio::Sequence::NA#gc_percent returns integer instead of float
! * Bio::Sequence::NA#gc (was aliased to gc_percent) is removed
! 
! In BioRuby, GC% is rounded to one decimal place.  However, how many digits
! should be left when rounding the value is not clear and as the GC% is an
! rough measure by its nature, we have changed to return integer part only.
! If you need a precise value, you can calculate it by values from the
! 'composition' method by your own criteria.
! 
! The 'gc' method is removed as the method name doesn't represent its value
! is ambiguous.