[BioRuby-cvs] bioruby ChangeLog,1.78,1.79 gemspec.rb,1.9,1.10

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv7972

Modified Files:
	ChangeLog gemspec.rb 
Log Message:
* preparation for BioRuby 1.2.1 release


Index: gemspec.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/gemspec.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** gemspec.rb	14 Dec 2007 16:22:58 -0000	1.9
--- gemspec.rb	29 Dec 2007 19:19:06 -0000	1.10
***************
*** 3,7 ****
  spec = Gem::Specification.new do |s|
    s.name = 'bio'
!   s.version = "1.2.0"
  
    s.author = "BioRuby project"
--- 3,7 ----
  spec = Gem::Specification.new do |s|
    s.name = 'bio'
!   s.version = "1.2.1"
  
    s.author = "BioRuby project"

Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.78
retrieving revision 1.79
diff -C2 -d -r1.78 -r1.79
*** ChangeLog	28 Dec 2007 14:31:06 -0000	1.78
--- ChangeLog	29 Dec 2007 19:19:06 -0000	1.79
***************
*** 1,34 ****
  2007-12-28  Naohisa Goto <ng at bioruby.org>
  
  	* lib/bio/appl/blast/report/format0.rb
  
! 	Fixed parse error when compisition-based statistics were enabled.
! 	In addition, Bio::Blast::Default::Report#references and
! 	Bio::Blast::Default::Report::HSP#stat_method methods are added.
! 	In NCBI BLAST 2.2.17, default option of composition-based
! 	statistics for blastp or tblastn are changed to be enabled
! 	by default.
  
  	* lib/bio/appl/blast/report/wublast.rb
  
! 	Changed to follow the above changes in format0.rb.
  
  	* lib/bio/sequence/common.rb
  
! 	Ruby 1.9 compliant: in window_search method, a local variable name
! 	outside the iterator loop is changed not to be shadowed by the
! 	iterator variable.
  
  	* lib/bio/db/pdb/pdb.rb
  
! 	Ruby 1.9 compliant: changed to avoid "RuntimeError: implicit
! 	argument passing of super from method defined by define_method()
! 	is not supported. Specify all arguments explicitly." error.
  
! 	Ruby 1.9 compliant: Bio::PDB::Record.get_record_class and
! 	Bio::PDB::Record.create_definition_hash (Note: they should only
! 	be internally used by PDB parser and users should not call them)
! 	are changed to follow the change of Module#constants which
! 	returns an array of Symbol instead of String.
  
  2007-12-26  Naohisa Goto <ng at bioruby.org>
--- 1,40 ----
+ 2007-12-30  Toshiaki Katayama <k at bioruby.org>
+ 
+ 	* BioRuby 1.2.1 released
+ 
+ 	  This version is not Ruby 1.9 (released few days ago) compliant yet.
+ 
  2007-12-28  Naohisa Goto <ng at bioruby.org>
  
  	* lib/bio/appl/blast/report/format0.rb
  
! 	  Fixed parse error when compisition-based statistics were enabled.
! 	  In addition, Bio::Blast::Default::Report#references and
! 	  Bio::Blast::Default::Report::HSP#stat_method methods are added.
! 	  In NCBI BLAST 2.2.17, default option of composition-based
! 	  statistics for blastp or tblastn are changed to be enabled
! 	  by default.
  
  	* lib/bio/appl/blast/report/wublast.rb
  
! 	  Changed to follow the above changes in format0.rb.
  
  	* lib/bio/sequence/common.rb
  
! 	  Ruby 1.9 compliant: in window_search method, a local variable name
! 	  outside the iterator loop is changed not to be shadowed by the
! 	  iterator variable.
  
  	* lib/bio/db/pdb/pdb.rb
  
! 	  Ruby 1.9 compliant: changed to avoid "RuntimeError: implicit
! 	  argument passing of super from method defined by define_method()
! 	  is not supported. Specify all arguments explicitly." error.
  
! 	  Ruby 1.9 compliant: Bio::PDB::Record.get_record_class and
! 	  Bio::PDB::Record.create_definition_hash (Note: they should only
! 	  be internally used by PDB parser and users should not call them)
! 	  are changed to follow the change of Module#constants which
! 	  returns an array of Symbol instead of String.
  
  2007-12-26  Naohisa Goto <ng at bioruby.org>
***************
*** 62,80 ****
  	* lib/bio/db/pdb/pdb.rb
  
! 	Bio::PDB#inspect is added to prevent memory exhaust problem.
! 	([BioRuby] Parse big PDB use up all memory)
  
  	* lib/bio/db/pdb/model.rb
  
! 	Bio::PDB::Model#inspect is added.
  
  	* lib/bio/db/pdb/chain.rb
  
! 	Bio::PDB::Chain#inspect is added.
  
  	* lib/bio/db/pdb/residue.rb
  
! 	Bio::PDB::Residue#inspect is added.
! 	This also affects Bio::PDB::Heterogen#inspect.
  
  2007-12-15  Toshiaki Katayama <k at bioruby.org>
--- 68,86 ----
  	* lib/bio/db/pdb/pdb.rb
  
! 	  Bio::PDB#inspect is added to prevent memory exhaust problem.
! 	  ([BioRuby] Parse big PDB use up all memory)
  
  	* lib/bio/db/pdb/model.rb
  
! 	  Bio::PDB::Model#inspect is added.
  
  	* lib/bio/db/pdb/chain.rb
  
! 	  Bio::PDB::Chain#inspect is added.
  
  	* lib/bio/db/pdb/residue.rb
  
! 	  Bio::PDB::Residue#inspect is added.
! 	  This also affects Bio::PDB::Heterogen#inspect.
  
  2007-12-15  Toshiaki Katayama <k at bioruby.org>