[BioRuby-cvs] bioruby ChangeLog,1.70,1.71

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv23421

Modified Files:
	ChangeLog 
Log Message:
* preparation for BioRuby 1.2 release


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.70
retrieving revision 1.71
diff -C2 -d -r1.70 -r1.71
*** ChangeLog	12 Dec 2007 16:06:22 -0000	1.70
--- ChangeLog	14 Dec 2007 16:22:24 -0000	1.71
***************
*** 1,2 ****
--- 1,21 ----
+ 2007-12-15  Toshiaki Katayama <k at bioruby.org>
+ 
+ 	* BioRuby 1.2.0 released
+ 
+ 	  * BioRuby shell is improved
+ 	    * file save functionality is fixed
+ 	    * deprecated require_gem is changed to gem to suppress warnings
+ 	    * deprecated end_form_tag is rewrited to suppress warnings
+ 	    * images for Rails shell are separated to the bioruby directory
+ 	    * spinner is shown during the evaluation
+ 	    * background image in the textarea is removed for the visibility
+ 	  * Bio::Blast is fixed to parse -m 8 formatted result correctly
+ 	  * Bio::PubMed is rewrited to enhance its functionality
+ 	    * e.g. 'rettype' => 'count' and 'retmode' => 'xml' are available
+ 	  * Bio::FlatFile is improved to accept recent MEDLINE format
+ 	  * Bio::KEGG::COMPOUND is enhanced to utilize REMARK field
+ 	  * Bio::KEGG::API is fixed to skip filter when the value is Fixnum
+ 	  * A number of minor bug fixes
+ 
  2007-12-12  Naohisa Goto <ng at bioruby.org>
  
***************
*** 14,18 ****
  	  Fixed a misspelling in Bio::FlatFileIndex.formatstring2class.
  
! 2007-11-10  Toshiaki Katayama <k at bioruby.org>
  
  	* lib/bio/io/pubmed.rb:
--- 33,37 ----
  	  Fixed a misspelling in Bio::FlatFileIndex.formatstring2class.
  
! 2007-11-28  Toshiaki Katayama <k at bioruby.org>
  
  	* lib/bio/io/pubmed.rb:
***************
*** 21,24 ****
--- 40,54 ----
  	  strongly recommended).
  
+ 	  efetch method is enhanced to accept any PubMed search options
+ 	  as a hash (to retrieve in XML format etc.)
+ 
+ 	  Changed to wait 3 seconds among each access by default to be
+ 	  compliant with the NCBI terms (Make no more than one request
+ 	  every 3 seconds).
+ 
+ 	  All Bio::PubMed.* class methods are changed to instance methods
+ 	  (interface as the class methods are remained for the backward
+ 	  compatibility).
+ 
  2007-07-19  Toshiaki Katayama <k at bioruby.org>