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* preparation for BioRuby 1.2.1 release

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commit 23cf32c712569314e16c57aeceae74e85e494772 1 parent 2b0f877
@ktym ktym authored
Showing with 33 additions and 27 deletions.
  1. +30 −24 ChangeLog
  2. +1 −1  gemspec.rb
  3. +2 −2 lib/bio.rb
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54 ChangeLog
@@ -1,35 +1,41 @@
+2007-12-30 Toshiaki Katayama <k@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@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.
+ 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.
+ 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.
+ 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: 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.
+ 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@bioruby.org>
@@ -61,21 +67,21 @@
* lib/bio/db/pdb/pdb.rb
- Bio::PDB#inspect is added to prevent memory exhaust problem.
- ([BioRuby] Parse big PDB use up all memory)
+ 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.
+ Bio::PDB::Model#inspect is added.
* lib/bio/db/pdb/chain.rb
- Bio::PDB::Chain#inspect is added.
+ 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.
+ Bio::PDB::Residue#inspect is added.
+ This also affects Bio::PDB::Heterogen#inspect.
2007-12-15 Toshiaki Katayama <k@bioruby.org>
View
2  gemspec.rb
@@ -2,7 +2,7 @@
spec = Gem::Specification.new do |s|
s.name = 'bio'
- s.version = "1.2.0"
+ s.version = "1.2.1"
s.author = "BioRuby project"
s.email = "staff@bioruby.org"
View
4 lib/bio.rb
@@ -5,12 +5,12 @@
# Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
-# $Id: bio.rb,v 1.87 2007/12/14 16:04:54 k Exp $
+# $Id: bio.rb,v 1.88 2007/12/29 19:19:07 k Exp $
#
module Bio
- BIORUBY_VERSION = [1, 2, 0].extend(Comparable)
+ BIORUBY_VERSION = [1, 2, 1].extend(Comparable)
### Basic data types
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