bio 1.5.2 → 1.6.0.pre.20181210

data/appveyor.yml

@@ -0,0 +1,21 @@
+---
+version: "{build}"
+branches:
+  only:
+    - master
+clone_depth: 10
+install:
+  - SET PATH=C:\Ruby%ruby_version%\bin;%PATH%
+  - ruby --version
+  - gem --version
+  - gem build bioruby.gemspec
+  - gem install *.gem
+build: off
+environment:
+  matrix:
+    - ruby_version: "21"
+    - ruby_version: "21-x64"
+    - ruby_version: "22"
+    - ruby_version: "22-x64"
+    - ruby_version: "23"
+    - ruby_version: "23-x64"

data/bioruby.gemspec

@@ -3,7 +3,7 @@
 # 
 Gem::Specification.new do |s|
   s.name = 'bio'
-  s.version = "1.5.2"
+  s.version = "1.6.0.pre.20181211"
 
   s.author = "BioRuby project"
   s.email = "staff@bioruby.org"
@@ -21,6 +21,7 @@ Gem::Specification.new do |s|
     "COPYING.ja",
     "ChangeLog",
     "GPL",
+    "Gemfile",
     "KNOWN_ISSUES.rdoc",
     "LEGAL",
     "LGPL",
@@ -28,14 +29,11 @@ Gem::Specification.new do |s|
     "README_DEV.rdoc",
     "RELEASE_NOTES.rdoc",
     "Rakefile",
-    "bin/bioruby",
-    "bin/br_biofetch.rb",
-    "bin/br_bioflat.rb",
-    "bin/br_biogetseq.rb",
-    "bin/br_pmfetch.rb",
+    "appveyor.yml",
     "bioruby.gemspec",
     "bioruby.gemspec.erb",
     "doc/ChangeLog-1.4.3",
+    "doc/ChangeLog-1.5.0",
     "doc/ChangeLog-before-1.3.1",
     "doc/ChangeLog-before-1.4.2",
     "doc/Changes-0.7.rd",
@@ -44,6 +42,7 @@ Gem::Specification.new do |s|
     "doc/RELEASE_NOTES-1.4.1.rdoc",
     "doc/RELEASE_NOTES-1.4.2.rdoc",
     "doc/RELEASE_NOTES-1.4.3.rdoc",
+    "doc/RELEASE_NOTES-1.5.0.rdoc",
     "doc/Tutorial.rd",
     "doc/Tutorial.rd.html",
     "doc/Tutorial.rd.ja",
@@ -55,7 +54,6 @@ Gem::Specification.new do |s|
     "gemfiles/Gemfile.travis-rbx",
     "gemfiles/Gemfile.travis-ruby1.8",
     "gemfiles/Gemfile.travis-ruby1.9",
-    "gemfiles/Gemfile.travis-ruby2.2",
     "gemfiles/modify-Gemfile.rb",
     "gemfiles/prepare-gemspec.rb",
     "lib/bio.rb",
@@ -120,8 +118,6 @@ Gem::Specification.new do |s|
     "lib/bio/data/na.rb",
     "lib/bio/db.rb",
     "lib/bio/db/aaindex.rb",
-    "lib/bio/db/biosql/biosql_to_biosequence.rb",
-    "lib/bio/db/biosql/sequence.rb",
     "lib/bio/db/embl/common.rb",
     "lib/bio/db/embl/embl.rb",
     "lib/bio/db/embl/embl_to_biosequence.rb",
@@ -180,10 +176,6 @@ Gem::Specification.new do |s|
     "lib/bio/db/pdb/pdb.rb",
     "lib/bio/db/pdb/residue.rb",
     "lib/bio/db/pdb/utils.rb",
-    "lib/bio/db/phyloxml/phyloxml.xsd",
-    "lib/bio/db/phyloxml/phyloxml_elements.rb",
-    "lib/bio/db/phyloxml/phyloxml_parser.rb",
-    "lib/bio/db/phyloxml/phyloxml_writer.rb",
     "lib/bio/db/prosite.rb",
     "lib/bio/db/rebase.rb",
     "lib/bio/db/sanger_chromatogram/abif.rb",
@@ -193,9 +185,6 @@ Gem::Specification.new do |s|
     "lib/bio/db/soft.rb",
     "lib/bio/db/transfac.rb",
     "lib/bio/feature.rb",
-    "lib/bio/io/biosql/ar-biosql.rb",
-    "lib/bio/io/biosql/biosql.rb",
-    "lib/bio/io/biosql/config/database.yml",
     "lib/bio/io/das.rb",
     "lib/bio/io/fastacmd.rb",
     "lib/bio/io/fetch.rb",
@@ -210,7 +199,6 @@ Gem::Specification.new do |s|
     "lib/bio/io/ncbirest.rb",
     "lib/bio/io/pubmed.rb",
     "lib/bio/io/registry.rb",
-    "lib/bio/io/sql.rb",
     "lib/bio/io/togows.rb",
     "lib/bio/location.rb",
     "lib/bio/map.rb",
@@ -228,44 +216,6 @@ Gem::Specification.new do |s|
     "lib/bio/sequence/na.rb",
     "lib/bio/sequence/quality_score.rb",
     "lib/bio/sequence/sequence_masker.rb",
-    "lib/bio/shell.rb",
-    "lib/bio/shell/core.rb",
-    "lib/bio/shell/demo.rb",
-    "lib/bio/shell/interface.rb",
-    "lib/bio/shell/irb.rb",
-    "lib/bio/shell/object.rb",
-    "lib/bio/shell/plugin/blast.rb",
-    "lib/bio/shell/plugin/codon.rb",
-    "lib/bio/shell/plugin/das.rb",
-    "lib/bio/shell/plugin/emboss.rb",
-    "lib/bio/shell/plugin/entry.rb",
-    "lib/bio/shell/plugin/flatfile.rb",
-    "lib/bio/shell/plugin/midi.rb",
-    "lib/bio/shell/plugin/ncbirest.rb",
-    "lib/bio/shell/plugin/obda.rb",
-    "lib/bio/shell/plugin/psort.rb",
-    "lib/bio/shell/plugin/seq.rb",
-    "lib/bio/shell/plugin/togows.rb",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif",
-    "lib/bio/shell/script.rb",
-    "lib/bio/shell/setup.rb",
-    "lib/bio/shell/web.rb",
     "lib/bio/tree.rb",
     "lib/bio/tree/output.rb",
     "lib/bio/util/color_scheme.rb",
@@ -363,7 +313,6 @@ Gem::Specification.new do |s|
     "sample/seqdatabase.ini",
     "sample/ssearch2tab.rb",
     "sample/tdiary.rb",
-    "sample/test_phyloxml_big.rb",
     "sample/test_restriction_enzyme_long.rb",
     "sample/tfastx2tab.rb",
     "sample/vs-genes.rb",
@@ -485,11 +434,6 @@ Gem::Specification.new do |s|
     "test/data/paml/codeml/models/results7-8.txt",
     "test/data/paml/codeml/output.txt",
     "test/data/paml/codeml/rates",
-    "test/data/phyloxml/apaf.xml",
-    "test/data/phyloxml/bcl_2.xml",
-    "test/data/phyloxml/made_up.xml",
-    "test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml",
-    "test/data/phyloxml/phyloxml_examples.xml",
     "test/data/pir/CRAB_ANAPL.pir",
     "test/data/prosite/prosite.dat",
     "test/data/refseq/nm_126355.entret",
@@ -539,8 +483,6 @@ Gem::Specification.new do |s|
     "test/unit/bio/data/test_aa.rb",
     "test/unit/bio/data/test_codontable.rb",
     "test/unit/bio/data/test_na.rb",
-    "test/unit/bio/db/biosql/tc_biosql.rb",
-    "test/unit/bio/db/biosql/ts_suite_biosql.rb",
     "test/unit/bio/db/embl/test_common.rb",
     "test/unit/bio/db/embl/test_embl.rb",
     "test/unit/bio/db/embl/test_embl_rel89.rb",
@@ -579,8 +521,6 @@ Gem::Specification.new do |s|
     "test/unit/bio/db/test_nbrf.rb",
     "test/unit/bio/db/test_newick.rb",
     "test/unit/bio/db/test_nexus.rb",
-    "test/unit/bio/db/test_phyloxml.rb",
-    "test/unit/bio/db/test_phyloxml_writer.rb",
     "test/unit/bio/db/test_prosite.rb",
     "test/unit/bio/db/test_qual.rb",
     "test/unit/bio/db/test_rebase.rb",
@@ -598,7 +538,6 @@ Gem::Specification.new do |s|
     "test/unit/bio/sequence/test_na.rb",
     "test/unit/bio/sequence/test_quality_score.rb",
     "test/unit/bio/sequence/test_sequence_masker.rb",
-    "test/unit/bio/shell/plugin/test_seq.rb",
     "test/unit/bio/test_alignment.rb",
     "test/unit/bio/test_command.rb",
     "test/unit/bio/test_db.rb",
@@ -608,7 +547,6 @@ Gem::Specification.new do |s|
     "test/unit/bio/test_pathway.rb",
     "test/unit/bio/test_reference.rb",
     "test/unit/bio/test_sequence.rb",
-    "test/unit/bio/test_shell.rb",
     "test/unit/bio/test_tree.rb",
     "test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb",
     "test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb",
@@ -643,7 +581,8 @@ Gem::Specification.new do |s|
     "doc/RELEASE_NOTES-1.4.0.rdoc",
     "doc/RELEASE_NOTES-1.4.1.rdoc",
     "doc/RELEASE_NOTES-1.4.2.rdoc",
-    "doc/RELEASE_NOTES-1.4.3.rdoc"
+    "doc/RELEASE_NOTES-1.4.3.rdoc",
+    "doc/RELEASE_NOTES-1.5.0.rdoc"
   ]
   s.rdoc_options << '--main' << 'README.rdoc'
   s.rdoc_options << '--title' << 'BioRuby API documentation'
@@ -651,14 +590,4 @@ Gem::Specification.new do |s|
   s.rdoc_options << '--line-numbers' << '--inline-source'
 
   s.require_path = 'lib'
-
-  s.bindir = "bin"
-  s.executables = [
-    "bioruby",
-    "br_biofetch.rb",
-    "br_bioflat.rb",
-    "br_biogetseq.rb",
-    "br_pmfetch.rb"
-  ]
-  s.default_executable = "bioruby"
 end

data/bioruby.gemspec.erb

@@ -7,18 +7,18 @@ Gem::Specification.new do |s|
 
     # By default, determined from lib/bio/version.rb
     load "./lib/bio/version.rb" unless defined?(BIO_VERSION_RB_LOADED)
+    ver = Bio::BIORUBY_VERSION.dup
     case Bio::BIORUBY_EXTRA_VERSION
     when nil
-      suffix = nil
-    when /\A\.(\d+)\z/
-      suffix = $1
-    when /\A\-dev\z/
-      suffix = Time.now.strftime("%Y%m%d")
+      # does nothing
+    when /\A\.(pre)\z/
+      ver.push $1
+      ver.push Time.now.strftime("%Y%m%d")
+    when /\A\.(.+)\z/
+      ver.push $1
     else
       raise "unsupported BIORUBY_EXTRA_VERSION"
     end
-    ver = Bio::BIORUBY_VERSION.dup
-    ver.push suffix if suffix
     %><%= 
     (env_ver || ver.join('.'))
        ###### Above is executed in ERB environment ######
@@ -48,7 +48,7 @@ Gem::Specification.new do |s|
           "bioruby.gemspec", "setup.rb",
           "extconf.rb", "LEGAL",
           "COPYING", "COPYING.ja", "GPL", "LGPL"
-        ] + Dir.glob("{bin,doc,etc,gemfiles,lib,sample,test}/**/*").delete_if do |item|
+        ] + Dir.glob("{doc,etc,gemfiles,lib,sample,test}/**/*").delete_if do |item|
               case item
               when /(\A|\/)CVS(\z|\/)/, /(\A|\/)rdoc(\z|\/)/, /\~\z/
                 true
@@ -90,23 +90,4 @@ Gem::Specification.new do |s|
   s.rdoc_options << '--line-numbers' << '--inline-source'
 
   s.require_path = 'lib'
-
-  s.bindir = "bin"
-  s.executables = [
-    <%= ###### Below is executed in ERB environment ######
-        # Files in bin/ directory are selected.
-        exec_files = files.find_all { |item| /\Abin\// =~ item }
-        # Non-executable files are removed from the list.
-        exec_files.delete_if { |item| !File.executable?(item) }
-        # strip "bin/"
-        exec_files.collect! { |item| item.sub(/\Abin\//, '') }
-        # Fail safe settings
-        if exec_files.empty? then
-            exec_files = [ "bioruby", "br_biofetch.rb", "br_biogetseq.rb", "br_bioflat.rb", "br_pmfetch.rb" ]
-        end
-        exec_files.sort.collect { |x| x.dump }.join(",\n    ")
-        ###### Above is executed in ERB environment ######
-    %>
-  ]
-  s.default_executable = "bioruby"
 end

data/doc/ChangeLog-1.5.0

@@ -0,0 +1,2919 @@
+commit 01ac93ca3b341716c85c571f1194834db0a68e52
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Jul 1 02:21:26 2015 +0900
+
+    update ChangeLog by rake rechangelog
+
+ ChangeLog |   28 ++++++++++++++++++++++++++++
+ 1 file changed, 28 insertions(+)
+
+commit cac63ff501df6a71afead77175db9fb491c2985b
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Jul 1 01:31:21 2015 +0900
+
+    .travis.yml: use Ruby 2.1.6 for tar and gem integration tests
+
+ .travis.yml |    8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+commit 5318c99249f34dacc788b82c658ea0e256770db0
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Jul 1 00:43:39 2015 +0900
+
+    known issues added about new BLAST XML format and BLAST+ text format
+
+ KNOWN_ISSUES.rdoc  |   11 +++++++++++
+ RELEASE_NOTES.rdoc |   11 +++++++++++
+ 2 files changed, 22 insertions(+)
+
+commit b61d8df0300ef366539e1154c9a2dac2f1f4ff18
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 23:57:01 2015 +0900
+
+    update ChangeLog with rake rechangelog
+
+ ChangeLog |   47 +++++++++++++++++++++++++++++++++++++++++++++++
+ 1 file changed, 47 insertions(+)
+
+commit 75cf6c31c57239b2e39a171e536ad5dddcaec94a
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 23:56:08 2015 +0900
+
+    regenerate bioruby.gemspec with rake regemspec
+
+ bioruby.gemspec |    1 +
+ 1 file changed, 1 insertion(+)
+
+commit 608850beb33f3f7333f05307202b766adb350eb9
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 23:54:59 2015 +0900
+
+    description about updating of Ruby's License
+
+ RELEASE_NOTES.rdoc |    9 +++++++++
+ 1 file changed, 9 insertions(+)
+
+commit f54bcfc20d20935db4e342e5988c0b7f59c131b3
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 23:16:51 2015 +0900
+
+    BSDL is referred in COPYING and COPYING.ja
+
+ BSDL |   22 ++++++++++++++++++++++
+ 1 file changed, 22 insertions(+)
+ create mode 100644 BSDL
+
+commit d1cbfb699259fd57af02181f4374d562dda3abe1
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 23:14:42 2015 +0900
+
+    changes of Ruby's License is reflected.
+
+ COPYING    |    4 ++--
+ COPYING.ja |   72 ++++++++++++++++++++++++++++++------------------------------
+ 2 files changed, 38 insertions(+), 38 deletions(-)
+
+commit 2d9de9a0e2abe7fa9f193e54af0cbfc24bf2c37b
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 22:50:37 2015 +0900
+
+    ChangeLog is regenerated by using "rake rechangelog"
+
+ ChangeLog | 2786 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
+ 1 file changed, 2780 insertions(+), 6 deletions(-)
+
+commit 70665a69a79d569d7bb37ef6d8c238534e6dae3a
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 22:49:55 2015 +0900
+
+    KNOWN_ISSUES.rdoc: change ruby versions and add descriptions
+
+ KNOWN_ISSUES.rdoc |   14 +++++++++-----
+ 1 file changed, 9 insertions(+), 5 deletions(-)
+
+commit 1054106f93b973b5a92f993c5b83b1444f96fffe
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 22:48:51 2015 +0900
+
+    prepare to release BioRuby 1.5.0
+
+ bioruby.gemspec    |    2 +-
+ lib/bio/version.rb |    2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+commit 0f150586904f7e423455615313992ccf77d7e123
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 22:44:58 2015 +0900
+
+    RELEASE_NOTES.rdoc: update many
+
+ RELEASE_NOTES.rdoc |  151 +++++++++++++++++++++++++++++++++++++++++++++-------
+ 1 file changed, 132 insertions(+), 19 deletions(-)
+
+commit 2924ca0b977da13d42f232f880fd2df0b2995677
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 21:55:52 2015 +0900
+
+    Bug fix: Bio::UniProtKB#gene_name should not raise NoMethodError
+    
+     * Bug fix: Bio::UniProtKB#gene_name raised NoMethodError when
+       gene_names method returns nil. It should return nil.
+       Thanks to Jose Irizarry who reports and sends suggested fix.
+       (https://github.com/bioruby/bioruby/pull/83 )
+
+ lib/bio/db/embl/uniprotkb.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 9bf9022007a0ff31a870b1ea08e423aebc487c17
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 18:45:51 2015 +0900
+
+    regenerate bioruby.gemspec with rake regemspec
+
+ bioruby.gemspec |    1 +
+ 1 file changed, 1 insertion(+)
+
+commit a151e51a44b3dd93e5d075d71954f639eaec339e
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 18:10:55 2015 +0900
+
+    update docs; change recommended Ruby versions
+
+ README.rdoc |    9 ++++++---
+ 1 file changed, 6 insertions(+), 3 deletions(-)
+
+commit e86e745c8a6c666c446fe2f9f47818140999e2db
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 18:08:53 2015 +0900
+
+    delete description about SOAP4R
+
+ README.rdoc |    5 -----
+ 1 file changed, 5 deletions(-)
+
+commit 7e4bfb6b3757872691487b080bfd87363a4f9480
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 03:22:35 2015 +0900
+
+    .travis.yml: test/unit no longer bundled with Ruby 2.2
+    
+     * For Ruby 2.2, use a new Gemfile named Gemfile.travis-ruby2.2
+       that include 'gem "test-unit"' line because test/unit have been
+       provided by bundled gem since Ruby 2.2.
+
+ .travis.yml                     |    7 ++++---
+ gemfiles/Gemfile.travis-ruby2.2 |    9 +++++++++
+ 2 files changed, 13 insertions(+), 3 deletions(-)
+ create mode 100644 gemfiles/Gemfile.travis-ruby2.2
+
+commit cac85ca215ed781c80d49a5bf3d5d37d808c783b
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 02:51:16 2015 +0900
+
+    bump up version to 1.5.0-dev; simplify the versioning rules
+    
+     * Bump up version to 1.5.0-dev (1.5.0.20150630)
+     * Simplify the versioning rules.
+     * We will adopt the Semantic Versioning since BioRuby 1.5.1.
+
+ bioruby.gemspec     |    2 +-
+ bioruby.gemspec.erb |   21 ++++-----------------
+ lib/bio/version.rb  |   17 ++++++++---------
+ 3 files changed, 13 insertions(+), 27 deletions(-)
+
+commit 1a24fb6840932499be833b5ec3bb36184b1334a1
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 02:14:01 2015 +0900
+
+    Bug fix: update Bio::Hinv::BASE_URI
+    
+     * Bug fix: update Bio::Hinv::BASE_URI to follow the server URI change.
+     * Update official documentation URL.
+
+ lib/bio/io/hinv.rb |    4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+commit a9a12fff70ca287aa098d1331a3146e2899cb709
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 02:08:40 2015 +0900
+
+    delete $Id:$ line
+
+ lib/bio/io/hinv.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 2bfa0f41969003f17c4b894b5279347616c8f187
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 01:58:01 2015 +0900
+
+    delete sections about SOAP4R issues
+
+ KNOWN_ISSUES.rdoc |   12 ------------
+ 1 file changed, 12 deletions(-)
+
+commit 9dbd83aa00acc5f78b5da68f000c305da9f31b66
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 01:54:16 2015 +0900
+
+    remove commented-out lines of soap4r-ruby1.9
+
+ gemfiles/Gemfile.travis-jruby1.9 |    3 ---
+ gemfiles/Gemfile.travis-rbx      |    3 ---
+ gemfiles/Gemfile.travis-ruby1.9  |    3 ---
+ 3 files changed, 9 deletions(-)
+
+commit 14d2f3e2fa15f94faeff4d28c957f581461eac82
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 01:50:30 2015 +0900
+
+    .travis.yml: update ruby versions, remove ruby 1.9.2
+
+ .travis.yml |    8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+commit 89f9b1fe2332584b5d63b1539b8e470d853478a3
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 00:36:42 2015 +0900
+
+    about removal of Bio::SOAPWSDL, Bio::EBI::SOAP, Bio::HGC::HiGet
+
+ RELEASE_NOTES.rdoc |   20 ++++++++++++++++++++
+ 1 file changed, 20 insertions(+)
+
+commit 29516d3d6d2f907f65822bcf4146e95785773a3a
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 00:50:47 2015 +0900
+
+    regenerate bioruby.gemspec with rake regemspec
+
+ bioruby.gemspec |    6 ------
+ 1 file changed, 6 deletions(-)
+
+commit 357a1afc5ef457326179142c163968aa5cd94864
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 00:49:42 2015 +0900
+
+    not to load deleted file lib/bio/shell/plugin/soap.rb
+
+ lib/bio/shell.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 956e475da52ea17f1022493f589489a3e7c06f93
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Jun 29 23:43:24 2015 +0900
+
+    deleted lib/bio/shell/plugin/soap.rb
+    
+     * deleted lib/bio/shell/plugin/soap.rb because Bio::SOAPWSDL and
+       all SOAP client classes in BioRuby are removed.
+
+ lib/bio/shell/plugin/soap.rb |   50 ------------------------------------------
+ 1 file changed, 50 deletions(-)
+ delete mode 100644 lib/bio/shell/plugin/soap.rb
+
+commit 00acae3c3a8066891e08dc225eae2c22c3415191
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Jun 29 23:41:20 2015 +0900
+
+    not to load removed Bio::EBI::SOAP from lib/bio/io/ebisoap.rb
+
+ lib/bio.rb |    4 ----
+ 1 file changed, 4 deletions(-)
+
+commit d4844b38b5ddaec7ec15b56ef66f6930f0e6cfc0
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Jun 29 23:38:26 2015 +0900
+
+    remove Bio::EBI::SOAP (lib/bio/io/ebisoap.rb)
+    
+     * Bio::EBI::SOAP (lib/bio/io/ebisoap.rb) is removed because
+       Bio::SOAPWSDL is removed.
+
+ lib/bio/io/ebisoap.rb |  158 -------------------------------------------------
+ 1 file changed, 158 deletions(-)
+ delete mode 100644 lib/bio/io/ebisoap.rb
+
+commit 79b4705bac82fe17b12c649172a629d3de41cbdf
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 30 00:12:36 2015 +0900
+
+    not to load removed Bio::SOAPWSDL from lib/bio/io/soapwsdl.rb
+
+ lib/bio.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 03ced6a70973557532517c70dac183775bd11fa7
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Jun 29 23:59:28 2015 +0900
+
+    remove Bio::SOAPWSDL (lib/bio/io/soapwsdl.rb) and tests
+    
+     * Bio::SOAPWSDL is removed because SOAP4R (SOAP/WSDL library in Ruby)
+       is no longer bundled with Ruby since Ruby 1.9. For Ruby 1.9 or later,
+       some gems of SOAP4R are available, but we think they are not
+       well-maintained. Moreover, many SOAP servers have been retired
+       (see previous commits). So, we give up maintaining Bio::SOAPWSDL.
+
+ lib/bio/io/soapwsdl.rb               |  119 ----------------------------------
+ test/network/bio/io/test_soapwsdl.rb |   53 ---------------
+ test/unit/bio/io/test_soapwsdl.rb    |   33 ----------
+ 3 files changed, 205 deletions(-)
+ delete mode 100644 lib/bio/io/soapwsdl.rb
+ delete mode 100644 test/network/bio/io/test_soapwsdl.rb
+ delete mode 100644 test/unit/bio/io/test_soapwsdl.rb
+
+commit d927652e9f5d241e3c1b13b7d760f5a190b72e50
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Jun 29 23:35:38 2015 +0900
+
+    delete old comment-out lines about Bio::DDBJ::XML
+
+ lib/bio.rb |    5 -----
+ 1 file changed, 5 deletions(-)
+
+commit b995251bf96b8983def36e77bc94d6f0c0f2c78c
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Jun 29 23:29:47 2015 +0900
+
+    do not load Bio::HGC::HiGet from deleted lib/bio/io/higet.rb
+
+ lib/bio.rb |    4 ----
+ 1 file changed, 4 deletions(-)
+
+commit 6191020ed1e150f9e70de687375528a899fcf8ef
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Jun 29 23:27:41 2015 +0900
+
+    remove lib/bio/io/higet.rb because of the server down for a long time
+
+ lib/bio/io/higet.rb |   73 ---------------------------------------------------
+ 1 file changed, 73 deletions(-)
+ delete mode 100644 lib/bio/io/higet.rb
+
+commit 5a527c5cdd513d72ad5817c66ac87e7613395e26
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Jun 27 02:33:46 2015 +0900
+
+    add/modify about removed features and incompatible changes
+
+ RELEASE_NOTES.rdoc |   71 +++++++++++++++++++++++++++++++++++++++++++++++++---
+ 1 file changed, 67 insertions(+), 4 deletions(-)
+
+commit 1886314d2b8dd7d4b3e86c7b93134facd881127a
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Jun 27 01:24:36 2015 +0900
+
+    regenerate bioruby.gemspec with rake regemspec
+
+ bioruby.gemspec |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 724e9c1c039dcc7fa19fb15de0313218a87f9868
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jun 25 23:34:44 2015 +0900
+
+    extconf.rb is deleted because no native extensions are included
+    
+     * extconf.rb is deleted because no native extensions are included in
+       BioRuby and to avoid potential confusions. Nowadays, extconf.rb is
+       usually used only for building native extensions. Use gem or
+       setup.rb to install BioRuby.
+
+ extconf.rb |    2 --
+ 1 file changed, 2 deletions(-)
+ delete mode 100644 extconf.rb
+
+commit d42a1cb1df17e0c11ca0407dc05e1271cd74a0d7
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Jun 24 22:29:28 2015 +0900
+
+    Ruby 2.3 support: IO#close to closed IO object is allowed without error.
+
+ test/unit/bio/io/flatfile/test_buffer.rb |    8 +++++++-
+ 1 file changed, 7 insertions(+), 1 deletion(-)
+
+commit 5ea39188ac3cc2609397b2d8864a2019ea6b93d2
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri May 1 23:42:39 2015 +0900
+
+    s.license = "Ruby"
+    
+     * bioruby.gemspec.erb, bioruby.gemspec: s.license = "Ruby"
+       Thanks to Peter Cock who reports a patch.
+       (https://github.com/bioruby/bioruby/issues/101 )
+
+ bioruby.gemspec     |    1 +
+ bioruby.gemspec.erb |    1 +
+ 2 files changed, 2 insertions(+)
+
+commit 2b18ae005a592ea4ae7b632f7e658d4bbf153fd8
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri May 1 23:39:36 2015 +0900
+
+    remove deprecated Gem::Specification#rubyforge_project
+
+ bioruby.gemspec     |    2 +-
+ bioruby.gemspec.erb |    2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+commit 3a1d89bde9af44793c850b1cde950e3e3042fb8d
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 01:52:31 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/db/gff.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 165ebf29ba192c7a7e7f1633809d34966c2aeed1
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 01:51:47 2015 +0900
+
+    suppress "character class has duplicated range" warnings
+
+ lib/bio/db/gff.rb |    4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+commit 715ee5aa3a797737d390365b2c202cc9a0effea5
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 01:37:35 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/appl/sosui/report.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 71e34938f1228911657ebf00720712a17bc89ea9
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 01:36:44 2015 +0900
+
+    comment out a line to suppress warning: assigned but unused variable - tmh
+
+ lib/bio/appl/sosui/report.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit fc518f3826bf60d70ebdbd70acdba512f1462c6f
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 01:34:22 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/db/sanger_chromatogram/chromatogram.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 516c467dfb245d99c4f7f77e251c77ffc5d274ca
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 01:33:19 2015 +0900
+
+    suppress warning: instance variable @aqual not initialized
+
+ lib/bio/db/sanger_chromatogram/chromatogram.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 56d2e472196ba03ba6aa2a2bdf8d3de81272fa15
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 01:30:26 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/db/kegg/module.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit fb6b9b6578d08a87c1974e58f6d1f231b4ad52c0
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 01:28:05 2015 +0900
+
+    suppress "instance variable @XXX not initialized" warnings
+
+ lib/bio/db/kegg/module.rb |    8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+commit 9f70b8d54abd9adbd50d46a3176f23f51af01cc7
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 01:25:50 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/db/kegg/pathway.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 3844b9bb69e1f657c9b85bb20a4d209828b78b12
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 01:25:03 2015 +0900
+
+    suppress "instance variable @XXX not initialized" warnings
+
+ lib/bio/db/kegg/pathway.rb |    8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+commit 8d857e246eacb6c9f8fbbceaa2fba7f1211e2b86
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 01:20:13 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/db/fasta/defline.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit aadf285bc9e618b7813b42fd39e0b1966a04385c
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 01:18:43 2015 +0900
+
+    suppress defline.rb:393: warning: character class has duplicated range
+
+ lib/bio/db/fasta/defline.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 5297db11eb165885c4f15b914c2132c4122ae5a9
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 01:11:43 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ test/unit/bio/test_db.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 20381ad45c674c0844a92891cb8ae71edaa6e333
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 01:08:04 2015 +0900
+
+    suppress "warning: instance variable @tagsize not initialized"
+    
+     * test/unit/bio/test_db.rb: to suppress "warning: instance variable
+       @tagsize not initialized" when executing Bio::TestDB#test_fetch,
+       @tagsize is set in setup.
+
+ test/unit/bio/test_db.rb |    5 ++++-
+ 1 file changed, 4 insertions(+), 1 deletion(-)
+
+commit d194edfc68bc10fde11f2cf014a59113ddc63b24
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 00:59:21 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/data/codontable.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit fac51f540dc7b33cd3ec51f97b5cb1ea587a461e
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 00:57:28 2015 +0900
+
+    suppress warning: instance variable @reverse not initialized
+
+ lib/bio/data/codontable.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 4e85315f03e374157f832c8435d0d2f43cd969af
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 00:55:25 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/appl/iprscan/report.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit dafa7ce62378ff1605a295f8c620eb3a0a4a3c57
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 00:54:37 2015 +0900
+
+    suppress warning: instance variable @ipr_ids not initialized
+
+ lib/bio/appl/iprscan/report.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 52b6073997c1b26fea9d4aae3154b37575944d4d
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 00:50:43 2015 +0900
+
+    suppress "method redefined" warnings and fill RDoc for some methods
+
+ lib/bio/db/phyloxml/phyloxml_elements.rb |   46 +++++++++++++++++++++++-------
+ 1 file changed, 35 insertions(+), 11 deletions(-)
+
+commit 3d2e99fe993d76d5ece5bdbcd2e9541fa098c4dd
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 28 00:36:51 2015 +0900
+
+    suppress "instance variable @XXX not initialized" warnings
+
+ lib/bio/db/phyloxml/phyloxml_elements.rb |   88 +++++++++++++++---------------
+ 1 file changed, 44 insertions(+), 44 deletions(-)
+
+commit 02d4f98eae3934d8ad9c950b41132eb14653fe27
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Mar 26 20:33:35 2015 +0900
+
+    suppress warning: instance variable @uri not initialized
+
+ lib/bio/db/phyloxml/phyloxml_elements.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 94277712e9dd000c2d9bf5b6ebfd84d0f2fc3b59
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Mar 26 01:47:45 2015 +0900
+
+    suppress warning: instance variable @format not initialized
+
+ lib/bio/db/fastq.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit e61e1071e4bb7dd9ee995c3a7f864c2ef4384edd
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Mar 26 01:40:33 2015 +0900
+
+    suppress "instance variable not initialized" warnings
+    
+     * suppress warning: instance variable @sc_match not initialized
+     * suppress warning: instance variable @sc_mismatch not initialized
+     * suppress warning: instance variable @gaps not initialized
+     * suppress warning: instance variable @hit_frame not initialized
+     * suppress warning: instance variable @query_frame not initialized
+
+ lib/bio/appl/blast/format0.rb |   13 ++++++++++---
+ 1 file changed, 10 insertions(+), 3 deletions(-)
+
+commit 08c458c74a7a34e340e09053cbc0f9c071e27395
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Mar 26 01:09:16 2015 +0900
+
+    suppress warning: instance variable @pattern not initialized
+
+ lib/bio/appl/blast/format0.rb |    8 ++++++--
+ 1 file changed, 6 insertions(+), 2 deletions(-)
+
+commit 33d7eed180fd601972724f4b992f1a17c689ef62
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Mar 26 00:57:02 2015 +0900
+
+    Test bug fix: fix typo of test target method
+
+ test/network/bio/test_command.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 76a98bce1affac03483c08f803d4314b42a0a3d3
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Mar 26 00:32:25 2015 +0900
+
+    Incompatible Change: Bio::Command.make_cgi_params rejects single String
+    
+     * Incompatible Change: Bio::Command.make_cgi_params no longer accepts a
+       single String as a form. Use Hash or Array containing key-value pairs
+       as String objects. This change also affects Bio::Command.post_form
+       and Bio::Command.http_post_form which internally use this method.
+
+ lib/bio/command.rb            |    2 +-
+ test/unit/bio/test_command.rb |    9 +++++----
+ 2 files changed, 6 insertions(+), 5 deletions(-)
+
+commit b1612545a7516befd850a6d5925aa73bbaa4b4b0
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Mar 25 02:36:41 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/io/togows.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 4d5a419cc78ff2a79cff2812adc6f16f286204e8
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Mar 25 02:35:45 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ test/network/bio/io/test_togows.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit a8d2c4cac665b4bb8140df329a9cc1d6e5e2d02d
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Mar 25 02:35:03 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ test/unit/bio/io/test_togows.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit dd0967db3743789ea5aa48623df8d97f93062694
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Mar 25 02:33:49 2015 +0900
+
+    test_make_path: add test data using Symbol objects
+
+ test/unit/bio/io/test_togows.rb |    4 +++-
+ 1 file changed, 3 insertions(+), 1 deletion(-)
+
+commit e07158a60ca666b5d625408bcf8fa602fd8114a8
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Mar 25 02:22:31 2015 +0900
+
+    Bio::TogoWS::REST#entry: comma between IDs should NOT be escaped to %2C
+
+ lib/bio/io/togows.rb |   11 +++++++++--
+ 1 file changed, 9 insertions(+), 2 deletions(-)
+
+commit 98546289b2f2da2dc7f9586fd5e2942da4d8f3a8
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Mar 25 02:00:17 2015 +0900
+
+    Bug fix: search with offset did not work due to TogoWS server change
+    
+     * lib/bio/io/togows.rb: Bug fix: Bio::TogoWS::REST#search with offset
+       and limit did not work due to TogoWS server change about URI escape.
+       For example,
+       http://togows.org/search/nuccore/Milnesium+tardigradum/2%2C3 fails,
+       http://togows.org/search/nuccore/Milnesium+tardigradum/2,3 works fine.
+
+ lib/bio/io/togows.rb |   24 +++++++++++++++++++++---
+ 1 file changed, 21 insertions(+), 3 deletions(-)
+
+commit 7097f80e315a0a6332e7a76a5bb261649e8dcc1a
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Mar 25 01:33:26 2015 +0900
+
+    Bug fix due to TogoWS convert method spec change
+    
+     * lib/bio/io/togows.rb: Bug fix: Bio::TogoWS::REST#convert did not work
+       because of the spec change of TogoWS REST API.
+
+ lib/bio/io/togows.rb |    7 +++----
+ 1 file changed, 3 insertions(+), 4 deletions(-)
+
+commit 1a9b1063af4c0b32cd287d4a2c2466343aeddb98
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Mar 25 01:30:34 2015 +0900
+
+    improve tests for bio/command.rb for methods using http protocol
+
+ test/network/bio/test_command.rb |   67 ++++++++++++++++++++++++++++++++++++--
+ 1 file changed, 65 insertions(+), 2 deletions(-)
+
+commit c63920e4d8569e3eaef201d4d60fcddfa15f1f34
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Mar 25 01:30:06 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/command.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 1683edac0e9ecbf819ffcd332a6db2d25c2d596a
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Mar 25 01:28:28 2015 +0900
+
+    new methods Bio::Command.http_post and Bio::Command.post to post raw data
+
+ lib/bio/command.rb |   61 ++++++++++++++++++++++++++++++++++++++++++++++++++++
+ 1 file changed, 61 insertions(+)
+
+commit a40157205282e148bf3a2e43aed1e08d713fb598
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Mar 24 00:46:23 2015 +0900
+
+    suppress warnings "instance variable @circular not initialized"
+
+ lib/bio/util/restriction_enzyme/range/sequence_range.rb |    4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+commit abcac8de85c9606f6a1879fe9d2ae559911708c9
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Mar 24 00:29:42 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ test/unit/bio/io/flatfile/test_autodetection.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 1b5bf586af238b712a9f640087421fd299376c2d
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Mar 24 00:28:38 2015 +0900
+
+    suppress warning: assigned but unused variable - length
+
+ test/unit/bio/io/flatfile/test_autodetection.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 5497068d17c2794ab2b6ef1e603e5478a86537c6
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Mar 24 00:22:54 2015 +0900
+
+    add/modify assertions to suppress "unused variable" warnings
+
+ test/unit/bio/db/genbank/test_genbank.rb |   12 +++++++++---
+ 1 file changed, 9 insertions(+), 3 deletions(-)
+
+commit d5bafd8b7ee28ab0418b09fd6dd47abcb9eb1ee5
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 23:57:56 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/appl/blast.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit bbd60d1aae7c894f914b7265d2de22fea5eb3faf
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 23:56:42 2015 +0900
+
+    suppress warning: assigned but unused variable - dummy
+
+ lib/bio/appl/blast.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 4a91502ccf14ab8655645144120aa97d0c8313a5
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 20:32:59 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/shell/setup.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit c437a4078ff8e2869b9c1ab3543022db373a93c3
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 20:32:20 2015 +0900
+
+    suppress warning: instance variable @mode not initialized
+
+ lib/bio/shell/setup.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 8967cf280d5ca8491d57a11e4f3ffab7369c4ea8
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 20:28:50 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/shell/irb.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 42b5f030067be4bc9c53ccb4c06ccfc5e8d9df03
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 20:28:27 2015 +0900
+
+    change deprecated method File.exists? to File.exist?
+
+ lib/bio/shell/irb.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 389ad2f311f161f235db2373aeb2f5500b1ea65f
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 20:27:01 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/shell/interface.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit de5949798d66c16d2b5e2cf8ba7192049ec99c5b
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 20:26:37 2015 +0900
+
+    change deprecated method File.exists? to File.exist?
+
+ lib/bio/shell/interface.rb |    6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+commit c8907059a716a8778e333755c8fb53bb2a0c7158
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 20:24:58 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/shell/core.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 1fe5903f8acd8045d203465a099a45218e7e3891
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 20:24:25 2015 +0900
+
+    change deprecated method File.exists? to File.exist?
+
+ lib/bio/shell/core.rb |   10 +++++-----
+ 1 file changed, 5 insertions(+), 5 deletions(-)
+
+commit 929207c6f186c81f076fab9b1bbbd23c4b966f4e
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 20:20:05 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ test/unit/bio/db/pdb/test_pdb.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit e75c57fcd7abc56ba6fcbf1996e491aca890f5b1
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 20:19:30 2015 +0900
+
+    suppress "assigned but unused variable" warnings
+
+ test/unit/bio/db/pdb/test_pdb.rb |   21 ++++++++++++++-------
+ 1 file changed, 14 insertions(+), 7 deletions(-)
+
+commit b458301f47322c265fce27efd0ed71443c17d9d7
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 18:34:12 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/shell/plugin/entry.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit c3f909fe06b82b3cbd4bdcbcdef668fc0727be9d
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 18:33:30 2015 +0900
+
+    change deprecated method File.exists? to File.exist?
+
+ lib/bio/shell/plugin/entry.rb |    4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+commit 7ba6349c2446aa03b843a2a8fb49505c8f63c6ca
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 18:20:44 2015 +0900
+
+    change deprecated method File.exists? to File.exist?
+
+ lib/bio/appl/meme/mast.rb |    8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+commit e7f78ea3c3fb1b78adcc6ae13f450cf2cda361cd
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 18:10:27 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/db/phyloxml/phyloxml_writer.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit b32eae0050a73bd5a2931c17a6694f494ad00bb2
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Mar 23 18:07:54 2015 +0900
+
+    suppress warning: mismatched indentations at 'end' with 'def' at 166
+
+ lib/bio/db/phyloxml/phyloxml_writer.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit bd735347283ce5d332245d0349186f300800a43f
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 21 12:57:03 2015 +0900
+
+    remove duplicated line and suppress Ruby 2.2 warning
+
+ setup.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 68ad10e178594691c77ba4b97c2449fecf0ac9de
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 21 12:50:46 2015 +0900
+
+    Ruby 1.9 support: suppress "shadowing outer local variable" warnings
+
+ setup.rb |   10 +++++-----
+ 1 file changed, 5 insertions(+), 5 deletions(-)
+
+commit 2343482078aec8373f7a2eb8ed4d7c44119f809c
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 21 12:16:45 2015 +0900
+
+    Ruby 2.2 support: Config was renamed to RbConfig
+
+ setup.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit d512712745142d6c6ebe9a6ef51c8c4773bd7c2c
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 21 11:52:47 2015 +0900
+
+    Ruby 1.9 support: suppress "shadowing outer local variable" warnings
+
+ lib/bio/db/embl/format_embl.rb |    6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+commit bfa75df9047ab6855c931558f6bf9fdbb1c3c288
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 21 11:36:01 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/io/flatfile/buffer.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit d6fbaa0c555117ebadd46e284ae357586856102d
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 21 11:35:07 2015 +0900
+
+    Ruby 1.9 support: suppress warning: shadowing outer local variable - fobj
+
+ lib/bio/io/flatfile/buffer.rb |    8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+commit 0083d3284ec181f4bcc3144f76b12f9d52e3eff6
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 21 11:29:39 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/io/fastacmd.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit d4909c0e80e572a639edba07388e430c7f5d6ce8
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 21 11:29:01 2015 +0900
+
+    remove old sample script in "if $0 == __FILE__" block
+
+ lib/bio/io/fastacmd.rb |   15 ---------------
+ 1 file changed, 15 deletions(-)
+
+commit 8171162d0a3991d5f0d9a8bccee57250248d6d3d
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 21 11:15:10 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/db/go.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit ed7c9a5335ef59399f3098311f47b8dec519281a
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 21 11:14:19 2015 +0900
+
+    Ruby 1.9 support: suppress warnings: "shadowing outer local variable - goid"
+
+ lib/bio/db/go.rb |    4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+commit dd543068b046c9a0c2a40159c830c92b680244f1
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 21 11:03:08 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/db/phyloxml/phyloxml_elements.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 4c74a6e3aeca30820b0be61e867c9201445542ec
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 21 10:24:40 2015 +0900
+
+    suppress warning: mismatched indentations at 'end' with 'class'
+
+ lib/bio/db/phyloxml/phyloxml_elements.rb |    4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+commit ee4ffdc748c1f9f45e97ff7f0da8350c5468c333
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 21 10:08:30 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/db/phyloxml/phyloxml_parser.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 46a4edc8729ff836ae28d11f1503c9923275b9f6
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Mar 21 10:00:04 2015 +0900
+
+    Ruby 1.9 support: suppress warning "shadowing outer local variable - flag"
+
+ lib/bio/db/phyloxml/phyloxml_parser.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit db3552c683edf79adbfa5ed897f5ef91e8417585
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Mar 20 16:33:45 2015 +0900
+
+    Bug fix: Bio::PhyloXML::Parser.open_uri did not return block return value
+    
+     * Bug fix: Bio::PhyloXML::Parser.open_uri did not return block
+       return value when giving block.
+     * Suppress warning "assigned but unused variable - ret"
+
+ lib/bio/db/phyloxml/phyloxml_parser.rb |    1 +
+ 1 file changed, 1 insertion(+)
+
+commit 84c2c4e94352cc9cef982d3b505b4f439617e01e
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Mar 20 16:21:49 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/appl/genscan/report.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 05c55d0aaf1dc130ac04155622ccebb3394fc3c0
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Mar 20 16:21:06 2015 +0900
+
+    Ruby 1.9 support: suppress warning "shadowing outer local variable - i"
+
+ lib/bio/appl/genscan/report.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 5edcc1c97ca7c292fa6551509570daf68ac36837
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Mar 20 16:13:57 2015 +0900
+
+    Ruby 1.9 support: suppress warning "shadowing outer local variable - y"
+
+ lib/bio/appl/blast/format0.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 813d53a06258244a47784697e8fc95f1f15db8da
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Mar 20 16:03:19 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/io/das.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit b6ae4a423dd763969c8e18ca6a578fd0600d6159
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Mar 20 16:02:20 2015 +0900
+
+    Ruby 1.9 support: suppress "warning: shadowing outer local variable - e"
+
+ lib/bio/io/das.rb |   80 ++++++++++++++++++++++++++---------------------------
+ 1 file changed, 40 insertions(+), 40 deletions(-)
+
+commit 7fa75a644167dd8c189f681e29c1cf5f1bf2fe0b
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Mar 20 15:36:00 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ lib/bio/shell/plugin/seq.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 051aba1519d71f1205363c4421feb6c06881ab0c
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Mar 20 15:29:02 2015 +0900
+
+    Bug fix: Ruby 1.9 support: did not yield the last part of the string
+    
+     * lib/bio/shell/plugin/seq.rb: Bug fix: Ruby 1.9 support:
+       String#step and #skip (extended by bioruby-shell) did not yield
+       the last part of the string due to a change from Ruby 1.8 to 1.9.
+     * Suppress warning message "shadowing outer local variable - i"
+
+ lib/bio/shell/plugin/seq.rb |   12 +++++++-----
+ 1 file changed, 7 insertions(+), 5 deletions(-)
+
+commit a9f2bff92de58c2ab4cefc67e721d3ad69e9de98
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Mar 20 15:09:16 2015 +0900
+
+    Ruby 2.2 support: suppress a "shadowing outer local variable" warning
+
+ lib/bio/alignment.rb |    6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+commit d0bcc8766d91eb7cacea2a6d5b32b3e0b3c5ce56
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Mar 20 14:31:04 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ test/unit/bio/test_alignment.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 0c8fa8fd558088822a98e11b6fa4bec9b37ebec7
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Mar 20 14:26:38 2015 +0900
+
+    Ruby 2.2 support: comment out duplicated line to suppress warning
+    
+     * Ruby 2.2 support: test/unit/bio/test_alignment.rb:
+       Suppress warning: duplicated key at line 182 ignored: "t"
+
+ test/unit/bio/test_alignment.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit ab17c40e1ce492dc924205e8e2f90d31adae4464
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Mar 20 14:18:08 2015 +0900
+
+    Ruby 2.2 support: some tests did not run with test-unit gem
+    
+     * Ruby 2.2 support: test/unit/bio/db/test_fastq.rb
+       Support for test-unit gem bundled in Ruby 2.2.
+       See commit log b9488a64abb780c5e9b6cd28e8264bad399fa749 for details.
+
+ test/unit/bio/db/test_fastq.rb |   18 ++++++++++++++----
+ 1 file changed, 14 insertions(+), 4 deletions(-)
+
+commit ea668d73c18e3df33625cba4352ad5f6966e0eb4
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Mar 20 14:03:43 2015 +0900
+
+    delete obsolete $Id:$ line
+
+ test/unit/bio/appl/sim4/test_report.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 1abb8d362a0f2443b48923bcccba3d7d0caa1f1d
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Mar 20 13:57:33 2015 +0900
+
+    Ruby 2.2 support: some tests did not run with test-unit gem
+    
+     * Ruby 2.2 support: test/unit/bio/appl/sim4/test_report.rb
+       Support for test-unit gem bundled in Ruby 2.2.
+       See commit log b9488a64abb780c5e9b6cd28e8264bad399fa749 for details.
+
+ test/unit/bio/appl/sim4/test_report.rb |   62 +++++++++++++++++++++++---------
+ 1 file changed, 46 insertions(+), 16 deletions(-)
+
+commit b9488a64abb780c5e9b6cd28e8264bad399fa749
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Mar 20 13:13:28 2015 +0900
+
+    Ruby 2.2 support: some tests did not run with test-unit gem
+    
+     *  Ruby 2.2 support: test/unit/bio/appl/blast/test_report.rb:
+        With test-unit gem bundled in Ruby 2.2, test methods inherited
+        from a parent class and executed in the parent class do not
+        run in the child class. To avoid the behavior, test methods
+        are moved to modules and test classes are changed to include
+        the modules.
+
+ test/unit/bio/appl/blast/test_report.rb |  156 ++++++++++++++++++++++---------
+ 1 file changed, 110 insertions(+), 46 deletions(-)
+
+commit febe8bbf614e530f597d7306d33df5f5f4ee6699
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Mar 19 00:55:09 2015 +0900
+
+    try to use bio-old-biofetch-emulator gem
+    
+     * bin/br_biofetch.rb: try to use bio-old-biofetch-emulator gem.
+       Without bio-old-biofetch-emulator, the program exits with error
+       message when default BioRuby BioFetch server is specified.
+
+ bin/br_biofetch.rb |   19 +++++++++++++++++++
+ 1 file changed, 19 insertions(+)
+
+commit 08450e0a35cbf5596dd30238d23aa7a7296c8f67
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Mar 19 00:36:10 2015 +0900
+
+    do not repeat default_url and another_url
+
+ bin/br_biofetch.rb |   14 ++++++++++----
+ 1 file changed, 10 insertions(+), 4 deletions(-)
+
+commit 8e39d3411405b09cc6ea55ba31e5206536ebf59d
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Mar 18 23:57:59 2015 +0900
+
+    Revert e29fc5fadbe0dae6528cf49637496dc2df3ec0dc
+    
+     * bin/br_biofetch.rb: revert e29fc5fadbe0dae6528cf49637496dc2df3ec0dc
+       because the old deprecated bioruby biofetch server can be emulated
+       by bio-old-biofetch-emulator gem package.
+
+ bin/br_biofetch.rb |   15 ++++++++-------
+ 1 file changed, 8 insertions(+), 7 deletions(-)
+
+commit 849c38931a64b7ff2ba7ec46a495e65a99a869fb
+Author: Ben J. Woodcroft <donttrustben near gmail.com>
+Date:   Wed Aug 8 09:44:09 2012 +1000
+
+    add FastaFormat#first_name method
+
+ lib/bio/db/fasta.rb            |   17 ++++++++++++++++
+ test/unit/bio/db/test_fasta.rb |   42 +++++++++++++++++++++++++++++++++++++++-
+ 2 files changed, 58 insertions(+), 1 deletion(-)
+
+commit 888a70508c0392cae89021feba5c4a6a62228a11
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Nov 14 15:08:35 2014 +0900
+
+    fix typo
+    
+     * fix typo. Thanks to Iain Barnett who reported the bug in
+       https://github.com/bioruby/bioruby/pull/93
+       (c4843d65447f6a434da523c9c313f34d025f36f8)
+
+ lib/bio/sequence/compat.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit afc6df190109649e8eb11b2af1184ddfcf5327d3
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Nov 14 14:29:42 2014 +0900
+
+    add documentation when gc_percent is not enough
+
+ lib/bio/sequence/na.rb |    8 ++++++++
+ 1 file changed, 8 insertions(+)
+
+commit bb63f67f2dfe6dba5c70ada033ca0cc1ecaa7783
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Nov 13 21:43:00 2014 +0900
+
+    Add tests for Bio::PubMed#search, query, pmfetch
+    
+     * Add tests for Bio::PubMed#search, query, pmfetch, although
+       they will be deprecated in the future.
+     * This commit and commit bfe4292c51bba5c4032027c36c35e98f28a9605a
+       are inspired by https://github.com/bioruby/bioruby/pull/76
+       (though the pull request have not been merged), and the commits
+       fix the issue https://github.com/bioruby/bioruby/issues/75.
+       Thanks to Paul Leader who reported the issue and the pull request.
+
+ test/network/bio/io/test_pubmed.rb |   49 ++++++++++++++++++++++++++++++++++++
+ 1 file changed, 49 insertions(+)
+
+commit 74edba100da83c27f2edb7a9edc9ec98265a7cff
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Nov 13 12:05:12 2014 +0900
+
+    Change default tool and email values
+    
+     * Default "tool" and "email" values are changed to "bioruby" and
+       "staff@bioruby.org" respectively. Now, the author of a script
+       do not need to set his/her email address unless the script makes
+       excess traffic to NCBI.
+     * Update RDoc documentation
+
+ lib/bio/io/ncbirest.rb |   48 +++++++++++++++++++++++++++++++++++++++++++-----
+ 1 file changed, 43 insertions(+), 5 deletions(-)
+
+commit bfe4292c51bba5c4032027c36c35e98f28a9605a
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Nov 13 11:54:53 2014 +0900
+
+    Bug fix: use NCBI E-Utilities instead of old deprecated API
+    
+     * Bio::PubMed#search, query, pmfetch: remove old code using deprecated
+       and/or unofficial web API, and change use esearch or efetch methods
+       which use NCBI E-utilities. These methods will be deprecated in the
+       future. To indicate this, show warning message if $VERBOSE is true.
+     * Update RDoc documentation
+
+ lib/bio/io/pubmed.rb |  157 ++++++++++++++++++++++++--------------------------
+ 1 file changed, 76 insertions(+), 81 deletions(-)
+
+commit d78173a6eb6d8177e733decc0b8137fac067aa82
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Nov 11 17:41:32 2014 +0900
+
+    remove unused $Id:$ line
+
+ bin/br_biofetch.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit e29fc5fadbe0dae6528cf49637496dc2df3ec0dc
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Nov 11 17:31:38 2014 +0900
+
+    Change default server to EBI Dbfetch server; remove BioRuby BioFetch server
+    
+     * Change default server to EBI Dbfetch server.
+     * The BioRuby BioFetch server is removed. When "-r" option (force to use
+       BioRuby server) is specified, warning message is shown, and the program
+       exits with code 1 (abnormal exit).
+     * Usage message is also changed.
+
+ bin/br_biofetch.rb |   15 +++++++--------
+ 1 file changed, 7 insertions(+), 8 deletions(-)
+
+commit 94ecac33e87e444d9fe991340c2d8f3709bc6d90
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Nov 11 17:19:30 2014 +0900
+
+    fix documentation reflecting recent changes of Bio::Fetch
+
+ lib/bio/io/fetch.rb |   33 ++++++++++++++++++++-------------
+ 1 file changed, 20 insertions(+), 13 deletions(-)
+
+commit 06a9db014614818ef35108928415ef18e8c8ae2c
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Nov 11 16:41:26 2014 +0900
+
+    documentation about incompatible changes of Bio::Fetch
+
+ RELEASE_NOTES.rdoc |   22 ++++++++++++++++++++++
+ 1 file changed, 22 insertions(+)
+
+commit 6d94e949b6d325f27b45b816a8305f828d049ec6
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Nov 11 16:35:50 2014 +0900
+
+    Issue about Bio::Fetch and BioRuby BioFetch server is resolved
+    
+     * Issue about Bio::Fetch is resolved by recent commits.
+    
+     * The BioRuby BioFetch server is deprecated. There is no hope to restart
+       the service again. EBI Dbfetch server is an alternative.
+
+ KNOWN_ISSUES.rdoc |    9 ---------
+ 1 file changed, 9 deletions(-)
+
+commit 699cd3ff136310a551d30e0ddd7fbe66e483b5be
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Nov 11 15:27:11 2014 +0900
+
+    update RDoc documents for Bio::Fetch
+
+ lib/bio/io/fetch.rb |   61 +++++++++++++++++++++++++++++++++------------------
+ 1 file changed, 40 insertions(+), 21 deletions(-)
+
+commit c7837f8e5ee2cc1c3085da74567a2b25280bbb8f
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Nov 11 14:48:48 2014 +0900
+
+    Incompatibile change: remove Bio::Fetch.query; add Bio::Fetch::EBI.query
+    
+     * Incompatible change: remove a class method Bio::Fetch.query because
+       default server URL in Bio::Fetch is deprecated.
+    
+     * New class method: Bio::Fetch::EBI.query. This can be used as an
+       alternative method of deprecated Bio::Fetch.query method.
+
+ lib/bio/io/fetch.rb |   35 ++++++++++++++++++-----------------
+ 1 file changed, 18 insertions(+), 17 deletions(-)
+
+commit f9048684acaff0fcd00b458a946d5f692706325b
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Nov 11 14:24:22 2014 +0900
+
+    Incompatible change: Default server in Bio::Fetch.new is deperecated
+    
+     * Incompatible change: Default server URL in Bio::Fetch.new is deprecated.
+       Users must explicitly specify the URL. Alternatively, users must change
+       their code to use Bio::Fetch::EBI.
+    
+     * New class Bio::Fetch::EBI, EBI Dbfetch client. This acts the same as
+       Bio::Fetch.new(Bio::Fetch::EBI::URL) with default database name
+       "ena_sequence".
+
+ lib/bio/io/fetch.rb |   36 +++++++++++++++++++++++++++++++++---
+ 1 file changed, 33 insertions(+), 3 deletions(-)
+
+commit e8919f4f57fc545ca194bebb08c11159b36071cb
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Nov 11 13:43:28 2014 +0900
+
+    removed unused variables
+
+ lib/bio/io/fetch.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit faec95656b846a7a17cd6a1dbc633dda63cb5b6e
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Nov 11 11:44:00 2014 +0900
+
+    Updated URL of EMBL-EBI Dbfetch
+
+ lib/bio/io/fetch.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 85be893655f68aafbf7e13badd20bf7f26cd7328
+Author: Jose Irizarry <protechpr@gmail.com>
+Date:   Mon Dec 24 12:30:55 2012 -0400
+
+    Update lib/bio/io/fetch.rb
+    
+    Use EBI's dbfetch endpoint as default since BioRuby's endpoint has been disabled for a while now.
+
+ lib/bio/io/fetch.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 163cc06547beed653e19b8c6e71e829d85f2f99c
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Oct 21 16:42:30 2014 +0900
+
+    Doc bug fix: wrong sample code
+
+ lib/bio/appl/paml/codeml.rb |    4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+commit 97143139d2d4a66366576a8e62518e93fa5afccf
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Oct 21 15:47:52 2014 +0900
+
+    Prevent to repeat calculations of total bases
+    
+     * Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Prevent to
+       repeat calculations of total bases.
+
+ lib/bio/sequence/na.rb |   20 ++++++++++++--------
+ 1 file changed, 12 insertions(+), 8 deletions(-)
+
+commit b5dbd882e000842fef65e10290b379bfafdddf06
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Oct 21 15:41:13 2014 +0900
+
+    Documentation bug fix: Return value is Rational or Float.
+    
+     * Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Return value
+       is Rational or Float in recent versions of Ruby. Documentation added for
+       the treatment of "u" and to return 0.0 if there are no bases.
+       Reported by ctSkennerton (https://github.com/bioruby/bioruby/issues/73 ).
+
+ lib/bio/sequence/na.rb |   47 +++++++++++++++++++++++++++++++++++++++++++----
+ 1 file changed, 43 insertions(+), 4 deletions(-)
+
+commit 3ba98d52ce57488e604dd7ac388a874e5b40ae9d
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Aug 12 00:58:38 2014 +0900
+
+    regenerate bioruby.gemspec with rake regemspec
+
+ bioruby.gemspec |   14 ++++++--------
+ 1 file changed, 6 insertions(+), 8 deletions(-)
+
+commit a9724d339582952b40c928beccf91376d4e63315
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Aug 5 19:20:42 2014 +0900
+
+    Update URIs
+    
+     * Update URIs.
+     * Remove links to RubyForge and RAA which have already been closed.
+     * Add some words for Ruby 1.9 or later.
+
+ README.rdoc |   24 +++++++++++-------------
+ 1 file changed, 11 insertions(+), 13 deletions(-)
+
+commit 5f3569faaf89ebcd2b2cf9cbe6b3c1f0544b2679
+Author: Iain Barnett <iainspeed@gmail.com>
+Date:   Wed Mar 5 02:11:07 2014 +0000
+
+    Refactor Bio::AminoAcid#weight: Early return clearer and idiomatic.
+
+ lib/bio/data/aa.rb |   26 ++++++++++++--------------
+ 1 file changed, 12 insertions(+), 14 deletions(-)
+
+commit c229a20887fcb6df9a7ba49ad5a23e175056fa8d
+Author: Iain Barnett <iainspeed@gmail.com>
+Date:   Wed Mar 5 02:02:45 2014 +0000
+
+    Fixed the stack level too deep errors by using Hash#invert.
+
+ lib/bio/data/aa.rb |   18 +-----------------
+ 1 file changed, 1 insertion(+), 17 deletions(-)
+
+commit 08dd928df30f5b39c255f9f70dbed8410d395cdf
+Author: Iain Barnett <iainspeed@gmail.com>
+Date:   Tue Mar 4 01:22:51 2014 +0000
+
+    Refactored to shorten, remove rescues, and clarify.
+
+ lib/bio/alignment.rb |   19 +++++++------------
+ 1 file changed, 7 insertions(+), 12 deletions(-)
+
+commit 112aa284cb1ebecc1d5de186edf2b385649a7268
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Mar 19 14:48:32 2014 +0900
+
+    Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008)
+    
+    * Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008).
+      Thanks to a researcher who reports the patch via email.
+
+ lib/bio/db/pdb/pdb.rb |    4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+commit ecd5e0c86b04aa918b71c859568425fa39ebbde5
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Jan 18 04:22:51 2014 +0900
+
+    suppress "source :rubygems is deprecated" warning
+
+ gemfiles/Gemfile.travis-jruby1.8 |    2 +-
+ gemfiles/Gemfile.travis-jruby1.9 |    2 +-
+ gemfiles/Gemfile.travis-ruby1.8  |    2 +-
+ gemfiles/Gemfile.travis-ruby1.9  |    2 +-
+ 4 files changed, 4 insertions(+), 4 deletions(-)
+
+commit 4bda345fe3de9cf1b64c26f3dca1cb3727c946d0
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Jan 18 04:22:03 2014 +0900
+
+    gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci
+    
+     * gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci
+     * .travis.yml is modified to use gemfile/Gemfile.travis-rbx for rbx.
+
+ .travis.yml                 |    4 ++--
+ gemfiles/Gemfile.travis-rbx |   16 ++++++++++++++++
+ 2 files changed, 18 insertions(+), 2 deletions(-)
+ create mode 100644 gemfiles/Gemfile.travis-rbx
+
+commit dcff544d6d0a967eb853b97ba9faa30eaa6fd9dc
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Jan 18 04:13:50 2014 +0900
+
+    .travis.yml: fix mistakes
+
+ .travis.yml |    8 +-------
+ 1 file changed, 1 insertion(+), 7 deletions(-)
+
+commit f0f67f295f05a5e1e30c479621c25498e2c8f6f2
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Jan 18 03:56:54 2014 +0900
+
+    Ruby 2.1 workaround: Array#uniq does not always choose the first item
+    
+     * Ruby 2.1 workaround: Array#uniq does not always choose the first item.
+       Thanks to Andrew Grimm who reported the issue.
+       (https://github.com/bioruby/bioruby/issues/92 )
+       Note that the behavior change is also regarded as a bug in Ruby and
+       is fixed. (https://bugs.ruby-lang.org/issues/9340 )
+
+ test/unit/bio/test_pathway.rb |   35 +++++++++++++++++++++++++----------
+ 1 file changed, 25 insertions(+), 10 deletions(-)
+
+commit e92e09edf5904f51d3e73e61d13fce4159a543c5
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Jan 18 03:32:05 2014 +0900
+
+    .travis.yml: workaround to avoid error in Ruby 1.8.7 and jruby-18mode
+    
+     * workaround to avoid error in Ruby 1.8.7 and jruby-18mode
+       (reference: https://github.com/rubygems/rubygems/pull/763 )
+
+ .travis.yml |    2 ++
+ 1 file changed, 2 insertions(+)
+
+commit 655a675096962710896fb458afcac9b5deb1fa5f
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Jan 18 03:22:44 2014 +0900
+
+    .travis.yml: rbx version is changed to 2.2.3
+    
+     * rbx version is changed to 2.2.3
+     * add dependent gems for rbx platforms, described in
+       http://docs.travis-ci.com/user/languages/ruby/
+
+ .travis.yml |    7 ++++++-
+ 1 file changed, 6 insertions(+), 1 deletion(-)
+
+commit d2f5b882d5e2acf35d0c783a56aa47533b9f2bd5
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Jan 11 03:46:45 2014 +0900
+
+    .travis.yml: change ruby versions for tar and gem integration tests
+    
+     * In tar and gem integration tests, Ruby versions are changed to
+       MRI 2.0.0 and jruby-19mode.
+     * Add jruby-18mode
+     * Add rbx-2.1.1
+
+ .travis.yml |   32 ++++++++++++++++++++++----------
+ 1 file changed, 22 insertions(+), 10 deletions(-)
+
+commit 71991af394b937d35e2bbbc84a21e65ffba7714d
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jan 9 00:57:25 2014 +0900
+
+    .travis.yml: Add 2.1.0 and 2.0.0, remove rbx-XXmode
+    
+     * Add 2.1.0 and 2.0.0
+     * Remove rbx-18mode and rbx-19mode
+     * 1.9.2 is moved from "include" to "rvm".
+     * 1.8.7 is moved from "rvm" to "include", and remove
+       "gemfiles/Gemfile.travis-ruby1.8" line from "gemfile".
+     * Remove "exclude" and simplify build matrix.
+     * Suggested by agrimm in https://github.com/bioruby/bioruby/pull/91
+
+ .travis.yml |   27 +++++----------------------
+ 1 file changed, 5 insertions(+), 22 deletions(-)
+
+commit 80966bc875cc6e01978b6c9272f6ddd8f344aa62
+Author: Brynjar Smari Bjarnason <binni@binnisb.com>
+Date:   Mon Dec 9 14:57:42 2013 +0100
+
+    Bug fix: Only do gsub on bio_ref.reference.authors if it exists.
+    
+     * Bug fix: Only do gsub on bio_ref.reference.authors if it exists.
+       Fix https://github.com/bioruby/bioruby/issues/89
+
+ lib/bio/db/biosql/sequence.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 3337bbd3be2affcef44202a0c924b3e22dafd856
+Author: Brynjar Smari Bjarnason <binni@binnisb.com>
+Date:   Mon Dec 9 14:55:24 2013 +0100
+
+    Bug fix: Missing require when generating genbank output for BioSQL sequence
+    
+     * Bug fix: Missing require when generating genbank output for BioSQL
+       sequence. Partly fix https://github.com/bioruby/bioruby/issues/89
+
+ lib/bio/db/biosql/biosql_to_biosequence.rb |    1 +
+ 1 file changed, 1 insertion(+)
+
+commit 1f829ae8e8c89c5c24e7bc7aa8ed5fa25e8ef6c2
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Nov 23 18:17:43 2013 +0900
+
+    Benchmark example1-seqnos.aln in addition to example1.aln
+    
+     * sample/benchmark_clustalw_report.rb: Benchmark parsing speed of
+       example1-seqnos.aln in addition to example1.aln.
+
+ sample/benchmark_clustalw_report.rb |   28 ++++++++++++++++++++++------
+ 1 file changed, 22 insertions(+), 6 deletions(-)
+
+commit c5d3e761859fa72c18f9301d84c31070f35e733e
+Author: Andrew Grimm <andrew.j.grimm@gmail.com>
+Date:   Tue Sep 17 21:15:56 2013 +1000
+
+    Add benchmark script for Bio::ClustalW::Report.
+
+ sample/benchmark_clustalw_report.rb |   31 +++++++++++++++++++++++++++++++
+ 1 file changed, 31 insertions(+)
+ create mode 100644 sample/benchmark_clustalw_report.rb
+
+commit 07c14e94cdb94cf9ba8a2bf050572ae1cbf24cff
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Nov 23 17:49:54 2013 +0900
+
+    Bio::ClustalW::Report#do_parse speed optimization
+    
+     * Bio::ClustalW::Report#do_parse speed optimization. Thanks to
+       Andrew Grimm who indicates the optimization point.
+       (https://github.com/bioruby/bioruby/pull/86 )
+     * "$" in the regular expression is changed to "\z". In this context,
+       the "$" was intended to be matched with only the end of the string.
+
+ lib/bio/appl/clustalw/report.rb |    4 +++-
+ 1 file changed, 3 insertions(+), 1 deletion(-)
+
+commit 6a78028d4f595ecb5b4600d0f238b07a2d80bdd5
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Nov 23 15:52:15 2013 +0900
+
+    New test data: ClustalW with -SEQNOS=ON option
+    
+     * test/data/clustalw/example1-seqnos.aln: New test data: ClustalW
+       running with -SEQNOS=ON option.
+     * Bio::TestClustalWReport::TestClustalWReportSeqnos: new test class
+       that parses the above data.
+
+ test/data/clustalw/example1-seqnos.aln     |   58 ++++++++++++++++++++++++++++
+ test/unit/bio/appl/clustalw/test_report.rb |   11 ++++++
+ 2 files changed, 69 insertions(+)
+ create mode 100644 test/data/clustalw/example1-seqnos.aln
+
+commit f5da0bbb4b1639616bb8c63ff8c58840e140ef8b
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Nov 23 15:35:31 2013 +0900
+
+    Simplify test data path in setup
+    
+     * Bio::TestClustalWReport::TestClustalWReport#setup: simplify test data
+       filename path.
+     * Modify indentes and void lines.
+
+ test/unit/bio/appl/clustalw/test_report.rb |   10 +++-------
+ 1 file changed, 3 insertions(+), 7 deletions(-)
+
+commit 8f0bea1d3252d0de9e2d91dc31ef8a9552c2d758
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Nov 23 15:21:38 2013 +0900
+
+    Common test methods are moved to a module
+    
+     * New namespace module Bio::TestClustalWReport.
+     * Common test methods are moved to CommonTestMethods,
+       and test classes using the methods include it.
+     * The test_sequences method is split into two methods
+       CommonTestMethods#test_sequence0 and test_sequence1.
+
+ test/unit/bio/appl/clustalw/test_report.rb |   97 +++++++++++++++-------------
+ 1 file changed, 53 insertions(+), 44 deletions(-)
+
+commit edda65b8fb32c2eee6b0652074981c31aa68b0eb
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Aug 23 23:51:59 2013 +0900
+
+    Test bug fix: Read test file with binary mode to avoid encoding error
+    
+     * Test bug fix: Read test file with binary mode to avoid string encoding
+       error. Thanks to nieder (github.com/nieder) who reports the bug.
+       (https://github.com/bioruby/bioruby/issues/84)
+
+ test/unit/bio/db/test_phyloxml.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 011d6fe5f016408891c5da3143c83e2564ccbf27
+Author: meso_cacase <y-naito@dbcls.rois.ac.jp>
+Date:   Fri Apr 5 01:13:27 2013 +0900
+
+    Modified siRNA design rules by Ui-Tei and Reynolds
+    
+     * Ui-Tei rule: Avoided contiguous GCs 10 nt or more.
+     * Reynolds rule: Total score of eight criteria is calculated.
+       * Returns numerical score for functional siRNA instead of returning 'true'.
+       * Returns 'false' for non-functional siRNA, as usual.
+     * Unit tests are modified to reflect these changes.
+
+ lib/bio/util/sirna.rb            |   92 +++++++++++++++++++++++++++++++-------
+ test/unit/bio/util/test_sirna.rb |   44 +++++++++---------
+ 2 files changed, 98 insertions(+), 38 deletions(-)
+
+commit b6e7953108ebf34d61bc79ee4bdae1092cfe339f
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jun 28 15:40:57 2013 +0900
+
+    Use Bio::UniProtKB instead of Bio::UniProt
+    
+     * Use Bio::UniProtKB instead of Bio::UniProt.
+     * Test class names are also changed from UniProt to UniProtKB.
+
+ test/unit/bio/db/embl/test_uniprotkb_new_part.rb |   22 +++++++++++-----------
+ 1 file changed, 11 insertions(+), 11 deletions(-)
+
+commit cddd35cf8d64abfff8bd6a8372d019fc4c32848c
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jun 28 15:26:20 2013 +0900
+
+    rename test/unit/bio/db/embl/test_uniprot_new_part.rb to test_uniprotkb_new_part.rb
+
+ test/unit/bio/db/embl/test_uniprot_new_part.rb   |  208 ----------------------
+ test/unit/bio/db/embl/test_uniprotkb_new_part.rb |  208 ++++++++++++++++++++++
+ 2 files changed, 208 insertions(+), 208 deletions(-)
+ delete mode 100644 test/unit/bio/db/embl/test_uniprot_new_part.rb
+ create mode 100644 test/unit/bio/db/embl/test_uniprotkb_new_part.rb
+
+commit 1b51d0940712a6f144f8268dc77048bc7ec7d983
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jun 28 15:21:36 2013 +0900
+
+    Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB.
+    
+     * Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB.
+     * Test class names are also changed.
+
+ test/unit/bio/db/embl/test_uniprotkb.rb |  223 +++++++++++++++----------------
+ 1 file changed, 111 insertions(+), 112 deletions(-)
+
+commit 68494aa862c3495def713e6cad6fc478f223416f
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jun 28 15:01:15 2013 +0900
+
+    test_sptr.rb is renamed to test_uniprotkb.rb
+
+ test/unit/bio/db/embl/test_sptr.rb      | 1807 -------------------------------
+ test/unit/bio/db/embl/test_uniprotkb.rb | 1807 +++++++++++++++++++++++++++++++
+ 2 files changed, 1807 insertions(+), 1807 deletions(-)
+ delete mode 100644 test/unit/bio/db/embl/test_sptr.rb
+ create mode 100644 test/unit/bio/db/embl/test_uniprotkb.rb
+
+commit e1ed7fab4c0350e6866dd420a93e950c53063f38
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jun 28 14:52:08 2013 +0900
+
+    Add autoload of Bio::UniProtKB, and modify comments of deprecated classes.
+
+ lib/bio.rb |   18 ++++++++++--------
+ 1 file changed, 10 insertions(+), 8 deletions(-)
+
+commit 7c78cb1b275a845e215f9a6da67026836efc5807
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jun 28 14:28:02 2013 +0900
+
+    Bio::SwissProt and Bio::TrEMBL are deprecated
+    
+     * Bio::SwissProt and Bio::TrEMBL are deprecated.
+     * Show warning messages when using these classes.
+
+ lib/bio/db/embl/swissprot.rb |   41 ++++++++++++----------------------------
+ lib/bio/db/embl/trembl.rb    |   43 +++++++++++++-----------------------------
+ 2 files changed, 25 insertions(+), 59 deletions(-)
+
+commit b998ad13849ff7f1d69ed0c640a2e1bafe3fc957
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jun 28 14:27:36 2013 +0900
+
+    Bio::UniProt is changed to be an alias of Bio::UniProtKB.
+
+ lib/bio/db/embl/uniprot.rb |   41 ++++++++++++-----------------------------
+ 1 file changed, 12 insertions(+), 29 deletions(-)
+
+commit f46324e2fb6a2bc3e4680c8064dc0fc3d89e6f24
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jun 28 14:21:56 2013 +0900
+
+    Bio::SPTR is renamed as Bio::UniProtKB and changed to an alias
+    
+     * Bio::SPTR is renamed to Bio::UniProtKB.
+     * For older programs which use Bio::SPTR, set Bio::SPTR as an alias of
+       Bio::UniProtKB.
+
+ lib/bio/db/embl/sptr.rb      |   20 ++++++
+ lib/bio/db/embl/uniprotkb.rb |  147 +++++++++++++++++++++---------------------
+ 2 files changed, 93 insertions(+), 74 deletions(-)
+ create mode 100644 lib/bio/db/embl/sptr.rb
+
+commit 70816d90a6ef290c7ca7f50d492e7c4f836aadd8
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jun 27 18:16:38 2013 +0900
+
+    Rename lib/bio/db/embl/sptr.rb to uniprotkb.rb
+
+ lib/bio/db/embl/sptr.rb      | 1456 ------------------------------------------
+ lib/bio/db/embl/uniprotkb.rb | 1456 ++++++++++++++++++++++++++++++++++++++++++
+ 2 files changed, 1456 insertions(+), 1456 deletions(-)
+ delete mode 100644 lib/bio/db/embl/sptr.rb
+ create mode 100644 lib/bio/db/embl/uniprotkb.rb
+
+commit 2a10ded8e1502e0db5ec3b2e060f658ee53aafd0
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jun 27 16:36:58 2013 +0900
+
+    Bio::RefSeq and Bio::DDBJ are deprecated. Show warnings.
+    
+     * Bio::RefSeq and Bio::DDBJ are deprecated because they were only
+       an alias of Bio::GenBank. Please use Bio::GenBank instead.
+     * Show warning message when loading the classes and initializing
+       a new instance.
+     * Changed to require genbank.rb only when GenBank is not defined.
+       This might reduce the possibility of circular require.
+
+ lib/bio/db/genbank/ddbj.rb   |   11 +++++++++--
+ lib/bio/db/genbank/refseq.rb |   14 +++++++++++---
+ 2 files changed, 20 insertions(+), 5 deletions(-)
+
+commit 118d0bff58b48f69505eef5dcc2f961ac6e0d9de
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jun 27 16:08:55 2013 +0900
+
+    Remove descriptions about DDBJ Web API (WABI)
+
+ KNOWN_ISSUES.rdoc |    8 --------
+ 1 file changed, 8 deletions(-)
+
+commit fe8f976c7ced4d525a4eabd728269f71326cf001
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jun 27 13:41:19 2013 +0900
+
+    Remove ddbjsoap method that uses Bio::DDBJ::XML
+
+ lib/bio/shell/plugin/soap.rb |   28 ----------------------------
+ 1 file changed, 28 deletions(-)
+
+commit 54bef3fc48bb48eb198537a9fba6379f33f036cc
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jun 27 13:39:42 2013 +0900
+
+    Remove Bio::Blast::Remote::DDBJ from the comment line
+
+ test/network/bio/appl/blast/test_remote.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit a7c5a656dab1bb8ada6b36ec003a89aec9e26671
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 25 18:34:46 2013 +0900
+
+    Delete sample/demo_ddbjxml.rb which uses Bio::DDBJ::XML
+
+ sample/demo_ddbjxml.rb |  212 ------------------------------------------------
+ 1 file changed, 212 deletions(-)
+ delete mode 100644 sample/demo_ddbjxml.rb
+
+commit e55293b67d305382cfb30b45aa30af82a574b580
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 25 18:29:54 2013 +0900
+
+    Remove Bio::Blast::Remote::DDBJ, Bio::Blast.ddbj and related components
+    
+     * Remove Bio::Blast::Remote::DDBJ, Bio::Blast.ddbj and related components
+       which use Bio::DDBJ::XML or Bio::DDBJ::REST.
+
+ lib/bio/appl/blast/ddbj.rb                 |  131 ----------------------------
+ lib/bio/appl/blast/remote.rb               |    9 --
+ test/network/bio/appl/blast/test_remote.rb |   14 ---
+ test/network/bio/appl/test_blast.rb        |   12 ---
+ 4 files changed, 166 deletions(-)
+ delete mode 100644 lib/bio/appl/blast/ddbj.rb
+
+commit 19a5c992096a68a26f8684ee2ae128d17f2a49fd
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Jun 25 16:52:05 2013 +0900
+
+    Remove Bio::DDBJ::XML and REST due to suspension of DDBJ Web API (WABI)
+    
+     * Remove Bio::DDBJ::XML and Bio::DDBJ::REST due to suspension of
+       DDBJ Web API (WABI). DDBJ says that it is now under reconstruction
+       and the API will be completely changed. Thus, I've decided to throw
+       away current API client in Ruby and to implement new one with the new
+       API.
+     * Autoload lines in lib/bio/db/genbank/ddbj.rb are removed.
+     * Tests are also removed.
+
+ lib/bio/db/genbank/ddbj.rb           |    3 -
+ lib/bio/io/ddbjrest.rb               |  344 -------------------------
+ lib/bio/io/ddbjxml.rb                |  458 ----------------------------------
+ test/network/bio/io/test_ddbjrest.rb |   47 ----
+ test/unit/bio/io/test_ddbjxml.rb     |   81 ------
+ 5 files changed, 933 deletions(-)
+ delete mode 100644 lib/bio/io/ddbjrest.rb
+ delete mode 100644 lib/bio/io/ddbjxml.rb
+ delete mode 100644 test/network/bio/io/test_ddbjrest.rb
+ delete mode 100644 test/unit/bio/io/test_ddbjxml.rb
+
+commit 1f852e0bf3c830aaa40dc7fc2bd535418af8dfd1
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat May 25 03:00:08 2013 +0900
+
+    regenerate bioruby.gemspec with rake regemspec
+
+ bioruby.gemspec |    2 --
+ 1 file changed, 2 deletions(-)
+
+commit 5b90959ab399f961823a7c4453392c75cf971333
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat May 25 02:58:50 2013 +0900
+
+    Update files and directories used to create package without git
+
+ bioruby.gemspec.erb |    6 ++++--
+ 1 file changed, 4 insertions(+), 2 deletions(-)
+
+commit df29f057ded6ac73fbdce7ae04a70ead28f4cc9f
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat May 25 02:46:32 2013 +0900
+
+    Ruby 2.0 support: not to add ChangeLog and LEGAL to rdoc_files
+    
+     * Ruby 2.0 support: not to add ChangeLog and LEGAL to rdoc_files.
+       Because ChangeLog is not rdoc format, rdoc bundled with Ruby 2.0
+       raises error during parsing.
+
+ bioruby.gemspec.erb |    4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+commit 930a5fcf5e38ae2bdfeee62eed9a46db1c519fae
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:29:33 2013 +0900
+
+    Remove unused variable in lib/bio/util/contingency_table.rb
+    
+    This commit removes below interpreter warning.
+    
+    * warning: assigned but unused variable
+
+ lib/bio/util/contingency_table.rb |    2 --
+ 1 file changed, 2 deletions(-)
+
+commit 490b3f7ca3b987c1a17852b641aad3125fc565cd
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:28:30 2013 +0900
+
+    Rename unused variable in lib/bio/tree.rb
+    
+    This commit removes below interpreter warning.
+    
+    * warning: assigned but unused variable
+
+ lib/bio/tree.rb |    4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+commit c024fb972edb52e213165149273fc7ac4bec2f6e
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu May 16 21:26:44 2013 +0900
+
+    Refactoring to suppress "warning: assigned but unused variable"
+
+ lib/bio/pathway.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit b3b2a268d6118307eed88fce1d805a61c6fb843d
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:18:44 2013 +0900
+
+    Remove unused variable in lib/bio/db/transfac.rb
+    
+    This commit removes below interpreter warning.
+    
+    * warning: assigned but unused variable
+
+ lib/bio/db/transfac.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit dd8abf1f95af4a70cf0b86b0e719e3dcfd8abecf
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu May 16 21:13:34 2013 +0900
+
+    Refactoring to suppress warnings "assigned but unused variable"
+
+ lib/bio/db/nexus.rb |    5 +++--
+ 1 file changed, 3 insertions(+), 2 deletions(-)
+
+commit b37512fb8028cf30bb2f813928aed49a5b39dce3
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:15:59 2013 +0900
+
+    Rename unused variable in lib/bio/db/kegg/reaction.rb
+    
+    This commit removes below interpreter warning.
+    
+    * warning: assigned but unused variable
+
+ lib/bio/db/kegg/reaction.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit a81fca3b1247ae4a3e05bfa912c8181efdfca81b
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:15:09 2013 +0900
+
+    Remove unused variable in lib/bio/db/go.rb
+    
+    This commit removes below interpreter warning.
+    
+    * warning: assigned but unused variable
+
+ lib/bio/db/go.rb |    6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+commit 69b0c433e76faffba6a48dfc38dcc2b1444ce2b7
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:13:24 2013 +0900
+
+    Rename unused variable in lib/bio/db/gff.rb
+    
+    This commit removes below interpreter warning.
+    
+    * warning: assigned but unused variable
+
+ lib/bio/db/gff.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 88c214fe3183c161cda94a3a4cda442b3a769965
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu May 9 23:46:28 2013 +0900
+
+    add a dummy line to suppress "warning: assigned but unused variable"
+
+ lib/bio/db/embl/sptr.rb |    1 +
+ 1 file changed, 1 insertion(+)
+
+commit 1ead12f9c951a983c6775f79ca1b6944f95a61b9
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu May 9 23:41:54 2013 +0900
+
+    Refactoring to suppress warnings "assigned but unused variable"
+
+ lib/bio/db/embl/embl.rb |    7 ++++---
+ 1 file changed, 4 insertions(+), 3 deletions(-)
+
+commit 8d0eb5105eb2f419f5b4f4fbb191b8fb2032664b
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:01:27 2013 +0900
+
+    Remove unused variable in lib/bio/appl/paml/common
+    
+    This commit removes below interpreter warning.
+    
+    * warning: assigned but unused variable
+
+ lib/bio/appl/paml/common.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit c6cf0d2e2a3a0b9062f9464dba0e363f460d04e4
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu May 9 23:27:54 2013 +0900
+
+    suppress warning "assigned but unused variable"
+
+ lib/bio/appl/paml/codeml/report.rb |    1 +
+ 1 file changed, 1 insertion(+)
+
+commit 8834d50544b03a92a3ca816704b179e4333d1dfc
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 16:59:18 2013 +0900
+
+    Remove unused variable in lib/bio/appl/meme/mast/report
+    
+    This commit removes below interpreter warning.
+    
+    * warning: assigned but unused variable
+
+ lib/bio/appl/meme/mast/report.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit fe51a49ee68c41a3ce0c48c39db6e8a28d1689ee
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 16:57:44 2013 +0900
+
+    Remove unused variable in lib/bio/appl/blast/report
+    
+    This commit removes below interpreter warning.
+    
+    * warning: assigned but unused variable
+
+ lib/bio/appl/blast/report.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 622497ff309412fb986c5315d55d41c3ca48d362
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:25:29 2013 +0900
+
+    Fix indent in lib/bio/map
+    
+    This commit removes below interpreter warning.
+    
+    * warning: mismatched indentations at ...
+
+ lib/bio/map.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 3ea6bcaf229fd1a71a0192253cc47e817bb64b82
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 18:05:04 2013 +0900
+
+    Remove unused variable in test/unit/bio/appl/blast/test_report
+    
+    This commit removes below interpreter warning.
+    
+    * warning: assigned but unused variable
+
+ test/unit/bio/appl/blast/test_report.rb |    2 --
+ 1 file changed, 2 deletions(-)
+
+commit 178ca9e5244cc3aa7f0507c7d5528bb57b0858be
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 18:03:46 2013 +0900
+
+    Remove unused variable in test/unit/bio/appl/bl2seq/test_report
+    
+    This commit removes below interpreter warning.
+    
+    * warning: assigned but unused variable
+
+ test/unit/bio/appl/bl2seq/test_report.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit b8a5c1cb9f54d9199200b406f77e8152eef96f02
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu May 9 21:20:10 2013 +0900
+
+    Add assertions and suppress "unused variable" warnings
+    
+     * Add assertions to check object id returned by forward_complement
+       and reverse_complement methods. This change also aims to suppress
+       "assigned but unused variable" warnings.
+
+ test/unit/bio/sequence/test_na.rb |    4 +++-
+ 1 file changed, 3 insertions(+), 1 deletion(-)
+
+commit bd8fc9b197c54c108d74fea9161c8f0dd3b041fc
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:59:09 2013 +0900
+
+    Remove unused variable in test/unit/bio/io/flatfile/test_splitter
+    
+    This commit removes below interpreter warning.
+    
+    * warning: assigned but unused variable
+
+ test/unit/bio/io/flatfile/test_splitter.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 0a87c9e265c4560453faf84fc009b60319c75416
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:57:51 2013 +0900
+
+    Remove unused variable in test/unit/bio/db/test_phyloxml_writer
+    
+    This commit removes below interpreter warning.
+    
+    * warning: assigned but unused variable
+
+ test/unit/bio/db/test_phyloxml_writer.rb |    4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+commit 95b2614eb32eb12428df29360d0c1f146f39a469
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu May 9 20:56:43 2013 +0900
+
+    Comment out some lines to suppress "unused variable" warnings
+
+ test/unit/bio/db/test_gff.rb |    4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+commit b8917841559fbd506c73fdf374a8097f23a1bc37
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:51:11 2013 +0900
+
+    Remove unused variable in test/unit/bio/db/embl/test_sptr.rb
+    
+     * Remove warnings "warning: assigned but unused variable"
+     * Note that the sequence in TestSPTRUniProtRel7_6#test_10000aa is
+       a fragment of human p53 protein, and is not related with Q09165.
+
+ test/unit/bio/db/embl/test_sptr.rb |    3 ---
+ 1 file changed, 3 deletions(-)
+
+commit 6b46d324a545f509bbd238ae7ec009d586469314
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:45:47 2013 +0900
+
+    Remove unused variable in test/unit/bio/db/embl/test_embl_rel89
+    
+    This commit removes below interpreter warning.
+    
+    * warning: assigned but unused variable
+
+ test/unit/bio/db/embl/test_embl_rel89.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit f36eeb0107e7a8315c66888ec8292ed33bd959cc
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:45:21 2013 +0900
+
+    Remove unused variable in test/unit/bio/db/embl/test_embl
+    
+    This commit removes below interpreter warning.
+    
+    * warning: assigned but unused variable
+
+ test/unit/bio/db/embl/test_embl.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit a1a2ad9b963d9bb2da8d07ae7b182bd339bea88e
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:36:59 2013 +0900
+
+    Fix indent in test/unit/bio/sequence/test_dblink
+    
+    This commit removes below interpreter warning.
+    
+    * warning: mismatched indentations at ...
+
+ test/unit/bio/sequence/test_dblink.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 345a8eb4408ca241c13c410a578490c905eb7391
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:36:21 2013 +0900
+
+    Fix indent in test/unit/bio/db/test_phyloxml
+    
+    This commit removes below interpreter warning.
+    
+    * warning: mismatched indentations at ...
+
+ test/unit/bio/db/test_phyloxml.rb |   58 ++++++++++++++++++-------------------
+ 1 file changed, 29 insertions(+), 29 deletions(-)
+
+commit ae8c7a6705a30c0c18c57df9869979a968aa63ac
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:35:07 2013 +0900
+
+    Fix indent in test/unit/bio/db/genbank/test_genbank
+    
+    This commit removes below interpreter warning.
+    
+    * warning: mismatched indentations at ...
+
+ test/unit/bio/db/genbank/test_genbank.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 872d8954e1351251fbace20e331035251ae5f806
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Thu Apr 4 17:33:23 2013 +0900
+
+    Fix indent in test/unit/bio/appl/test_blast
+    
+    This commit removes below interpreter warning.
+    
+    * warning: mismatched indentations at ...
+
+ test/unit/bio/appl/test_blast.rb |    4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+commit bd973e084695c4d777c8ecf6d566788838158165
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Mar 27 03:03:49 2013 +0900
+
+    .travis.yml: rbx-18mode is moved to allow_failures
+
+ .travis.yml |    8 +++++---
+ 1 file changed, 5 insertions(+), 3 deletions(-)
+
+commit 63e93faba74a8143a0be9595fdf87329f3015745
+Author: Andrew Grimm <andrew.j.grimm@gmail.com>
+Date:   Tue Mar 26 20:20:11 2013 +1100
+
+    Squash warning in alignment.rb: assigned but unused variable - oldkeys
+
+ lib/bio/alignment.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit bd735d6f9d6edfd1550a4279167ac06b372f847a
+Author: Andrew Grimm <andrew.j.grimm@gmail.com>
+Date:   Tue Mar 26 20:14:46 2013 +1100
+
+    Squash warning in alignment.rb: assigned but unused variable - lines
+
+ lib/bio/alignment.rb |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit 3e7b27f96a901a3abfc338572f98d60a9e3be498
+Author: Andrew Grimm <andrew.j.grimm@gmail.com>
+Date:   Tue Mar 26 19:44:49 2013 +1100
+
+    Squash warning in defline.rb: assigned but unused variable - idtype
+
+ lib/bio/db/fasta/defline.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit aafc03330fa79243cfa4097d356a7c304ddb7980
+Author: Kenichi Kamiya <kachick1@gmail.com>
+Date:   Sat Feb 16 21:22:55 2013 +0900
+
+    Simplify some regular expressions
+    
+    * /\w/ including /\d/
+    * /\s/ including [/\r/, /\t/, /\n/]
+
+ lib/bio/appl/blast/format0.rb |    2 +-
+ lib/bio/db/embl/common.rb     |    2 +-
+ lib/bio/db/embl/embl.rb       |    2 +-
+ lib/bio/db/embl/sptr.rb       |    2 +-
+ lib/bio/db/gff.rb             |    2 +-
+ 5 files changed, 5 insertions(+), 5 deletions(-)
+
+commit 623ad4011fa8b56f3c9f50a859d1fa26f6570700
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jan 11 16:41:12 2013 +0900
+
+    Improvement of parameter checks and error output
+    
+     * Improvement of parameter checks
+     * To avoid potential XSS in old MSIE which ignores content-type,
+       always do CGI.escapeHTML for parameters in error messages
+
+ sample/biofetch.rb |   91 ++++++++++++++++++++++++++++++++++++----------------
+ 1 file changed, 63 insertions(+), 28 deletions(-)
+
+commit 03d48c43f1de7ebc9104b9aa972f226774a0bf49
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jan 11 15:32:05 2013 +0900
+
+    Add metadata cache
+    
+     * Add metadata cache. It caches the list of databases and a list of
+       available formats for each database. Database entries are not cached.
+     * charset=utf-8 in CGI header.
+
+ sample/biofetch.rb |  110 +++++++++++++++++++++++++++++++++++++++++-----------
+ 1 file changed, 87 insertions(+), 23 deletions(-)
+
+commit 114d29d4bdfc328f5e91adee9bea465622248e0d
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jan 11 09:10:08 2013 +0900
+
+    remove excess double quotations in html part
+
+ sample/biofetch.rb |    8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+commit 949311648b92d51a2596f896fdae8d74ac0608a3
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jan 11 08:59:18 2013 +0900
+
+    add magic comment: coding utf-8
+
+ sample/biofetch.rb |    1 +
+ 1 file changed, 1 insertion(+)
+
+commit 4ae509273134c5deca7910847063ed07c56150db
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jan 10 23:27:09 2013 +0900
+
+    Rewrite to use TogoWS REST API instead of SOAP-based KEGG API.
+    
+     * Rewrite to use TogoWS REST API instead of deprecated SOAP-based
+       KEGG API.
+     * Examples are changed to fit with current TogoWS.
+     * Now, the script does not depend on any non-standard libraries
+       including BioRuby. This means that one can put this script on
+       a server without installing BioRuby.
+     * New constans SCRIPT_NAME and BASE_URL for easy customizing.
+     * Many changes. See "git diff" for details.
+
+ sample/biofetch.rb |  265 ++++++++++++++++++++++++++--------------------------
+ 1 file changed, 131 insertions(+), 134 deletions(-)
+
+commit bc98bc54c59be98425d66c64b19a3b9612993beb
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jan 10 15:17:42 2013 +0900
+
+    Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
+
+ gemfiles/Gemfile.travis-ruby1.9 |    1 +
+ 1 file changed, 1 insertion(+)
+
+commit dfe54b2fbe303f56a868404173fe346724b7aa4a
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jan 10 14:06:45 2013 +0900
+
+    Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
+
+ gemfiles/Gemfile.travis-jruby1.8 |    1 +
+ gemfiles/Gemfile.travis-jruby1.9 |    1 +
+ 2 files changed, 2 insertions(+)
+
+commit f07ec6ac326d51c055496983abba54afd00c35d4
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jan 10 01:38:00 2013 +0900
+
+    Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
+
+ gemfiles/Gemfile.travis-ruby1.8 |    1 +
+ 1 file changed, 1 insertion(+)
+
+commit 4221d52055087f85daa1c23349d10ecdb4d01a31
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jan 10 01:27:03 2013 +0900
+
+    Ruby 2.0 support: Set script encoding to US-ASCII for gff.rb.
+
+ lib/bio/db/gff.rb |    1 +
+ 1 file changed, 1 insertion(+)
+
+commit 1526df8273e9d2283fd4a921d4cf8c0c664fe71c
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jan 10 00:45:36 2013 +0900
+
+    Convert encoding of the Japanese tutorial files to UTF-8
+
+ doc/Tutorial.rd.ja      | 1920 +++++++++++++++++++++++------------------------
+ doc/Tutorial.rd.ja.html | 1918 +++++++++++++++++++++++-----------------------
+ 2 files changed, 1919 insertions(+), 1919 deletions(-)
+
+commit 3215570185a46dd0d6c4cd96d583b2487636b483
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jan 10 00:41:51 2013 +0900
+
+    updated doc/Tutorial.rd.html and doc/Tutorial.rd.ja.html
+
+ doc/Tutorial.rd.html    |   19 ++---
+ doc/Tutorial.rd.ja.html |  202 +++++++++++++----------------------------------
+ 2 files changed, 63 insertions(+), 158 deletions(-)
+
+commit 8db12935a9cc15bae92bdb7183476cfea9e1f819
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jan 10 00:38:18 2013 +0900
+
+    Set html title when generating tutorial html
+
+ Rakefile |    3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+commit 644d438decceb072475877a749435fba543ff8ea
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jan 4 03:19:00 2013 +0900
+
+    regenerate bioruby.gemspec with rake regemspec
+
+ bioruby.gemspec |    6 ------
+ 1 file changed, 6 deletions(-)
+
+commit 54dc9b9f68ee2de9ee005a772ce000277a073d97
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jan 4 02:35:01 2013 +0900
+
+    Remove sample/psortplot_html.rb which depend on Bio::KEGG::API.
+    
+     * Remove sample/psortplot_html.rb because it strongly depend on
+       removed Bio::KEGG::API and discontinued SOAP-based KEGG API.
+       It is hard to re-write by using new REST-based KEGG API because
+       the new API seems to lack color_pathway_by_objects that returns
+       image URL. Moreover, there is no one-by-one API migration guide.
+
+ sample/psortplot_html.rb |  214 ----------------------------------------------
+ 1 file changed, 214 deletions(-)
+ delete mode 100644 sample/psortplot_html.rb
+
+commit dbdf2dad3dec9d10141b891a481b9b05e1561708
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jan 4 02:34:05 2013 +0900
+
+    Remove descriptions about KEGG API and Bio::KEGG::API.
+
+ doc/Tutorial.rd    |    6 ---
+ doc/Tutorial.rd.ja |  106 +---------------------------------------------------
+ 2 files changed, 1 insertion(+), 111 deletions(-)
+
+commit 3ca725dc1e07f794344c9fcae43d4972ed2895da
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Jan 4 02:33:09 2013 +0900
+
+    Remove description about KEGG API and Bio::KEGG::API.
+
+ README.rdoc |    6 ++----
+ 1 file changed, 2 insertions(+), 4 deletions(-)
+
+commit d4568788069f2d998a78ad72b1d906aae13e85f4
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jan 3 23:55:58 2013 +0900
+
+    Remove KEGG API plugin of BioRuby Shell, due to the removal of Bio::KEGG::API.
+
+ lib/bio/shell.rb                |    1 -
+ lib/bio/shell/plugin/keggapi.rb |  181 ---------------------------------------
+ 2 files changed, 182 deletions(-)
+ delete mode 100644 lib/bio/shell/plugin/keggapi.rb
+
+commit 22c8f4945d622f8f22c08b262c6caf81a0261284
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jan 3 23:52:36 2013 +0900
+
+    Delete autoload lines for removed Bio::KEGG::API
+
+ lib/bio.rb |    4 ----
+ 1 file changed, 4 deletions(-)
+
+commit b56ec0984d5001c3a4d3b4f0ba8fbbbf79835747
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jan 3 23:51:24 2013 +0900
+
+    Remove Bio::KEGG::API and its sample code and documentation files.
+    
+     * Remove Bio::KEGG::API and its sample code and documentation files.
+       * deleted: lib/bio/io/keggapi.rb
+       * deleted: doc/KEGG_API.rd
+       * deleted: doc/KEGG_API.rd.ja
+       * deleted: sample/demo_keggapi.rb
+
+ doc/KEGG_API.rd        | 1843 ------------------------------------------------
+ doc/KEGG_API.rd.ja     | 1834 -----------------------------------------------
+ lib/bio/io/keggapi.rb  |  363 ----------
+ sample/demo_keggapi.rb |  502 -------------
+ 4 files changed, 4542 deletions(-)
+ delete mode 100644 doc/KEGG_API.rd
+ delete mode 100644 doc/KEGG_API.rd.ja
+ delete mode 100644 lib/bio/io/keggapi.rb
+ delete mode 100644 sample/demo_keggapi.rb
+
+commit 63af413c122b4531193153fbfee034deaf0a9606
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Mon Oct 1 21:11:14 2012 +0900
+
+    Bug fix: parse error when subject sequence contains spaces
+    
+     * Bug fix: parse error when subject sequence contains spaces.
+       Thanks to Edward Rice who reports the bug. (Bug #3385)
+       (https://redmine.open-bio.org/issues/3385)
+
+ lib/bio/appl/blast/format0.rb |   38 +++++++++++++++++++-------------------
+ 1 file changed, 19 insertions(+), 19 deletions(-)
+
+commit 9f2f682ec6624ff356bea7aca76365ba95d33549
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Sep 7 16:50:44 2012 +0900
+
+    add an env line to be recognized in allow_failures
+
+ .travis.yml |    1 +
+ 1 file changed, 1 insertion(+)
+
+commit fead6dda526081db09c56c2262f111338b7d8cd7
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Fri Sep 7 16:08:57 2012 +0900
+
+    environment variable TESTOPTS=-v for verbose output of rake test
+
+ .travis.yml |   22 ++++++++++++++--------
+ 1 file changed, 14 insertions(+), 8 deletions(-)
+
+commit 3de19895140502898c77fc83d9ad6fae47331763
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 6 18:17:22 2012 +0900
+
+    Remove Bio.method_missing because it is broken.
+    
+     * Bio.method_missing, the hook of undefined methods, providing
+       shortcut of Bio::Shell methods, is now removed, because it does
+       not work correctly, and because the use of method_missing should
+       normally be avoided unless it is really necessary. Alternatively,
+       use Bio::Shell.xxxxx (xxxxx is a method name).
+
+ lib/bio.rb |   13 -------------
+ 1 file changed, 13 deletions(-)
+
+commit a358584c4a76be6a38ab38a18e6dc66840030450
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 6 16:48:51 2012 +0900
+
+    Delete autoload line of a removed class Bio::NCBI::SOAP.
+
+ lib/bio/io/ncbirest.rb |    1 -
+ 1 file changed, 1 deletion(-)
+
+commit 340d665775b862da638e4d12751b84d2ccd83e82
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 6 16:47:03 2012 +0900
+
+    Delete autoload lines of removed classes.
+
+ lib/bio.rb |    4 ----
+ 1 file changed, 4 deletions(-)
+
+commit c7c29a672b38d2182cf4afc9a970b854af1149a7
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 6 16:43:25 2012 +0900
+
+    regenerate bioruby.gemspec with rake regemspec
+
+ bioruby.gemspec |    3 ---
+ 1 file changed, 3 deletions(-)
+
+commit 09bb4b8a8b7e01a36dbe0cf44a5c2a6a6b5750f1
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 6 16:23:17 2012 +0900
+
+    Remove Bio::Shell#ncbisoap which uses removed Bio::NCBI::SOAP.
+
+ lib/bio/shell/plugin/soap.rb |    9 ---------
+ 1 file changed, 9 deletions(-)
+
+commit a5e46acdaf06568bea6cb773200bbf3881b5670e
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Sep 6 16:02:32 2012 +0900
+
+    Remove issues about removed classes Bio::NCBI::SOAP and Bio::KEGG::Taxonomy
+
+ KNOWN_ISSUES.rdoc |   10 ----------
+ 1 file changed, 10 deletions(-)
+
+commit 529815acb1b57486bd506b81eec6be80277cbae7
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Sep 5 11:33:27 2012 +0900
+
+    Remove Bio::KEGG::Taxonomy which is old and broken
+    
+     * Remove Bio::KEGG::Taxonomy because it raises error or the data
+       structure in the return value seems to be broken. In addition,
+       running the sample script sample/demo_kegg_taxonomy.rb shows
+       error or falls into infinite loop. Moreover, KEGG closes public
+       FTP site and the target data file of the class ("taxonomy")
+       can only be obtained by paid subscribers. From the above reasons,
+       it seems there are no users of this class now.
+     * Deleted files: lib/bio/db/kegg/taxonomy.rb,
+       sample/demo_kegg_taxonomy.rb
+
+ lib/bio/db/kegg/taxonomy.rb  |  280 ------------------------------------------
+ sample/demo_kegg_taxonomy.rb |   92 --------------
+ 2 files changed, 372 deletions(-)
+ delete mode 100644 lib/bio/db/kegg/taxonomy.rb
+ delete mode 100644 sample/demo_kegg_taxonomy.rb
+
+commit dc47fb46e86bba15ba43de31075eaba3cf811fa3
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Sep 5 11:26:00 2012 +0900
+
+    Remove Bio::NCBI::SOAP which is broken
+    
+     * Remove Bio::NCBI::SOAP in lib/bio/io/ncbisoap.rb, because it always
+       raises error during the parsing of WSDL files provided by NCBI, both
+       with Ruby 1.8.X (with bundled SOAP4R) and Ruby 1.9.X (with
+       soap4r-ruby1.9 gem). To solve the error, modifying SOAP4R may be
+       needed, that seems very difficult. The alternative is Bio::NCBI::REST,
+       REST client class for the NCBI EUtil web services.
+
+ lib/bio/io/ncbisoap.rb |  156 ------------------------------------------------
+ 1 file changed, 156 deletions(-)
+ delete mode 100644 lib/bio/io/ncbisoap.rb
+
+commit 314e06e54603bb238015c391904f414b3da48752
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Sep 4 11:13:47 2012 +0900
+
+    regenerate bioruby.gemspec with rake regemspec
+
+ bioruby.gemspec |   10 ++++------
+ 1 file changed, 4 insertions(+), 6 deletions(-)
+
+commit e929d5d23a9b489ef42f30b33959f059baf1e185
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Sep 4 11:09:36 2012 +0900
+
+    Remove issues about removed classes Bio::Ensembl and Bio::DBGET.
+
+ KNOWN_ISSUES.rdoc |   16 ----------------
+ 1 file changed, 16 deletions(-)
+
+commit 550a5440490012f73b6d38d84238cd498f2ebb02
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Sep 4 10:57:20 2012 +0900
+
+    Remove Bio::Ensembl because it does not work
+    
+     * Remove Bio::Ensembl because it does not work after the renewal of
+       the Ensembl web site in 2008.
+     * Alternative is io-ensembl gem which supports current Ensembl API.
+       http://rubygems.org/gems/bio-ensembl
+     * Deleted files: lib/bio/io/ensembl.rb,
+       test/network/bio/io/test_ensembl.rb, test/unit/bio/io/test_ensembl.rb.
+
+ lib/bio/io/ensembl.rb               |  229 ----------------------------------
+ test/network/bio/io/test_ensembl.rb |  230 -----------------------------------
+ test/unit/bio/io/test_ensembl.rb    |  111 -----------------
+ 3 files changed, 570 deletions(-)
+ delete mode 100644 lib/bio/io/ensembl.rb
+ delete mode 100644 test/network/bio/io/test_ensembl.rb
+ delete mode 100644 test/unit/bio/io/test_ensembl.rb
+
+commit 61301a8ec252f3623f994edd59f597360f73448b
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Tue Sep 4 10:47:52 2012 +0900
+
+    Remove obsolete Bio::DBGET
+    
+     * Remove Bio::DBGET because it uses old original protocol that was
+       discontinued about 8 years ago.
+     * Remove lib/bio/io/dbget.rb and sample/dbget.
+
+ lib/bio/io/dbget.rb |  194 ---------------------------------------------------
+ sample/dbget        |   37 ----------
+ 2 files changed, 231 deletions(-)
+ delete mode 100644 lib/bio/io/dbget.rb
+ delete mode 100755 sample/dbget
+
+commit 3c5e288a8685ba3279a3ba73f1b31056c1b6f7a8
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Aug 23 00:25:43 2012 +0900
+
+    Refresh ChangeLog, showing changes after 1.4.3 release.
+    
+     * Refresh to the new ChangeLog, showing changes after 1.4.3 release.
+       For the changes before 1.4.3, see doc/ChangeLog-1.4.3.
+       For the changes before 1.4.2, see doc/ChangeLog-before-1.4.2.
+       For the changes before 1.3.1, see doc/ChangeLog-before-1.3.1.
+
+ ChangeLog |   61 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ 1 file changed, 61 insertions(+)
+ create mode 100644 ChangeLog
+
+commit 63c13ad8516b9dcacbe001137666c3468968542b
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Aug 23 00:25:07 2012 +0900
+
+    Rakefile: Update hardcoded git tag name for updating of ChangeLog.
+
+ Rakefile |    2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+commit b10c7ad2db24d88726ffb8c63078baa217aeac43
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Aug 23 00:20:01 2012 +0900
+
+    renamed ChangeLog to doc/ChangeLog-1.4.3
+
+ ChangeLog           | 1478 ---------------------------------------------------
+ doc/ChangeLog-1.4.3 | 1478 +++++++++++++++++++++++++++++++++++++++++++++++++++
+ 2 files changed, 1478 insertions(+), 1478 deletions(-)
+ delete mode 100644 ChangeLog
+ create mode 100644 doc/ChangeLog-1.4.3
+
+commit 0c20cb62ba6b253098e7198c14de1829f72474f5
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Aug 23 00:18:50 2012 +0900
+
+    ChangeLog updated: add log about 1.4.3 release.
+
+ ChangeLog |    9 +++++++++
+ 1 file changed, 9 insertions(+)
+
+commit 5e88ccbe0fefdd4d57f144aaf9073f5e7d93281c
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Aug 23 00:16:25 2012 +0900
+
+    New RELEASE_NOTES.rdoc for the next release version.
+
+ RELEASE_NOTES.rdoc |   47 +++++++++++++++++++++++++++++++++++++++++++++++
+ 1 file changed, 47 insertions(+)
+ create mode 100644 RELEASE_NOTES.rdoc
+
+commit e3d40b90d88ab0d0a91d8e32ebf97c16097f0996
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Aug 23 00:12:40 2012 +0900
+
+    Renamed RELEASE_NOTES.rdoc to doc/RELEASE_NOTES-1.4.3.rdoc
+
+ RELEASE_NOTES.rdoc           |  204 ------------------------------------------
+ doc/RELEASE_NOTES-1.4.3.rdoc |  204 ++++++++++++++++++++++++++++++++++++++++++
+ 2 files changed, 204 insertions(+), 204 deletions(-)
+ delete mode 100644 RELEASE_NOTES.rdoc
+ create mode 100644 doc/RELEASE_NOTES-1.4.3.rdoc
+
+commit 08bcabecccb271385d38a0f807e8c408def5a128
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Aug 23 00:00:15 2012 +0900
+
+    Bio::BIORUBY_EXTRA_VERSION set to ".5000" (unstable version).
+
+ bioruby.gemspec    |    2 +-
+ lib/bio/version.rb |    2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)