bio 1.5.2 → 1.6.0.pre.20181210

checksums.yaml

@@ -1,7 +1,7 @@
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-  metadata.gz: 7d762b4e5d063e187234682d669984b9c043ef2e
-  data.tar.gz: d050ee03ce8b66ca9dde030cf16b5c0f01540966
+SHA256:
+  metadata.gz: e7709c923030d4637615ea2e30de470129ab4947321320ec59c725f5959ce360
+  data.tar.gz: b8d7f1e108ffc6be38e05c31bc97013bbc4a3d9590e702bf2ca486aa8483e6c7
 SHA512:
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data/.travis.yml

@@ -1,6 +1,7 @@
+sudo: false
 language: ruby
 rvm:
-  - 2.1.6
+  - 2.1.10
   - 2.0.0
   - 1.9.3
 env:
@@ -8,8 +9,6 @@ env:
 gemfile:
   - gemfiles/Gemfile.travis-ruby1.9
 before_install:
-  - gem update --system 2.1.11
-  - gem --version
   - mkdir /tmp/bioruby
   - ruby gemfiles/modify-Gemfile.rb
   - ruby gemfiles/prepare-gemspec.rb
@@ -18,7 +17,7 @@ matrix:
     - rvm: 1.8.7
       gemfile: gemfiles/Gemfile.travis-ruby1.8
       env: TESTOPTS=-v
-    - rvm: rbx-2.2.3
+    - rvm: rbx-3.29
       gemfile: gemfiles/Gemfile.travis-rbx
       env: TESTOPTS=-v
     - rvm: jruby-18mode
@@ -27,13 +26,15 @@ matrix:
     - rvm: jruby-19mode
       gemfile: gemfiles/Gemfile.travis-jruby1.9
       env: TMPDIR=/tmp/bioruby TESTOPTS=-v
-    - rvm: 2.2.2
-      gemfile: gemfiles/Gemfile.travis-ruby2.2
-    - rvm: 2.1.6
-      gemfile: gemfiles/Gemfile.travis-ruby1.9
+    - rvm: 2.3.1
+      gemfile: Gemfile
+    - rvm: 2.2.5
+      gemfile: Gemfile
+    - rvm: 2.2.5
+      gemfile: Gemfile
       env: BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test TESTOPTS=-v
-    - rvm: 2.1.6
-      gemfile: gemfiles/Gemfile.travis-ruby1.9
+    - rvm: 2.2.5
+      gemfile: Gemfile
       env: BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
     - rvm: jruby-19mode
       gemfile: gemfiles/Gemfile.travis-jruby1.9
@@ -42,7 +43,7 @@ matrix:
       gemfile: gemfiles/Gemfile.travis-jruby1.9
       env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
   allow_failures:
-    - rvm: rbx-2.2.3
+    - rvm: rbx-3.29
       gemfile: gemfiles/Gemfile.travis-rbx
       env: TESTOPTS=-v
     - rvm: jruby-18mode

data/ChangeLog

@@ -1,204 +1,31 @@
-commit 68f87dc3c4488155992f88c3cf1db27061948315
+commit e066e3c8bcf0c6b7eadd3573576d4550aca77cc5
 Author: Naohisa Goto <ng@bioruby.org>
-Date:   Thu Sep 20 13:25:35 2018 +0900
+Date:   Thu Jul 2 22:17:06 2015 +0900
 
-    add changes made for bioruby-1.5.2
+    ChangeLog is moved to doc/ChangeLog-1.5.0
 
- RELEASE_NOTES.rdoc | 14 ++++++++++++++
- 1 file changed, 14 insertions(+)
+ ChangeLog           | 2919 ---------------------------------------------------
+ doc/ChangeLog-1.5.0 | 2919 +++++++++++++++++++++++++++++++++++++++++++++++++++
+ 2 files changed, 2919 insertions(+), 2919 deletions(-)
+ delete mode 100644 ChangeLog
+ create mode 100644 doc/ChangeLog-1.5.0
 
-commit 6b7e87abfbab88a3bb1b80227ab4b0cfaaeae26e
+commit dd53e885c1baa765bc094897d53309af7b15497b
 Author: Naohisa Goto <ng@bioruby.org>
-Date:   Thu Sep 20 13:24:45 2018 +0900
+Date:   Thu Jul 2 22:09:26 2015 +0900
 
-    regenerate bioruby.gemspec with rake regemspec
+    change version for generating ChangeLog to 1.5.0
 
- bioruby.gemspec | 2 +-
+ Rakefile |    2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 
-commit a7dbefeef20d6dea18f0bdd67df24e00c5e9ede6
-Author: Naohisa Goto <ng@bioruby.org>
-Date:   Thu Sep 20 13:23:31 2018 +0900
-
-    version changed to 1.5.2
-
- lib/bio/version.rb | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-commit e00134a1a31db46421b6d468ea1c1d0368bfbb6c
-Author: Naohisa Goto <ng@bioruby.org>
-Date:   Thu Sep 20 12:55:32 2018 +0900
-
-    Bug fix: printf format syntax error about single percent character
-    
-     * Bio::Shell#seqstat: Fix format specifier syntax error.
-       Recent version of Ruby raised error: 'ArgumentError:
-       incomplete format specifier;use %% (double %) instead'.
-
- lib/bio/shell/plugin/seq.rb | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-commit df61cdba5ba3e90fda6c70cc9f880567656a5a82
-Author: Naohisa Goto <ng@bioruby.org>
-Date:   Thu Sep 20 07:06:08 2018 +0900
-
-    Improvement documentation
-    
-     * Improve documentation.
-     * Close https://github.com/bioruby/bioruby/pull/120 .
-
- lib/bio/db/aaindex.rb | 79 +++++++++++++++++++++++++++++++++++++++++++++++----
- 1 file changed, 74 insertions(+), 5 deletions(-)
-
-commit 35bcc5008c7721afb3c16467ae6dc782651f4c39
-Author: Naohisa Goto <ng@bioruby.org>
-Date:   Thu Sep 20 05:01:12 2018 +0900
-
-    Bug fix: Bio::Command.new_https should support proxy
-
- lib/bio/command.rb | 18 +++++++-----------
- 1 file changed, 7 insertions(+), 11 deletions(-)
-
-commit 88b58e94d4612f39abb14b89779ceeb533cd552e
-Author: Naohisa Goto <ng@bioruby.org>
-Date:   Thu Sep 20 04:58:56 2018 +0900
-
-    https support for Bio::Blast::Remote::GenomeNet::Information
-
- lib/bio/appl/blast/genomenet.rb | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-commit dfccbdf32bf819f941f2bcb4f63b2f0ce12cacfa
-Author: ramadis <rramiro.o@hotmail.com>
-Date:   Sat Jul 7 15:12:33 2018 -0300
-
-    Add https requests in command. Fix genomenet query by allowing https requests.
-
- lib/bio/appl/blast/genomenet.rb |  2 +-
- lib/bio/command.rb              | 14 ++++++++++++++
- 2 files changed, 15 insertions(+), 1 deletion(-)
-
-commit d1e1358c1a5c7c7f4aa093a09d5bb45b60f7e7ee
-Author: markwilkinson <markw@illuminae.com>
-Date:   Tue Dec 12 14:13:51 2017 +0100
-
-    fixing Fasta Report parser for fasta36 -m10
-
- lib/bio/appl/fasta/format10.rb | 3 ++-
- 1 file changed, 2 insertions(+), 1 deletion(-)
-
-commit b9b11f66733e20e1ee6d2b5e0aab813b5b5d0000
-Author: Naohisa Goto <ng@bioruby.org>
-Date:   Wed Sep 13 22:13:59 2017 +0900
-
-    Suppress warning "assigned but unused variable"
-
- lib/bio/io/flatfile/autodetection.rb | 5 +++++
- 1 file changed, 5 insertions(+)
-
-commit 580dd6bb9344c2afd0fe60b0cf53a4b28734fbbf
-Author: Naohisa Goto <ng@bioruby.org>
-Date:   Wed Sep 13 22:10:53 2017 +0900
-
-    Suppress warning: "instance variable @top_strand not initialized"
-    
-     * Suppress warning: "instance variable @top_strand not initialized".
-       To do so, force to raise NoMethodError when @top_strand is not
-       initialized or is nil. This should be changed to appropriate
-       exception in the future.
-
- lib/bio/util/sirna.rb | 2 ++
- 1 file changed, 2 insertions(+)
-
-commit 9d7ef4e66ecdc1aadc08fda4b332a51ca7739c82
-Author: Naohisa Goto <ng@bioruby.org>
-Date:   Wed Sep 13 21:31:38 2017 +0900
-
-    Suppress warning in Ruby 2.4: "constant ::Fixnum is deprecated"
-
- lib/bio/db/soft.rb                                                    | 4 ++--
- .../util/restriction_enzyme/range/sequence_range/calculated_cuts.rb   | 2 +-
- test/unit/bio/test_alignment.rb                                       | 4 ++--
- 3 files changed, 5 insertions(+), 5 deletions(-)
-
-commit 2747ee11392068de88e044abf52d12a88a0624ea
-Author: Naohisa Goto <ng@bioruby.org>
-Date:   Wed Sep 13 21:19:12 2017 +0900
-
-    Suppress warning "parentheses after method name is interpreted as an argument list, not a decomposed argument" in Ruby 2.4
-
- lib/bio/map.rb | 8 ++++----
- 1 file changed, 4 insertions(+), 4 deletions(-)
-
-commit 1edbd88a703d3cff0f5a29e45fa51058405ab58c
-Author: Naohisa Goto <ng@bioruby.org>
-Date:   Wed Sep 7 22:06:32 2016 +0900
-
-    BioRuby 1.5.1 is released
-
- ChangeLog | 690 +++++++++++++++++++++++++++++++++++---------------------------
- 1 file changed, 385 insertions(+), 305 deletions(-)
-
-commit 917fe0d0e9910267cd54bf48c2caabe89875a299
-Author: Naohisa Goto <ng@bioruby.org>
-Date:   Wed Sep 7 22:00:56 2016 +0900
-
-    regenerate bioruby.gemspec with rake regemspec
-
- bioruby.gemspec | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-commit 1cfa823572742ea46f14420481c10f05fdbce862
-Author: Naohisa Goto <ng@bioruby.org>
-Date:   Wed Sep 7 21:51:28 2016 +0900
-
-    Bio::BIORUBY_EXTRA_VERSION set to nil (Release version)
-
- lib/bio/version.rb | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-commit 8c27599ef5b8ee33cd074feadd089de01a8fa8e6
-Author: Naohisa Goto <ng@bioruby.org>
-Date:   Wed Sep 7 21:49:20 2016 +0900
-
-    Added release notes for 1.5.1 release
-
- RELEASE_NOTES.rdoc | 26 ++++++++++++++++++++++++++
- 1 file changed, 26 insertions(+)
-
-commit 47ada241ad6f3632dbbd77542befb82500b7195e
-Author: Naohisa Goto <ng@bioruby.org>
-Date:   Sat Aug 13 08:22:22 2016 +0900
-
-    Update URLs and use https for NCBI REST web services
-
- lib/bio/io/ncbirest.rb | 50 ++++++++++++++++++++++++++------------------------
- 1 file changed, 26 insertions(+), 24 deletions(-)
-
-commit 018c2aff1c7813e7b07362ecc8a25db334c0ae95
-Author: Naohisa Goto <ng@bioruby.org>
-Date:   Sat Aug 13 08:12:08 2016 +0900
-
-    New method Bio::Command#start_http_uri(uri) with tests
-    
-     * lib/bio/command.rb: New method Bio::Command#start_http_uri(uri)
-       that supports HTTPS. Note that this method is intended to be
-       called only from BioRuby internals.
-     * lib/bio/command.rb: Bio::Command#post and #post_form are changed
-       to use the start_http_uri().
-     * test/network/bio/test_command.rb: tests for start_http_uri().
-
- lib/bio/command.rb               | 42 ++++++++++++++++++++++++++++++++++++++--
- test/network/bio/test_command.rb | 17 ++++++++++++++++
- 2 files changed, 57 insertions(+), 2 deletions(-)
-
 commit 7a5d897ebc45d9ec5357918a42eb2980decf01e4
 Author: Naohisa Goto <ng@bioruby.org>
 Date:   Thu Jul 2 21:52:17 2015 +0900
 
     version changed to 1.5.1-dev (pre-release version of 1.5.1)
 
- lib/bio/version.rb | 4 ++--
+ lib/bio/version.rb |    4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 
 commit 8fc4d6c64f6958a352c36b171b00d1f1ff2a2354
@@ -207,2924 +34,5 @@ Date:   Thu Jul 2 21:47:28 2015 +0900
 
     fix English syntax and unexpected word insertion
 
- RELEASE_NOTES.rdoc | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-commit 1d165c5def88fdeb8f3beeba1f9e6ab0ce71c2a1
-Author: Naohisa Goto <ng@bioruby.org>
-Date:   Wed Jul 1 17:28:17 2015 +0900
-
-    BioRuby 1.5.0 is released
-
- ChangeLog | 9 +++++++++
- 1 file changed, 9 insertions(+)
-
-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 ++--
+ RELEASE_NOTES.rdoc |    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
-
- .../bio/db/embl/{test_uniprot_new_part.rb => test_uniprotkb_new_part.rb}  | 0
- 1 file changed, 0 insertions(+), 0 deletions(-)
- rename test/unit/bio/db/embl/{test_uniprot_new_part.rb => test_uniprotkb_new_part.rb} (100%)
-
-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 => test_uniprotkb.rb} | 0
- 1 file changed, 0 insertions(+), 0 deletions(-)
- rename test/unit/bio/db/embl/{test_sptr.rb => test_uniprotkb.rb} (100%)
-
-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 => uniprotkb.rb} | 0
- 1 file changed, 0 insertions(+), 0 deletions(-)
- rename lib/bio/db/embl/{sptr.rb => uniprotkb.rb} (100%)
-
-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 => doc/ChangeLog-1.4.3 | 0
- 1 file changed, 0 insertions(+), 0 deletions(-)
- rename ChangeLog => doc/ChangeLog-1.4.3 (100%)
-
-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 => doc/RELEASE_NOTES-1.4.3.rdoc | 0
- 1 file changed, 0 insertions(+), 0 deletions(-)
- rename RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.4.3.rdoc (100%)
-
-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(-)