commit 1bc877e557e165b42eea992d89f19a63996cb586
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Sep 13 21:19:01 2022 +0900

    regenerate bioruby.gemspec with rake regemspec

 bioruby.gemspec | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

commit 190e4751b84cc45cbce636c4414482a8169b08df
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Sep 13 21:18:06 2022 +0900

    prepare for BioRuby 2.0.4 release

 lib/bio/version.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit a666639e0393e96b2de0bbcb447c13f8a14ad06d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Sep 13 21:17:11 2022 +0900

    update release notes for upcoming BioRuby 2.0.4

 RELEASE_NOTES.rdoc | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

commit c0d197343dd7fd8999d04083c9e8f24fa37a2f93
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Sep 13 21:13:40 2022 +0900

    License of UniProt data is CC BY 4.0

 LEGAL | 9 +++++++++
 1 file changed, 9 insertions(+)

commit e670102e6d4deb04c1fcae62459cc02861132d25
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Sep 13 21:01:50 2022 +0900

    Bug fix: Bio::UniProtKB#protein_name and #synonyms may raise error
    
     * Bug fix: Bio::UniProtKB#protein_name and #synonyms may raise error
       after calling Bio::UniProtKB#de method.

 lib/bio/db/embl/uniprotkb.rb                   | 25 ++++++++++++++++++-------
 test/unit/bio/db/embl/test_uniprotkb_P28907.rb | 11 +++++++++++
 2 files changed, 29 insertions(+), 7 deletions(-)

commit 9c04e08e8d1316ffd7fc15ab311cea5dd6937d36
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Sep 13 20:44:46 2022 +0900

    Supports format change of FT lines since UniProt release 2019_11
    
     * Bio::UniProtKB#ft: Supports text format change of FT lines since
       UniProt release 2019_11. (Details of the format changes:
       https://www.uniprot.org/release-notes/2019-12-18-release#text%5Fft )
    
       This closes https://github.com/bioruby/bioruby/issues/147 .
    
     * Tests are added with a new test data

 lib/bio/db/embl/uniprotkb.rb                   | 122 +++++-
 test/data/uniprot/P28907.uniprot               | 551 +++++++++++++++++++++++++
 test/unit/bio/db/embl/test_uniprotkb_P28907.rb | 314 ++++++++++++++
 3 files changed, 983 insertions(+), 4 deletions(-)
 create mode 100644 test/data/uniprot/P28907.uniprot
 create mode 100644 test/unit/bio/db/embl/test_uniprotkb_P28907.rb

commit b18ee463d4328b5ef619733b46f568b18459be7a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 5 23:49:18 2021 +0900

    BioRuby 2.0.3 is released

 ChangeLog | 136 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 136 insertions(+)

commit c16e230d15cf30478a3739563b4e4745dc57ef82
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 5 23:44:45 2021 +0900

    regenerate bioruby.gemspec with rake regemspec

 bioruby.gemspec | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

commit 1a8c44dc5b8d24342550273a594e5f75e41f41df
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 5 23:41:29 2021 +0900

    prepare for BioRuby 2.0.3 release

 lib/bio/version.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 863242cdb9a748ba9efb3be3b39f92c17ed3ea84
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 5 23:36:27 2021 +0900

    update release notes for upcoming BioRuby 2.0.3

 RELEASE_NOTES.rdoc | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

commit b97794d632c73dc45639cec000fb11238740eb30
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 5 23:26:20 2021 +0900

    Ruby 3.0 compatibility fix: Bio::Sequence::*#partition, #rpartiton
    
     * Behaviors of Bio::Sequence::*#partition and #rpartition in Ruby 3.0
       are changed to mimic those in Ruby 2.x.

 lib/bio/sequence/common.rb           | 17 +++++++
 test/unit/bio/sequence/test_ruby3.rb | 94 ++++++++++++++++++++++++++++++++++++
 2 files changed, 111 insertions(+)

commit 7ff79cd449ee03e0063120fb9abec50d9b08e979
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 5 22:24:16 2021 +0900

    remove resolved Ruby 3.0 issue

 KNOWN_ISSUES.rdoc | 8 --------
 1 file changed, 8 deletions(-)

commit 24bb3c3cf417837ad63a27913db7237aef1414c6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 5 21:24:26 2021 +0900

    Bio::Sequence::NA,AA,Generic: workaround for Ruby 3.0.0 incompatible change
    
     * Since Ruby 3.0.0, over 30 methods in subclass of String class are
       changed to return/yield String instance instead of the subclass
       instance. (https://github.com/ruby/ruby/blob/v3_0_0/NEWS.md )
    
     * In this commit, workaround is made for the following methods:
       * *
       * capitalize
       * center
       * chomp
       * chop
       * delete
       * delete_prefix
       * delete_suffix
       * downcase
       * each_char
       * each_grapheme_cluster
       * each_line
       * gsub
       * gsub!
       * ljust
       * lstrip
       * revserse
       * rjust
       * rstrip
       * slice!
       * slice / []
       * split
       * squeeze
       * strip
       * sub
       * sub!
       * succ / next
       * swapcase
       * tr
       * tr_s
       * upcase
     * Note: sub! and gsub! are not described in the NEWS.md
       but are also affected by this Ruby 3.0.0 incompatible changes.
    
     * The following methods are not patched i.e. they return/yield
       String instances.
       * dump
       * partition
       * rpartition
       * scrub
     * Note: In Ruby 2.7 or earlier, Bio::Sequence::NA#partition
       and #rpartition methods return an array that may contain
       mixture of Bio::Sequence::NA instances and String instances.
    
     * test/unit/bio/sequence/test_ruby3.rb: unit tests for the
       above methods.
    
     * Close https://github.com/bioruby/bioruby/issues/137

 lib/bio/sequence/common.rb           |  95 +++++++++
 test/unit/bio/sequence/test_ruby3.rb | 368 +++++++++++++++++++++++++++++++++++
 2 files changed, 463 insertions(+)
 create mode 100644 test/unit/bio/sequence/test_ruby3.rb

commit 0efc0a54685d43645daa9c53d7140bfb81577777
Author: kojix2 <2xijok@gmail.com>
Date:   Tue Aug 31 19:39:25 2021 +0900

    Fix typos: Retrun -> Return

 lib/bio/appl/iprscan/report.rb | 6 +++---
 lib/bio/appl/sosui/report.rb   | 2 +-
 lib/bio/db/embl/uniprotkb.rb   | 2 +-
 lib/bio/db/go.rb               | 4 ++--
 lib/bio/tree.rb                | 2 +-
 5 files changed, 8 insertions(+), 8 deletions(-)

commit a291b5a72da12a5cc8b006d1dd63d002fda5dff3
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 31 23:52:54 2020 +0900

    BioRuby 2.0.2 is released

 ChangeLog | 98 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 98 insertions(+)

commit fd420b713ca364e677ef3551919ec907791df86d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 31 23:51:08 2020 +0900

    RELEASE_NOTES.rdoc: change some description

 RELEASE_NOTES.rdoc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 0ed9b37f38fa1b00dcc1d422914e4cbdbbc5f6ab
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 31 23:46:46 2020 +0900

    regenerate bioruby.gemspec with rake regemspec

 bioruby.gemspec | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit fa84b8fac653c26b9f8db429321ef49202554a69
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 31 23:45:38 2020 +0900

    prepare for BioRuby 2.0.2 release

 lib/bio/version.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 32c5efccbad4e0d3440726383f863520ee242cc5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 31 23:39:18 2020 +0900

    update release notes for upcoming BioRuby 2.0.2

 RELEASE_NOTES.rdoc | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

commit c2f6e62ab64bc532f442bccc0d76ced5380664ec
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 31 23:38:43 2020 +0900

    add a known issue about Ruby 3.0

 KNOWN_ISSUES.rdoc | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

commit a733c0816da7c97ca0c23016b473b004fb755f54
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 31 23:04:55 2020 +0900

    remove deprecation warning of Gem::Specification#has_rdoc=
    
    Gem::Specification#has_rdoc= have been deprecated since RubyGems 1.3.3
    in 2009. (https://blog.rubygems.org/2009/05/04/1.3.3-released.html )
    RDoc is always generated regardless of the value, and the line is
    safely removed.
    
    This fixes https://github.com/bioruby/bioruby/issues/138 .
    Thanks to @jaysonvirissimo for reporting the issue.

 bioruby.gemspec     | 1 -
 bioruby.gemspec.erb | 1 -
 2 files changed, 2 deletions(-)

commit bed6746ce62059795996eeb6e5ac65655bab12b5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 31 22:51:56 2020 +0900

    require ruby's date library to avoid NameError for Date
    
    In Bio::Sequence#output(:embl), NameError (uninitialized constant
    Bio::Sequence::Format::INSDFeatureHelper::Date) is observed.
    The error message is misleading because Date is provided by Ruby's
    standard date library.
    
    This fixes https://github.com/bioruby/bioruby/issues/135 .
    Thanks to Dr. Mark Wilkinson for reporting the issue.

 lib/bio/sequence/format.rb | 1 +
 1 file changed, 1 insertion(+)

commit 5f3aa79fdaf6dd5551d51663ca2e9b6f5e56d855
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 6 17:45:12 2020 +0900

    fix mistaken URLs

 README.rdoc | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

commit d5e1670ee4863cc60d3aa08432a7ee3b1e445439
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 6 15:48:45 2019 +0900

    BioRuby 2.0.1 is released

 ChangeLog | 185 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 185 insertions(+)

commit 21bf51a1ec8c18c9cdf8528ffc3c59c503cef042
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 6 15:45:47 2019 +0900

    RELEASE_NOTES.rdoc: describe notable changes since 2.0.0

 RELEASE_NOTES.rdoc | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

commit 9092a629e0e28b416ee7288d349fb9d73dd2b961
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 6 15:06:11 2019 +0900

    regenerate bioruby.gemspec with rake regemspec

 bioruby.gemspec | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

commit 59e24b6e55d2c9a8887e8e01a91999d33a008042
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 6 15:04:33 2019 +0900

    prepare for BioRuby 2.0.1 release

 lib/bio/version.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 9635a38a158db434fd2b6aff7a2ee75622ddecef
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 6 14:51:23 2019 +0900

    sample/fastq2html.rb: A html visualization of FASTQ sequences
    
     * sample/fastq2html: A html visualization of FASTQ sequences.
       Each sequence is colored with the quality score.
     * sample/fastq2html.cwl: CWL workflow for the above sample script
     * sample/fastq2html.testdata.yaml: Test data for the above workflow

 sample/fastq2html.cwl           | 23 ++++++++++
 sample/fastq2html.rb            | 94 +++++++++++++++++++++++++++++++++++++++++
 sample/fastq2html.testdata.yaml |  5 +++
 3 files changed, 122 insertions(+)
 create mode 100644 sample/fastq2html.cwl
 create mode 100644 sample/fastq2html.rb
 create mode 100644 sample/fastq2html.testdata.yaml

commit 6bbcf8b66310c225d686f2c59359680a0bc0b4b6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 6 14:42:19 2019 +0900

    sample/rev_comp.rb: Generates reverse-complement sequences
    
     * sample/rev_comp.rb: Generates reverse-complement sequences of
       the given nucleotide sequences.
     * sample/rev_comp.cwl: CWL cowkflow for the sample script
     * sample/rev_comp.testdata.yaml: Test data for the above CWL workflow

 sample/rev_comp.cwl           | 23 +++++++++++++++++++++++
 sample/rev_comp.rb            | 20 ++++++++++++++++++++
 sample/rev_comp.testdata.yaml |  7 +++++++
 3 files changed, 50 insertions(+)
 create mode 100644 sample/rev_comp.cwl
 create mode 100644 sample/rev_comp.rb
 create mode 100644 sample/rev_comp.testdata.yaml

commit ff0e6c3c6b6f1b56d81b5a4b579a6d0984bfc607
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 6 14:40:45 2019 +0900

    sample/color_scheme_(na|aa).rb: use String#each_char instead of each_byte

 sample/color_scheme_aa.rb | 6 +++---
 sample/color_scheme_na.rb | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

commit 6f7c1be09aa3d6cdb76fd029fc0f84efda31c907
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Sep 5 17:32:07 2019 +0900

    sample/color_scheme_aa.rb: new sample based on color_scheme_na.rb

 sample/color_scheme_aa.rb | 82 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)
 create mode 100644 sample/color_scheme_aa.rb

commit 51864c3857178f58133b759f7608b8d6d8991c44
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Sep 5 17:13:20 2019 +0900

    sample/color_scheme_na.rb: use const_get instead of eval

 sample/color_scheme_na.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit ba0b554971a9a387a54fc04c5002853d91357347
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Sep 5 17:02:20 2019 +0900

    sample/na2aa.cwl: inputBinding position -1 for the script
    
     * sample/na2aa.cwl: inputBinding position -1 is used for the script
       to emphasize that the argument is the first one.

 sample/na2aa.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 26a27ec261e2251f3ff3a85007147d33682778d0
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Sep 5 16:56:08 2019 +0900

    sample/color_scheme_na.rb: Supports more file formats
    
     * sample/color_scheme_na.rb: Supports more file formats other than
       fasta format, by using Bio::Flatfile.

 sample/color_scheme_na.rb | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

commit 5c053a606382bb578a2b6884ee639805154433e5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Sep 5 12:32:00 2019 +0900

    sample/na2aa.cwl: use inputBinding

 sample/na2aa.cwl | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

commit 6a3c3e02f08549d47dda00dca92d55bbadfc468f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Sep 4 22:59:21 2019 +0900

    Sample CWL workflow to run sample/na2aa.rb
    
     * na2aa.cwl: A sample CWL workflow to run na2aa.rb in sample/ dir
     * na2aa.testdata.yaml: Test data for the workflow

 sample/na2aa.cwl           | 20 ++++++++++++++++++++
 sample/na2aa.testdata.yaml |  7 +++++++
 2 files changed, 27 insertions(+)
 create mode 100644 sample/na2aa.cwl
 create mode 100644 sample/na2aa.testdata.yaml

commit 960b885036f549863e3cfe9c693c90f9bef27d3d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Sep 4 21:00:50 2019 +0900

    LEGAL: na2aa.rb is now Ruby's License

 LEGAL | 1 -
 1 file changed, 1 deletion(-)

commit 7af9e81988939007eb36dab6b102a7422e8196d8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Sep 4 14:34:05 2019 +0900

    sample/na2aa.rb: Completely rewritten
    
     * sample/na2aa.rb: Completely rewritten. License is changed because
       old code is completely wiped out. Note that the old code always
       raises error due to a bug in the code.
     * The old code was trying to replace 'X' (any) to '-' (gap) but
       the new code does not modify translated sequences anymore.

 sample/na2aa.rb | 36 +++++++++++-------------------------
 1 file changed, 11 insertions(+), 25 deletions(-)

commit cf8cac5e32db42b6683c1a837adc9e1c04994062
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Sep 2 17:11:08 2019 +0900

    Bug fix: Bio::GFF::GFF2::Record.parse did not return correct object

 lib/bio/db/gff.rb            | 4 +++-
 test/unit/bio/db/test_gff.rb | 5 +++++
 2 files changed, 8 insertions(+), 1 deletion(-)

commit 80b387e7e2bb8570d9204e389b6c5d90c6ea31de
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 14 14:33:19 2019 +0900

    BioRuby 2.0.0 is released

 ChangeLog | 1051 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 1043 insertions(+), 8 deletions(-)

commit 2e4046517fd8ee1c105ef53131e69f787d790099
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 14 14:23:19 2019 +0900

    Add "Recommended Plugins" section and description is moved to it

 README.rdoc | 22 +++++++++++++++-------
 1 file changed, 15 insertions(+), 7 deletions(-)

commit 7a533e4f57edcebb5dfe15fdddc9fbc986d2b7ec
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 14 14:17:08 2019 +0900

    fix directory name

 README.rdoc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 805266c9c900903156efd0baa8c1e6ee524a8147
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 14 14:14:52 2019 +0900

    add description about recommended plugins

 README.rdoc | 11 +++++++++++
 1 file changed, 11 insertions(+)

commit 02b7d8b9bc5dcd56f501a15e5e820f450153aa1c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 14 13:33:30 2019 +0900

    prepare to release BioRuby 2.0.0

 lib/bio/version.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

commit f1fed8dacb425d19c12abec5d4faeb733827f80f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 14 13:31:08 2019 +0900

    regenerate bioruby.gemspec with rake regemspec

 bioruby.gemspec | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

commit 3952ec9d5ce1e3ceea9734f667d36595808c4989
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 14 13:28:19 2019 +0900

    Remove xmlparser dependency from Gemfile and gemfiles/Gemfile.*

 Gemfile                         | 2 --
 gemfiles/Gemfile.travis-rbx     | 2 --
 gemfiles/Gemfile.travis-ruby1.8 | 2 --
 gemfiles/Gemfile.travis-ruby1.9 | 2 --
 gemfiles/Gemfile.windows        | 2 --
 5 files changed, 10 deletions(-)

commit d4a8ee7ae3d3b13a8be4c57c1f8db5b29f2c4a13
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 14 12:34:45 2019 +0900

    RELEASE_NOTES.rdoc: update aboue new features and improvements

 RELEASE_NOTES.rdoc | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

commit 2d4170a2a0262f5d75cef5a54b5d6f3da298f145
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 14 12:24:12 2019 +0900

    Tests added in the previous commit is moved and modified
    
     * test/network/bio/db/kegg/test_genes_hsa7422.rb: tests added in the
       previous commit is moved to the file and modified to get data
       from the internet for avoiding KEGG data license issue.
       Note that some of the tests might be fail in the near future due to
       the database entry updates.

 test/network/bio/db/kegg/test_genes_hsa7422.rb | 91 ++++++++++++++++++++++++++
 test/unit/bio/db/kegg/test_genes.rb            | 51 ---------------
 2 files changed, 91 insertions(+), 51 deletions(-)
 create mode 100644 test/network/bio/db/kegg/test_genes_hsa7422.rb

commit 67f8105acf22e88a7624305743ad13802ffed124
Author: kojix2 <2xijok@gmail.com>
Date:   Mon Oct 22 00:46:31 2018 +0900

    add DiseasesAsHash to KEGG/Common

 lib/bio/db/kegg/common.rb           | 14 ++++++++++
 lib/bio/db/kegg/genes.rb            | 26 +++++++++++++++++++
 lib/bio/db/kegg/pathway.rb          | 16 ++++--------
 test/unit/bio/db/kegg/test_genes.rb | 51 +++++++++++++++++++++++++++++++++++++
 4 files changed, 96 insertions(+), 11 deletions(-)

commit 9dbb655e1c3ec7460b77f1d0ea475531ac3a9361
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 14 11:37:11 2019 +0900

    update documents for upcoming new release

 KNOWN_ISSUES.rdoc  | 14 +++-----
 LEGAL              |  9 ------
 README.rdoc        | 92 +++++++----------------------------------------------
 README_DEV.rdoc    | 10 +++---
 RELEASE_NOTES.rdoc | 93 +++++++++++++++++++++++++++++++++++++++++++-----------
 5 files changed, 96 insertions(+), 122 deletions(-)

commit 6f388019a035a41a8867c6a03ef7e2707d1edce4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 14 11:32:40 2019 +0900

    .travis.yml: move 1.8.7 and 1.9.3 to allow_failures; update ruby versions

 .travis.yml | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

commit f2cbe9db9b78df653d774a7676e00f6f1a212b23
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 14 11:18:27 2019 +0900

    .travis.yml: Remove jobs using "tar-integration-test"

 .travis.yml | 9 ---------
 1 file changed, 9 deletions(-)

commit 68f28e81e3fa566843b548f1899549adcad5225a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 14 11:10:18 2019 +0900

    remove "rake tar-install" and "rake tar-integration-test" tasks
    
     * Rakefile: Remove "tar-install" and "tar-integration-test" tasks
       because they use setup.rb that is removed from the repository.

 Rakefile | 34 ----------------------------------
 1 file changed, 34 deletions(-)

commit 0cbdb4586f2231a68579105dbc7f0fb413b38a96
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 14 10:48:15 2019 +0900

    next bioruby version will be 2.0.0

 lib/bio/version.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 300d10b9791b7f0c0eff1d0544cae63fecc3b31a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 14 10:41:12 2019 +0900

    Remove setup.rb. Use RubyGems to install BioRuby.

 setup.rb | 1600 --------------------------------------------------------------
 1 file changed, 1600 deletions(-)
 delete mode 100644 setup.rb

commit a74683d9acfc16d0d715b020839839afc8b43350
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 14 02:28:31 2019 +0900

    try to require "bio-blast-xmlparser" provided by separete gem

 lib/bio/appl/blast/report.rb | 8 ++++++++
 1 file changed, 8 insertions(+)

commit de1c1e33aed392d4e2265a028b8acb50501f56bd
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Sep 16 04:49:21 2017 +0900

    check existance of a private method instead of XMLParser constant

 test/unit/bio/appl/blast/test_report.rb | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

commit 3f54d19c44411e845b32c522fc0deca4288dcf07
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Sep 16 04:39:19 2017 +0900

    xml_set_parameter is moved from xmlparser.rb etc.
    
     * The method xml_set_parameter is moved from
       lib/bio/appl/blast/xmlparser.rb because it is used by
       the REXML parser.
     * The method Bio::Blast::Report.xmlparser is move to
       lib/bio/appl/blast/xmlparser.rb in the separate repo.
     * Use "defined? xmlparser_parse" for checking existance of
       the blast xmlparser component.
     * Removed line to require bio/appl/blast/xmlparser.

 lib/bio/appl/blast/report.rb | 40 ++++++++++++++++++++++++++++++++--------
 1 file changed, 32 insertions(+), 8 deletions(-)

commit b19cd507c432739c5aaac700e222e6e4ecc63ddc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Sep 16 03:32:54 2017 +0900

    lib/bio/appl/blast/xmlparser.rb is removed and moved to separate gem
    
     * lib/bio/appl/blast/xmlparser.rb is removed and moved to separate gem
       to eliminate dependency to xmlparser that includes native extension.

 lib/bio/appl/blast/xmlparser.rb | 236 ----------------------------------------
 1 file changed, 236 deletions(-)
 delete mode 100644 lib/bio/appl/blast/xmlparser.rb

commit 525d3450ad3440bfbbe3a1540fe60d83c3845ec7
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Dec 15 11:33:08 2018 +0900

    .travis.yml: remove jruby-18mode and jruby-19mode; add jruby and truffleruby

 .travis.yml | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

commit 5bc0042b7fc39c62222534e0e4129d3f9794fd8c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 14 22:46:08 2018 +0900

    appveyor.yml: regenerate bioruby.gemspec before creating gem

 appveyor.yml | 1 +
 1 file changed, 1 insertion(+)

commit 5582dc1db60ffc812211d9803d5adce9c0dd70d3
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 14 22:39:35 2018 +0900

    appveyor.yml: modify gemfile/Gemfile.windows after bundle install

 appveyor.yml | 1 +
 1 file changed, 1 insertion(+)

commit 09031bcae0a42fe93d07b46eb489ffbabc8c1319
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 14 22:30:09 2018 +0900

    appveyor.yml: give up using vendor/bundle; set BUNDLE_GEMFILE

 appveyor.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

commit 44fb6c67aef1b0311d32ac806fc9a62f09d401d5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 14 21:59:44 2018 +0900

    appveyor.yml: Specify gemfiles/Gemfile.windows
    
     * appveyor.yml: Specify gemfiles/Gemfile.windows in which xmlparser gem
       is excluded because of build failure of the xmlparser gem on Windows.
     * gemfiles/Gemfile.windows: Gemfile for Appveyor, running on Microsoft
       Windows.

 appveyor.yml             | 2 +-
 gemfiles/Gemfile.windows | 8 ++++++++
 2 files changed, 9 insertions(+), 1 deletion(-)
 create mode 100644 gemfiles/Gemfile.windows

commit fe55e52b42660dda1d21749bf714e989e7db754e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 14 21:48:06 2018 +0900

    appveyor.yml: update ruby versions and test procedure

 appveyor.yml | 22 +++++++++++++++-------
 1 file changed, 15 insertions(+), 7 deletions(-)

commit 739f5c9a512074a7de25d87e8104ed15bdb28b5d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 14 11:57:43 2018 +0900

    .travis.yml: change default Gemfile
    
     * Change default Gemfile to Gemfile
     * Move old Ruby versions to "include" matrix.
     * Change ruby version for gem-integration-test and tar-integration-test

 .travis.yml | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

commit 2f54a9cbf8fb6d8580d488b20007d5ce4562e5e9
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 14 11:42:58 2018 +0900

    .travis.yml: No more limit to master branch. Instead, add blocklist.

 .travis.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

commit 9ac3e44318c67fd4415a2118dd5631902e784e12
Author: Kozo Nishida <knishida@riken.jp>
Date:   Thu Dec 13 22:47:54 2018 +0900

    ci(travis): Add rvm versions

 .travis.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

commit 258dd67c9d65f1247e56d5c5228cc6f9c019d133
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 10 21:56:16 2018 +0900

    regenerate bioruby.gemspec with rake regemspec

 bioruby.gemspec | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 3920483d6b5a3759e6c610d7ee9fb1a63dcc9ce4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 10 21:55:19 2018 +0900

    Simplify version number processing

 bioruby.gemspec.erb | 14 +++++++-------
 lib/bio/version.rb  | 12 +++++-------
 2 files changed, 12 insertions(+), 14 deletions(-)

commit 80949a10ea5e4f88d21d893905b720925f5a9e7b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 10 18:54:00 2018 +0900

    next bioruby version will be 1.6.0

 lib/bio/version.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 2b542865a4d4af2684ace41f79e273ebceb51807
Merge: 02a96424 d71e07a0
Author: Toshiaki Katayama <k@bioruby.org>
Date:   Fri Oct 19 06:45:49 2018 +0900

    Merge pull request #125 from kojix2/master
    
    update TogoWS documentation. genbank -> ncbi-nucleotide

commit d71e07a0cb1cc441241be91273bd44e3717b8773
Author: kojix2 <2xijok@gmail.com>
Date:   Thu Oct 18 19:10:29 2018 +0900

    update TogoWS documentation. genbank -> ncbi-nucleotide

 lib/bio/io/togows.rb                   | 10 +++++-----
 sample/test_restriction_enzyme_long.rb |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

commit 02a964241b79e2307d0a00473427ea6bc2ea6932
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 6bfef40ae87099565371abf94cf2cc8bfac76b12
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 4e3251d2172f58239f103e7edf8f4c351140f378
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 6dd1f9fb8c2b4ba95086eab7bffc01583feccf3a
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 4b6f87c9fd2dc62418ddfc4b57bcc4b73287a603
Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>
Date:   Sat Mar 31 13:08:07 2018 +0900

    directly refer to the given hash

 lib/bio/data/codontable.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit 25636ffa08c6ea9a9e4d1b451a456bc1f482ad40
Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>
Date:   Sat Jun 2 15:10:12 2018 +0900

    precalculated ambiguity codontable

 lib/bio/data/codontable.rb | 55 +++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 52 insertions(+), 3 deletions(-)

commit b2d924045202ec3aa4e1b79341fd939a881d4c2e
Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>
Date:   Sat Mar 31 11:55:57 2018 +0900

    construct ambiguity nucleotide to amino acid table

 lib/bio/data/codontable.rb            | 49 ++++++++++++++++++++++++++++++++++-
 test/unit/bio/data/test_codontable.rb |  3 +++
 2 files changed, 51 insertions(+), 1 deletion(-)

commit a7378b6b269ea1c0391e259dd8e4868f03b064ea
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 c89c40c29c3c92f8e548c79d2d04698123559007
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 15 16:33:19 2017 +0900

    Remove settings about executables
    
     * Definitions and settings about executables are removed because
       all files in bin/ have been moved to separate gem packages
       (bio-shell and bio-executables).

 bioruby.gemspec     | 13 -------------
 bioruby.gemspec.erb | 21 +--------------------
 2 files changed, 1 insertion(+), 33 deletions(-)

commit b5a8d385da8f2c1b6e1caf77295e590f55595944
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 15 16:20:03 2017 +0900

    bin/br_*.rb is moved to bio-executables gem
    
     * The following executable files are moved to "bio-executables" gem.
       * bin/br_biofetch.rb
       * bin/br_bioflat.rb
       * bin/br_biogetseq.rb
       * bin/br_pmfetch.rb

 bin/br_biofetch.rb  |  71 ---------
 bin/br_bioflat.rb   | 293 ------------------------------------
 bin/br_biogetseq.rb |  45 ------
 bin/br_pmfetch.rb   | 422 ----------------------------------------------------
 4 files changed, 831 deletions(-)
 delete mode 100755 bin/br_biofetch.rb
 delete mode 100755 bin/br_bioflat.rb
 delete mode 100755 bin/br_biogetseq.rb
 delete mode 100755 bin/br_pmfetch.rb

commit eb61d89a366437570a0590a629cb75718866b236
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 15 09:31:14 2017 +0900

    regenerate bioruby.gemspec with rake regemspec

 bioruby.gemspec | 44 +-------------------------------------------
 1 file changed, 1 insertion(+), 43 deletions(-)

commit 6d40721d039fdb6b77af656f32ccabeabc427409
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 15 09:29:33 2017 +0900

    Remove BioRuby Shell files that are released as independent gem package

 bin/bioruby                                        |  47 --
 lib/bio/shell.rb                                   |  44 --
 lib/bio/shell/core.rb                              | 578 ---------------------
 lib/bio/shell/demo.rb                              | 146 ------
 lib/bio/shell/interface.rb                         | 217 --------
 lib/bio/shell/irb.rb                               |  94 ----
 lib/bio/shell/object.rb                            |  71 ---
 lib/bio/shell/plugin/blast.rb                      |  42 --
 lib/bio/shell/plugin/codon.rb                      | 218 --------
 lib/bio/shell/plugin/das.rb                        |  58 ---
 lib/bio/shell/plugin/emboss.rb                     |  23 -
 lib/bio/shell/plugin/entry.rb                      | 137 -----
 lib/bio/shell/plugin/flatfile.rb                   | 101 ----
 lib/bio/shell/plugin/midi.rb                       | 430 ---------------
 lib/bio/shell/plugin/ncbirest.rb                   |  68 ---
 lib/bio/shell/plugin/obda.rb                       |  45 --
 lib/bio/shell/plugin/psort.rb                      |  56 --
 lib/bio/shell/plugin/seq.rb                        | 248 ---------
 lib/bio/shell/plugin/togows.rb                     |  40 --
 .../generators/bioruby/bioruby_generator.rb        |  29 --
 .../generators/bioruby/templates/_classes.rhtml    |   4 -
 .../generators/bioruby/templates/_log.rhtml        |  27 -
 .../generators/bioruby/templates/_methods.rhtml    |  11 -
 .../generators/bioruby/templates/_modules.rhtml    |   4 -
 .../generators/bioruby/templates/_variables.rhtml  |   7 -
 .../generators/bioruby/templates/bioruby-bg.gif    | Bin 1431 -> 0 bytes
 .../generators/bioruby/templates/bioruby-gem.png   | Bin 6951 -> 0 bytes
 .../generators/bioruby/templates/bioruby-link.gif  | Bin 2758 -> 0 bytes
 .../generators/bioruby/templates/bioruby.css       | 368 -------------
 .../generators/bioruby/templates/bioruby.rhtml     |  47 --
 .../bioruby/templates/bioruby_controller.rb        | 144 -----
 .../generators/bioruby/templates/bioruby_helper.rb |  47 --
 .../generators/bioruby/templates/commands.rhtml    |   8 -
 .../generators/bioruby/templates/history.rhtml     |  10 -
 .../generators/bioruby/templates/index.rhtml       |  26 -
 .../generators/bioruby/templates/spinner.gif       | Bin 1542 -> 0 bytes
 lib/bio/shell/script.rb                            |  25 -
 lib/bio/shell/setup.rb                             | 108 ----
 lib/bio/shell/web.rb                               | 102 ----
 test/unit/bio/shell/plugin/test_seq.rb             | 187 -------
 test/unit/bio/test_shell.rb                        |  20 -
 41 files changed, 3837 deletions(-)
 delete mode 100755 bin/bioruby
 delete mode 100644 lib/bio/shell.rb
 delete mode 100644 lib/bio/shell/core.rb
 delete mode 100644 lib/bio/shell/demo.rb
 delete mode 100644 lib/bio/shell/interface.rb
 delete mode 100644 lib/bio/shell/irb.rb
 delete mode 100644 lib/bio/shell/object.rb
 delete mode 100644 lib/bio/shell/plugin/blast.rb
 delete mode 100644 lib/bio/shell/plugin/codon.rb
 delete mode 100644 lib/bio/shell/plugin/das.rb
 delete mode 100644 lib/bio/shell/plugin/emboss.rb
 delete mode 100644 lib/bio/shell/plugin/entry.rb
 delete mode 100644 lib/bio/shell/plugin/flatfile.rb
 delete mode 100644 lib/bio/shell/plugin/midi.rb
 delete mode 100644 lib/bio/shell/plugin/ncbirest.rb
 delete mode 100644 lib/bio/shell/plugin/obda.rb
 delete mode 100644 lib/bio/shell/plugin/psort.rb
 delete mode 100644 lib/bio/shell/plugin/seq.rb
 delete mode 100644 lib/bio/shell/plugin/togows.rb
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml
 delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif
 delete mode 100644 lib/bio/shell/script.rb
 delete mode 100644 lib/bio/shell/setup.rb
 delete mode 100644 lib/bio/shell/web.rb
 delete mode 100644 test/unit/bio/shell/plugin/test_seq.rb
 delete mode 100644 test/unit/bio/test_shell.rb

commit ab9feb6f1f495a2b3ca350005c6162c51178aecb
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 cf486e327c253482f54e59b2e18f73db27641135
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 88477698f0e1b5a74f9682f26e97c5f90f6912b4
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 f8cff14179cfeea0d685f4df756db71ceb6d5fab
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 ddb25c2bf3872c6306a91e407d95caa2e136cee9
Author: Jun Aruga <jaruga@redhat.com>
Date:   Fri Nov 18 11:14:38 2016 +0100

    Gemfile for local development.

 .travis.yml                                | 8 ++++----
 gemfiles/Gemfile.travis-ruby2.2 => Gemfile | 0
 bioruby.gemspec                            | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)
 rename gemfiles/Gemfile.travis-ruby2.2 => Gemfile (100%)

commit 16faf6473b74eb172716b713ab757cb2ab2bcacc
Author: Jun Aruga <jaruga@redhat.com>
Date:   Thu Nov 17 17:50:40 2016 +0100

    Fixes ruby1.8 Travis failure that is because rdoc 4.3.0 requires Ruby >= 1.9.3.

 gemfiles/Gemfile.travis-jruby1.8 | 3 ++-
 gemfiles/Gemfile.travis-ruby1.8  | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

commit 146fd66b3a14972bcfd0e9bf8ec007d38c55ac39
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 7abd46f058a17ac34b263714449756383622012d
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 11c680f6d64a60bdc0f4248951bf2d2ebafbc433
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 17 20:40:41 2016 +0900

    gemfiles/Gemfile.*: remove dependency on libxml-ruby
    
     * gemfiles/Gemfile.*: remove dependency on libxml-ruby.
       Bio::PhyloXML required libxml-ruby but was already removed.

 gemfiles/Gemfile.travis-jruby1.8 | 3 ---
 gemfiles/Gemfile.travis-jruby1.9 | 3 ---
 gemfiles/Gemfile.travis-rbx      | 1 -
 gemfiles/Gemfile.travis-ruby1.8  | 1 -
 gemfiles/Gemfile.travis-ruby1.9  | 1 -
 gemfiles/Gemfile.travis-ruby2.2  | 1 -
 6 files changed, 10 deletions(-)

commit 09fa57f987445e8654de6a0d0cf7c45f7625600c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 17 16:16:40 2016 +0900

    regenerate bioruby.gemspec with rake regemspec

 bioruby.gemspec | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

commit 87812d119820bf66767c7767cfec7554d7a00f3b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 17 15:45:46 2016 +0900

    README.rdoc: about bioruby-phyloxml and bio-biosql

 README.rdoc | 10 ++++++++++
 1 file changed, 10 insertions(+)

commit 2294f255f5f05f9f629a1e88c0e1f59bb74b32bc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 17 15:42:46 2016 +0900

    KNOWN_ISSUES.rdoc: remove descriptions about Bio::SQL

 KNOWN_ISSUES.rdoc | 5 -----
 1 file changed, 5 deletions(-)

commit 35a6f761dc5fa493b8311747dde7f2a54d8aee75
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 17 15:40:57 2016 +0900

    README.rdoc: remove descriptions about Bio::SQL

 README.rdoc | 13 +------------
 1 file changed, 1 insertion(+), 12 deletions(-)

commit 46a5bf7acdc803b7e75225c41b23396c4619f25d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 17 14:59:41 2016 +0900

    remove autoload of Bio::SQL

 lib/bio.rb | 1 -
 1 file changed, 1 deletion(-)

commit 57bf535da34715beafccb902404cf1bb35b18af4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 17 14:48:46 2016 +0900

    Removed Bio::SQL that have been moved to separate repository
    
     * Bio::SQL is moved to https://github.com/bioruby/bioruby-biosql
       and removed from this repository.
    
     * List of deleted files:
       * deleted:    lib/bio/db/biosql/biosql_to_biosequence.rb
       * deleted:    lib/bio/db/biosql/sequence.rb
       * deleted:    lib/bio/io/biosql/ar-biosql.rb
       * deleted:    lib/bio/io/biosql/biosql.rb
       * deleted:    lib/bio/io/biosql/config/database.yml
       * deleted:    lib/bio/io/sql.rb
       * deleted:    test/unit/bio/db/biosql/tc_biosql.rb
       * deleted:    test/unit/bio/db/biosql/ts_suite_biosql.rb

 lib/bio/db/biosql/biosql_to_biosequence.rb |  78 -----
 lib/bio/db/biosql/sequence.rb              | 444 -----------------------------
 lib/bio/io/biosql/ar-biosql.rb             | 257 -----------------
 lib/bio/io/biosql/biosql.rb                |  39 ---
 lib/bio/io/biosql/config/database.yml      |  21 --
 lib/bio/io/sql.rb                          |  79 -----
 test/unit/bio/db/biosql/tc_biosql.rb       | 114 --------
 test/unit/bio/db/biosql/ts_suite_biosql.rb |   8 -
 8 files changed, 1040 deletions(-)
 delete mode 100644 lib/bio/db/biosql/biosql_to_biosequence.rb
 delete mode 100644 lib/bio/db/biosql/sequence.rb
 delete mode 100644 lib/bio/io/biosql/ar-biosql.rb
 delete mode 100644 lib/bio/io/biosql/biosql.rb
 delete mode 100644 lib/bio/io/biosql/config/database.yml
 delete mode 100644 lib/bio/io/sql.rb
 delete mode 100644 test/unit/bio/db/biosql/tc_biosql.rb
 delete mode 100644 test/unit/bio/db/biosql/ts_suite_biosql.rb

commit 476dcdbe2b21cd5adb641952ee3da92c2d593121
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jun 8 12:38:22 2016 +0900

    appveyor.yml: eliminate old Ruby versions and add Ruby 2.3

 appveyor.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

commit c26e2b77b75b5505a274822f53c6c5a8f842f6c0
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jun 8 01:50:19 2016 +0900

    .travis.yml: fix to use rbx-3.29

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit b524abedac9c85d4f8259191b973bc38a9fc557c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jun 8 01:45:48 2016 +0900

    gemfiles/Gemfile.travis-jruby1.8: use old gem versions supporting Ruby 1.8

 gemfiles/Gemfile.travis-jruby1.8 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

commit c5df9268b77f1d4dc2b29e7cfb7baf3c528c1558
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jun 8 01:42:40 2016 +0900

    .travis.yml: use rbx-3.29 instead of rbx-3

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

commit b51b54894ca2d76d9c13680fd72b87951a10a1df
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jun 8 01:25:18 2016 +0900

    Workaround to avoid bug in old versions of Bundler
    
     * gemfiles/prepare-gemspec.rb: execute "gem update bundler" to avoid
       "NoMethodError: undefined method `spec' for nil:NilClass"
       during "bundle install". This error may be due to a bug of Bundler
       and the bug seems to be fixed in the latest version of Budler.

 gemfiles/prepare-gemspec.rb | 4 ++++
 1 file changed, 4 insertions(+)

commit a82424b4864e243ebf1f8cc7f181044798b34b5a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jun 8 01:20:15 2016 +0900

    .travis.yml: add Ruby 2.3.1; use Ruby 2.2.5 instead of 2.2

 .travis.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

commit ae927514a5c2853d3839750af86bfcc1fc53e4f1
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jun 8 00:54:22 2016 +0900

    .travis.yml: add "sudo: false" for faster testing

 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

commit 832c4dd94a5602a9deadf599ce1778fac870ac81
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jun 8 00:46:26 2016 +0900

    gemfiles/Gemfile.travis-ruby1.8: use old gem versions supporting Ruby 1.8

 gemfiles/Gemfile.travis-ruby1.8 | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

commit 6cf0ab84cd67aab0f6f4012438c1852a19f3ac7a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jun 8 00:04:36 2016 +0900

    regenerate bioruby.gemspec with rake regemspec

 bioruby.gemspec | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

commit 8e986984892d661b4f09a06158a634554d931718
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Jun 7 23:59:35 2016 +0900

    .travis.yml: Update ruby versions and remove temporary workaround
    
     * Update Ruby versions to 2.2, 2.1.10, and rbx-3.
     * Remove temporary workaround about RubyGems introduced in
       e92e09edf5904f51d3e73e61d13fce4159a543c5.

 .travis.yml | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

commit 90e678d6d74d86c45631128c0f16181679f0d599
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Jun 7 23:37:45 2016 +0900

    Test bug: fix gem version mismatch error on Travis-CI
    
     * Rakefile: prefer to use spec read from existing bioruby.gemspec file
       instead of that of generated from bioruby.gemspec.erb.
       This fixes "can't activate bio (= 1.5.1.2016XXXX), already activated
       bio-1.5.1.2015NNNN" occurred on Travis-CI during gem integration tests.

 Rakefile | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

commit bdb33fe752b7dddcb35f57d826f85dbdd512c3c1
Author: Kozo Nishida <knishida@riken.jp>
Date:   Wed Nov 4 12:08:24 2015 +0900

    add appveyor.yml

 appveyor.yml | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 appveyor.yml

commit 8b0fa73c57232a6a86d2d6fd0711f51bc50aa333
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Sep 17 23:34:34 2015 +0900

    regenerate bioruby.gemspec with rake regemspec

 bioruby.gemspec | 14 +-------------
 1 file changed, 1 insertion(+), 13 deletions(-)

commit 813fc808e9a235e03ed2d5bad2d15f74946bd65a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Sep 17 23:30:46 2015 +0900

    Tutorial.rd.html is regenerated by rake retutorial2html

 doc/Tutorial.rd.html | 117 +++++++++------------------------------------------
 1 file changed, 19 insertions(+), 98 deletions(-)

commit 756f14122a45973289172a88241490a1bcc0054a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Sep 17 23:25:07 2015 +0900

    Delete Bio::PhyloXML tutorial
    
     * Tutorial for Bio::PhyloXML is deleted from BioRuby core.
       It is now moved to bio-phyloxml gem. New tutorial for
       Bio::PhyloXML is available at:
       https://github.com/bioruby/bioruby-phyloxml/blob/master/doc/Tutorial.rd

 doc/Tutorial.rd | 114 +++-----------------------------------------------------
 1 file changed, 6 insertions(+), 108 deletions(-)

commit bb42efdd2eec380c99cbd3e505577a550dda8ce7
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Sep 17 23:20:50 2015 +0900

    Delete description of Bio::PhyloXML and its dependency libxml-ruby.

 README.rdoc | 6 ------
 1 file changed, 6 deletions(-)

commit 4202ae936baf0f4c8a722af240a6613f4e8a8cee
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Sep 17 22:48:23 2015 +0900

    Remove PhyloXML (split out bio-phyloxml gem)
    
     * Bio::PhyloXML is removed from BioRuby core.
       It will soon be released as separate bio-phyloxml gem.
       The development repository of the new Bio::PhyloXML is
       https://github.com/bioruby/bioruby-phyloxml

 lib/bio/db/phyloxml/phyloxml.xsd                   |  582 ------
 lib/bio/db/phyloxml/phyloxml_elements.rb           | 1194 -----------
 lib/bio/db/phyloxml/phyloxml_parser.rb             | 1001 ----------
 lib/bio/db/phyloxml/phyloxml_writer.rb             |  227 ---
 sample/test_phyloxml_big.rb                        |  205 --
 test/data/phyloxml/apaf.xml                        |  666 -------
 test/data/phyloxml/bcl_2.xml                       | 2097 --------------------
 test/data/phyloxml/made_up.xml                     |  144 --
 .../data/phyloxml/ncbi_taxonomy_mollusca_short.xml |   65 -
 test/data/phyloxml/phyloxml_examples.xml           |  415 ----
 test/unit/bio/db/test_phyloxml.rb                  |  821 --------
 test/unit/bio/db/test_phyloxml_writer.rb           |  334 ----
 12 files changed, 7751 deletions(-)
 delete mode 100644 lib/bio/db/phyloxml/phyloxml.xsd
 delete mode 100644 lib/bio/db/phyloxml/phyloxml_elements.rb
 delete mode 100644 lib/bio/db/phyloxml/phyloxml_parser.rb
 delete mode 100644 lib/bio/db/phyloxml/phyloxml_writer.rb
 delete mode 100644 sample/test_phyloxml_big.rb
 delete mode 100644 test/data/phyloxml/apaf.xml
 delete mode 100644 test/data/phyloxml/bcl_2.xml
 delete mode 100644 test/data/phyloxml/made_up.xml
 delete mode 100644 test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml
 delete mode 100644 test/data/phyloxml/phyloxml_examples.xml
 delete mode 100644 test/unit/bio/db/test_phyloxml.rb
 delete mode 100644 test/unit/bio/db/test_phyloxml_writer.rb

commit e3a85ad9eb6d258e79fdfbe600711a5296a20e8c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Sep 17 22:45:32 2015 +0900

    Delete autoload of Bio::PhyloXML
    
     * Delete autoload of Bio::PhyloXML, for preparation of spliting
       out Bio::PhyloXML.

 lib/bio.rb | 7 -------
 1 file changed, 7 deletions(-)

commit 422ffe6fedecf41d83327c01f7a55ebce4afd70d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Sep 15 22:33:14 2015 +0900

    Incompatible change about deprecated Bio::Taxonomy is described.

 RELEASE_NOTES.rdoc | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

commit 3ea10d73340d8ad571ab6ca386cffca18ec725d1
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Sep 15 21:06:29 2015 +0900

    Bio::Taxonomy is removed and merged to Bio::PhyloXML::Taxonomy
    
     * Bio::Taxonomy in lib/bio/db/phyloxml/phyloxml_elements.rb was
       written for PhyloXML, but it was intended to become general
       taxonomy data class in BioRuby. However, no efforts have been
       made to improve the Bio::Taxonomy class, and it still remains
       to be a PhyloXML specific class. As the first step to split out
       Bio::PhyloXML to a new Gem (Biogem) package, we now decide to
       remove Bio::Taxonomy and merge it to Bio::PhyloXML::Taxonomy.
    
     * Codes using Bio::Taxonomy should be modified. Changing
       Bio::Taxonomy to Bio::PhyloXML::Taxonomy, or adding the
       following monkey patch is needed.
    
          module Bio
             unless defined? Taxonomy
                Taxonomy = Bio::PhyloXML::Taxonomy
             end
          end

 lib/bio.rb                               |  2 --
 lib/bio/db/phyloxml/phyloxml_elements.rb | 21 +++++++++------------
 2 files changed, 9 insertions(+), 14 deletions(-)

commit f89f49223f7d6ed74a8fc50aa2355fb5912c885f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Sep 14 15:15:56 2015 +0900

    regenerate bioruby.gemspec with rake regemspec

 bioruby.gemspec | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

commit 809e190d710caceee1c213da1aa067dee87e6ebd
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Sep 14 15:14:05 2015 +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 a44257e933165509f3d2b164ea547ed8fba18ea5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Sep 14 15:10:42 2015 +0900

    move RELEASE_NOTES.rdoc to doc/RELEASE_NOTES-1.5.0.rdoc

 RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.5.0.rdoc | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.5.0.rdoc (100%)

commit 4d53755b0181255e2ee69193a5a3b064ef4f4b77
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jul 2 22:19:03 2015 +0900

    ChangeLog since 1.5.0 release

 ChangeLog | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 ChangeLog

commit e066e3c8bcf0c6b7eadd3573576d4550aca77cc5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jul 2 22:17:06 2015 +0900

    ChangeLog is moved to doc/ChangeLog-1.5.0

 ChangeLog => doc/ChangeLog-1.5.0 | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename ChangeLog => doc/ChangeLog-1.5.0 (100%)

commit dd53e885c1baa765bc094897d53309af7b15497b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jul 2 22:09:26 2015 +0900

    change version for generating ChangeLog to 1.5.0

 Rakefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

commit 8fc4d6c64f6958a352c36b171b00d1f1ff2a2354
Author: Naohisa Goto <ng@bioruby.org>
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(-)
