commit 51ab2dec144c99a14ca9009c7b589b500f1cad5f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Aug 22 00:12:47 2012 +0900

    Preparation to re-release BioRuby 1.4.3

 ChangeLog |   22 ++++++++++++++++++++++
 1 files changed, 22 insertions(+), 0 deletions(-)

commit 5ff159d12252393ff04afe52b59a315d15c63d18
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Aug 22 00:00:40 2012 +0900

    Bug fix: bin/bioruby failed to save object
    
     * Bug fix: bin/bioruby: Failed to save object with error message
       "can't convert Symbol into String" on Ruby 1.9.

 RELEASE_NOTES.rdoc    |    2 ++
 lib/bio/shell/core.rb |    1 +
 2 files changed, 3 insertions(+), 0 deletions(-)

commit 74c6ce09413e7ddde1431d74e10cc9c4cdbb95ba
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Aug 21 22:35:18 2012 +0900

    BioRuby 1.4.3 is released.

 ChangeLog |   21 +++++++++++++++++++++
 1 files changed, 21 insertions(+), 0 deletions(-)

commit 61af85b6cfc7bb1f3668ed68232113eb0751e7ea
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Aug 21 22:33:30 2012 +0900

    preparation for BioRuby 1.4.3 release version

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

commit 1ec68beac42a06e9ef0a9c953650ef4d599e4e65
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Aug 21 20:53:04 2012 +0900

    ChangeLog modified; release candidate version 1.4.3-rc2

 ChangeLog          | 1353 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 bioruby.gemspec    |    2 +-
 lib/bio/version.rb |    4 +-
 3 files changed, 1356 insertions(+), 3 deletions(-)

commit e0d570b237a8b96ae0c1e7b1ad72c7333be07c52
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Aug 20 20:35:58 2012 +0900

    version changed to 1.4.3-rc1

 bioruby.gemspec    |    3 ++-
 lib/bio/version.rb |    2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

commit 511c81ba67f7b8dc9cff85cf68db654d2feaf52e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Aug 20 20:17:14 2012 +0900

    document JRUBY-5678 (resolved) and related issue with the workaround.

 KNOWN_ISSUES.rdoc  |    9 +++++++++
 RELEASE_NOTES.rdoc |    9 +++++++++
 2 files changed, 18 insertions(+), 0 deletions(-)

commit 2fdd7a3b3555a33dead31181c9526af22f24916f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Aug 20 19:44:39 2012 +0900

    update recommended Ruby versions and the year in copyright lines

 README.rdoc |    7 +++----
 1 files changed, 3 insertions(+), 4 deletions(-)

commit b156227749e5ada74330e837c9ce48a16e6a6a2f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Aug 20 19:16:25 2012 +0900

    Bug fix: Bio::EMBL#os raises error, with incompatible change
    
     * Bug fix: Bio::EMBL#os raises error. The bug is reported by
       Marc P. Hoeppner in the BioRuby mailing list
       (https://redmine.open-bio.org/issues/3294).
     * Incompatible change: Bio::EMBL#os no longer splits the content with
       comma, and it no longer raises error even if the OS line is not in
       the "Genus species (name)" format. The changes may affect the parsing
       of old EMBL files which contain two or more species names in an OS line.
     * Unit tests are modified to catch up the above incompatible changes.

 RELEASE_NOTES.rdoc                       |   14 ++++++
 lib/bio/db/embl/embl.rb                  |   74 ++++++++++++++++++++++++++++++
 test/unit/bio/db/embl/test_embl.rb       |    9 +---
 test/unit/bio/db/embl/test_embl_rel89.rb |    9 +---
 4 files changed, 92 insertions(+), 14 deletions(-)

commit 31c8b4cb6ce2364aacee8137ddec3aa5f7d2d0d8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Aug 20 19:04:50 2012 +0900

    Workaround for jruby-1.7.0.preview2 bugs JRUBY-6195, JRUBY-6818
    
     * Workaroud for jruby-1.7.0.preview2 bugs JRUBY-6195 and JRUBY-6818.
     * Refactoring of call_command_popen: split _call_command_popen_ruby18
       and _call_command_popen_ruby19, add _call_command_popen_jruby19.
       Note that _call_command_popen_jruby19 will be removed in the future
       after the bugs are fixed.

 lib/bio/command.rb |   98 ++++++++++++++++++++++++++++++++++++++++++++++-----
 1 files changed, 88 insertions(+), 10 deletions(-)

commit 05f51fa2e871e71c2b20559eb05e456768a4f7d6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Aug 18 00:32:31 2012 +0900

    New default etc/bioinformatics/seqdatabase.ini
    
     * New default etc/bioinformatics/seqdatabase.ini, with currently
       available services.

 etc/bioinformatics/seqdatabase.ini |   27 +++++++++++++++++++++++++++
 1 files changed, 27 insertions(+), 0 deletions(-)
 create mode 100644 etc/bioinformatics/seqdatabase.ini

commit a4264cc3667b98289c09efc7ccba9c8e86f6d89c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Aug 18 00:31:10 2012 +0900

    etc/bioinformatics/seqdatabase.ini is moved to sample/

 etc/bioinformatics/seqdatabase.ini |  210 ------------------------------------
 sample/seqdatabase.ini             |  210 ++++++++++++++++++++++++++++++++++++
 2 files changed, 210 insertions(+), 210 deletions(-)
 delete mode 100644 etc/bioinformatics/seqdatabase.ini
 create mode 100644 sample/seqdatabase.ini

commit 04b7a27b557576f5325b3ee420262922ab66ca3b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Aug 18 00:30:38 2012 +0900

    known issue about http://bioruby.org/cgi-bin/biofetch.rb server down

 KNOWN_ISSUES.rdoc |    9 +++++++++
 1 files changed, 9 insertions(+), 0 deletions(-)

commit 4a8193f7b91ff703c8f3dc6e6a6ae0c981a404e6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 17 23:45:41 2012 +0900

    Update descriptions about JRuby and Rubinius bugs

 KNOWN_ISSUES.rdoc  |   14 ++++++++++----
 RELEASE_NOTES.rdoc |   14 ++++++++++----
 2 files changed, 20 insertions(+), 8 deletions(-)

commit a2d8dd8ccebde84e91f82c59e531cc08fbf0f3fe
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 17 17:19:22 2012 +0900

    Remove the suffix .rb in require, to avoid potential multiple loading.

 test/unit/bio/db/fasta/test_defline.rb        |    2 +-
 test/unit/bio/db/genbank/test_genpept.rb      |    2 +-
 test/unit/bio/db/kegg/test_drug.rb            |    2 +-
 test/unit/bio/db/kegg/test_genome.rb          |    2 +-
 test/unit/bio/db/kegg/test_glycan.rb          |    2 +-
 test/unit/bio/util/test_restriction_enzyme.rb |    2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

commit 1d2e8b02db3699c2cd4f4890abc078ffd2b503aa
Author: Ben J. Woodcroft <donttrustben near gmail.com>
Date:   Wed Aug 8 09:41:20 2012 +1000

    fill in missing piece of documentation in FastaFormat

 lib/bio/db/fasta.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 83bf09d4d81803c8d06e0d45ca25e7c09016161c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Aug 8 00:08:26 2012 +0900

    RELEASE_NOTE.rdoc modified to reflect recent changes

 RELEASE_NOTES.rdoc |  107 ++++++++++++++++++++++++++++++++++++++++++++-------
 1 files changed, 92 insertions(+), 15 deletions(-)

commit c3afb1eb98cf8777ee021624c3d2eab92b3543f2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Aug 8 00:06:09 2012 +0900

    Descriptions about JRuby, Rubinius, DDBJ Web API, SOAP4R etc.

 KNOWN_ISSUES.rdoc |   45 +++++++++++++++++++++++++++++++++++++++++++--
 1 files changed, 43 insertions(+), 2 deletions(-)

commit 01da7401a011aa519c43a021f89f6e7f769b4649
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Aug 7 23:55:09 2012 +0900

    regenerate bioruby.gemspec with rake regemspec

 bioruby.gemspec |    3 +--
 1 files changed, 1 insertions(+), 2 deletions(-)

commit 9f70c27d9b75408fddae8384a2a09715b959dcb5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Aug 7 23:51:56 2012 +0900

    improve documentation; version changed to 1.4.3-pre1

 lib/bio/version.rb |   13 +++++++++++--
 1 files changed, 11 insertions(+), 2 deletions(-)

commit c11f12c8aa56b8509cd082f3478e96374210e5d7
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Aug 7 23:31:41 2012 +0900

    Remove autorequire which have been deprecated

 bioruby.gemspec.erb |    1 -
 1 files changed, 0 insertions(+), 1 deletions(-)

commit 7792b092033d2c819f2bcad0e206f27608481db5
Author: Ben J Woodcroft <donttrustben@gmail.com>
Date:   Mon Aug 6 09:40:55 2012 +1000

    flesh out FastaFormat documentation

 lib/bio/db/fasta.rb         |  102 ++++++++++++++++++++++++-------------------
 lib/bio/db/fasta/defline.rb |    2 +-
 2 files changed, 58 insertions(+), 46 deletions(-)

commit 9a2fe67c247cdc7c9ddc9f8b8de771515ba76ac1
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 3 22:36:12 2012 +0900

    .travis.yml: restructure matrix, add allow_failures lines
    
     * Add allow_failures lines
     * Restructure matrix: remove many exclude lines and add some
       include lines.
     * When running jruby, Set TMPDIR to avoid known issue about
       FileUtils#remove_entry_secure.

 .travis.yml |   52 ++++++++++++++++++----------------------------------
 1 files changed, 18 insertions(+), 34 deletions(-)

commit 553fd102c533c42675f93895557e3e00d36fd3e7
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 3 22:05:39 2012 +0900

    Improve tests for BLAST "-m 8" tabular format parser

 test/unit/bio/appl/blast/test_report.rb |  119 +++++++++++++++++++++++++++++++
 1 files changed, 119 insertions(+), 0 deletions(-)

commit 3e1c062dbc168bd558ca8408a6da115aa570f3a7
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 3 22:05:07 2012 +0900

    Improve test and suppress warning: assigned but unused variable

 test/unit/bio/io/flatfile/test_buffer.rb |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

commit 7e29ce1f050e9e5b23299372d8ddfae781447dc3
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 3 22:02:21 2012 +0900

    Improve test and suppress warning: assigned but unused variable

 test/unit/bio/db/test_newick.rb |    2 ++
 1 files changed, 2 insertions(+), 0 deletions(-)

commit 1053b62069df74f336934e4ed0f3f217e4ad3312
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jul 27 13:56:53 2012 +0900

    Suppress warnings: shadowing outer local variable
    
     * Suppress warnings: shadowing outer local variable.
       Thanks to Andrew Grimm: https://github.com/bioruby/bioruby/pull/64

 lib/bio/db/gff.rb |    8 ++++----
 1 files changed, 4 insertions(+), 4 deletions(-)

commit e55794f65b3fb45c99e61d45220fe42f718426a3
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jul 25 23:29:17 2012 +0900

    Suppress warnings in lib/bio/alignment.rb:2322
    
     * A space is inserted to suppress warnings in lib/bio/alignment.rb:2322.
       * warning: :' after local variable is interpreted as binary operator
       * warning: even though it seems like symbol literal

 lib/bio/alignment.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 174a38ea8c4ecea70724bf6ec8e72b2e4259853b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jul 25 23:12:51 2012 +0900

    Modified to follow changes of GenomeNet BLAST site

 lib/bio/appl/blast/genomenet.rb |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit 93e24935840dcdec76984313719700134d69daf2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jul 25 15:21:32 2012 +0900

    suppress warnings: instance variable @comment not initialized

 lib/bio/db/gff.rb |    6 ++++--
 1 files changed, 4 insertions(+), 2 deletions(-)

commit 0ad3818fedb707a26e849877bde1f8dab006b848
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jul 25 00:54:02 2012 +0900

    suppress warnings: URI.escape/URI.unescape is obsolete

 lib/bio/db/gff.rb |   39 +++++++++++++++++++++++++++++++++------
 1 files changed, 33 insertions(+), 6 deletions(-)

commit 1263938742e7eeedb4a877aff7314e304320eca9
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Jul 23 21:15:52 2012 +0900

    Added link to blastall options reference
    
     * Added link to blastall options reference.
       Thanks to Gareth Rees who sent a pull request.
       (https://github.com/bioruby/bioruby/pull/49)

 lib/bio/appl/blast/genomenet.rb |    5 +++++
 1 files changed, 5 insertions(+), 0 deletions(-)

commit 2ec5f4fd5abd0db7ec79ab3a9fd4adde7c9384a8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Jul 23 17:26:45 2012 +0900

    Next bioruby release version will be 1.4.3.

 RELEASE_NOTES.rdoc |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 6cf1318507a5d82bb93acdfe33e96723a2e742fc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Jul 23 17:25:35 2012 +0900

    fix typo

 README.rdoc |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 2fd71cac315affe6e4d90b03dadac782f11553a5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Jul 23 17:21:57 2012 +0900

    Bug fix: Genomenet remote blast: catch up changes of the server

 lib/bio/appl/blast/genomenet.rb |   33 +++++++++++++++++++++++----------
 1 files changed, 23 insertions(+), 10 deletions(-)

commit 69d9717da11b2fe81a8f840bbafcc5fbb0dbe688
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jul 20 11:24:37 2012 +0900

    regenerate bioruby.gemspec with rake regemspec

 bioruby.gemspec |    2 ++
 1 files changed, 2 insertions(+), 0 deletions(-)

commit 9683da186579dbfa5da1bb1a32edc49cfdc026b8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jul 18 23:19:33 2012 +0900

    Incompatible changes in Bio::KEGG::KGML are documented.
    
     * Incompatible changes in Bio::KEGG::KGML are documented.
     * Next BioRuby release version will be 1.4.3.

 RELEASE_NOTES.rdoc |   44 +++++++++++++++++++++++++++++++++++++++++---
 1 files changed, 41 insertions(+), 3 deletions(-)

commit 6cab377ae760d1abfda06caafe4a04ecd549e21d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jul 18 22:56:00 2012 +0900

    Incompatible changes: Bio::KEGG::KGML::Reaction#substrates, products
    
     * Incompatible changes: Bio::KEGG::KGML::Reaction#substrates and
       Bio::KEGG::KGML::Reaction#products are changed to return an array
       containing Bio::KEGG::KGML::Substrate and Bio::KEGG::KGML::Product
       objects, respectively. The aim of these changes are to store ID
       of substrates and products that were thrown away in the previous
       versions.

 lib/bio/db/kegg/kgml.rb            |   48 ++++++++++++++--
 test/unit/bio/db/kegg/test_kgml.rb |  104 +++++++++++++++++++++++++++++++++++-
 2 files changed, 144 insertions(+), 8 deletions(-)

commit 3cb1e09709d3c6b934028e28f9cafed149c9c751
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jul 18 22:16:46 2012 +0900

    Bio::KEGG::KGML#parse_* :use new attribute names
    
     * In Bio::KEGG::KGML#parse_* (private methods) new attribute method
       names should be used instead of deprecated old names.

 lib/bio/db/kegg/kgml.rb |   18 +++++++++---------
 1 files changed, 9 insertions(+), 9 deletions(-)

commit c5ef981db6add98dc6778cd9809aff38a7071593
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jul 18 22:14:33 2012 +0900

    modified documentation for Bio::KEGG::KGML

 lib/bio/db/kegg/kgml.rb |   73 +++++++++++++++++++++++++++--------------------
 1 files changed, 42 insertions(+), 31 deletions(-)

commit 5416b84eaa37b5abf15f905586a5eee65c4026f0
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jul 18 15:01:58 2012 +0900

    New class Bio::KEGG::KGML::Graphics with tests for Bio::KEGG::KGML
    
     * New class Bio::KEGG::KGML::Graphics for storing a graphics element.
       This fixes https://github.com/bioruby/bioruby/issues/51.
     * Unit tests for Bio::KEGG::KGML are added with mock test data.
     * Improve rdoc documentation for Bio::KEGG::KGML.
     * New method Bio::KEGG::KGML::Reaction#id
     * Attribute methods that were different from the KGML attribute
       names are renamed to the names of the KGML attribute names.
       Old method names are deprecated and are changed to aliases
       and will be removed in the future.
        * Bio::KEGG::KGML::Entry#id (old name: entry_id)
        * Bio::KEGG::KGML::Entry#type (old name: category)
        * Bio::KEGG::KGML::Entry#entry1 (old name: node1)
        * Bio::KEGG::KGML::Entry#entry2 (old name: node2)
        * Bio::KEGG::KGML::Entry#type (old name: rel)
        * Bio::KEGG::KGML::Reaction#name (old name: entry_id)
        * Bio::KEGG::KGML::Reaction#type (old name: direction)
     * Following attribute methods are deprecated because two or more
       graphics elements may exist in an entry element. They will be
       removed in the future.
        * Bio::KEGG::KGML::Entry#label
        * Bio::KEGG::KGML::Entry#shape
        * Bio::KEGG::KGML::Entry#x
        * Bio::KEGG::KGML::Entry#y
        * Bio::KEGG::KGML::Entry#width
        * Bio::KEGG::KGML::Entry#height
        * Bio::KEGG::KGML::Entry#fgcolor
        * Bio::KEGG::KGML::Entry#bgcolor

 lib/bio/db/kegg/kgml.rb            |  321 ++++++++++---
 test/data/KEGG/test.kgml           |   37 ++
 test/unit/bio/db/kegg/test_kgml.rb |  922 ++++++++++++++++++++++++++++++++++++
 3 files changed, 1223 insertions(+), 57 deletions(-)
 create mode 100644 test/data/KEGG/test.kgml
 create mode 100644 test/unit/bio/db/kegg/test_kgml.rb

commit e5478363ef6969ec14c4e09c2bd7c6d27c12cf5b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Jul 17 22:23:28 2012 +0900

    rdoc documentation for Bio::KEGG::KGML

 lib/bio/db/kegg/kgml.rb |  166 ++++++++++++++++++++++++++++++++++++++++++++---
 1 files changed, 157 insertions(+), 9 deletions(-)

commit 4a97e7034cae835b3bbc8ef918b9c6c48910dec5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jul 11 15:16:49 2012 +0900

    autoload should not be used for libraries outside bio

 lib/bio/db/kegg/kgml.rb |    3 +--
 1 files changed, 1 insertions(+), 2 deletions(-)

commit 338d4cd9913d70041349c5201f80f7a65e7135a6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jul 6 00:50:01 2012 +0900

    remove unnecessary require "bio/db" in lib/bio/db/pdb.rb

 lib/bio/db/pdb.rb |    5 +----
 1 files changed, 1 insertions(+), 4 deletions(-)

commit 87c806a480fcacb0fc610c9669de19e4cb661a9c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jul 6 00:47:20 2012 +0900

    workaround to avoid circular require about Bio::PDB

 lib/bio/db/pdb/atom.rb              |    5 +++--
 lib/bio/db/pdb/chain.rb             |    5 ++---
 lib/bio/db/pdb/chemicalcomponent.rb |    5 +++--
 lib/bio/db/pdb/model.rb             |    4 ++--
 lib/bio/db/pdb/pdb.rb               |    3 ++-
 lib/bio/db/pdb/residue.rb           |    4 ++--
 lib/bio/db/pdb/utils.rb             |   11 +++++++----
 7 files changed, 21 insertions(+), 16 deletions(-)

commit 874f35c3930506fa029b419aa84677d1fea6681a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jul 6 00:24:24 2012 +0900

    regenerate bioruby.gemspec with rake regemspec

 bioruby.gemspec |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

commit 090d4edb5698135f87df450a963ef35a307349c4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jul 6 00:19:54 2012 +0900

    Tree output (formatter) methods moved to lib/bio/tree/output.rb
    
     * To avoid circular require about bio/tree, phylogenetic tree output
      (formatter) methods are moved to lib/bio/tree/output.rb.

 lib/bio/db/newick.rb   |  244 --------------------------------------------
 lib/bio/tree.rb        |    3 +-
 lib/bio/tree/output.rb |  264 ++++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 265 insertions(+), 246 deletions(-)
 create mode 100644 lib/bio/tree/output.rb

commit b3d12b63097a5141b029bbfb3690870cd1935a60
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jul 6 00:18:44 2012 +0900

    Workaround to avoid circular require for Bio::Blast

 lib/bio/appl/bl2seq/report.rb     |    6 +++---
 lib/bio/appl/blast/ddbj.rb        |    3 ---
 lib/bio/appl/blast/format0.rb     |    3 +++
 lib/bio/appl/blast/genomenet.rb   |    2 --
 lib/bio/appl/blast/ncbioptions.rb |   11 ++++++++---
 lib/bio/appl/blast/remote.rb      |   11 ++++++-----
 lib/bio/appl/blast/report.rb      |   16 ++++++++++------
 lib/bio/appl/blast/rpsblast.rb    |    5 +++--
 lib/bio/appl/blast/wublast.rb     |    6 +++---
 9 files changed, 36 insertions(+), 27 deletions(-)

commit 8f6c906c7b0d65b93ebf0a1e1307259e6eab8465
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jul 5 23:29:42 2012 +0900

    remove old require lines that are commented out

 lib/bio/appl/blast/format0.rb |    5 -----
 1 files changed, 0 insertions(+), 5 deletions(-)

commit c632fbf2d0320860eadfacb196d51d80ed3a2b34
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jul 5 23:16:49 2012 +0900

    Remove old workaround of strscan.so for Ruby 1.7 or earlier

 lib/bio/appl/blast/format0.rb |   18 +-----------------
 1 files changed, 1 insertions(+), 17 deletions(-)

commit c81dce87f53d3ea7c7d2335e077fa609f2737779
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jul 5 23:03:40 2012 +0900

    .travis.yml: include ruby 1.9.2 test

 .travis.yml |    2 ++
 1 files changed, 2 insertions(+), 0 deletions(-)

commit 34709d114089c722b5da796028ffb91021761fdd
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jul 5 23:00:37 2012 +0900

    Remove old comment lines

 lib/bio/sequence/format.rb |    6 ------
 1 files changed, 0 insertions(+), 6 deletions(-)

commit e0d5ed61e0101e2e72ad024dccd58c8c90def2b9
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jul 5 22:42:17 2012 +0900

    Finalizer for Bio::Command::Tmpdir is changed to suppress test failure
    
     * New class Bio::Command::Tmpdir::Remover for removing temporary
       directory in finilizer. This class is BioRuby internal use only.
       Users should not use this class.
     * Finalizer for Bio::Command::Tmpdir is changed from a Proc object
       to an instance of the Remover class.
     * Test failure fix: In some environment, with Ruby 1.9.2,
       test_output_embl(Bio::FuncTestSequenceOutputEMBL) was failed with
       "<#<ArgumentError: wrong number of arguments (1 for 0)>" that was
       raised in the finalizer callback of Bio::Command::Tmpdir. This
       commit fixes the problem.

 lib/bio/command.rb |   56 +++++++++++++++++++++++++++------------------------
 1 files changed, 30 insertions(+), 26 deletions(-)

commit cca98d1378ce66d6db84cc9c1beadd39ed0e0fee
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jul 5 22:21:34 2012 +0900

    Workaround to avoid circular require and JRuby autoload bug
    
     * "require" lines are modified to avoid circular require.
     * In files that would be required directly from outside bio/sequence
       (aa.rb, adapter.rb, common.rb, compat.rb, dblink.rb, generic.rb,
       na.rb, quality_score.rb, sequence_masker.rb), because of avoiding
       potential mismatch of superclass and/or lack of some methods,
       bio/sequence.rb is required when Bio::Sequence is not defined.
     * workaround to avoid JRuby autoload bug

 lib/bio/sequence.rb                 |   10 ++++++----
 lib/bio/sequence/aa.rb              |    8 +++-----
 lib/bio/sequence/adapter.rb         |   12 ++++++------
 lib/bio/sequence/common.rb          |    2 ++
 lib/bio/sequence/compat.rb          |    9 ++-------
 lib/bio/sequence/dblink.rb          |   11 ++++++-----
 lib/bio/sequence/generic.rb         |    7 +++----
 lib/bio/sequence/na.rb              |   10 ++++------
 lib/bio/sequence/quality_score.rb   |    2 ++
 lib/bio/sequence/sequence_masker.rb |    3 +++
 10 files changed, 37 insertions(+), 37 deletions(-)

commit d2915c33ae7f330837688195a58c1e60fe78402a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jul 5 21:04:28 2012 +0900

    workaround to avoid circular require in Bio::RestrictionEnzyme
    
     * Workaround to avoid circular require in Bio::RestrictionEnzyme
     * Special care was needed for Bio::RestrictionEnzyme::Analysis
       because its method definitions are divided into two files:
       analysis.rb, analysis_basic.rb.

 lib/bio/util/restriction_enzyme/analysis.rb        |   13 ++++++++-----
 lib/bio/util/restriction_enzyme/analysis_basic.rb  |    7 ++++---
 lib/bio/util/restriction_enzyme/cut_symbol.rb      |    5 +++--
 lib/bio/util/restriction_enzyme/dense_int_array.rb |    3 +++
 lib/bio/util/restriction_enzyme/double_stranded.rb |    7 +++----
 .../double_stranded/aligned_strands.rb             |    7 +++----
 .../double_stranded/cut_location_pair.rb           |    7 +++----
 .../cut_location_pair_in_enzyme_notation.rb        |    7 +++----
 .../double_stranded/cut_locations.rb               |    7 +++----
 .../cut_locations_in_enzyme_notation.rb            |    7 +++----
 lib/bio/util/restriction_enzyme/range/cut_range.rb |    7 +++----
 .../util/restriction_enzyme/range/cut_ranges.rb    |    7 +++----
 .../range/horizontal_cut_range.rb                  |    7 +++----
 .../restriction_enzyme/range/sequence_range.rb     |    7 +++----
 .../range/sequence_range/calculated_cuts.rb        |    7 +++----
 .../range/sequence_range/fragment.rb               |    7 +++----
 .../range/sequence_range/fragments.rb              |    7 +++----
 .../restriction_enzyme/range/vertical_cut_range.rb |    7 +++----
 lib/bio/util/restriction_enzyme/single_strand.rb   |    6 +++---
 .../cut_locations_in_enzyme_notation.rb            |    7 +++----
 .../restriction_enzyme/single_strand_complement.rb |    7 +++----
 .../util/restriction_enzyme/sorted_num_array.rb    |    3 +++
 .../util/restriction_enzyme/string_formatting.rb   |    7 +++----
 23 files changed, 75 insertions(+), 81 deletions(-)

commit 7df4843288ffde6d7132a5651fe978301f8ebd2b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jul 5 20:18:08 2012 +0900

    workaround to avoid JRuby autoload bug

 lib/bio/util/restriction_enzyme.rb |    4 +---
 1 files changed, 1 insertions(+), 3 deletions(-)

commit 97d95f2b400006d4229a7ce69d7d8a5cdce42764
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jul 4 22:00:27 2012 +0900

    changed require to autoload for the workaround of JRuby autoload bug

 lib/bio/feature.rb |    5 ++---
 1 files changed, 2 insertions(+), 3 deletions(-)

commit 530b82a45731c2a71a110826341be425de1271e0
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jul 4 22:00:06 2012 +0900

    workaround to avoid JRuby autoload bug

 lib/bio/sequence/common.rb |    4 +---
 1 files changed, 1 insertions(+), 3 deletions(-)

commit 8614f31b36fb93d6e49d109268d646ff3032cd1a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jul 4 21:28:52 2012 +0900

    workaround to avoid JRuby autoload bug
    
     * Workaround to avoid JRuby autoload bug.
     * Changed to require bio/db.rb because it is always loaded.

 lib/bio/db/kegg/genes.rb |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit ea500006ed56857139c858bdfeb98773e5ca541e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jun 28 21:36:35 2012 +0900

    Rakefile: use own mktmpdir

 Rakefile |   59 +++++++++++++++++++++++++++++++++++++++++++----------------
 1 files changed, 43 insertions(+), 16 deletions(-)

commit 452fadcab61083dcb9d01ee05d300eae5cb23fee
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jun 28 20:37:59 2012 +0900

    .travis.yml: remove "rake regemspec" from after_install

 .travis.yml |    2 --
 1 files changed, 0 insertions(+), 2 deletions(-)

commit 3fad822af3d7e558a58b71fd8ec2a7061b49f9f2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jun 28 20:36:59 2012 +0900

    regenerate bioruby.gemspec with rake regemspec

 bioruby.gemspec |    2 ++
 1 files changed, 2 insertions(+), 0 deletions(-)

commit ea6e96fc654c797664b118a6326a84e4f9b1a8a3
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jun 28 20:35:49 2012 +0900

    print message when doing Dir.chdir

 Rakefile |   17 +++++++++++------
 1 files changed, 11 insertions(+), 6 deletions(-)

commit c2fcd5e8cc71da38dc3c6d1f8c8d0233e47398b3
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jun 28 20:28:41 2012 +0900

    In tar-install, removed dependency to regemspec

 Rakefile |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 67a7e83d516aab5d60f8263525b359be8b0ffc0b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jun 28 20:23:24 2012 +0900

    Rakefile: give up using Dir.mktmpdir because of JRuby's behavior
    
     * Rakefile: give up using Dir.mktmpdir because of JRuby's behavior
       that may be related with http://jira.codehaus.org/browse/JRUBY-5678

 Rakefile |   61 ++++++++++++++++++++++++++++++++++++++++++++++---------------
 1 files changed, 46 insertions(+), 15 deletions(-)

commit cff098034a338bbe9579d6c7b4380c7132a38ef5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jun 28 19:23:57 2012 +0900

    gem-integration-test, gem-install and gem-install-nodoc are removed
    
     * gem-integration-test, gem-install and gem-install-nodoc are removed
       because they are useless with Bundler

 Rakefile |   13 -------------
 1 files changed, 0 insertions(+), 13 deletions(-)

commit d5c054265af4f80318cbfa5a5bbdee6125219de2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jun 28 18:10:05 2012 +0900

    .travis.yml: .gemspec is needed to install local gem

 .travis.yml                 |    1 +
 gemfiles/prepare-gemspec.rb |   25 +++++++++++++++++++++++++
 2 files changed, 26 insertions(+), 0 deletions(-)
 create mode 100644 gemfiles/prepare-gemspec.rb

commit 05b6172123f42a1d8d46668d8a3d5f698c371704
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jun 28 17:51:43 2012 +0900

    remove 1.9.2; add tar/gem integration tests
    
     * Remove ruby version 1.9.2 from matrix for reducing builds
     * Add tar/gem integration tests
     * Add a new helper script gemfiles/modify-Gemfile.rb,
       modifying gemfile when running gem integration test.
     * Remove jruby version comments

 .travis.yml                |   26 +++++++++++++++++---------
 gemfiles/modify-Gemfile.rb |   28 ++++++++++++++++++++++++++++
 2 files changed, 45 insertions(+), 9 deletions(-)
 create mode 100644 gemfiles/modify-Gemfile.rb

commit 6813f91893e7ddc3000047357c9ed2dafb32a722
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jun 28 17:06:28 2012 +0900

    descriptions are modified for danger operations

 Rakefile |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit a209688952c922d9ba45c227874990bccd3da7c0
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Jun 25 23:25:51 2012 +0900

    regenerate bioruby.gemspec with rake regemspec

 bioruby.gemspec |    5 +++++
 1 files changed, 5 insertions(+), 0 deletions(-)

commit 8f6459497be0e9ca7dc3eb2eb9606e42d97ad60c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Jun 25 21:01:06 2012 +0900

    rake tasks added and default task is changed
    
     * New tasks:
       * gem-install: build gem and install it
       * gem-install-nodoc: build gem and install it with --no-ri --no-rdoc.
       * gem-test: test installed bioruby gem installed with gem-install
         (or gem-install-nodoc)
       * gem-integration-test: build gem, install and run test (with --no-ri
         --no-rdoc)
       * tar-install: DANGER: build tar and install by using setup.rb
       * installed-test: test installed bioruby
       * tar-integration-test: DANGER: build tar, install and run test
       * see-env: see BIORUBY_RAKE_DEFAULT_TASK environment variable and
         invoke the specified task. If the variable did not exist, it
         invokes "test" which is previously the default task. It is added
         for selecting task on Travis-ci. It is not recommended to invoke
         the task explicitly by hand.
     * Default task is changed from "test" to "see-env".

 Rakefile |  110 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 files changed, 107 insertions(+), 3 deletions(-)

commit 3b400042cd361e1ab6d0fb0d8c8cce14a6c2ae10
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Jun 25 20:58:13 2012 +0900

    BIORUBY_TEST_LIB is always added on the top of $LOAD_PATH
    
     * When BIORUBY_TEST_LIB is specified, the specified directory name
       is always added on the top of $LOAD_PATH even if it is already
       included in the middle of $LOAD_PATH.

 test/bioruby_test_helper.rb |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit 848304b6f90310f8fa15c80ba06655ae5cae5053
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Jun 25 20:42:07 2012 +0900

    New env BIORUBY_TEST_GEM and BIORUBY_TEST_LIB behavior changed
    
     * New environment variable BIORUBY_TEST_GEM for testing installed
       bio-X.X.X gem. Version number can be specified.
       Example with version number:
        % env BIORUBY_TEST_GEM=1.4.2.5000 ruby test/runner.rb
       Example without version number:
        % env BIORUBY_TEST_GEM="" ruby test/runner.rb
     * When BIORUBY_TEST_LIB is empty, it no longer add an empty string to
       $LOAD_PATH. Moreover, when BIORUBY_TEST_GEM is set, the variable is
       ignored.

 test/bioruby_test_helper.rb |   49 ++++++++++++++++++++++++++++++++----------
 1 files changed, 37 insertions(+), 12 deletions(-)

commit 9453a6773c24f866698370195fd8e767443a38b9
Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>
Date:   Fri Jun 1 18:06:40 2012 +0900

    broader FASTQ file recognition
    
     * Because PacBio RS sequencer may produce kilobases long reads and
       read buffer size (default 31 lines) for file format detection
       may not be sufficient to find the second id line starting with "+",
       the regular expression for FASTQ is truncated only to check the
       first id line starting with "@".
     * Test code is added.

 lib/bio/io/flatfile/autodetection.rb            |    2 +-
 test/unit/bio/io/flatfile/test_autodetection.rb |    6 ++++++
 2 files changed, 7 insertions(+), 1 deletions(-)

commit 120e780c023cba06b83899c2f8a17c8fc1de4faa
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jun 8 15:36:29 2012 +0900

    Retry sequence randomize test up to 10 times when fails
    
     * To suppress rare failure of chi-square equiprobability tests for
       Bio::Sequence::Common#randomize, test code changed to retry
       up to 10 times if the chi-square test fails.  The assertion fails
       if the chi-square test fails 10 consecutive times, and this
       strongly suggests bugs in codes or in the random number generator.
     * The chi-square equiprobability tests are separated into a new
       test class.

 test/unit/bio/sequence/test_common.rb |   40 +++++++++++++++++++++++++++++---
 1 files changed, 36 insertions(+), 4 deletions(-)

commit 20dde52f7da784d4d9ac551957700cd96e842ef6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat May 19 18:14:19 2012 +0900

    libxml-ruby is disabled because of build error on Travis-ci

 gemfiles/Gemfile.travis-jruby1.8 |    3 ++-
 gemfiles/Gemfile.travis-jruby1.9 |    3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

commit 3c5c1cc277d30737815c7e44a2abbb308f5324b0
Author: Clayton Wheeler <cswh@umich.edu>
Date:   Mon May 14 21:48:41 2012 -0400

    Use libxml-ruby instead of libxml-jruby to fix JRuby test failures.
    
    The travis-ci Gemfiles currently call for libxml-jruby; this appears
    not to support the same API as libxml-ruby, resulting in several tests
    in test/unit/bio/db/test_phyloxml.rb failing with "NameError:
    uninitialized constant LibXMLJRuby::XML::Parser::Options". Switching
    to the C libxml-ruby library allows these tests to pass under JRuby in
    1.8 mode.
    
    JRuby in 1.9 mode still fails a few PhyloXML tests due to
    https://jira.codehaus.org/browse/JRUBY-6662.

 gemfiles/Gemfile.travis-jruby1.8 |    2 +-
 gemfiles/Gemfile.travis-jruby1.9 |    2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

commit 01a618242d67f0d00fe681dfd85e68bb393513fc
Author: Clayton Wheeler <cswh@umich.edu>
Date:   Thu May 10 23:13:56 2012 -0400

    test_tree.rb: to use %f instead of %g to prevent odd behavior.

 test/unit/bio/test_tree.rb |   22 +++++++++++-----------
 1 files changed, 11 insertions(+), 11 deletions(-)

commit 5e80e4394bf2a5e4ee472fe84ab76239b293e1b5
Author: Clayton Wheeler <cswh@umich.edu>
Date:   Thu May 10 23:04:55 2012 -0400

    Fixed spurious JRuby failures in test_tree.rb due to floating point differences.

 test/unit/bio/test_tree.rb |   14 +++++++-------
 1 files changed, 7 insertions(+), 7 deletions(-)

commit 459d4da894e9a9b9db0d793e3711dc45bae2089b
Author: Artem Tarasov <lomereiter@gmail.com>
Date:   Thu May 10 16:23:13 2012 +0400

    Test bug fix: order of hash keys are not guaranteed
    
     * Test bug fix: Bio::TestSOFT#test_dataset: order of hash keys are
       not guaranteed.

 test/unit/bio/db/test_soft.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 7e730691d6ec597a610dc0d4665db3598fcfde59
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu May 10 00:06:19 2012 +0900

    removed potential circular require about Bio::Sequence::Format

 lib/bio/db/embl/format_embl.rb       |    4 ----
 lib/bio/db/fasta/format_fasta.rb     |    4 ----
 lib/bio/db/fasta/format_qual.rb      |    5 -----
 lib/bio/db/fastq/format_fastq.rb     |    1 -
 lib/bio/db/genbank/format_genbank.rb |    4 ----
 lib/bio/sequence/format_raw.rb       |    4 ----
 6 files changed, 0 insertions(+), 22 deletions(-)

commit f1c398fdc3488bd18bd13ac864920ce6db4dab9e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed May 9 15:54:20 2012 +0900

    .travis.yml: comment out apt-get lines
    
     * .travis.yml: comment out apt-get lines because libxml2-dev
       and libexpat1-dev are already installed.

 .travis.yml |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit bc5ef4959e51f4a199d9f740b07812e9b8216255
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed May 9 15:47:11 2012 +0900

    travis-ci: comment out soap4r-ruby1.9 in Gemfile because of error
    
     * travis-ci: soap4r-ruby1.9 gem in Gemfile.travis-ruby1.9 and
       Gemfile.travis-jruby1.9 is commented out because of an error
       "uninitialized constant XML::SaxParser".

 gemfiles/Gemfile.travis-jruby1.9 |    4 +++-
 gemfiles/Gemfile.travis-ruby1.9  |    4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

commit 7e8153c09660c31d6286c1924680b8c5073a10b6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue May 1 18:11:09 2012 +0900

    config files for Travis CI continuous integration service

 .travis.yml                      |   73 ++++++++++++++++++++++++++++++++++++++
 gemfiles/Gemfile.travis-jruby1.8 |    6 +++
 gemfiles/Gemfile.travis-jruby1.9 |    7 ++++
 gemfiles/Gemfile.travis-ruby1.8  |    7 ++++
 gemfiles/Gemfile.travis-ruby1.9  |    8 ++++
 5 files changed, 101 insertions(+), 0 deletions(-)
 create mode 100644 .travis.yml
 create mode 100644 gemfiles/Gemfile.travis-jruby1.8
 create mode 100644 gemfiles/Gemfile.travis-jruby1.9
 create mode 100644 gemfiles/Gemfile.travis-ruby1.8
 create mode 100644 gemfiles/Gemfile.travis-ruby1.9

commit f1ecae7763648cb735a885ddb6c46d71c59b0694
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Mar 23 01:36:59 2012 +0900

    Test bug fix: tests affected by the bug of Bio::NucleicAcid.to_re("s")

 test/unit/bio/data/test_na.rb     |    2 +-
 test/unit/bio/sequence/test_na.rb |    2 +-
 test/unit/bio/test_sequence.rb    |    4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

commit 3fd9384b1b59140a929c81dcc4b07cb3c2e47525
Author: Trevor Wennblom <trevor@well.com>
Date:   Sat Feb 25 15:26:27 2012 -0600

    Bug fix: Bio::NucleicAcid.to_re("s") typo

 lib/bio/data/na.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit c552aa3a6773139b14ae95e79e0fb43a2f91c6fb
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jan 12 22:24:37 2012 +0900

    Bug fix: GenomeNet BLAST server URI changed.
    
     * Bug fix: GenomeNet BLAST server URI changed.
       Reported by joaocardoso via GitHub.
       ( https://github.com/bioruby/bioruby/issues/44 )

 lib/bio/appl/blast/genomenet.rb |    3 ++-
 1 files changed, 2 insertions(+), 1 deletions(-)

commit f33abf9bbd90c3c1e320f06447fdb54ffd094c5d
Author: peterjc <p.j.a.cock@googlemail.com>
Date:   Fri Nov 25 11:20:08 2011 +0000

    Mark echoarg2.bat and echoarg2.sh as world executable

 0 files changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 test/data/command/echoarg2.bat
 mode change 100644 => 100755 test/data/command/echoarg2.sh

commit d2d66f833d0b20647e8d761d2a240b99b206eaa8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 24 13:32:37 2011 +0900

    Bug fix: rake aborted without git

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

commit c2139739988ef731d61bf1a8cdba2dc5c48393bd
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 24 13:07:10 2011 +0900

    regenerate bioruby.gemspec with rake regemspec.

 bioruby.gemspec |   18 ++++++++++--------
 1 files changed, 10 insertions(+), 8 deletions(-)

commit 6213b45d28bfea2cc8c838813b524d48c369266b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 24 13:05:07 2011 +0900

    Added workaround for changes of a module name and file names to require.

 Rakefile |   21 +++++++++++++++++++--
 1 files changed, 19 insertions(+), 2 deletions(-)

commit 39f847cf8d453476275361078b831da43d400816
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 24 12:08:47 2011 +0900

    Use binary mode to open files.

 Rakefile |    6 ++++--
 1 files changed, 4 insertions(+), 2 deletions(-)

commit 688779e71a27e861fb01e07f816384561b8cfe45
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 24 11:49:30 2011 +0900

    Rakefile: new tasks: test-all to run all tests, etc.
    
     * Rakefile: new tasks: test-all to run all tests, and test-network
       to run tests in test/network.

 Rakefile |   10 ++++++++++
 1 files changed, 10 insertions(+), 0 deletions(-)

commit 53719535defcb0fefb3cf8bebe3fad6716bf7de2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 24 11:28:38 2011 +0900

    test/runner.rb: Run tests only in test/unit and test/functional.

 test/runner.rb |   22 ++++++++++++++++------
 1 files changed, 16 insertions(+), 6 deletions(-)

commit fb9ee403db6b447aee73ebb7f12ff5a5b73d6c52
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 23 20:36:36 2011 +0900

    A test class using network connection is moved under test/network/.

 test/functional/bio/test_command.rb |   16 ----------------
 test/network/bio/test_command.rb    |   35 +++++++++++++++++++++++++++++++++++
 2 files changed, 35 insertions(+), 16 deletions(-)
 create mode 100644 test/network/bio/test_command.rb

commit a6dda2215aa686a9ca4af7484aa190f726d51e69
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 23 20:28:58 2011 +0900

    Tests using network connections are moved to test/network/
    
     * Tests using network connections are moved to test/network/.
       * renamed: test/functional/bio/appl -> test/network/bio/appl
       * renamed: test/functional/bio/io   -> test/network/bio/io

 test/functional/bio/appl/blast/test_remote.rb |   93 ---------
 test/functional/bio/appl/test_blast.rb        |   61 ------
 test/functional/bio/appl/test_pts1.rb         |  117 -----------
 test/functional/bio/io/test_ddbjrest.rb       |   47 -----
 test/functional/bio/io/test_ensembl.rb        |  230 ---------------------
 test/functional/bio/io/test_pubmed.rb         |  135 -------------
 test/functional/bio/io/test_soapwsdl.rb       |   53 -----
 test/functional/bio/io/test_togows.rb         |  268 -------------------------
 test/network/bio/appl/blast/test_remote.rb    |   93 +++++++++
 test/network/bio/appl/test_blast.rb           |   61 ++++++
 test/network/bio/appl/test_pts1.rb            |  117 +++++++++++
 test/network/bio/io/test_ddbjrest.rb          |   47 +++++
 test/network/bio/io/test_ensembl.rb           |  230 +++++++++++++++++++++
 test/network/bio/io/test_pubmed.rb            |  135 +++++++++++++
 test/network/bio/io/test_soapwsdl.rb          |   53 +++++
 test/network/bio/io/test_togows.rb            |  268 +++++++++++++++++++++++++
 16 files changed, 1004 insertions(+), 1004 deletions(-)
 delete mode 100644 test/functional/bio/appl/blast/test_remote.rb
 delete mode 100644 test/functional/bio/appl/test_blast.rb
 delete mode 100644 test/functional/bio/appl/test_pts1.rb
 delete mode 100644 test/functional/bio/io/test_ddbjrest.rb
 delete mode 100644 test/functional/bio/io/test_ensembl.rb
 delete mode 100644 test/functional/bio/io/test_pubmed.rb
 delete mode 100644 test/functional/bio/io/test_soapwsdl.rb
 delete mode 100644 test/functional/bio/io/test_togows.rb
 create mode 100644 test/network/bio/appl/blast/test_remote.rb
 create mode 100644 test/network/bio/appl/test_blast.rb
 create mode 100644 test/network/bio/appl/test_pts1.rb
 create mode 100644 test/network/bio/io/test_ddbjrest.rb
 create mode 100644 test/network/bio/io/test_ensembl.rb
 create mode 100644 test/network/bio/io/test_pubmed.rb
 create mode 100644 test/network/bio/io/test_soapwsdl.rb
 create mode 100644 test/network/bio/io/test_togows.rb

commit ec747aa33d06e08a6469dfd330360161d1b0f8e2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 23 15:03:08 2011 +0900

    Test bug fix: use binmode to disable CR/LF conversion (fail on Windows)

 test/unit/bio/appl/blast/test_rpsblast.rb |    1 +
 test/unit/bio/io/flatfile/test_buffer.rb  |    1 +
 2 files changed, 2 insertions(+), 0 deletions(-)

commit 07ce32da009baa2c4e81f6d96f45e3dac49da183
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 23 14:47:33 2011 +0900

    Test bug fix: Read Sanger chromatogram files with binary mode
    
     * Test bug fix: Read Sanger chromatogram files with binary mode.
       Fix error/failure on Windows due to default text mode reading.

 test/unit/bio/db/sanger_chromatogram/test_abif.rb |    3 ++-
 test/unit/bio/db/sanger_chromatogram/test_scf.rb  |    6 ++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

commit 20d9068643214e3482d18c36028e50b3c9109755
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 23 14:17:25 2011 +0900

    Incompatible change: Bio::FlatFile.open and auto use binary mode
    
     * Incompatible change: Bio::FlatFile.open and auto use binary mode
       (binmode) unless text mode option is explicitly given.

 RELEASE_NOTES.rdoc                       |    7 ++
 lib/bio/io/flatfile/buffer.rb            |   84 ++++++++++++++++++
 test/unit/bio/io/flatfile/test_buffer.rb |  139 ++++++++++++++++++++++++++++++
 3 files changed, 230 insertions(+), 0 deletions(-)

commit 48bd150a6180d59879872bd85dd95c7ddf1a19c0
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 22 17:32:23 2011 +0900

    Test bug fix: fixed incomplete Windows platform detection.

 test/unit/bio/test_command.rb |   13 +++++++++----
 1 files changed, 9 insertions(+), 4 deletions(-)

commit d499bcee7956b1a0a4c04aeb106e50a0839167b0
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 22 16:15:05 2011 +0900

    FuncTestCommandCall is changed to test various command-lines.
    
     * New file test/data/command/echoarg2.sh shell script, which acts
       like echoarg2.bat for Windows.
     * FuncTestCommandCall is changed to test various command-lines.

 test/data/command/echoarg2.sh       |    4 ++
 test/functional/bio/test_command.rb |   70 +++++++++++++++++++++++++++++------
 2 files changed, 62 insertions(+), 12 deletions(-)
 create mode 100644 test/data/command/echoarg2.sh

commit d45e311c09ad2f4116770dd903f81e652a63ca2a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 22 14:21:34 2011 +0900

    Test bug fix: Opened files should be closed.
    
     * Test bug fix: Opened files should be closed.  When finalizing writer
       tests, temporary files are not properly closed after verify reading,
       and removing the temporary files raise erro on Windows.

 test/unit/bio/db/test_phyloxml_writer.rb |   24 +++++++++++++++---------
 1 files changed, 15 insertions(+), 9 deletions(-)

commit a9022c61b98746e98a83f1cfd902e0e6b11c7bbb
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 22 13:55:15 2011 +0900

    New method Bio::PhyloXML::Parser#closed?, and Bio::PhyloXML::Parser.open with block.
    
     * New method Bio::PhyloXML::Parser#closed? to check if it is closed
       or not.
     * Bio::PhyloXML::Parser.open and open_uri now can get a block.
       When a block is given, a Bio::PhyloXML::Parser object is passed
       to the block as an argument. When the block terminates, the object
       is closed.
     * Added tests about the above changes.

 lib/bio/db/phyloxml/phyloxml_parser.rb |   57 +++++++++++++++++++++++++++++---
 test/unit/bio/db/test_phyloxml.rb      |   56 ++++++++++++++++++++++++++++++-
 2 files changed, 106 insertions(+), 7 deletions(-)

commit 893cbe6ca993eca08427074059c2ba03621ea889
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Nov 5 00:49:10 2011 +0900

    Ruby 1.9 should be fully supported, and optional requirements are revised.

 README.rdoc |   48 +++++++++++++++++++++++++++++++++---------------
 1 files changed, 33 insertions(+), 15 deletions(-)

commit 38b1715c2d6bad39560e0846781ca903b1c16eda
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 4 22:12:38 2011 +0900

    Added REFERENCE.

 README.rdoc |   12 ++++++++++++
 1 files changed, 12 insertions(+), 0 deletions(-)

commit 9a766cd17236bbe1e28d6972001dd5e3ed596123
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 4 21:39:20 2011 +0900

    Removed "setup.rb test" and added about running tests.

 README.rdoc |   39 ++++++++++++++++++++++++++++++++++-----
 1 files changed, 34 insertions(+), 5 deletions(-)

commit 39737179b06366e1d5acf2e5ac930e41b3a4ee38
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Fri Oct 14 08:58:01 2011 +0200

    Tutorial: added info on biogems

 doc/Tutorial.rd      |   16 ++++++++++++++++
 doc/Tutorial.rd.html |   23 +++++++++++++++--------
 2 files changed, 31 insertions(+), 8 deletions(-)

commit e84400c5e9e94d95d6a8d3c4b72388b94d204766
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Fri Oct 14 08:49:41 2011 +0200

    Tutorial: small updates

 doc/Tutorial.rd      |    8 +++++---
 doc/Tutorial.rd.html |    9 +++++----
 2 files changed, 10 insertions(+), 7 deletions(-)

commit 9fe07345b3b7be890d5baad9a51f0752af5e0ac4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Sep 13 23:05:39 2011 +0900

    README_DEV.rdoc: added git tips and policies, etc.
    
     * Added Git tips about sending a patch or a pull request.
     * Added Git management policies for the blessed repository.
     * Added some coding styles.
     * Added descriptions about Ruby versions and OS.

 README_DEV.rdoc |   95 +++++++++++++++++++++++++++++++++++++++++++++++++++++-
 1 files changed, 93 insertions(+), 2 deletions(-)

commit 3c952c4a782501b21f36ece5bcab672dab12fc6d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Sep 13 13:21:20 2011 +0900

    README.rdoc: for release notes and changelog, about sample files.

 README.rdoc |   10 +++++++++-
 1 files changed, 9 insertions(+), 1 deletions(-)

commit fba9a6c0f1f79dd567ca54ba085b6258ac8efb31
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Sep 13 13:20:05 2011 +0900

    RELEASE_NOTES.rdoc: mentioned about removal of rdoc.zsh.

 RELEASE_NOTES.rdoc |    6 +++++-
 1 files changed, 5 insertions(+), 1 deletions(-)

commit 685b6bb7b98083e1b50e73baf4e7fa71bc9a39fa
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Sep 12 21:23:34 2011 +0900

    bioruby.gemspec.erb: LEGAL is added to rdoc files
    
     * bioruby.gemspec.erb: LEGAL is added to rdoc files.
     * bioruby.gemspec is updated by "rake regemspec".

 bioruby.gemspec     |    9 ++++++---
 bioruby.gemspec.erb |    6 +++++-
 2 files changed, 11 insertions(+), 4 deletions(-)

commit 414a6331f40fc99f554042e9a031689ea6d76da4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Sep 12 20:54:06 2011 +0900

    deleted rdoc.zsh which is obsolete and unused
    
     * Deleted rdoc.zsh which is obsolete and unused.
       To generate rdoc html, "rake rdoc" or "rake rerdoc".
       See "rake -T" for more information.

 rdoc.zsh |    8 --------
 1 files changed, 0 insertions(+), 8 deletions(-)
 delete mode 100644 rdoc.zsh

commit 272d9106cec43b0f219edd92a6f7bd3f9875a761
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Sep 12 20:35:47 2011 +0900

    Added new ChangeLog, showing changes after 1.4.2 release.
    
     * Added new ChangeLog, showing changes after 1.4.2 release.
       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 |   64 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 64 insertions(+), 0 deletions(-)
 create mode 100644 ChangeLog

commit 941493378f9884978c81d5f63ee4ed5c175d4bea
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Sep 12 20:28:28 2011 +0900

    Rakefile: add new task :rechangelog to update ChangeLog using git log.
    
     * Rakefile: add new task :rechangelog to update ChangeLog using
       git log. Note that the tag name (currently 1.4.2) is hardcoded
       in Rakefile.

 Rakefile |    9 +++++++++
 1 files changed, 9 insertions(+), 0 deletions(-)

commit 1c89e6546223c3c05ea79b8ade4b493580851efa
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Sep 12 20:24:49 2011 +0900

    renamed ChangeLog to doc/ChangeLog-before-1.4.2

 ChangeLog                  | 5013 --------------------------------------------
 doc/ChangeLog-before-1.4.2 | 5013 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 5013 insertions(+), 5013 deletions(-)
 delete mode 100644 ChangeLog
 create mode 100644 doc/ChangeLog-before-1.4.2

commit 2233fbada55034bd16fb5b9c642292b4b6ccca83
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Sep 12 20:22:49 2011 +0900

    ChangeLog updated: add log about 1.4.2 release

 ChangeLog |    9 +++++++++
 1 files changed, 9 insertions(+), 0 deletions(-)

commit 1c02ab0488e4097a2cf5c16180c3179c78e3d572
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Sep 12 19:40:54 2011 +0900

    New RELEASE_NOTES.rdoc for next release version.

 RELEASE_NOTES.rdoc |   47 +++++++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 47 insertions(+), 0 deletions(-)
 create mode 100644 RELEASE_NOTES.rdoc

commit 4e63e69e98c0c440ec476ef3407fcc8fd2411056
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Sep 12 19:32:48 2011 +0900

    renamed RELEASE_NOTES.rdoc to doc/RELEASE_NOTES-1.4.2.rdoc

 RELEASE_NOTES.rdoc           |  132 ------------------------------------------
 doc/RELEASE_NOTES-1.4.2.rdoc |  132 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 132 insertions(+), 132 deletions(-)
 delete mode 100644 RELEASE_NOTES.rdoc
 create mode 100644 doc/RELEASE_NOTES-1.4.2.rdoc

commit 9c5c8cafc3ec372ef80aa20d01d13034f94d5af2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 2 12:02:41 2011 +0900

    Bio::BIORUBY_EXTRA_VERSION set to ".5000" (unstable version).

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