bio 1.5.2 → 1.6.0.pre.20181210

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Files changed (93) hide show
  1. checksums.yaml +5 -5
  2. data/.travis.yml +12 -11
  3. data/ChangeLog +14 -3106
  4. data/{gemfiles/Gemfile.travis-ruby2.2 → Gemfile} +0 -1
  5. data/KNOWN_ISSUES.rdoc +0 -5
  6. data/README.rdoc +11 -18
  7. data/RELEASE_NOTES.rdoc +34 -291
  8. data/Rakefile +13 -9
  9. data/appveyor.yml +21 -0
  10. data/bioruby.gemspec +7 -78
  11. data/bioruby.gemspec.erb +8 -27
  12. data/doc/ChangeLog-1.5.0 +2919 -0
  13. data/doc/RELEASE_NOTES-1.5.0.rdoc +285 -0
  14. data/doc/Tutorial.rd +6 -108
  15. data/doc/Tutorial.rd.html +19 -98
  16. data/gemfiles/Gemfile.travis-jruby1.8 +3 -5
  17. data/gemfiles/Gemfile.travis-jruby1.9 +0 -3
  18. data/gemfiles/Gemfile.travis-rbx +0 -1
  19. data/gemfiles/Gemfile.travis-ruby1.8 +4 -4
  20. data/gemfiles/Gemfile.travis-ruby1.9 +0 -1
  21. data/gemfiles/prepare-gemspec.rb +4 -0
  22. data/lib/bio.rb +0 -10
  23. data/lib/bio/data/codontable.rb +99 -3
  24. data/lib/bio/io/togows.rb +5 -5
  25. data/lib/bio/version.rb +6 -8
  26. data/sample/test_restriction_enzyme_long.rb +1 -1
  27. data/test/unit/bio/data/test_codontable.rb +3 -0
  28. metadata +11 -77
  29. data/bin/bioruby +0 -47
  30. data/bin/br_biofetch.rb +0 -71
  31. data/bin/br_bioflat.rb +0 -293
  32. data/bin/br_biogetseq.rb +0 -45
  33. data/bin/br_pmfetch.rb +0 -422
  34. data/lib/bio/db/biosql/biosql_to_biosequence.rb +0 -78
  35. data/lib/bio/db/biosql/sequence.rb +0 -444
  36. data/lib/bio/db/phyloxml/phyloxml.xsd +0 -582
  37. data/lib/bio/db/phyloxml/phyloxml_elements.rb +0 -1197
  38. data/lib/bio/db/phyloxml/phyloxml_parser.rb +0 -1001
  39. data/lib/bio/db/phyloxml/phyloxml_writer.rb +0 -227
  40. data/lib/bio/io/biosql/ar-biosql.rb +0 -257
  41. data/lib/bio/io/biosql/biosql.rb +0 -39
  42. data/lib/bio/io/biosql/config/database.yml +0 -21
  43. data/lib/bio/io/sql.rb +0 -79
  44. data/lib/bio/shell.rb +0 -44
  45. data/lib/bio/shell/core.rb +0 -578
  46. data/lib/bio/shell/demo.rb +0 -146
  47. data/lib/bio/shell/interface.rb +0 -217
  48. data/lib/bio/shell/irb.rb +0 -94
  49. data/lib/bio/shell/object.rb +0 -71
  50. data/lib/bio/shell/plugin/blast.rb +0 -42
  51. data/lib/bio/shell/plugin/codon.rb +0 -218
  52. data/lib/bio/shell/plugin/das.rb +0 -58
  53. data/lib/bio/shell/plugin/emboss.rb +0 -23
  54. data/lib/bio/shell/plugin/entry.rb +0 -137
  55. data/lib/bio/shell/plugin/flatfile.rb +0 -101
  56. data/lib/bio/shell/plugin/midi.rb +0 -430
  57. data/lib/bio/shell/plugin/ncbirest.rb +0 -68
  58. data/lib/bio/shell/plugin/obda.rb +0 -45
  59. data/lib/bio/shell/plugin/psort.rb +0 -56
  60. data/lib/bio/shell/plugin/seq.rb +0 -248
  61. data/lib/bio/shell/plugin/togows.rb +0 -40
  62. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +0 -29
  63. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +0 -4
  64. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +0 -27
  65. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +0 -11
  66. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +0 -4
  67. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +0 -7
  68. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
  69. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
  70. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
  71. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +0 -368
  72. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +0 -47
  73. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +0 -144
  74. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +0 -47
  75. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +0 -8
  76. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +0 -10
  77. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +0 -26
  78. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
  79. data/lib/bio/shell/script.rb +0 -25
  80. data/lib/bio/shell/setup.rb +0 -108
  81. data/lib/bio/shell/web.rb +0 -102
  82. data/sample/test_phyloxml_big.rb +0 -205
  83. data/test/data/phyloxml/apaf.xml +0 -666
  84. data/test/data/phyloxml/bcl_2.xml +0 -2097
  85. data/test/data/phyloxml/made_up.xml +0 -144
  86. data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +0 -65
  87. data/test/data/phyloxml/phyloxml_examples.xml +0 -415
  88. data/test/unit/bio/db/biosql/tc_biosql.rb +0 -114
  89. data/test/unit/bio/db/biosql/ts_suite_biosql.rb +0 -8
  90. data/test/unit/bio/db/test_phyloxml.rb +0 -821
  91. data/test/unit/bio/db/test_phyloxml_writer.rb +0 -334
  92. data/test/unit/bio/shell/plugin/test_seq.rb +0 -187
  93. data/test/unit/bio/test_shell.rb +0 -20
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@@ -1,6 +1,7 @@
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+ sudo: false
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  language: ruby
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  rvm:
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- - 2.1.6
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+ - 2.1.10
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  - 2.0.0
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  - 1.9.3
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  env:
@@ -8,8 +9,6 @@ env:
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  gemfile:
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  - gemfiles/Gemfile.travis-ruby1.9
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  before_install:
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- - gem update --system 2.1.11
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- - gem --version
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  - mkdir /tmp/bioruby
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  - ruby gemfiles/modify-Gemfile.rb
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  - ruby gemfiles/prepare-gemspec.rb
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  - rvm: 1.8.7
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  gemfile: gemfiles/Gemfile.travis-ruby1.8
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  env: TESTOPTS=-v
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- - rvm: rbx-2.2.3
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+ - rvm: rbx-3.29
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  gemfile: gemfiles/Gemfile.travis-rbx
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  env: TESTOPTS=-v
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  - rvm: jruby-18mode
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  - rvm: jruby-19mode
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  gemfile: gemfiles/Gemfile.travis-jruby1.9
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  env: TMPDIR=/tmp/bioruby TESTOPTS=-v
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- - rvm: 2.2.2
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- gemfile: gemfiles/Gemfile.travis-ruby2.2
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- - rvm: 2.1.6
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- gemfile: gemfiles/Gemfile.travis-ruby1.9
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+ - rvm: 2.3.1
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+ gemfile: Gemfile
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+ - rvm: 2.2.5
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+ gemfile: Gemfile
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+ - rvm: 2.2.5
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+ gemfile: Gemfile
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  env: BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test TESTOPTS=-v
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- - rvm: 2.1.6
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- gemfile: gemfiles/Gemfile.travis-ruby1.9
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+ - rvm: 2.2.5
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+ gemfile: Gemfile
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  env: BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
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  - rvm: jruby-19mode
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  gemfile: gemfiles/Gemfile.travis-jruby1.9
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  gemfile: gemfiles/Gemfile.travis-jruby1.9
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  env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
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  allow_failures:
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- - rvm: rbx-2.2.3
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+ - rvm: rbx-3.29
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  gemfile: gemfiles/Gemfile.travis-rbx
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  env: TESTOPTS=-v
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  - rvm: jruby-18mode
data/ChangeLog CHANGED
@@ -1,204 +1,31 @@
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- commit 68f87dc3c4488155992f88c3cf1db27061948315
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+ commit e066e3c8bcf0c6b7eadd3573576d4550aca77cc5
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  Author: Naohisa Goto <ng@bioruby.org>
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- Date: Thu Sep 20 13:25:35 2018 +0900
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+ Date: Thu Jul 2 22:17:06 2015 +0900
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- add changes made for bioruby-1.5.2
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+ ChangeLog is moved to doc/ChangeLog-1.5.0
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- RELEASE_NOTES.rdoc | 14 ++++++++++++++
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- 1 file changed, 14 insertions(+)
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+ ChangeLog | 2919 ---------------------------------------------------
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+ doc/ChangeLog-1.5.0 | 2919 +++++++++++++++++++++++++++++++++++++++++++++++++++
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+ 2 files changed, 2919 insertions(+), 2919 deletions(-)
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+ delete mode 100644 ChangeLog
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+ create mode 100644 doc/ChangeLog-1.5.0
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- commit 6b7e87abfbab88a3bb1b80227ab4b0cfaaeae26e
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+ commit dd53e885c1baa765bc094897d53309af7b15497b
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  Author: Naohisa Goto <ng@bioruby.org>
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- Date: Thu Sep 20 13:24:45 2018 +0900
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+ Date: Thu Jul 2 22:09:26 2015 +0900
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- regenerate bioruby.gemspec with rake regemspec
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+ change version for generating ChangeLog to 1.5.0
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- bioruby.gemspec | 2 +-
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+ Rakefile | 2 +-
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  1 file changed, 1 insertion(+), 1 deletion(-)
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- commit a7dbefeef20d6dea18f0bdd67df24e00c5e9ede6
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Thu Sep 20 13:23:31 2018 +0900
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-
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- version changed to 1.5.2
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-
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- lib/bio/version.rb | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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-
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- commit e00134a1a31db46421b6d468ea1c1d0368bfbb6c
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Thu Sep 20 12:55:32 2018 +0900
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-
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- Bug fix: printf format syntax error about single percent character
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-
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- * Bio::Shell#seqstat: Fix format specifier syntax error.
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- Recent version of Ruby raised error: 'ArgumentError:
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- incomplete format specifier;use %% (double %) instead'.
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-
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- lib/bio/shell/plugin/seq.rb | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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-
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- commit df61cdba5ba3e90fda6c70cc9f880567656a5a82
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Thu Sep 20 07:06:08 2018 +0900
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-
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- Improvement documentation
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-
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- * Improve documentation.
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- * Close https://github.com/bioruby/bioruby/pull/120 .
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- lib/bio/db/aaindex.rb | 79 +++++++++++++++++++++++++++++++++++++++++++++++----
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- 1 file changed, 74 insertions(+), 5 deletions(-)
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- commit 35bcc5008c7721afb3c16467ae6dc782651f4c39
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Thu Sep 20 05:01:12 2018 +0900
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-
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- Bug fix: Bio::Command.new_https should support proxy
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- lib/bio/command.rb | 18 +++++++-----------
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- 1 file changed, 7 insertions(+), 11 deletions(-)
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- commit 88b58e94d4612f39abb14b89779ceeb533cd552e
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Thu Sep 20 04:58:56 2018 +0900
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-
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- https support for Bio::Blast::Remote::GenomeNet::Information
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- lib/bio/appl/blast/genomenet.rb | 6 +++---
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- 1 file changed, 3 insertions(+), 3 deletions(-)
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- commit dfccbdf32bf819f941f2bcb4f63b2f0ce12cacfa
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- Author: ramadis <rramiro.o@hotmail.com>
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- Date: Sat Jul 7 15:12:33 2018 -0300
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- Add https requests in command. Fix genomenet query by allowing https requests.
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- lib/bio/appl/blast/genomenet.rb | 2 +-
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- lib/bio/command.rb | 14 ++++++++++++++
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- 2 files changed, 15 insertions(+), 1 deletion(-)
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- commit d1e1358c1a5c7c7f4aa093a09d5bb45b60f7e7ee
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- Author: markwilkinson <markw@illuminae.com>
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- Date: Tue Dec 12 14:13:51 2017 +0100
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-
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- fixing Fasta Report parser for fasta36 -m10
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- lib/bio/appl/fasta/format10.rb | 3 ++-
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- 1 file changed, 2 insertions(+), 1 deletion(-)
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- commit b9b11f66733e20e1ee6d2b5e0aab813b5b5d0000
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Sep 13 22:13:59 2017 +0900
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-
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- Suppress warning "assigned but unused variable"
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- lib/bio/io/flatfile/autodetection.rb | 5 +++++
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- 1 file changed, 5 insertions(+)
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- commit 580dd6bb9344c2afd0fe60b0cf53a4b28734fbbf
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Sep 13 22:10:53 2017 +0900
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-
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- Suppress warning: "instance variable @top_strand not initialized"
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- * Suppress warning: "instance variable @top_strand not initialized".
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- To do so, force to raise NoMethodError when @top_strand is not
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- initialized or is nil. This should be changed to appropriate
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- exception in the future.
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- lib/bio/util/sirna.rb | 2 ++
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- 1 file changed, 2 insertions(+)
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- commit 9d7ef4e66ecdc1aadc08fda4b332a51ca7739c82
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Sep 13 21:31:38 2017 +0900
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- Suppress warning in Ruby 2.4: "constant ::Fixnum is deprecated"
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- lib/bio/db/soft.rb | 4 ++--
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- .../util/restriction_enzyme/range/sequence_range/calculated_cuts.rb | 2 +-
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- test/unit/bio/test_alignment.rb | 4 ++--
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- 3 files changed, 5 insertions(+), 5 deletions(-)
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- commit 2747ee11392068de88e044abf52d12a88a0624ea
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Sep 13 21:19:12 2017 +0900
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- Suppress warning "parentheses after method name is interpreted as an argument list, not a decomposed argument" in Ruby 2.4
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- lib/bio/map.rb | 8 ++++----
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- 1 file changed, 4 insertions(+), 4 deletions(-)
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- commit 1edbd88a703d3cff0f5a29e45fa51058405ab58c
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Sep 7 22:06:32 2016 +0900
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- BioRuby 1.5.1 is released
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- ChangeLog | 690 +++++++++++++++++++++++++++++++++++---------------------------
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- 1 file changed, 385 insertions(+), 305 deletions(-)
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- commit 917fe0d0e9910267cd54bf48c2caabe89875a299
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Sep 7 22:00:56 2016 +0900
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- regenerate bioruby.gemspec with rake regemspec
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- bioruby.gemspec | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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- commit 1cfa823572742ea46f14420481c10f05fdbce862
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Sep 7 21:51:28 2016 +0900
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- Bio::BIORUBY_EXTRA_VERSION set to nil (Release version)
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- lib/bio/version.rb | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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- commit 8c27599ef5b8ee33cd074feadd089de01a8fa8e6
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Sep 7 21:49:20 2016 +0900
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- Added release notes for 1.5.1 release
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- RELEASE_NOTES.rdoc | 26 ++++++++++++++++++++++++++
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- 1 file changed, 26 insertions(+)
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- commit 47ada241ad6f3632dbbd77542befb82500b7195e
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Aug 13 08:22:22 2016 +0900
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- Update URLs and use https for NCBI REST web services
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- lib/bio/io/ncbirest.rb | 50 ++++++++++++++++++++++++++------------------------
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- 1 file changed, 26 insertions(+), 24 deletions(-)
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- commit 018c2aff1c7813e7b07362ecc8a25db334c0ae95
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Aug 13 08:12:08 2016 +0900
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- New method Bio::Command#start_http_uri(uri) with tests
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- * lib/bio/command.rb: New method Bio::Command#start_http_uri(uri)
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- that supports HTTPS. Note that this method is intended to be
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- * lib/bio/command.rb: Bio::Command#post and #post_form are changed
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- * test/network/bio/test_command.rb: tests for start_http_uri().
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- lib/bio/command.rb | 42 ++++++++++++++++++++++++++++++++++++++--
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- test/network/bio/test_command.rb | 17 ++++++++++++++++
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- 2 files changed, 57 insertions(+), 2 deletions(-)
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- RELEASE_NOTES.rdoc | 4 ++--
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- 1 file changed, 2 insertions(+), 2 deletions(-)
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- commit 1d165c5def88fdeb8f3beeba1f9e6ab0ce71c2a1
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Jul 1 17:28:17 2015 +0900
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- BioRuby 1.5.0 is released
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- ChangeLog | 9 +++++++++
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- 1 file changed, 9 insertions(+)
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- commit 01ac93ca3b341716c85c571f1194834db0a68e52
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Jul 1 02:21:26 2015 +0900
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- update ChangeLog by rake rechangelog
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-
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- ChangeLog | 28 ++++++++++++++++++++++++++++
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- 1 file changed, 28 insertions(+)
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-
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- commit cac63ff501df6a71afead77175db9fb491c2985b
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Jul 1 01:31:21 2015 +0900
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-
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- .travis.yml: use Ruby 2.1.6 for tar and gem integration tests
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-
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- .travis.yml | 8 ++++----
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- 1 file changed, 4 insertions(+), 4 deletions(-)
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-
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- commit 5318c99249f34dacc788b82c658ea0e256770db0
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Jul 1 00:43:39 2015 +0900
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-
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- known issues added about new BLAST XML format and BLAST+ text format
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-
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- KNOWN_ISSUES.rdoc | 11 +++++++++++
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- RELEASE_NOTES.rdoc | 11 +++++++++++
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- 2 files changed, 22 insertions(+)
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-
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- commit b61d8df0300ef366539e1154c9a2dac2f1f4ff18
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 23:57:01 2015 +0900
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-
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- update ChangeLog with rake rechangelog
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-
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- ChangeLog | 47 +++++++++++++++++++++++++++++++++++++++++++++++
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- 1 file changed, 47 insertions(+)
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-
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- commit 75cf6c31c57239b2e39a171e536ad5dddcaec94a
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 23:56:08 2015 +0900
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-
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- regenerate bioruby.gemspec with rake regemspec
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-
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- bioruby.gemspec | 1 +
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- 1 file changed, 1 insertion(+)
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-
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- commit 608850beb33f3f7333f05307202b766adb350eb9
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 23:54:59 2015 +0900
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-
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- description about updating of Ruby's License
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-
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- RELEASE_NOTES.rdoc | 9 +++++++++
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- 1 file changed, 9 insertions(+)
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-
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- commit f54bcfc20d20935db4e342e5988c0b7f59c131b3
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 23:16:51 2015 +0900
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-
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- BSDL is referred in COPYING and COPYING.ja
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-
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- BSDL | 22 ++++++++++++++++++++++
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- 1 file changed, 22 insertions(+)
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- create mode 100644 BSDL
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-
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- commit d1cbfb699259fd57af02181f4374d562dda3abe1
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 23:14:42 2015 +0900
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-
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- changes of Ruby's License is reflected.
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-
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- COPYING | 4 ++--
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- COPYING.ja | 72 +++++++++++++++++++++++++++++++-------------------------------
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- 2 files changed, 38 insertions(+), 38 deletions(-)
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-
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- commit 2d9de9a0e2abe7fa9f193e54af0cbfc24bf2c37b
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 22:50:37 2015 +0900
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-
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- ChangeLog is regenerated by using "rake rechangelog"
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-
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- ChangeLog | 2786 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
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- 1 file changed, 2780 insertions(+), 6 deletions(-)
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-
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- commit 70665a69a79d569d7bb37ef6d8c238534e6dae3a
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 22:49:55 2015 +0900
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-
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- KNOWN_ISSUES.rdoc: change ruby versions and add descriptions
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-
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- KNOWN_ISSUES.rdoc | 14 +++++++++-----
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- 1 file changed, 9 insertions(+), 5 deletions(-)
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-
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- commit 1054106f93b973b5a92f993c5b83b1444f96fffe
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 22:48:51 2015 +0900
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-
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- prepare to release BioRuby 1.5.0
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-
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- bioruby.gemspec | 2 +-
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- lib/bio/version.rb | 2 +-
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- 2 files changed, 2 insertions(+), 2 deletions(-)
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-
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- commit 0f150586904f7e423455615313992ccf77d7e123
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 22:44:58 2015 +0900
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-
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- RELEASE_NOTES.rdoc: update many
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-
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- RELEASE_NOTES.rdoc | 151 ++++++++++++++++++++++++++++++++++++++++++++++-------
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- 1 file changed, 132 insertions(+), 19 deletions(-)
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-
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- commit 2924ca0b977da13d42f232f880fd2df0b2995677
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 21:55:52 2015 +0900
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-
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- Bug fix: Bio::UniProtKB#gene_name should not raise NoMethodError
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-
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- * Bug fix: Bio::UniProtKB#gene_name raised NoMethodError when
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- gene_names method returns nil. It should return nil.
342
- Thanks to Jose Irizarry who reports and sends suggested fix.
343
- (https://github.com/bioruby/bioruby/pull/83 )
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-
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- lib/bio/db/embl/uniprotkb.rb | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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-
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- commit 9bf9022007a0ff31a870b1ea08e423aebc487c17
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 18:45:51 2015 +0900
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-
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- regenerate bioruby.gemspec with rake regemspec
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-
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- bioruby.gemspec | 1 +
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- 1 file changed, 1 insertion(+)
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-
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- commit a151e51a44b3dd93e5d075d71954f639eaec339e
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 18:10:55 2015 +0900
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-
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- update docs; change recommended Ruby versions
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-
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- README.rdoc | 9 ++++++---
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- 1 file changed, 6 insertions(+), 3 deletions(-)
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-
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- commit e86e745c8a6c666c446fe2f9f47818140999e2db
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 18:08:53 2015 +0900
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-
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- delete description about SOAP4R
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-
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- README.rdoc | 5 -----
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- 1 file changed, 5 deletions(-)
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-
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- commit 7e4bfb6b3757872691487b080bfd87363a4f9480
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 03:22:35 2015 +0900
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-
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- .travis.yml: test/unit no longer bundled with Ruby 2.2
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-
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- * For Ruby 2.2, use a new Gemfile named Gemfile.travis-ruby2.2
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- that include 'gem "test-unit"' line because test/unit have been
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- provided by bundled gem since Ruby 2.2.
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-
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- .travis.yml | 7 ++++---
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- gemfiles/Gemfile.travis-ruby2.2 | 9 +++++++++
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- 2 files changed, 13 insertions(+), 3 deletions(-)
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- create mode 100644 gemfiles/Gemfile.travis-ruby2.2
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-
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- commit cac85ca215ed781c80d49a5bf3d5d37d808c783b
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 02:51:16 2015 +0900
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-
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- bump up version to 1.5.0-dev; simplify the versioning rules
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-
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- * Bump up version to 1.5.0-dev (1.5.0.20150630)
397
- * Simplify the versioning rules.
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- * We will adopt the Semantic Versioning since BioRuby 1.5.1.
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-
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- bioruby.gemspec | 2 +-
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- bioruby.gemspec.erb | 21 ++++-----------------
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- lib/bio/version.rb | 17 ++++++++---------
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- 3 files changed, 13 insertions(+), 27 deletions(-)
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-
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- commit 1a24fb6840932499be833b5ec3bb36184b1334a1
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 02:14:01 2015 +0900
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-
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- Bug fix: update Bio::Hinv::BASE_URI
410
-
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- * Bug fix: update Bio::Hinv::BASE_URI to follow the server URI change.
412
- * Update official documentation URL.
413
-
414
- lib/bio/io/hinv.rb | 4 ++--
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- 1 file changed, 2 insertions(+), 2 deletions(-)
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-
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- commit a9a12fff70ca287aa098d1331a3146e2899cb709
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 02:08:40 2015 +0900
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-
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- delete $Id:$ line
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-
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- lib/bio/io/hinv.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit 2bfa0f41969003f17c4b894b5279347616c8f187
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 01:58:01 2015 +0900
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-
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- delete sections about SOAP4R issues
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-
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- KNOWN_ISSUES.rdoc | 12 ------------
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- 1 file changed, 12 deletions(-)
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-
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- commit 9dbd83aa00acc5f78b5da68f000c305da9f31b66
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 01:54:16 2015 +0900
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-
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- remove commented-out lines of soap4r-ruby1.9
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-
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- gemfiles/Gemfile.travis-jruby1.9 | 3 ---
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- gemfiles/Gemfile.travis-rbx | 3 ---
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- gemfiles/Gemfile.travis-ruby1.9 | 3 ---
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- 3 files changed, 9 deletions(-)
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-
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- commit 14d2f3e2fa15f94faeff4d28c957f581461eac82
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 01:50:30 2015 +0900
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-
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- .travis.yml: update ruby versions, remove ruby 1.9.2
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-
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- .travis.yml | 8 ++++----
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- 1 file changed, 4 insertions(+), 4 deletions(-)
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-
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- commit 89f9b1fe2332584b5d63b1539b8e470d853478a3
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 00:36:42 2015 +0900
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-
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- about removal of Bio::SOAPWSDL, Bio::EBI::SOAP, Bio::HGC::HiGet
460
-
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- RELEASE_NOTES.rdoc | 20 ++++++++++++++++++++
462
- 1 file changed, 20 insertions(+)
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-
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- commit 29516d3d6d2f907f65822bcf4146e95785773a3a
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 00:50:47 2015 +0900
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-
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- regenerate bioruby.gemspec with rake regemspec
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-
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- bioruby.gemspec | 6 ------
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- 1 file changed, 6 deletions(-)
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-
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- commit 357a1afc5ef457326179142c163968aa5cd94864
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 00:49:42 2015 +0900
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-
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- not to load deleted file lib/bio/shell/plugin/soap.rb
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-
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- lib/bio/shell.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit 956e475da52ea17f1022493f589489a3e7c06f93
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Mon Jun 29 23:43:24 2015 +0900
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-
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- deleted lib/bio/shell/plugin/soap.rb
487
-
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- * deleted lib/bio/shell/plugin/soap.rb because Bio::SOAPWSDL and
489
- all SOAP client classes in BioRuby are removed.
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-
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- lib/bio/shell/plugin/soap.rb | 50 --------------------------------------------
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- 1 file changed, 50 deletions(-)
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- delete mode 100644 lib/bio/shell/plugin/soap.rb
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-
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- commit 00acae3c3a8066891e08dc225eae2c22c3415191
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Mon Jun 29 23:41:20 2015 +0900
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-
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- not to load removed Bio::EBI::SOAP from lib/bio/io/ebisoap.rb
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-
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- lib/bio.rb | 4 ----
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- 1 file changed, 4 deletions(-)
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-
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- commit d4844b38b5ddaec7ec15b56ef66f6930f0e6cfc0
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Mon Jun 29 23:38:26 2015 +0900
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-
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- remove Bio::EBI::SOAP (lib/bio/io/ebisoap.rb)
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-
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- * Bio::EBI::SOAP (lib/bio/io/ebisoap.rb) is removed because
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- Bio::SOAPWSDL is removed.
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-
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- lib/bio/io/ebisoap.rb | 158 --------------------------------------------------
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- 1 file changed, 158 deletions(-)
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- delete mode 100644 lib/bio/io/ebisoap.rb
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-
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- commit 79b4705bac82fe17b12c649172a629d3de41cbdf
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Jun 30 00:12:36 2015 +0900
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-
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- not to load removed Bio::SOAPWSDL from lib/bio/io/soapwsdl.rb
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-
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- lib/bio.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit 03ced6a70973557532517c70dac183775bd11fa7
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Mon Jun 29 23:59:28 2015 +0900
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-
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- remove Bio::SOAPWSDL (lib/bio/io/soapwsdl.rb) and tests
531
-
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- * Bio::SOAPWSDL is removed because SOAP4R (SOAP/WSDL library in Ruby)
533
- is no longer bundled with Ruby since Ruby 1.9. For Ruby 1.9 or later,
534
- some gems of SOAP4R are available, but we think they are not
535
- well-maintained. Moreover, many SOAP servers have been retired
536
- (see previous commits). So, we give up maintaining Bio::SOAPWSDL.
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-
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- lib/bio/io/soapwsdl.rb | 119 -----------------------------------
539
- test/network/bio/io/test_soapwsdl.rb | 53 ----------------
540
- test/unit/bio/io/test_soapwsdl.rb | 33 ----------
541
- 3 files changed, 205 deletions(-)
542
- delete mode 100644 lib/bio/io/soapwsdl.rb
543
- delete mode 100644 test/network/bio/io/test_soapwsdl.rb
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- delete mode 100644 test/unit/bio/io/test_soapwsdl.rb
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-
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- commit d927652e9f5d241e3c1b13b7d760f5a190b72e50
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Mon Jun 29 23:35:38 2015 +0900
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-
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- delete old comment-out lines about Bio::DDBJ::XML
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-
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- lib/bio.rb | 5 -----
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- 1 file changed, 5 deletions(-)
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-
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- commit b995251bf96b8983def36e77bc94d6f0c0f2c78c
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Mon Jun 29 23:29:47 2015 +0900
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-
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- do not load Bio::HGC::HiGet from deleted lib/bio/io/higet.rb
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-
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- lib/bio.rb | 4 ----
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- 1 file changed, 4 deletions(-)
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-
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- commit 6191020ed1e150f9e70de687375528a899fcf8ef
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Mon Jun 29 23:27:41 2015 +0900
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-
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- remove lib/bio/io/higet.rb because of the server down for a long time
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-
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- lib/bio/io/higet.rb | 73 -----------------------------------------------------
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- 1 file changed, 73 deletions(-)
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- delete mode 100644 lib/bio/io/higet.rb
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-
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- commit 5a527c5cdd513d72ad5817c66ac87e7613395e26
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Jun 27 02:33:46 2015 +0900
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-
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- add/modify about removed features and incompatible changes
579
-
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- RELEASE_NOTES.rdoc | 71 +++++++++++++++++++++++++++++++++++++++++++++++++++---
581
- 1 file changed, 67 insertions(+), 4 deletions(-)
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-
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- commit 1886314d2b8dd7d4b3e86c7b93134facd881127a
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Jun 27 01:24:36 2015 +0900
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-
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- regenerate bioruby.gemspec with rake regemspec
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-
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- bioruby.gemspec | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit 724e9c1c039dcc7fa19fb15de0313218a87f9868
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Thu Jun 25 23:34:44 2015 +0900
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-
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- extconf.rb is deleted because no native extensions are included
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-
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- * extconf.rb is deleted because no native extensions are included in
599
- BioRuby and to avoid potential confusions. Nowadays, extconf.rb is
600
- usually used only for building native extensions. Use gem or
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- setup.rb to install BioRuby.
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-
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- extconf.rb | 2 --
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- 1 file changed, 2 deletions(-)
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- delete mode 100644 extconf.rb
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-
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- commit d42a1cb1df17e0c11ca0407dc05e1271cd74a0d7
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Jun 24 22:29:28 2015 +0900
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-
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- Ruby 2.3 support: IO#close to closed IO object is allowed without error.
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-
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- test/unit/bio/io/flatfile/test_buffer.rb | 8 +++++++-
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- 1 file changed, 7 insertions(+), 1 deletion(-)
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-
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- commit 5ea39188ac3cc2609397b2d8864a2019ea6b93d2
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- Author: Naohisa Goto <ng@bioruby.org>
618
- Date: Fri May 1 23:42:39 2015 +0900
619
-
620
- s.license = "Ruby"
621
-
622
- * bioruby.gemspec.erb, bioruby.gemspec: s.license = "Ruby"
623
- Thanks to Peter Cock who reports a patch.
624
- (https://github.com/bioruby/bioruby/issues/101 )
625
-
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- bioruby.gemspec | 1 +
627
- bioruby.gemspec.erb | 1 +
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- 2 files changed, 2 insertions(+)
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-
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- commit 2b18ae005a592ea4ae7b632f7e658d4bbf153fd8
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Fri May 1 23:39:36 2015 +0900
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-
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- remove deprecated Gem::Specification#rubyforge_project
635
-
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- bioruby.gemspec | 2 +-
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- bioruby.gemspec.erb | 2 +-
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- 2 files changed, 2 insertions(+), 2 deletions(-)
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-
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- commit 3a1d89bde9af44793c850b1cde950e3e3042fb8d
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 01:52:31 2015 +0900
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-
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- delete obsolete $Id:$ line
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-
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- lib/bio/db/gff.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit 165ebf29ba192c7a7e7f1633809d34966c2aeed1
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- Author: Naohisa Goto <ng@bioruby.org>
651
- Date: Sat Mar 28 01:51:47 2015 +0900
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-
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- suppress "character class has duplicated range" warnings
654
-
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- lib/bio/db/gff.rb | 4 ++--
37
+ RELEASE_NOTES.rdoc | 4 ++--
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38
  1 file changed, 2 insertions(+), 2 deletions(-)
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-
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- commit 715ee5aa3a797737d390365b2c202cc9a0effea5
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 01:37:35 2015 +0900
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-
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- delete obsolete $Id:$ line
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-
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- lib/bio/appl/sosui/report.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit 71e34938f1228911657ebf00720712a17bc89ea9
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 01:36:44 2015 +0900
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-
671
- comment out a line to suppress warning: assigned but unused variable - tmh
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-
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- lib/bio/appl/sosui/report.rb | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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-
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- commit fc518f3826bf60d70ebdbd70acdba512f1462c6f
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 01:34:22 2015 +0900
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-
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- delete obsolete $Id:$ line
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-
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- lib/bio/db/sanger_chromatogram/chromatogram.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit 516c467dfb245d99c4f7f77e251c77ffc5d274ca
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 01:33:19 2015 +0900
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-
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- suppress warning: instance variable @aqual not initialized
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-
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- lib/bio/db/sanger_chromatogram/chromatogram.rb | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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-
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- commit 56d2e472196ba03ba6aa2a2bdf8d3de81272fa15
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 01:30:26 2015 +0900
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-
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- delete obsolete $Id:$ line
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-
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- lib/bio/db/kegg/module.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit fb6b9b6578d08a87c1974e58f6d1f231b4ad52c0
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 01:28:05 2015 +0900
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-
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- suppress "instance variable @XXX not initialized" warnings
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-
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- lib/bio/db/kegg/module.rb | 8 ++++----
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- 1 file changed, 4 insertions(+), 4 deletions(-)
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-
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- commit 9f70b8d54abd9adbd50d46a3176f23f51af01cc7
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 01:25:50 2015 +0900
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-
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- delete obsolete $Id:$ line
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-
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- lib/bio/db/kegg/pathway.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit 3844b9bb69e1f657c9b85bb20a4d209828b78b12
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 01:25:03 2015 +0900
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-
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- suppress "instance variable @XXX not initialized" warnings
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-
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- lib/bio/db/kegg/pathway.rb | 8 ++++----
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- 1 file changed, 4 insertions(+), 4 deletions(-)
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-
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- commit 8d857e246eacb6c9f8fbbceaa2fba7f1211e2b86
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 01:20:13 2015 +0900
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- delete obsolete $Id:$ line
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-
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- lib/bio/db/fasta/defline.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit aadf285bc9e618b7813b42fd39e0b1966a04385c
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 01:18:43 2015 +0900
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-
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- suppress defline.rb:393: warning: character class has duplicated range
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-
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- lib/bio/db/fasta/defline.rb | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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-
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- commit 5297db11eb165885c4f15b914c2132c4122ae5a9
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 01:11:43 2015 +0900
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-
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- delete obsolete $Id:$ line
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-
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- test/unit/bio/test_db.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit 20381ad45c674c0844a92891cb8ae71edaa6e333
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 01:08:04 2015 +0900
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-
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- suppress "warning: instance variable @tagsize not initialized"
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-
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- * test/unit/bio/test_db.rb: to suppress "warning: instance variable
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- @tagsize not initialized" when executing Bio::TestDB#test_fetch,
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- @tagsize is set in setup.
766
-
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- test/unit/bio/test_db.rb | 5 ++++-
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- 1 file changed, 4 insertions(+), 1 deletion(-)
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-
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- commit d194edfc68bc10fde11f2cf014a59113ddc63b24
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 00:59:21 2015 +0900
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-
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- delete obsolete $Id:$ line
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-
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- lib/bio/data/codontable.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit fac51f540dc7b33cd3ec51f97b5cb1ea587a461e
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 00:57:28 2015 +0900
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-
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- suppress warning: instance variable @reverse not initialized
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-
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- lib/bio/data/codontable.rb | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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-
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- commit 4e85315f03e374157f832c8435d0d2f43cd969af
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 00:55:25 2015 +0900
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- delete obsolete $Id:$ line
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-
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- lib/bio/appl/iprscan/report.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit dafa7ce62378ff1605a295f8c620eb3a0a4a3c57
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 00:54:37 2015 +0900
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-
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- suppress warning: instance variable @ipr_ids not initialized
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-
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- lib/bio/appl/iprscan/report.rb | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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-
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- commit 52b6073997c1b26fea9d4aae3154b37575944d4d
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 00:50:43 2015 +0900
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-
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- suppress "method redefined" warnings and fill RDoc for some methods
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-
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- lib/bio/db/phyloxml/phyloxml_elements.rb | 46 ++++++++++++++++++++++++--------
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- 1 file changed, 35 insertions(+), 11 deletions(-)
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-
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- commit 3d2e99fe993d76d5ece5bdbcd2e9541fa098c4dd
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 28 00:36:51 2015 +0900
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-
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- suppress "instance variable @XXX not initialized" warnings
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-
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- lib/bio/db/phyloxml/phyloxml_elements.rb | 88 ++++++++++++++++----------------
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- 1 file changed, 44 insertions(+), 44 deletions(-)
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-
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- commit 02d4f98eae3934d8ad9c950b41132eb14653fe27
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Thu Mar 26 20:33:35 2015 +0900
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-
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- suppress warning: instance variable @uri not initialized
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-
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- lib/bio/db/phyloxml/phyloxml_elements.rb | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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-
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- commit 94277712e9dd000c2d9bf5b6ebfd84d0f2fc3b59
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Thu Mar 26 01:47:45 2015 +0900
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- suppress warning: instance variable @format not initialized
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-
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- lib/bio/db/fastq.rb | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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-
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- commit e61e1071e4bb7dd9ee995c3a7f864c2ef4384edd
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Thu Mar 26 01:40:33 2015 +0900
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- suppress "instance variable not initialized" warnings
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-
848
- * suppress warning: instance variable @sc_match not initialized
849
- * suppress warning: instance variable @sc_mismatch not initialized
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- * suppress warning: instance variable @gaps not initialized
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- * suppress warning: instance variable @hit_frame not initialized
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- * suppress warning: instance variable @query_frame not initialized
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-
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- lib/bio/appl/blast/format0.rb | 13 ++++++++++---
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- 1 file changed, 10 insertions(+), 3 deletions(-)
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-
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- commit 08c458c74a7a34e340e09053cbc0f9c071e27395
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Thu Mar 26 01:09:16 2015 +0900
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- suppress warning: instance variable @pattern not initialized
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-
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- lib/bio/appl/blast/format0.rb | 8 ++++++--
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- 1 file changed, 6 insertions(+), 2 deletions(-)
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-
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- commit 33d7eed180fd601972724f4b992f1a17c689ef62
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Thu Mar 26 00:57:02 2015 +0900
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-
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- Test bug fix: fix typo of test target method
871
-
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- test/network/bio/test_command.rb | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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-
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- commit 76a98bce1affac03483c08f803d4314b42a0a3d3
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Thu Mar 26 00:32:25 2015 +0900
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-
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- Incompatible Change: Bio::Command.make_cgi_params rejects single String
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-
881
- * Incompatible Change: Bio::Command.make_cgi_params no longer accepts a
882
- single String as a form. Use Hash or Array containing key-value pairs
883
- as String objects. This change also affects Bio::Command.post_form
884
- and Bio::Command.http_post_form which internally use this method.
885
-
886
- lib/bio/command.rb | 2 +-
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- test/unit/bio/test_command.rb | 9 +++++----
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- 2 files changed, 6 insertions(+), 5 deletions(-)
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-
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- commit b1612545a7516befd850a6d5925aa73bbaa4b4b0
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Mar 25 02:36:41 2015 +0900
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- delete obsolete $Id:$ line
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-
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- lib/bio/io/togows.rb | 1 -
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- 1 file changed, 1 deletion(-)
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- commit 4d5a419cc78ff2a79cff2812adc6f16f286204e8
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Mar 25 02:35:45 2015 +0900
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- delete obsolete $Id:$ line
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-
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- test/network/bio/io/test_togows.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit a8d2c4cac665b4bb8140df329a9cc1d6e5e2d02d
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Mar 25 02:35:03 2015 +0900
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- delete obsolete $Id:$ line
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-
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- test/unit/bio/io/test_togows.rb | 1 -
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- 1 file changed, 1 deletion(-)
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- commit dd0967db3743789ea5aa48623df8d97f93062694
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Mar 25 02:33:49 2015 +0900
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-
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- test_make_path: add test data using Symbol objects
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-
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- test/unit/bio/io/test_togows.rb | 4 +++-
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- 1 file changed, 3 insertions(+), 1 deletion(-)
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-
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- commit e07158a60ca666b5d625408bcf8fa602fd8114a8
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Mar 25 02:22:31 2015 +0900
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-
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- Bio::TogoWS::REST#entry: comma between IDs should NOT be escaped to %2C
931
-
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- lib/bio/io/togows.rb | 11 +++++++++--
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- 1 file changed, 9 insertions(+), 2 deletions(-)
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-
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- commit 98546289b2f2da2dc7f9586fd5e2942da4d8f3a8
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Mar 25 02:00:17 2015 +0900
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939
- Bug fix: search with offset did not work due to TogoWS server change
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-
941
- * lib/bio/io/togows.rb: Bug fix: Bio::TogoWS::REST#search with offset
942
- and limit did not work due to TogoWS server change about URI escape.
943
- For example,
944
- http://togows.org/search/nuccore/Milnesium+tardigradum/2%2C3 fails,
945
- http://togows.org/search/nuccore/Milnesium+tardigradum/2,3 works fine.
946
-
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- lib/bio/io/togows.rb | 24 +++++++++++++++++++++---
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- 1 file changed, 21 insertions(+), 3 deletions(-)
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-
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- commit 7097f80e315a0a6332e7a76a5bb261649e8dcc1a
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Mar 25 01:33:26 2015 +0900
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-
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- Bug fix due to TogoWS convert method spec change
955
-
956
- * lib/bio/io/togows.rb: Bug fix: Bio::TogoWS::REST#convert did not work
957
- because of the spec change of TogoWS REST API.
958
-
959
- lib/bio/io/togows.rb | 7 +++----
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- 1 file changed, 3 insertions(+), 4 deletions(-)
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-
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- commit 1a9b1063af4c0b32cd287d4a2c2466343aeddb98
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Mar 25 01:30:34 2015 +0900
965
-
966
- improve tests for bio/command.rb for methods using http protocol
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-
968
- test/network/bio/test_command.rb | 67 ++++++++++++++++++++++++++++++++++++++--
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- 1 file changed, 65 insertions(+), 2 deletions(-)
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-
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- commit c63920e4d8569e3eaef201d4d60fcddfa15f1f34
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Mar 25 01:30:06 2015 +0900
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- delete obsolete $Id:$ line
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-
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- lib/bio/command.rb | 1 -
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- 1 file changed, 1 deletion(-)
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- commit 1683edac0e9ecbf819ffcd332a6db2d25c2d596a
981
- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Wed Mar 25 01:28:28 2015 +0900
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984
- new methods Bio::Command.http_post and Bio::Command.post to post raw data
985
-
986
- lib/bio/command.rb | 61 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
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- 1 file changed, 61 insertions(+)
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- commit a40157205282e148bf3a2e43aed1e08d713fb598
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Mar 24 00:46:23 2015 +0900
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- suppress warnings "instance variable @circular not initialized"
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-
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- lib/bio/util/restriction_enzyme/range/sequence_range.rb | 4 ++--
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- 1 file changed, 2 insertions(+), 2 deletions(-)
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-
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- commit abcac8de85c9606f6a1879fe9d2ae559911708c9
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Mar 24 00:29:42 2015 +0900
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- delete obsolete $Id:$ line
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- test/unit/bio/io/flatfile/test_autodetection.rb | 1 -
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- 1 file changed, 1 deletion(-)
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- commit 1b5bf586af238b712a9f640087421fd299376c2d
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Mar 24 00:28:38 2015 +0900
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1011
- suppress warning: assigned but unused variable - length
1012
-
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- test/unit/bio/io/flatfile/test_autodetection.rb | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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- commit 5497068d17c2794ab2b6ef1e603e5478a86537c6
1017
- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Tue Mar 24 00:22:54 2015 +0900
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- add/modify assertions to suppress "unused variable" warnings
1021
-
1022
- test/unit/bio/db/genbank/test_genbank.rb | 12 +++++++++---
1023
- 1 file changed, 9 insertions(+), 3 deletions(-)
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-
1025
- commit d5bafd8b7ee28ab0418b09fd6dd47abcb9eb1ee5
1026
- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Mon Mar 23 23:57:56 2015 +0900
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- delete obsolete $Id:$ line
1030
-
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- lib/bio/appl/blast.rb | 1 -
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- 1 file changed, 1 deletion(-)
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- commit bbd60d1aae7c894f914b7265d2de22fea5eb3faf
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Mon Mar 23 23:56:42 2015 +0900
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- suppress warning: assigned but unused variable - dummy
1039
-
1040
- lib/bio/appl/blast.rb | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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1043
- commit 4a91502ccf14ab8655645144120aa97d0c8313a5
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Mon Mar 23 20:32:59 2015 +0900
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- delete obsolete $Id:$ line
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-
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- lib/bio/shell/setup.rb | 1 -
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- 1 file changed, 1 deletion(-)
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- commit c437a4078ff8e2869b9c1ab3543022db373a93c3
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Mon Mar 23 20:32:20 2015 +0900
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1056
- suppress warning: instance variable @mode not initialized
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1058
- lib/bio/shell/setup.rb | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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- commit 8967cf280d5ca8491d57a11e4f3ffab7369c4ea8
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Mon Mar 23 20:28:50 2015 +0900
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- delete obsolete $Id:$ line
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- lib/bio/shell/irb.rb | 1 -
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- 1 file changed, 1 deletion(-)
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- commit 42b5f030067be4bc9c53ccb4c06ccfc5e8d9df03
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Mon Mar 23 20:28:27 2015 +0900
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- change deprecated method File.exists? to File.exist?
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- lib/bio/shell/irb.rb | 2 +-
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- 1 file changed, 1 insertion(+), 1 deletion(-)
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- commit 389ad2f311f161f235db2373aeb2f5500b1ea65f
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- Author: Naohisa Goto <ng@bioruby.org>
1081
- Date: Mon Mar 23 20:27:01 2015 +0900
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- delete obsolete $Id:$ line
1084
-
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- lib/bio/shell/interface.rb | 1 -
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- 1 file changed, 1 deletion(-)
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- commit de5949798d66c16d2b5e2cf8ba7192049ec99c5b
1089
- Author: Naohisa Goto <ng@bioruby.org>
1090
- Date: Mon Mar 23 20:26:37 2015 +0900
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1092
- change deprecated method File.exists? to File.exist?
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-
1094
- lib/bio/shell/interface.rb | 6 +++---
1095
- 1 file changed, 3 insertions(+), 3 deletions(-)
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-
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- commit c8907059a716a8778e333755c8fb53bb2a0c7158
1098
- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Mon Mar 23 20:24:58 2015 +0900
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- delete obsolete $Id:$ line
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-
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- lib/bio/shell/core.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit 1fe5903f8acd8045d203465a099a45218e7e3891
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- Author: Naohisa Goto <ng@bioruby.org>
1108
- Date: Mon Mar 23 20:24:25 2015 +0900
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1110
- change deprecated method File.exists? to File.exist?
1111
-
1112
- lib/bio/shell/core.rb | 10 +++++-----
1113
- 1 file changed, 5 insertions(+), 5 deletions(-)
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-
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- commit 929207c6f186c81f076fab9b1bbbd23c4b966f4e
1116
- Author: Naohisa Goto <ng@bioruby.org>
1117
- Date: Mon Mar 23 20:20:05 2015 +0900
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-
1119
- delete obsolete $Id:$ line
1120
-
1121
- test/unit/bio/db/pdb/test_pdb.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit e75c57fcd7abc56ba6fcbf1996e491aca890f5b1
1125
- Author: Naohisa Goto <ng@bioruby.org>
1126
- Date: Mon Mar 23 20:19:30 2015 +0900
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1128
- suppress "assigned but unused variable" warnings
1129
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1130
- test/unit/bio/db/pdb/test_pdb.rb | 21 ++++++++++++++-------
1131
- 1 file changed, 14 insertions(+), 7 deletions(-)
1132
-
1133
- commit b458301f47322c265fce27efd0ed71443c17d9d7
1134
- Author: Naohisa Goto <ng@bioruby.org>
1135
- Date: Mon Mar 23 18:34:12 2015 +0900
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1137
- delete obsolete $Id:$ line
1138
-
1139
- lib/bio/shell/plugin/entry.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
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- commit c3f909fe06b82b3cbd4bdcbcdef668fc0727be9d
1143
- Author: Naohisa Goto <ng@bioruby.org>
1144
- Date: Mon Mar 23 18:33:30 2015 +0900
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- change deprecated method File.exists? to File.exist?
1147
-
1148
- lib/bio/shell/plugin/entry.rb | 4 ++--
1149
- 1 file changed, 2 insertions(+), 2 deletions(-)
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-
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- commit 7ba6349c2446aa03b843a2a8fb49505c8f63c6ca
1152
- Author: Naohisa Goto <ng@bioruby.org>
1153
- Date: Mon Mar 23 18:20:44 2015 +0900
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1155
- change deprecated method File.exists? to File.exist?
1156
-
1157
- lib/bio/appl/meme/mast.rb | 8 ++++----
1158
- 1 file changed, 4 insertions(+), 4 deletions(-)
1159
-
1160
- commit e7f78ea3c3fb1b78adcc6ae13f450cf2cda361cd
1161
- Author: Naohisa Goto <ng@bioruby.org>
1162
- Date: Mon Mar 23 18:10:27 2015 +0900
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- delete obsolete $Id:$ line
1165
-
1166
- lib/bio/db/phyloxml/phyloxml_writer.rb | 1 -
1167
- 1 file changed, 1 deletion(-)
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-
1169
- commit b32eae0050a73bd5a2931c17a6694f494ad00bb2
1170
- Author: Naohisa Goto <ng@bioruby.org>
1171
- Date: Mon Mar 23 18:07:54 2015 +0900
1172
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1173
- suppress warning: mismatched indentations at 'end' with 'def' at 166
1174
-
1175
- lib/bio/db/phyloxml/phyloxml_writer.rb | 2 +-
1176
- 1 file changed, 1 insertion(+), 1 deletion(-)
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-
1178
- commit bd735347283ce5d332245d0349186f300800a43f
1179
- Author: Naohisa Goto <ng@bioruby.org>
1180
- Date: Sat Mar 21 12:57:03 2015 +0900
1181
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1182
- remove duplicated line and suppress Ruby 2.2 warning
1183
-
1184
- setup.rb | 1 -
1185
- 1 file changed, 1 deletion(-)
1186
-
1187
- commit 68ad10e178594691c77ba4b97c2449fecf0ac9de
1188
- Author: Naohisa Goto <ng@bioruby.org>
1189
- Date: Sat Mar 21 12:50:46 2015 +0900
1190
-
1191
- Ruby 1.9 support: suppress "shadowing outer local variable" warnings
1192
-
1193
- setup.rb | 10 +++++-----
1194
- 1 file changed, 5 insertions(+), 5 deletions(-)
1195
-
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- commit 2343482078aec8373f7a2eb8ed4d7c44119f809c
1197
- Author: Naohisa Goto <ng@bioruby.org>
1198
- Date: Sat Mar 21 12:16:45 2015 +0900
1199
-
1200
- Ruby 2.2 support: Config was renamed to RbConfig
1201
-
1202
- setup.rb | 2 +-
1203
- 1 file changed, 1 insertion(+), 1 deletion(-)
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-
1205
- commit d512712745142d6c6ebe9a6ef51c8c4773bd7c2c
1206
- Author: Naohisa Goto <ng@bioruby.org>
1207
- Date: Sat Mar 21 11:52:47 2015 +0900
1208
-
1209
- Ruby 1.9 support: suppress "shadowing outer local variable" warnings
1210
-
1211
- lib/bio/db/embl/format_embl.rb | 6 +++---
1212
- 1 file changed, 3 insertions(+), 3 deletions(-)
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-
1214
- commit bfa75df9047ab6855c931558f6bf9fdbb1c3c288
1215
- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 21 11:36:01 2015 +0900
1217
-
1218
- delete obsolete $Id:$ line
1219
-
1220
- lib/bio/io/flatfile/buffer.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
1223
- commit d6fbaa0c555117ebadd46e284ae357586856102d
1224
- Author: Naohisa Goto <ng@bioruby.org>
1225
- Date: Sat Mar 21 11:35:07 2015 +0900
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-
1227
- Ruby 1.9 support: suppress warning: shadowing outer local variable - fobj
1228
-
1229
- lib/bio/io/flatfile/buffer.rb | 8 ++++----
1230
- 1 file changed, 4 insertions(+), 4 deletions(-)
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-
1232
- commit 0083d3284ec181f4bcc3144f76b12f9d52e3eff6
1233
- Author: Naohisa Goto <ng@bioruby.org>
1234
- Date: Sat Mar 21 11:29:39 2015 +0900
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-
1236
- delete obsolete $Id:$ line
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-
1238
- lib/bio/io/fastacmd.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
1241
- commit d4909c0e80e572a639edba07388e430c7f5d6ce8
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 21 11:29:01 2015 +0900
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-
1245
- remove old sample script in "if $0 == __FILE__" block
1246
-
1247
- lib/bio/io/fastacmd.rb | 15 ---------------
1248
- 1 file changed, 15 deletions(-)
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-
1250
- commit 8171162d0a3991d5f0d9a8bccee57250248d6d3d
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 21 11:15:10 2015 +0900
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-
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- delete obsolete $Id:$ line
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-
1256
- lib/bio/db/go.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
1259
- commit ed7c9a5335ef59399f3098311f47b8dec519281a
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- Author: Naohisa Goto <ng@bioruby.org>
1261
- Date: Sat Mar 21 11:14:19 2015 +0900
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-
1263
- Ruby 1.9 support: suppress warnings: "shadowing outer local variable - goid"
1264
-
1265
- lib/bio/db/go.rb | 4 ++--
1266
- 1 file changed, 2 insertions(+), 2 deletions(-)
1267
-
1268
- commit dd543068b046c9a0c2a40159c830c92b680244f1
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- Author: Naohisa Goto <ng@bioruby.org>
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- Date: Sat Mar 21 11:03:08 2015 +0900
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-
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- delete obsolete $Id:$ line
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-
1274
- lib/bio/db/phyloxml/phyloxml_elements.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
1277
- commit 4c74a6e3aeca30820b0be61e867c9201445542ec
1278
- Author: Naohisa Goto <ng@bioruby.org>
1279
- Date: Sat Mar 21 10:24:40 2015 +0900
1280
-
1281
- suppress warning: mismatched indentations at 'end' with 'class'
1282
-
1283
- lib/bio/db/phyloxml/phyloxml_elements.rb | 4 ++--
1284
- 1 file changed, 2 insertions(+), 2 deletions(-)
1285
-
1286
- commit ee4ffdc748c1f9f45e97ff7f0da8350c5468c333
1287
- Author: Naohisa Goto <ng@bioruby.org>
1288
- Date: Sat Mar 21 10:08:30 2015 +0900
1289
-
1290
- delete obsolete $Id:$ line
1291
-
1292
- lib/bio/db/phyloxml/phyloxml_parser.rb | 1 -
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- 1 file changed, 1 deletion(-)
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-
1295
- commit 46a4edc8729ff836ae28d11f1503c9923275b9f6
1296
- Author: Naohisa Goto <ng@bioruby.org>
1297
- Date: Sat Mar 21 10:00:04 2015 +0900
1298
-
1299
- Ruby 1.9 support: suppress warning "shadowing outer local variable - flag"
1300
-
1301
- lib/bio/db/phyloxml/phyloxml_parser.rb | 2 +-
1302
- 1 file changed, 1 insertion(+), 1 deletion(-)
1303
-
1304
- commit db3552c683edf79adbfa5ed897f5ef91e8417585
1305
- Author: Naohisa Goto <ng@bioruby.org>
1306
- Date: Fri Mar 20 16:33:45 2015 +0900
1307
-
1308
- Bug fix: Bio::PhyloXML::Parser.open_uri did not return block return value
1309
-
1310
- * Bug fix: Bio::PhyloXML::Parser.open_uri did not return block
1311
- return value when giving block.
1312
- * Suppress warning "assigned but unused variable - ret"
1313
-
1314
- lib/bio/db/phyloxml/phyloxml_parser.rb | 1 +
1315
- 1 file changed, 1 insertion(+)
1316
-
1317
- commit 84c2c4e94352cc9cef982d3b505b4f439617e01e
1318
- Author: Naohisa Goto <ng@bioruby.org>
1319
- Date: Fri Mar 20 16:21:49 2015 +0900
1320
-
1321
- delete obsolete $Id:$ line
1322
-
1323
- lib/bio/appl/genscan/report.rb | 1 -
1324
- 1 file changed, 1 deletion(-)
1325
-
1326
- commit 05c55d0aaf1dc130ac04155622ccebb3394fc3c0
1327
- Author: Naohisa Goto <ng@bioruby.org>
1328
- Date: Fri Mar 20 16:21:06 2015 +0900
1329
-
1330
- Ruby 1.9 support: suppress warning "shadowing outer local variable - i"
1331
-
1332
- lib/bio/appl/genscan/report.rb | 2 +-
1333
- 1 file changed, 1 insertion(+), 1 deletion(-)
1334
-
1335
- commit 5edcc1c97ca7c292fa6551509570daf68ac36837
1336
- Author: Naohisa Goto <ng@bioruby.org>
1337
- Date: Fri Mar 20 16:13:57 2015 +0900
1338
-
1339
- Ruby 1.9 support: suppress warning "shadowing outer local variable - y"
1340
-
1341
- lib/bio/appl/blast/format0.rb | 2 +-
1342
- 1 file changed, 1 insertion(+), 1 deletion(-)
1343
-
1344
- commit 813d53a06258244a47784697e8fc95f1f15db8da
1345
- Author: Naohisa Goto <ng@bioruby.org>
1346
- Date: Fri Mar 20 16:03:19 2015 +0900
1347
-
1348
- delete obsolete $Id:$ line
1349
-
1350
- lib/bio/io/das.rb | 1 -
1351
- 1 file changed, 1 deletion(-)
1352
-
1353
- commit b6ae4a423dd763969c8e18ca6a578fd0600d6159
1354
- Author: Naohisa Goto <ng@bioruby.org>
1355
- Date: Fri Mar 20 16:02:20 2015 +0900
1356
-
1357
- Ruby 1.9 support: suppress "warning: shadowing outer local variable - e"
1358
-
1359
- lib/bio/io/das.rb | 80 +++++++++++++++++++++++++++----------------------------
1360
- 1 file changed, 40 insertions(+), 40 deletions(-)
1361
-
1362
- commit 7fa75a644167dd8c189f681e29c1cf5f1bf2fe0b
1363
- Author: Naohisa Goto <ng@bioruby.org>
1364
- Date: Fri Mar 20 15:36:00 2015 +0900
1365
-
1366
- delete obsolete $Id:$ line
1367
-
1368
- lib/bio/shell/plugin/seq.rb | 1 -
1369
- 1 file changed, 1 deletion(-)
1370
-
1371
- commit 051aba1519d71f1205363c4421feb6c06881ab0c
1372
- Author: Naohisa Goto <ng@bioruby.org>
1373
- Date: Fri Mar 20 15:29:02 2015 +0900
1374
-
1375
- Bug fix: Ruby 1.9 support: did not yield the last part of the string
1376
-
1377
- * lib/bio/shell/plugin/seq.rb: Bug fix: Ruby 1.9 support:
1378
- String#step and #skip (extended by bioruby-shell) did not yield
1379
- the last part of the string due to a change from Ruby 1.8 to 1.9.
1380
- * Suppress warning message "shadowing outer local variable - i"
1381
-
1382
- lib/bio/shell/plugin/seq.rb | 12 +++++++-----
1383
- 1 file changed, 7 insertions(+), 5 deletions(-)
1384
-
1385
- commit a9f2bff92de58c2ab4cefc67e721d3ad69e9de98
1386
- Author: Naohisa Goto <ng@bioruby.org>
1387
- Date: Fri Mar 20 15:09:16 2015 +0900
1388
-
1389
- Ruby 2.2 support: suppress a "shadowing outer local variable" warning
1390
-
1391
- lib/bio/alignment.rb | 6 +++---
1392
- 1 file changed, 3 insertions(+), 3 deletions(-)
1393
-
1394
- commit d0bcc8766d91eb7cacea2a6d5b32b3e0b3c5ce56
1395
- Author: Naohisa Goto <ng@bioruby.org>
1396
- Date: Fri Mar 20 14:31:04 2015 +0900
1397
-
1398
- delete obsolete $Id:$ line
1399
-
1400
- test/unit/bio/test_alignment.rb | 1 -
1401
- 1 file changed, 1 deletion(-)
1402
-
1403
- commit 0c8fa8fd558088822a98e11b6fa4bec9b37ebec7
1404
- Author: Naohisa Goto <ng@bioruby.org>
1405
- Date: Fri Mar 20 14:26:38 2015 +0900
1406
-
1407
- Ruby 2.2 support: comment out duplicated line to suppress warning
1408
-
1409
- * Ruby 2.2 support: test/unit/bio/test_alignment.rb:
1410
- Suppress warning: duplicated key at line 182 ignored: "t"
1411
-
1412
- test/unit/bio/test_alignment.rb | 2 +-
1413
- 1 file changed, 1 insertion(+), 1 deletion(-)
1414
-
1415
- commit ab17c40e1ce492dc924205e8e2f90d31adae4464
1416
- Author: Naohisa Goto <ng@bioruby.org>
1417
- Date: Fri Mar 20 14:18:08 2015 +0900
1418
-
1419
- Ruby 2.2 support: some tests did not run with test-unit gem
1420
-
1421
- * Ruby 2.2 support: test/unit/bio/db/test_fastq.rb
1422
- Support for test-unit gem bundled in Ruby 2.2.
1423
- See commit log b9488a64abb780c5e9b6cd28e8264bad399fa749 for details.
1424
-
1425
- test/unit/bio/db/test_fastq.rb | 18 ++++++++++++++----
1426
- 1 file changed, 14 insertions(+), 4 deletions(-)
1427
-
1428
- commit ea668d73c18e3df33625cba4352ad5f6966e0eb4
1429
- Author: Naohisa Goto <ng@bioruby.org>
1430
- Date: Fri Mar 20 14:03:43 2015 +0900
1431
-
1432
- delete obsolete $Id:$ line
1433
-
1434
- test/unit/bio/appl/sim4/test_report.rb | 1 -
1435
- 1 file changed, 1 deletion(-)
1436
-
1437
- commit 1abb8d362a0f2443b48923bcccba3d7d0caa1f1d
1438
- Author: Naohisa Goto <ng@bioruby.org>
1439
- Date: Fri Mar 20 13:57:33 2015 +0900
1440
-
1441
- Ruby 2.2 support: some tests did not run with test-unit gem
1442
-
1443
- * Ruby 2.2 support: test/unit/bio/appl/sim4/test_report.rb
1444
- Support for test-unit gem bundled in Ruby 2.2.
1445
- See commit log b9488a64abb780c5e9b6cd28e8264bad399fa749 for details.
1446
-
1447
- test/unit/bio/appl/sim4/test_report.rb | 62 +++++++++++++++++++++++++---------
1448
- 1 file changed, 46 insertions(+), 16 deletions(-)
1449
-
1450
- commit b9488a64abb780c5e9b6cd28e8264bad399fa749
1451
- Author: Naohisa Goto <ng@bioruby.org>
1452
- Date: Fri Mar 20 13:13:28 2015 +0900
1453
-
1454
- Ruby 2.2 support: some tests did not run with test-unit gem
1455
-
1456
- * Ruby 2.2 support: test/unit/bio/appl/blast/test_report.rb:
1457
- With test-unit gem bundled in Ruby 2.2, test methods inherited
1458
- from a parent class and executed in the parent class do not
1459
- run in the child class. To avoid the behavior, test methods
1460
- are moved to modules and test classes are changed to include
1461
- the modules.
1462
-
1463
- test/unit/bio/appl/blast/test_report.rb | 156 ++++++++++++++++++++++----------
1464
- 1 file changed, 110 insertions(+), 46 deletions(-)
1465
-
1466
- commit febe8bbf614e530f597d7306d33df5f5f4ee6699
1467
- Author: Naohisa Goto <ng@bioruby.org>
1468
- Date: Thu Mar 19 00:55:09 2015 +0900
1469
-
1470
- try to use bio-old-biofetch-emulator gem
1471
-
1472
- * bin/br_biofetch.rb: try to use bio-old-biofetch-emulator gem.
1473
- Without bio-old-biofetch-emulator, the program exits with error
1474
- message when default BioRuby BioFetch server is specified.
1475
-
1476
- bin/br_biofetch.rb | 19 +++++++++++++++++++
1477
- 1 file changed, 19 insertions(+)
1478
-
1479
- commit 08450e0a35cbf5596dd30238d23aa7a7296c8f67
1480
- Author: Naohisa Goto <ng@bioruby.org>
1481
- Date: Thu Mar 19 00:36:10 2015 +0900
1482
-
1483
- do not repeat default_url and another_url
1484
-
1485
- bin/br_biofetch.rb | 14 ++++++++++----
1486
- 1 file changed, 10 insertions(+), 4 deletions(-)
1487
-
1488
- commit 8e39d3411405b09cc6ea55ba31e5206536ebf59d
1489
- Author: Naohisa Goto <ng@bioruby.org>
1490
- Date: Wed Mar 18 23:57:59 2015 +0900
1491
-
1492
- Revert e29fc5fadbe0dae6528cf49637496dc2df3ec0dc
1493
-
1494
- * bin/br_biofetch.rb: revert e29fc5fadbe0dae6528cf49637496dc2df3ec0dc
1495
- because the old deprecated bioruby biofetch server can be emulated
1496
- by bio-old-biofetch-emulator gem package.
1497
-
1498
- bin/br_biofetch.rb | 15 ++++++++-------
1499
- 1 file changed, 8 insertions(+), 7 deletions(-)
1500
-
1501
- commit 849c38931a64b7ff2ba7ec46a495e65a99a869fb
1502
- Author: Ben J. Woodcroft <donttrustben near gmail.com>
1503
- Date: Wed Aug 8 09:44:09 2012 +1000
1504
-
1505
- add FastaFormat#first_name method
1506
-
1507
- lib/bio/db/fasta.rb | 17 +++++++++++++++++
1508
- test/unit/bio/db/test_fasta.rb | 42 +++++++++++++++++++++++++++++++++++++++++-
1509
- 2 files changed, 58 insertions(+), 1 deletion(-)
1510
-
1511
- commit 888a70508c0392cae89021feba5c4a6a62228a11
1512
- Author: Naohisa Goto <ng@bioruby.org>
1513
- Date: Fri Nov 14 15:08:35 2014 +0900
1514
-
1515
- fix typo
1516
-
1517
- * fix typo. Thanks to Iain Barnett who reported the bug in
1518
- https://github.com/bioruby/bioruby/pull/93
1519
- (c4843d65447f6a434da523c9c313f34d025f36f8)
1520
-
1521
- lib/bio/sequence/compat.rb | 2 +-
1522
- 1 file changed, 1 insertion(+), 1 deletion(-)
1523
-
1524
- commit afc6df190109649e8eb11b2af1184ddfcf5327d3
1525
- Author: Naohisa Goto <ng@bioruby.org>
1526
- Date: Fri Nov 14 14:29:42 2014 +0900
1527
-
1528
- add documentation when gc_percent is not enough
1529
-
1530
- lib/bio/sequence/na.rb | 8 ++++++++
1531
- 1 file changed, 8 insertions(+)
1532
-
1533
- commit bb63f67f2dfe6dba5c70ada033ca0cc1ecaa7783
1534
- Author: Naohisa Goto <ng@bioruby.org>
1535
- Date: Thu Nov 13 21:43:00 2014 +0900
1536
-
1537
- Add tests for Bio::PubMed#search, query, pmfetch
1538
-
1539
- * Add tests for Bio::PubMed#search, query, pmfetch, although
1540
- they will be deprecated in the future.
1541
- * This commit and commit bfe4292c51bba5c4032027c36c35e98f28a9605a
1542
- are inspired by https://github.com/bioruby/bioruby/pull/76
1543
- (though the pull request have not been merged), and the commits
1544
- fix the issue https://github.com/bioruby/bioruby/issues/75.
1545
- Thanks to Paul Leader who reported the issue and the pull request.
1546
-
1547
- test/network/bio/io/test_pubmed.rb | 49 ++++++++++++++++++++++++++++++++++++++
1548
- 1 file changed, 49 insertions(+)
1549
-
1550
- commit 74edba100da83c27f2edb7a9edc9ec98265a7cff
1551
- Author: Naohisa Goto <ng@bioruby.org>
1552
- Date: Thu Nov 13 12:05:12 2014 +0900
1553
-
1554
- Change default tool and email values
1555
-
1556
- * Default "tool" and "email" values are changed to "bioruby" and
1557
- "staff@bioruby.org" respectively. Now, the author of a script
1558
- do not need to set his/her email address unless the script makes
1559
- excess traffic to NCBI.
1560
- * Update RDoc documentation
1561
-
1562
- lib/bio/io/ncbirest.rb | 48 +++++++++++++++++++++++++++++++++++++++++++-----
1563
- 1 file changed, 43 insertions(+), 5 deletions(-)
1564
-
1565
- commit bfe4292c51bba5c4032027c36c35e98f28a9605a
1566
- Author: Naohisa Goto <ng@bioruby.org>
1567
- Date: Thu Nov 13 11:54:53 2014 +0900
1568
-
1569
- Bug fix: use NCBI E-Utilities instead of old deprecated API
1570
-
1571
- * Bio::PubMed#search, query, pmfetch: remove old code using deprecated
1572
- and/or unofficial web API, and change use esearch or efetch methods
1573
- which use NCBI E-utilities. These methods will be deprecated in the
1574
- future. To indicate this, show warning message if $VERBOSE is true.
1575
- * Update RDoc documentation
1576
-
1577
- lib/bio/io/pubmed.rb | 157 +++++++++++++++++++++++++--------------------------
1578
- 1 file changed, 76 insertions(+), 81 deletions(-)
1579
-
1580
- commit d78173a6eb6d8177e733decc0b8137fac067aa82
1581
- Author: Naohisa Goto <ng@bioruby.org>
1582
- Date: Tue Nov 11 17:41:32 2014 +0900
1583
-
1584
- remove unused $Id:$ line
1585
-
1586
- bin/br_biofetch.rb | 1 -
1587
- 1 file changed, 1 deletion(-)
1588
-
1589
- commit e29fc5fadbe0dae6528cf49637496dc2df3ec0dc
1590
- Author: Naohisa Goto <ng@bioruby.org>
1591
- Date: Tue Nov 11 17:31:38 2014 +0900
1592
-
1593
- Change default server to EBI Dbfetch server; remove BioRuby BioFetch server
1594
-
1595
- * Change default server to EBI Dbfetch server.
1596
- * The BioRuby BioFetch server is removed. When "-r" option (force to use
1597
- BioRuby server) is specified, warning message is shown, and the program
1598
- exits with code 1 (abnormal exit).
1599
- * Usage message is also changed.
1600
-
1601
- bin/br_biofetch.rb | 15 +++++++--------
1602
- 1 file changed, 7 insertions(+), 8 deletions(-)
1603
-
1604
- commit 94ecac33e87e444d9fe991340c2d8f3709bc6d90
1605
- Author: Naohisa Goto <ng@bioruby.org>
1606
- Date: Tue Nov 11 17:19:30 2014 +0900
1607
-
1608
- fix documentation reflecting recent changes of Bio::Fetch
1609
-
1610
- lib/bio/io/fetch.rb | 33 ++++++++++++++++++++-------------
1611
- 1 file changed, 20 insertions(+), 13 deletions(-)
1612
-
1613
- commit 06a9db014614818ef35108928415ef18e8c8ae2c
1614
- Author: Naohisa Goto <ng@bioruby.org>
1615
- Date: Tue Nov 11 16:41:26 2014 +0900
1616
-
1617
- documentation about incompatible changes of Bio::Fetch
1618
-
1619
- RELEASE_NOTES.rdoc | 22 ++++++++++++++++++++++
1620
- 1 file changed, 22 insertions(+)
1621
-
1622
- commit 6d94e949b6d325f27b45b816a8305f828d049ec6
1623
- Author: Naohisa Goto <ng@bioruby.org>
1624
- Date: Tue Nov 11 16:35:50 2014 +0900
1625
-
1626
- Issue about Bio::Fetch and BioRuby BioFetch server is resolved
1627
-
1628
- * Issue about Bio::Fetch is resolved by recent commits.
1629
-
1630
- * The BioRuby BioFetch server is deprecated. There is no hope to restart
1631
- the service again. EBI Dbfetch server is an alternative.
1632
-
1633
- KNOWN_ISSUES.rdoc | 9 ---------
1634
- 1 file changed, 9 deletions(-)
1635
-
1636
- commit 699cd3ff136310a551d30e0ddd7fbe66e483b5be
1637
- Author: Naohisa Goto <ng@bioruby.org>
1638
- Date: Tue Nov 11 15:27:11 2014 +0900
1639
-
1640
- update RDoc documents for Bio::Fetch
1641
-
1642
- lib/bio/io/fetch.rb | 61 +++++++++++++++++++++++++++++++++++------------------
1643
- 1 file changed, 40 insertions(+), 21 deletions(-)
1644
-
1645
- commit c7837f8e5ee2cc1c3085da74567a2b25280bbb8f
1646
- Author: Naohisa Goto <ng@bioruby.org>
1647
- Date: Tue Nov 11 14:48:48 2014 +0900
1648
-
1649
- Incompatibile change: remove Bio::Fetch.query; add Bio::Fetch::EBI.query
1650
-
1651
- * Incompatible change: remove a class method Bio::Fetch.query because
1652
- default server URL in Bio::Fetch is deprecated.
1653
-
1654
- * New class method: Bio::Fetch::EBI.query. This can be used as an
1655
- alternative method of deprecated Bio::Fetch.query method.
1656
-
1657
- lib/bio/io/fetch.rb | 35 ++++++++++++++++++-----------------
1658
- 1 file changed, 18 insertions(+), 17 deletions(-)
1659
-
1660
- commit f9048684acaff0fcd00b458a946d5f692706325b
1661
- Author: Naohisa Goto <ng@bioruby.org>
1662
- Date: Tue Nov 11 14:24:22 2014 +0900
1663
-
1664
- Incompatible change: Default server in Bio::Fetch.new is deperecated
1665
-
1666
- * Incompatible change: Default server URL in Bio::Fetch.new is deprecated.
1667
- Users must explicitly specify the URL. Alternatively, users must change
1668
- their code to use Bio::Fetch::EBI.
1669
-
1670
- * New class Bio::Fetch::EBI, EBI Dbfetch client. This acts the same as
1671
- Bio::Fetch.new(Bio::Fetch::EBI::URL) with default database name
1672
- "ena_sequence".
1673
-
1674
- lib/bio/io/fetch.rb | 36 +++++++++++++++++++++++++++++++++---
1675
- 1 file changed, 33 insertions(+), 3 deletions(-)
1676
-
1677
- commit e8919f4f57fc545ca194bebb08c11159b36071cb
1678
- Author: Naohisa Goto <ng@bioruby.org>
1679
- Date: Tue Nov 11 13:43:28 2014 +0900
1680
-
1681
- removed unused variables
1682
-
1683
- lib/bio/io/fetch.rb | 1 -
1684
- 1 file changed, 1 deletion(-)
1685
-
1686
- commit faec95656b846a7a17cd6a1dbc633dda63cb5b6e
1687
- Author: Naohisa Goto <ng@bioruby.org>
1688
- Date: Tue Nov 11 11:44:00 2014 +0900
1689
-
1690
- Updated URL of EMBL-EBI Dbfetch
1691
-
1692
- lib/bio/io/fetch.rb | 2 +-
1693
- 1 file changed, 1 insertion(+), 1 deletion(-)
1694
-
1695
- commit 85be893655f68aafbf7e13badd20bf7f26cd7328
1696
- Author: Jose Irizarry <protechpr@gmail.com>
1697
- Date: Mon Dec 24 12:30:55 2012 -0400
1698
-
1699
- Update lib/bio/io/fetch.rb
1700
-
1701
- Use EBI's dbfetch endpoint as default since BioRuby's endpoint has been disabled for a while now.
1702
-
1703
- lib/bio/io/fetch.rb | 2 +-
1704
- 1 file changed, 1 insertion(+), 1 deletion(-)
1705
-
1706
- commit 163cc06547beed653e19b8c6e71e829d85f2f99c
1707
- Author: Naohisa Goto <ng@bioruby.org>
1708
- Date: Tue Oct 21 16:42:30 2014 +0900
1709
-
1710
- Doc bug fix: wrong sample code
1711
-
1712
- lib/bio/appl/paml/codeml.rb | 4 ++--
1713
- 1 file changed, 2 insertions(+), 2 deletions(-)
1714
-
1715
- commit 97143139d2d4a66366576a8e62518e93fa5afccf
1716
- Author: Naohisa Goto <ng@bioruby.org>
1717
- Date: Tue Oct 21 15:47:52 2014 +0900
1718
-
1719
- Prevent to repeat calculations of total bases
1720
-
1721
- * Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Prevent to
1722
- repeat calculations of total bases.
1723
-
1724
- lib/bio/sequence/na.rb | 20 ++++++++++++--------
1725
- 1 file changed, 12 insertions(+), 8 deletions(-)
1726
-
1727
- commit b5dbd882e000842fef65e10290b379bfafdddf06
1728
- Author: Naohisa Goto <ng@bioruby.org>
1729
- Date: Tue Oct 21 15:41:13 2014 +0900
1730
-
1731
- Documentation bug fix: Return value is Rational or Float.
1732
-
1733
- * Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Return value
1734
- is Rational or Float in recent versions of Ruby. Documentation added for
1735
- the treatment of "u" and to return 0.0 if there are no bases.
1736
- Reported by ctSkennerton (https://github.com/bioruby/bioruby/issues/73 ).
1737
-
1738
- lib/bio/sequence/na.rb | 47 +++++++++++++++++++++++++++++++++++++++++++----
1739
- 1 file changed, 43 insertions(+), 4 deletions(-)
1740
-
1741
- commit 3ba98d52ce57488e604dd7ac388a874e5b40ae9d
1742
- Author: Naohisa Goto <ng@bioruby.org>
1743
- Date: Tue Aug 12 00:58:38 2014 +0900
1744
-
1745
- regenerate bioruby.gemspec with rake regemspec
1746
-
1747
- bioruby.gemspec | 14 ++++++--------
1748
- 1 file changed, 6 insertions(+), 8 deletions(-)
1749
-
1750
- commit a9724d339582952b40c928beccf91376d4e63315
1751
- Author: Naohisa Goto <ng@bioruby.org>
1752
- Date: Tue Aug 5 19:20:42 2014 +0900
1753
-
1754
- Update URIs
1755
-
1756
- * Update URIs.
1757
- * Remove links to RubyForge and RAA which have already been closed.
1758
- * Add some words for Ruby 1.9 or later.
1759
-
1760
- README.rdoc | 24 +++++++++++-------------
1761
- 1 file changed, 11 insertions(+), 13 deletions(-)
1762
-
1763
- commit 5f3569faaf89ebcd2b2cf9cbe6b3c1f0544b2679
1764
- Author: Iain Barnett <iainspeed@gmail.com>
1765
- Date: Wed Mar 5 02:11:07 2014 +0000
1766
-
1767
- Refactor Bio::AminoAcid#weight: Early return clearer and idiomatic.
1768
-
1769
- lib/bio/data/aa.rb | 26 ++++++++++++--------------
1770
- 1 file changed, 12 insertions(+), 14 deletions(-)
1771
-
1772
- commit c229a20887fcb6df9a7ba49ad5a23e175056fa8d
1773
- Author: Iain Barnett <iainspeed@gmail.com>
1774
- Date: Wed Mar 5 02:02:45 2014 +0000
1775
-
1776
- Fixed the stack level too deep errors by using Hash#invert.
1777
-
1778
- lib/bio/data/aa.rb | 18 +-----------------
1779
- 1 file changed, 1 insertion(+), 17 deletions(-)
1780
-
1781
- commit 08dd928df30f5b39c255f9f70dbed8410d395cdf
1782
- Author: Iain Barnett <iainspeed@gmail.com>
1783
- Date: Tue Mar 4 01:22:51 2014 +0000
1784
-
1785
- Refactored to shorten, remove rescues, and clarify.
1786
-
1787
- lib/bio/alignment.rb | 19 +++++++------------
1788
- 1 file changed, 7 insertions(+), 12 deletions(-)
1789
-
1790
- commit 112aa284cb1ebecc1d5de186edf2b385649a7268
1791
- Author: Naohisa Goto <ng@bioruby.org>
1792
- Date: Wed Mar 19 14:48:32 2014 +0900
1793
-
1794
- Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008)
1795
-
1796
- * Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008).
1797
- Thanks to a researcher who reports the patch via email.
1798
-
1799
- lib/bio/db/pdb/pdb.rb | 4 ++--
1800
- 1 file changed, 2 insertions(+), 2 deletions(-)
1801
-
1802
- commit ecd5e0c86b04aa918b71c859568425fa39ebbde5
1803
- Author: Naohisa Goto <ng@bioruby.org>
1804
- Date: Sat Jan 18 04:22:51 2014 +0900
1805
-
1806
- suppress "source :rubygems is deprecated" warning
1807
-
1808
- gemfiles/Gemfile.travis-jruby1.8 | 2 +-
1809
- gemfiles/Gemfile.travis-jruby1.9 | 2 +-
1810
- gemfiles/Gemfile.travis-ruby1.8 | 2 +-
1811
- gemfiles/Gemfile.travis-ruby1.9 | 2 +-
1812
- 4 files changed, 4 insertions(+), 4 deletions(-)
1813
-
1814
- commit 4bda345fe3de9cf1b64c26f3dca1cb3727c946d0
1815
- Author: Naohisa Goto <ng@bioruby.org>
1816
- Date: Sat Jan 18 04:22:03 2014 +0900
1817
-
1818
- gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci
1819
-
1820
- * gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci
1821
- * .travis.yml is modified to use gemfile/Gemfile.travis-rbx for rbx.
1822
-
1823
- .travis.yml | 4 ++--
1824
- gemfiles/Gemfile.travis-rbx | 16 ++++++++++++++++
1825
- 2 files changed, 18 insertions(+), 2 deletions(-)
1826
- create mode 100644 gemfiles/Gemfile.travis-rbx
1827
-
1828
- commit dcff544d6d0a967eb853b97ba9faa30eaa6fd9dc
1829
- Author: Naohisa Goto <ng@bioruby.org>
1830
- Date: Sat Jan 18 04:13:50 2014 +0900
1831
-
1832
- .travis.yml: fix mistakes
1833
-
1834
- .travis.yml | 8 +-------
1835
- 1 file changed, 1 insertion(+), 7 deletions(-)
1836
-
1837
- commit f0f67f295f05a5e1e30c479621c25498e2c8f6f2
1838
- Author: Naohisa Goto <ng@bioruby.org>
1839
- Date: Sat Jan 18 03:56:54 2014 +0900
1840
-
1841
- Ruby 2.1 workaround: Array#uniq does not always choose the first item
1842
-
1843
- * Ruby 2.1 workaround: Array#uniq does not always choose the first item.
1844
- Thanks to Andrew Grimm who reported the issue.
1845
- (https://github.com/bioruby/bioruby/issues/92 )
1846
- Note that the behavior change is also regarded as a bug in Ruby and
1847
- is fixed. (https://bugs.ruby-lang.org/issues/9340 )
1848
-
1849
- test/unit/bio/test_pathway.rb | 35 +++++++++++++++++++++++++----------
1850
- 1 file changed, 25 insertions(+), 10 deletions(-)
1851
-
1852
- commit e92e09edf5904f51d3e73e61d13fce4159a543c5
1853
- Author: Naohisa Goto <ng@bioruby.org>
1854
- Date: Sat Jan 18 03:32:05 2014 +0900
1855
-
1856
- .travis.yml: workaround to avoid error in Ruby 1.8.7 and jruby-18mode
1857
-
1858
- * workaround to avoid error in Ruby 1.8.7 and jruby-18mode
1859
- (reference: https://github.com/rubygems/rubygems/pull/763 )
1860
-
1861
- .travis.yml | 2 ++
1862
- 1 file changed, 2 insertions(+)
1863
-
1864
- commit 655a675096962710896fb458afcac9b5deb1fa5f
1865
- Author: Naohisa Goto <ng@bioruby.org>
1866
- Date: Sat Jan 18 03:22:44 2014 +0900
1867
-
1868
- .travis.yml: rbx version is changed to 2.2.3
1869
-
1870
- * rbx version is changed to 2.2.3
1871
- * add dependent gems for rbx platforms, described in
1872
- http://docs.travis-ci.com/user/languages/ruby/
1873
-
1874
- .travis.yml | 7 ++++++-
1875
- 1 file changed, 6 insertions(+), 1 deletion(-)
1876
-
1877
- commit d2f5b882d5e2acf35d0c783a56aa47533b9f2bd5
1878
- Author: Naohisa Goto <ng@bioruby.org>
1879
- Date: Sat Jan 11 03:46:45 2014 +0900
1880
-
1881
- .travis.yml: change ruby versions for tar and gem integration tests
1882
-
1883
- * In tar and gem integration tests, Ruby versions are changed to
1884
- MRI 2.0.0 and jruby-19mode.
1885
- * Add jruby-18mode
1886
- * Add rbx-2.1.1
1887
-
1888
- .travis.yml | 32 ++++++++++++++++++++++----------
1889
- 1 file changed, 22 insertions(+), 10 deletions(-)
1890
-
1891
- commit 71991af394b937d35e2bbbc84a21e65ffba7714d
1892
- Author: Naohisa Goto <ng@bioruby.org>
1893
- Date: Thu Jan 9 00:57:25 2014 +0900
1894
-
1895
- .travis.yml: Add 2.1.0 and 2.0.0, remove rbx-XXmode
1896
-
1897
- * Add 2.1.0 and 2.0.0
1898
- * Remove rbx-18mode and rbx-19mode
1899
- * 1.9.2 is moved from "include" to "rvm".
1900
- * 1.8.7 is moved from "rvm" to "include", and remove
1901
- "gemfiles/Gemfile.travis-ruby1.8" line from "gemfile".
1902
- * Remove "exclude" and simplify build matrix.
1903
- * Suggested by agrimm in https://github.com/bioruby/bioruby/pull/91
1904
-
1905
- .travis.yml | 27 +++++----------------------
1906
- 1 file changed, 5 insertions(+), 22 deletions(-)
1907
-
1908
- commit 80966bc875cc6e01978b6c9272f6ddd8f344aa62
1909
- Author: Brynjar Smari Bjarnason <binni@binnisb.com>
1910
- Date: Mon Dec 9 14:57:42 2013 +0100
1911
-
1912
- Bug fix: Only do gsub on bio_ref.reference.authors if it exists.
1913
-
1914
- * Bug fix: Only do gsub on bio_ref.reference.authors if it exists.
1915
- Fix https://github.com/bioruby/bioruby/issues/89
1916
-
1917
- lib/bio/db/biosql/sequence.rb | 2 +-
1918
- 1 file changed, 1 insertion(+), 1 deletion(-)
1919
-
1920
- commit 3337bbd3be2affcef44202a0c924b3e22dafd856
1921
- Author: Brynjar Smari Bjarnason <binni@binnisb.com>
1922
- Date: Mon Dec 9 14:55:24 2013 +0100
1923
-
1924
- Bug fix: Missing require when generating genbank output for BioSQL sequence
1925
-
1926
- * Bug fix: Missing require when generating genbank output for BioSQL
1927
- sequence. Partly fix https://github.com/bioruby/bioruby/issues/89
1928
-
1929
- lib/bio/db/biosql/biosql_to_biosequence.rb | 1 +
1930
- 1 file changed, 1 insertion(+)
1931
-
1932
- commit 1f829ae8e8c89c5c24e7bc7aa8ed5fa25e8ef6c2
1933
- Author: Naohisa Goto <ng@bioruby.org>
1934
- Date: Sat Nov 23 18:17:43 2013 +0900
1935
-
1936
- Benchmark example1-seqnos.aln in addition to example1.aln
1937
-
1938
- * sample/benchmark_clustalw_report.rb: Benchmark parsing speed of
1939
- example1-seqnos.aln in addition to example1.aln.
1940
-
1941
- sample/benchmark_clustalw_report.rb | 28 ++++++++++++++++++++++------
1942
- 1 file changed, 22 insertions(+), 6 deletions(-)
1943
-
1944
- commit c5d3e761859fa72c18f9301d84c31070f35e733e
1945
- Author: Andrew Grimm <andrew.j.grimm@gmail.com>
1946
- Date: Tue Sep 17 21:15:56 2013 +1000
1947
-
1948
- Add benchmark script for Bio::ClustalW::Report.
1949
-
1950
- sample/benchmark_clustalw_report.rb | 31 +++++++++++++++++++++++++++++++
1951
- 1 file changed, 31 insertions(+)
1952
- create mode 100644 sample/benchmark_clustalw_report.rb
1953
-
1954
- commit 07c14e94cdb94cf9ba8a2bf050572ae1cbf24cff
1955
- Author: Naohisa Goto <ng@bioruby.org>
1956
- Date: Sat Nov 23 17:49:54 2013 +0900
1957
-
1958
- Bio::ClustalW::Report#do_parse speed optimization
1959
-
1960
- * Bio::ClustalW::Report#do_parse speed optimization. Thanks to
1961
- Andrew Grimm who indicates the optimization point.
1962
- (https://github.com/bioruby/bioruby/pull/86 )
1963
- * "$" in the regular expression is changed to "\z". In this context,
1964
- the "$" was intended to be matched with only the end of the string.
1965
-
1966
- lib/bio/appl/clustalw/report.rb | 4 +++-
1967
- 1 file changed, 3 insertions(+), 1 deletion(-)
1968
-
1969
- commit 6a78028d4f595ecb5b4600d0f238b07a2d80bdd5
1970
- Author: Naohisa Goto <ng@bioruby.org>
1971
- Date: Sat Nov 23 15:52:15 2013 +0900
1972
-
1973
- New test data: ClustalW with -SEQNOS=ON option
1974
-
1975
- * test/data/clustalw/example1-seqnos.aln: New test data: ClustalW
1976
- running with -SEQNOS=ON option.
1977
- * Bio::TestClustalWReport::TestClustalWReportSeqnos: new test class
1978
- that parses the above data.
1979
-
1980
- test/data/clustalw/example1-seqnos.aln | 58 ++++++++++++++++++++++++++++++
1981
- test/unit/bio/appl/clustalw/test_report.rb | 11 ++++++
1982
- 2 files changed, 69 insertions(+)
1983
- create mode 100644 test/data/clustalw/example1-seqnos.aln
1984
-
1985
- commit f5da0bbb4b1639616bb8c63ff8c58840e140ef8b
1986
- Author: Naohisa Goto <ng@bioruby.org>
1987
- Date: Sat Nov 23 15:35:31 2013 +0900
1988
-
1989
- Simplify test data path in setup
1990
-
1991
- * Bio::TestClustalWReport::TestClustalWReport#setup: simplify test data
1992
- filename path.
1993
- * Modify indentes and void lines.
1994
-
1995
- test/unit/bio/appl/clustalw/test_report.rb | 10 +++-------
1996
- 1 file changed, 3 insertions(+), 7 deletions(-)
1997
-
1998
- commit 8f0bea1d3252d0de9e2d91dc31ef8a9552c2d758
1999
- Author: Naohisa Goto <ng@bioruby.org>
2000
- Date: Sat Nov 23 15:21:38 2013 +0900
2001
-
2002
- Common test methods are moved to a module
2003
-
2004
- * New namespace module Bio::TestClustalWReport.
2005
- * Common test methods are moved to CommonTestMethods,
2006
- and test classes using the methods include it.
2007
- * The test_sequences method is split into two methods
2008
- CommonTestMethods#test_sequence0 and test_sequence1.
2009
-
2010
- test/unit/bio/appl/clustalw/test_report.rb | 97 ++++++++++++++++--------------
2011
- 1 file changed, 53 insertions(+), 44 deletions(-)
2012
-
2013
- commit edda65b8fb32c2eee6b0652074981c31aa68b0eb
2014
- Author: Naohisa Goto <ng@bioruby.org>
2015
- Date: Fri Aug 23 23:51:59 2013 +0900
2016
-
2017
- Test bug fix: Read test file with binary mode to avoid encoding error
2018
-
2019
- * Test bug fix: Read test file with binary mode to avoid string encoding
2020
- error. Thanks to nieder (github.com/nieder) who reports the bug.
2021
- (https://github.com/bioruby/bioruby/issues/84)
2022
-
2023
- test/unit/bio/db/test_phyloxml.rb | 2 +-
2024
- 1 file changed, 1 insertion(+), 1 deletion(-)
2025
-
2026
- commit 011d6fe5f016408891c5da3143c83e2564ccbf27
2027
- Author: meso_cacase <y-naito@dbcls.rois.ac.jp>
2028
- Date: Fri Apr 5 01:13:27 2013 +0900
2029
-
2030
- Modified siRNA design rules by Ui-Tei and Reynolds
2031
-
2032
- * Ui-Tei rule: Avoided contiguous GCs 10 nt or more.
2033
- * Reynolds rule: Total score of eight criteria is calculated.
2034
- * Returns numerical score for functional siRNA instead of returning 'true'.
2035
- * Returns 'false' for non-functional siRNA, as usual.
2036
- * Unit tests are modified to reflect these changes.
2037
-
2038
- lib/bio/util/sirna.rb | 92 +++++++++++++++++++++++++++++++++-------
2039
- test/unit/bio/util/test_sirna.rb | 44 +++++++++----------
2040
- 2 files changed, 98 insertions(+), 38 deletions(-)
2041
-
2042
- commit b6e7953108ebf34d61bc79ee4bdae1092cfe339f
2043
- Author: Naohisa Goto <ng@bioruby.org>
2044
- Date: Fri Jun 28 15:40:57 2013 +0900
2045
-
2046
- Use Bio::UniProtKB instead of Bio::UniProt
2047
-
2048
- * Use Bio::UniProtKB instead of Bio::UniProt.
2049
- * Test class names are also changed from UniProt to UniProtKB.
2050
-
2051
- test/unit/bio/db/embl/test_uniprotkb_new_part.rb | 22 +++++++++++-----------
2052
- 1 file changed, 11 insertions(+), 11 deletions(-)
2053
-
2054
- commit cddd35cf8d64abfff8bd6a8372d019fc4c32848c
2055
- Author: Naohisa Goto <ng@bioruby.org>
2056
- Date: Fri Jun 28 15:26:20 2013 +0900
2057
-
2058
- rename test/unit/bio/db/embl/test_uniprot_new_part.rb to test_uniprotkb_new_part.rb
2059
-
2060
- .../bio/db/embl/{test_uniprot_new_part.rb => test_uniprotkb_new_part.rb} | 0
2061
- 1 file changed, 0 insertions(+), 0 deletions(-)
2062
- rename test/unit/bio/db/embl/{test_uniprot_new_part.rb => test_uniprotkb_new_part.rb} (100%)
2063
-
2064
- commit 1b51d0940712a6f144f8268dc77048bc7ec7d983
2065
- Author: Naohisa Goto <ng@bioruby.org>
2066
- Date: Fri Jun 28 15:21:36 2013 +0900
2067
-
2068
- Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB.
2069
-
2070
- * Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB.
2071
- * Test class names are also changed.
2072
-
2073
- test/unit/bio/db/embl/test_uniprotkb.rb | 223 ++++++++++++++++----------------
2074
- 1 file changed, 111 insertions(+), 112 deletions(-)
2075
-
2076
- commit 68494aa862c3495def713e6cad6fc478f223416f
2077
- Author: Naohisa Goto <ng@bioruby.org>
2078
- Date: Fri Jun 28 15:01:15 2013 +0900
2079
-
2080
- test_sptr.rb is renamed to test_uniprotkb.rb
2081
-
2082
- test/unit/bio/db/embl/{test_sptr.rb => test_uniprotkb.rb} | 0
2083
- 1 file changed, 0 insertions(+), 0 deletions(-)
2084
- rename test/unit/bio/db/embl/{test_sptr.rb => test_uniprotkb.rb} (100%)
2085
-
2086
- commit e1ed7fab4c0350e6866dd420a93e950c53063f38
2087
- Author: Naohisa Goto <ng@bioruby.org>
2088
- Date: Fri Jun 28 14:52:08 2013 +0900
2089
-
2090
- Add autoload of Bio::UniProtKB, and modify comments of deprecated classes.
2091
-
2092
- lib/bio.rb | 18 ++++++++++--------
2093
- 1 file changed, 10 insertions(+), 8 deletions(-)
2094
-
2095
- commit 7c78cb1b275a845e215f9a6da67026836efc5807
2096
- Author: Naohisa Goto <ng@bioruby.org>
2097
- Date: Fri Jun 28 14:28:02 2013 +0900
2098
-
2099
- Bio::SwissProt and Bio::TrEMBL are deprecated
2100
-
2101
- * Bio::SwissProt and Bio::TrEMBL are deprecated.
2102
- * Show warning messages when using these classes.
2103
-
2104
- lib/bio/db/embl/swissprot.rb | 41 ++++++++++++-----------------------------
2105
- lib/bio/db/embl/trembl.rb | 43 +++++++++++++------------------------------
2106
- 2 files changed, 25 insertions(+), 59 deletions(-)
2107
-
2108
- commit b998ad13849ff7f1d69ed0c640a2e1bafe3fc957
2109
- Author: Naohisa Goto <ng@bioruby.org>
2110
- Date: Fri Jun 28 14:27:36 2013 +0900
2111
-
2112
- Bio::UniProt is changed to be an alias of Bio::UniProtKB.
2113
-
2114
- lib/bio/db/embl/uniprot.rb | 41 ++++++++++++-----------------------------
2115
- 1 file changed, 12 insertions(+), 29 deletions(-)
2116
-
2117
- commit f46324e2fb6a2bc3e4680c8064dc0fc3d89e6f24
2118
- Author: Naohisa Goto <ng@bioruby.org>
2119
- Date: Fri Jun 28 14:21:56 2013 +0900
2120
-
2121
- Bio::SPTR is renamed as Bio::UniProtKB and changed to an alias
2122
-
2123
- * Bio::SPTR is renamed to Bio::UniProtKB.
2124
- * For older programs which use Bio::SPTR, set Bio::SPTR as an alias of
2125
- Bio::UniProtKB.
2126
-
2127
- lib/bio/db/embl/sptr.rb | 20 ++++++
2128
- lib/bio/db/embl/uniprotkb.rb | 147 +++++++++++++++++++++----------------------
2129
- 2 files changed, 93 insertions(+), 74 deletions(-)
2130
- create mode 100644 lib/bio/db/embl/sptr.rb
2131
-
2132
- commit 70816d90a6ef290c7ca7f50d492e7c4f836aadd8
2133
- Author: Naohisa Goto <ng@bioruby.org>
2134
- Date: Thu Jun 27 18:16:38 2013 +0900
2135
-
2136
- Rename lib/bio/db/embl/sptr.rb to uniprotkb.rb
2137
-
2138
- lib/bio/db/embl/{sptr.rb => uniprotkb.rb} | 0
2139
- 1 file changed, 0 insertions(+), 0 deletions(-)
2140
- rename lib/bio/db/embl/{sptr.rb => uniprotkb.rb} (100%)
2141
-
2142
- commit 2a10ded8e1502e0db5ec3b2e060f658ee53aafd0
2143
- Author: Naohisa Goto <ng@bioruby.org>
2144
- Date: Thu Jun 27 16:36:58 2013 +0900
2145
-
2146
- Bio::RefSeq and Bio::DDBJ are deprecated. Show warnings.
2147
-
2148
- * Bio::RefSeq and Bio::DDBJ are deprecated because they were only
2149
- an alias of Bio::GenBank. Please use Bio::GenBank instead.
2150
- * Show warning message when loading the classes and initializing
2151
- a new instance.
2152
- * Changed to require genbank.rb only when GenBank is not defined.
2153
- This might reduce the possibility of circular require.
2154
-
2155
- lib/bio/db/genbank/ddbj.rb | 11 +++++++++--
2156
- lib/bio/db/genbank/refseq.rb | 14 +++++++++++---
2157
- 2 files changed, 20 insertions(+), 5 deletions(-)
2158
-
2159
- commit 118d0bff58b48f69505eef5dcc2f961ac6e0d9de
2160
- Author: Naohisa Goto <ng@bioruby.org>
2161
- Date: Thu Jun 27 16:08:55 2013 +0900
2162
-
2163
- Remove descriptions about DDBJ Web API (WABI)
2164
-
2165
- KNOWN_ISSUES.rdoc | 8 --------
2166
- 1 file changed, 8 deletions(-)
2167
-
2168
- commit fe8f976c7ced4d525a4eabd728269f71326cf001
2169
- Author: Naohisa Goto <ng@bioruby.org>
2170
- Date: Thu Jun 27 13:41:19 2013 +0900
2171
-
2172
- Remove ddbjsoap method that uses Bio::DDBJ::XML
2173
-
2174
- lib/bio/shell/plugin/soap.rb | 28 ----------------------------
2175
- 1 file changed, 28 deletions(-)
2176
-
2177
- commit 54bef3fc48bb48eb198537a9fba6379f33f036cc
2178
- Author: Naohisa Goto <ng@bioruby.org>
2179
- Date: Thu Jun 27 13:39:42 2013 +0900
2180
-
2181
- Remove Bio::Blast::Remote::DDBJ from the comment line
2182
-
2183
- test/network/bio/appl/blast/test_remote.rb | 2 +-
2184
- 1 file changed, 1 insertion(+), 1 deletion(-)
2185
-
2186
- commit a7c5a656dab1bb8ada6b36ec003a89aec9e26671
2187
- Author: Naohisa Goto <ng@bioruby.org>
2188
- Date: Tue Jun 25 18:34:46 2013 +0900
2189
-
2190
- Delete sample/demo_ddbjxml.rb which uses Bio::DDBJ::XML
2191
-
2192
- sample/demo_ddbjxml.rb | 212 -------------------------------------------------
2193
- 1 file changed, 212 deletions(-)
2194
- delete mode 100644 sample/demo_ddbjxml.rb
2195
-
2196
- commit e55293b67d305382cfb30b45aa30af82a574b580
2197
- Author: Naohisa Goto <ng@bioruby.org>
2198
- Date: Tue Jun 25 18:29:54 2013 +0900
2199
-
2200
- Remove Bio::Blast::Remote::DDBJ, Bio::Blast.ddbj and related components
2201
-
2202
- * Remove Bio::Blast::Remote::DDBJ, Bio::Blast.ddbj and related components
2203
- which use Bio::DDBJ::XML or Bio::DDBJ::REST.
2204
-
2205
- lib/bio/appl/blast/ddbj.rb | 131 -----------------------------
2206
- lib/bio/appl/blast/remote.rb | 9 --
2207
- test/network/bio/appl/blast/test_remote.rb | 14 ---
2208
- test/network/bio/appl/test_blast.rb | 12 ---
2209
- 4 files changed, 166 deletions(-)
2210
- delete mode 100644 lib/bio/appl/blast/ddbj.rb
2211
-
2212
- commit 19a5c992096a68a26f8684ee2ae128d17f2a49fd
2213
- Author: Naohisa Goto <ng@bioruby.org>
2214
- Date: Tue Jun 25 16:52:05 2013 +0900
2215
-
2216
- Remove Bio::DDBJ::XML and REST due to suspension of DDBJ Web API (WABI)
2217
-
2218
- * Remove Bio::DDBJ::XML and Bio::DDBJ::REST due to suspension of
2219
- DDBJ Web API (WABI). DDBJ says that it is now under reconstruction
2220
- and the API will be completely changed. Thus, I've decided to throw
2221
- away current API client in Ruby and to implement new one with the new
2222
- API.
2223
- * Autoload lines in lib/bio/db/genbank/ddbj.rb are removed.
2224
- * Tests are also removed.
2225
-
2226
- lib/bio/db/genbank/ddbj.rb | 3 -
2227
- lib/bio/io/ddbjrest.rb | 344 --------------------------
2228
- lib/bio/io/ddbjxml.rb | 458 -----------------------------------
2229
- test/network/bio/io/test_ddbjrest.rb | 47 ----
2230
- test/unit/bio/io/test_ddbjxml.rb | 81 -------
2231
- 5 files changed, 933 deletions(-)
2232
- delete mode 100644 lib/bio/io/ddbjrest.rb
2233
- delete mode 100644 lib/bio/io/ddbjxml.rb
2234
- delete mode 100644 test/network/bio/io/test_ddbjrest.rb
2235
- delete mode 100644 test/unit/bio/io/test_ddbjxml.rb
2236
-
2237
- commit 1f852e0bf3c830aaa40dc7fc2bd535418af8dfd1
2238
- Author: Naohisa Goto <ng@bioruby.org>
2239
- Date: Sat May 25 03:00:08 2013 +0900
2240
-
2241
- regenerate bioruby.gemspec with rake regemspec
2242
-
2243
- bioruby.gemspec | 2 --
2244
- 1 file changed, 2 deletions(-)
2245
-
2246
- commit 5b90959ab399f961823a7c4453392c75cf971333
2247
- Author: Naohisa Goto <ng@bioruby.org>
2248
- Date: Sat May 25 02:58:50 2013 +0900
2249
-
2250
- Update files and directories used to create package without git
2251
-
2252
- bioruby.gemspec.erb | 6 ++++--
2253
- 1 file changed, 4 insertions(+), 2 deletions(-)
2254
-
2255
- commit df29f057ded6ac73fbdce7ae04a70ead28f4cc9f
2256
- Author: Naohisa Goto <ng@bioruby.org>
2257
- Date: Sat May 25 02:46:32 2013 +0900
2258
-
2259
- Ruby 2.0 support: not to add ChangeLog and LEGAL to rdoc_files
2260
-
2261
- * Ruby 2.0 support: not to add ChangeLog and LEGAL to rdoc_files.
2262
- Because ChangeLog is not rdoc format, rdoc bundled with Ruby 2.0
2263
- raises error during parsing.
2264
-
2265
- bioruby.gemspec.erb | 4 ++--
2266
- 1 file changed, 2 insertions(+), 2 deletions(-)
2267
-
2268
- commit 930a5fcf5e38ae2bdfeee62eed9a46db1c519fae
2269
- Author: Kenichi Kamiya <kachick1@gmail.com>
2270
- Date: Thu Apr 4 17:29:33 2013 +0900
2271
-
2272
- Remove unused variable in lib/bio/util/contingency_table.rb
2273
-
2274
- This commit removes below interpreter warning.
2275
-
2276
- * warning: assigned but unused variable
2277
-
2278
- lib/bio/util/contingency_table.rb | 2 --
2279
- 1 file changed, 2 deletions(-)
2280
-
2281
- commit 490b3f7ca3b987c1a17852b641aad3125fc565cd
2282
- Author: Kenichi Kamiya <kachick1@gmail.com>
2283
- Date: Thu Apr 4 17:28:30 2013 +0900
2284
-
2285
- Rename unused variable in lib/bio/tree.rb
2286
-
2287
- This commit removes below interpreter warning.
2288
-
2289
- * warning: assigned but unused variable
2290
-
2291
- lib/bio/tree.rb | 4 ++--
2292
- 1 file changed, 2 insertions(+), 2 deletions(-)
2293
-
2294
- commit c024fb972edb52e213165149273fc7ac4bec2f6e
2295
- Author: Naohisa Goto <ng@bioruby.org>
2296
- Date: Thu May 16 21:26:44 2013 +0900
2297
-
2298
- Refactoring to suppress "warning: assigned but unused variable"
2299
-
2300
- lib/bio/pathway.rb | 2 +-
2301
- 1 file changed, 1 insertion(+), 1 deletion(-)
2302
-
2303
- commit b3b2a268d6118307eed88fce1d805a61c6fb843d
2304
- Author: Kenichi Kamiya <kachick1@gmail.com>
2305
- Date: Thu Apr 4 17:18:44 2013 +0900
2306
-
2307
- Remove unused variable in lib/bio/db/transfac.rb
2308
-
2309
- This commit removes below interpreter warning.
2310
-
2311
- * warning: assigned but unused variable
2312
-
2313
- lib/bio/db/transfac.rb | 2 +-
2314
- 1 file changed, 1 insertion(+), 1 deletion(-)
2315
-
2316
- commit dd8abf1f95af4a70cf0b86b0e719e3dcfd8abecf
2317
- Author: Naohisa Goto <ng@bioruby.org>
2318
- Date: Thu May 16 21:13:34 2013 +0900
2319
-
2320
- Refactoring to suppress warnings "assigned but unused variable"
2321
-
2322
- lib/bio/db/nexus.rb | 5 +++--
2323
- 1 file changed, 3 insertions(+), 2 deletions(-)
2324
-
2325
- commit b37512fb8028cf30bb2f813928aed49a5b39dce3
2326
- Author: Kenichi Kamiya <kachick1@gmail.com>
2327
- Date: Thu Apr 4 17:15:59 2013 +0900
2328
-
2329
- Rename unused variable in lib/bio/db/kegg/reaction.rb
2330
-
2331
- This commit removes below interpreter warning.
2332
-
2333
- * warning: assigned but unused variable
2334
-
2335
- lib/bio/db/kegg/reaction.rb | 2 +-
2336
- 1 file changed, 1 insertion(+), 1 deletion(-)
2337
-
2338
- commit a81fca3b1247ae4a3e05bfa912c8181efdfca81b
2339
- Author: Kenichi Kamiya <kachick1@gmail.com>
2340
- Date: Thu Apr 4 17:15:09 2013 +0900
2341
-
2342
- Remove unused variable in lib/bio/db/go.rb
2343
-
2344
- This commit removes below interpreter warning.
2345
-
2346
- * warning: assigned but unused variable
2347
-
2348
- lib/bio/db/go.rb | 6 +++---
2349
- 1 file changed, 3 insertions(+), 3 deletions(-)
2350
-
2351
- commit 69b0c433e76faffba6a48dfc38dcc2b1444ce2b7
2352
- Author: Kenichi Kamiya <kachick1@gmail.com>
2353
- Date: Thu Apr 4 17:13:24 2013 +0900
2354
-
2355
- Rename unused variable in lib/bio/db/gff.rb
2356
-
2357
- This commit removes below interpreter warning.
2358
-
2359
- * warning: assigned but unused variable
2360
-
2361
- lib/bio/db/gff.rb | 2 +-
2362
- 1 file changed, 1 insertion(+), 1 deletion(-)
2363
-
2364
- commit 88c214fe3183c161cda94a3a4cda442b3a769965
2365
- Author: Naohisa Goto <ng@bioruby.org>
2366
- Date: Thu May 9 23:46:28 2013 +0900
2367
-
2368
- add a dummy line to suppress "warning: assigned but unused variable"
2369
-
2370
- lib/bio/db/embl/sptr.rb | 1 +
2371
- 1 file changed, 1 insertion(+)
2372
-
2373
- commit 1ead12f9c951a983c6775f79ca1b6944f95a61b9
2374
- Author: Naohisa Goto <ng@bioruby.org>
2375
- Date: Thu May 9 23:41:54 2013 +0900
2376
-
2377
- Refactoring to suppress warnings "assigned but unused variable"
2378
-
2379
- lib/bio/db/embl/embl.rb | 7 ++++---
2380
- 1 file changed, 4 insertions(+), 3 deletions(-)
2381
-
2382
- commit 8d0eb5105eb2f419f5b4f4fbb191b8fb2032664b
2383
- Author: Kenichi Kamiya <kachick1@gmail.com>
2384
- Date: Thu Apr 4 17:01:27 2013 +0900
2385
-
2386
- Remove unused variable in lib/bio/appl/paml/common
2387
-
2388
- This commit removes below interpreter warning.
2389
-
2390
- * warning: assigned but unused variable
2391
-
2392
- lib/bio/appl/paml/common.rb | 2 +-
2393
- 1 file changed, 1 insertion(+), 1 deletion(-)
2394
-
2395
- commit c6cf0d2e2a3a0b9062f9464dba0e363f460d04e4
2396
- Author: Naohisa Goto <ng@bioruby.org>
2397
- Date: Thu May 9 23:27:54 2013 +0900
2398
-
2399
- suppress warning "assigned but unused variable"
2400
-
2401
- lib/bio/appl/paml/codeml/report.rb | 1 +
2402
- 1 file changed, 1 insertion(+)
2403
-
2404
- commit 8834d50544b03a92a3ca816704b179e4333d1dfc
2405
- Author: Kenichi Kamiya <kachick1@gmail.com>
2406
- Date: Thu Apr 4 16:59:18 2013 +0900
2407
-
2408
- Remove unused variable in lib/bio/appl/meme/mast/report
2409
-
2410
- This commit removes below interpreter warning.
2411
-
2412
- * warning: assigned but unused variable
2413
-
2414
- lib/bio/appl/meme/mast/report.rb | 2 +-
2415
- 1 file changed, 1 insertion(+), 1 deletion(-)
2416
-
2417
- commit fe51a49ee68c41a3ce0c48c39db6e8a28d1689ee
2418
- Author: Kenichi Kamiya <kachick1@gmail.com>
2419
- Date: Thu Apr 4 16:57:44 2013 +0900
2420
-
2421
- Remove unused variable in lib/bio/appl/blast/report
2422
-
2423
- This commit removes below interpreter warning.
2424
-
2425
- * warning: assigned but unused variable
2426
-
2427
- lib/bio/appl/blast/report.rb | 2 +-
2428
- 1 file changed, 1 insertion(+), 1 deletion(-)
2429
-
2430
- commit 622497ff309412fb986c5315d55d41c3ca48d362
2431
- Author: Kenichi Kamiya <kachick1@gmail.com>
2432
- Date: Thu Apr 4 17:25:29 2013 +0900
2433
-
2434
- Fix indent in lib/bio/map
2435
-
2436
- This commit removes below interpreter warning.
2437
-
2438
- * warning: mismatched indentations at ...
2439
-
2440
- lib/bio/map.rb | 2 +-
2441
- 1 file changed, 1 insertion(+), 1 deletion(-)
2442
-
2443
- commit 3ea6bcaf229fd1a71a0192253cc47e817bb64b82
2444
- Author: Kenichi Kamiya <kachick1@gmail.com>
2445
- Date: Thu Apr 4 18:05:04 2013 +0900
2446
-
2447
- Remove unused variable in test/unit/bio/appl/blast/test_report
2448
-
2449
- This commit removes below interpreter warning.
2450
-
2451
- * warning: assigned but unused variable
2452
-
2453
- test/unit/bio/appl/blast/test_report.rb | 2 --
2454
- 1 file changed, 2 deletions(-)
2455
-
2456
- commit 178ca9e5244cc3aa7f0507c7d5528bb57b0858be
2457
- Author: Kenichi Kamiya <kachick1@gmail.com>
2458
- Date: Thu Apr 4 18:03:46 2013 +0900
2459
-
2460
- Remove unused variable in test/unit/bio/appl/bl2seq/test_report
2461
-
2462
- This commit removes below interpreter warning.
2463
-
2464
- * warning: assigned but unused variable
2465
-
2466
- test/unit/bio/appl/bl2seq/test_report.rb | 1 -
2467
- 1 file changed, 1 deletion(-)
2468
-
2469
- commit b8a5c1cb9f54d9199200b406f77e8152eef96f02
2470
- Author: Naohisa Goto <ng@bioruby.org>
2471
- Date: Thu May 9 21:20:10 2013 +0900
2472
-
2473
- Add assertions and suppress "unused variable" warnings
2474
-
2475
- * Add assertions to check object id returned by forward_complement
2476
- and reverse_complement methods. This change also aims to suppress
2477
- "assigned but unused variable" warnings.
2478
-
2479
- test/unit/bio/sequence/test_na.rb | 4 +++-
2480
- 1 file changed, 3 insertions(+), 1 deletion(-)
2481
-
2482
- commit bd8fc9b197c54c108d74fea9161c8f0dd3b041fc
2483
- Author: Kenichi Kamiya <kachick1@gmail.com>
2484
- Date: Thu Apr 4 17:59:09 2013 +0900
2485
-
2486
- Remove unused variable in test/unit/bio/io/flatfile/test_splitter
2487
-
2488
- This commit removes below interpreter warning.
2489
-
2490
- * warning: assigned but unused variable
2491
-
2492
- test/unit/bio/io/flatfile/test_splitter.rb | 2 +-
2493
- 1 file changed, 1 insertion(+), 1 deletion(-)
2494
-
2495
- commit 0a87c9e265c4560453faf84fc009b60319c75416
2496
- Author: Kenichi Kamiya <kachick1@gmail.com>
2497
- Date: Thu Apr 4 17:57:51 2013 +0900
2498
-
2499
- Remove unused variable in test/unit/bio/db/test_phyloxml_writer
2500
-
2501
- This commit removes below interpreter warning.
2502
-
2503
- * warning: assigned but unused variable
2504
-
2505
- test/unit/bio/db/test_phyloxml_writer.rb | 4 ++--
2506
- 1 file changed, 2 insertions(+), 2 deletions(-)
2507
-
2508
- commit 95b2614eb32eb12428df29360d0c1f146f39a469
2509
- Author: Naohisa Goto <ng@bioruby.org>
2510
- Date: Thu May 9 20:56:43 2013 +0900
2511
-
2512
- Comment out some lines to suppress "unused variable" warnings
2513
-
2514
- test/unit/bio/db/test_gff.rb | 4 ++--
2515
- 1 file changed, 2 insertions(+), 2 deletions(-)
2516
-
2517
- commit b8917841559fbd506c73fdf374a8097f23a1bc37
2518
- Author: Kenichi Kamiya <kachick1@gmail.com>
2519
- Date: Thu Apr 4 17:51:11 2013 +0900
2520
-
2521
- Remove unused variable in test/unit/bio/db/embl/test_sptr.rb
2522
-
2523
- * Remove warnings "warning: assigned but unused variable"
2524
- * Note that the sequence in TestSPTRUniProtRel7_6#test_10000aa is
2525
- a fragment of human p53 protein, and is not related with Q09165.
2526
-
2527
- test/unit/bio/db/embl/test_sptr.rb | 3 ---
2528
- 1 file changed, 3 deletions(-)
2529
-
2530
- commit 6b46d324a545f509bbd238ae7ec009d586469314
2531
- Author: Kenichi Kamiya <kachick1@gmail.com>
2532
- Date: Thu Apr 4 17:45:47 2013 +0900
2533
-
2534
- Remove unused variable in test/unit/bio/db/embl/test_embl_rel89
2535
-
2536
- This commit removes below interpreter warning.
2537
-
2538
- * warning: assigned but unused variable
2539
-
2540
- test/unit/bio/db/embl/test_embl_rel89.rb | 1 -
2541
- 1 file changed, 1 deletion(-)
2542
-
2543
- commit f36eeb0107e7a8315c66888ec8292ed33bd959cc
2544
- Author: Kenichi Kamiya <kachick1@gmail.com>
2545
- Date: Thu Apr 4 17:45:21 2013 +0900
2546
-
2547
- Remove unused variable in test/unit/bio/db/embl/test_embl
2548
-
2549
- This commit removes below interpreter warning.
2550
-
2551
- * warning: assigned but unused variable
2552
-
2553
- test/unit/bio/db/embl/test_embl.rb | 1 -
2554
- 1 file changed, 1 deletion(-)
2555
-
2556
- commit a1a2ad9b963d9bb2da8d07ae7b182bd339bea88e
2557
- Author: Kenichi Kamiya <kachick1@gmail.com>
2558
- Date: Thu Apr 4 17:36:59 2013 +0900
2559
-
2560
- Fix indent in test/unit/bio/sequence/test_dblink
2561
-
2562
- This commit removes below interpreter warning.
2563
-
2564
- * warning: mismatched indentations at ...
2565
-
2566
- test/unit/bio/sequence/test_dblink.rb | 2 +-
2567
- 1 file changed, 1 insertion(+), 1 deletion(-)
2568
-
2569
- commit 345a8eb4408ca241c13c410a578490c905eb7391
2570
- Author: Kenichi Kamiya <kachick1@gmail.com>
2571
- Date: Thu Apr 4 17:36:21 2013 +0900
2572
-
2573
- Fix indent in test/unit/bio/db/test_phyloxml
2574
-
2575
- This commit removes below interpreter warning.
2576
-
2577
- * warning: mismatched indentations at ...
2578
-
2579
- test/unit/bio/db/test_phyloxml.rb | 58 +++++++++++++++++++--------------------
2580
- 1 file changed, 29 insertions(+), 29 deletions(-)
2581
-
2582
- commit ae8c7a6705a30c0c18c57df9869979a968aa63ac
2583
- Author: Kenichi Kamiya <kachick1@gmail.com>
2584
- Date: Thu Apr 4 17:35:07 2013 +0900
2585
-
2586
- Fix indent in test/unit/bio/db/genbank/test_genbank
2587
-
2588
- This commit removes below interpreter warning.
2589
-
2590
- * warning: mismatched indentations at ...
2591
-
2592
- test/unit/bio/db/genbank/test_genbank.rb | 2 +-
2593
- 1 file changed, 1 insertion(+), 1 deletion(-)
2594
-
2595
- commit 872d8954e1351251fbace20e331035251ae5f806
2596
- Author: Kenichi Kamiya <kachick1@gmail.com>
2597
- Date: Thu Apr 4 17:33:23 2013 +0900
2598
-
2599
- Fix indent in test/unit/bio/appl/test_blast
2600
-
2601
- This commit removes below interpreter warning.
2602
-
2603
- * warning: mismatched indentations at ...
2604
-
2605
- test/unit/bio/appl/test_blast.rb | 4 ++--
2606
- 1 file changed, 2 insertions(+), 2 deletions(-)
2607
-
2608
- commit bd973e084695c4d777c8ecf6d566788838158165
2609
- Author: Naohisa Goto <ng@bioruby.org>
2610
- Date: Wed Mar 27 03:03:49 2013 +0900
2611
-
2612
- .travis.yml: rbx-18mode is moved to allow_failures
2613
-
2614
- .travis.yml | 8 +++++---
2615
- 1 file changed, 5 insertions(+), 3 deletions(-)
2616
-
2617
- commit 63e93faba74a8143a0be9595fdf87329f3015745
2618
- Author: Andrew Grimm <andrew.j.grimm@gmail.com>
2619
- Date: Tue Mar 26 20:20:11 2013 +1100
2620
-
2621
- Squash warning in alignment.rb: assigned but unused variable - oldkeys
2622
-
2623
- lib/bio/alignment.rb | 1 -
2624
- 1 file changed, 1 deletion(-)
2625
-
2626
- commit bd735d6f9d6edfd1550a4279167ac06b372f847a
2627
- Author: Andrew Grimm <andrew.j.grimm@gmail.com>
2628
- Date: Tue Mar 26 20:14:46 2013 +1100
2629
-
2630
- Squash warning in alignment.rb: assigned but unused variable - lines
2631
-
2632
- lib/bio/alignment.rb | 2 +-
2633
- 1 file changed, 1 insertion(+), 1 deletion(-)
2634
-
2635
- commit 3e7b27f96a901a3abfc338572f98d60a9e3be498
2636
- Author: Andrew Grimm <andrew.j.grimm@gmail.com>
2637
- Date: Tue Mar 26 19:44:49 2013 +1100
2638
-
2639
- Squash warning in defline.rb: assigned but unused variable - idtype
2640
-
2641
- lib/bio/db/fasta/defline.rb | 1 -
2642
- 1 file changed, 1 deletion(-)
2643
-
2644
- commit aafc03330fa79243cfa4097d356a7c304ddb7980
2645
- Author: Kenichi Kamiya <kachick1@gmail.com>
2646
- Date: Sat Feb 16 21:22:55 2013 +0900
2647
-
2648
- Simplify some regular expressions
2649
-
2650
- * /\w/ including /\d/
2651
- * /\s/ including [/\r/, /\t/, /\n/]
2652
-
2653
- lib/bio/appl/blast/format0.rb | 2 +-
2654
- lib/bio/db/embl/common.rb | 2 +-
2655
- lib/bio/db/embl/embl.rb | 2 +-
2656
- lib/bio/db/embl/sptr.rb | 2 +-
2657
- lib/bio/db/gff.rb | 2 +-
2658
- 5 files changed, 5 insertions(+), 5 deletions(-)
2659
-
2660
- commit 623ad4011fa8b56f3c9f50a859d1fa26f6570700
2661
- Author: Naohisa Goto <ng@bioruby.org>
2662
- Date: Fri Jan 11 16:41:12 2013 +0900
2663
-
2664
- Improvement of parameter checks and error output
2665
-
2666
- * Improvement of parameter checks
2667
- * To avoid potential XSS in old MSIE which ignores content-type,
2668
- always do CGI.escapeHTML for parameters in error messages
2669
-
2670
- sample/biofetch.rb | 91 +++++++++++++++++++++++++++++++++++++-----------------
2671
- 1 file changed, 63 insertions(+), 28 deletions(-)
2672
-
2673
- commit 03d48c43f1de7ebc9104b9aa972f226774a0bf49
2674
- Author: Naohisa Goto <ng@bioruby.org>
2675
- Date: Fri Jan 11 15:32:05 2013 +0900
2676
-
2677
- Add metadata cache
2678
-
2679
- * Add metadata cache. It caches the list of databases and a list of
2680
- available formats for each database. Database entries are not cached.
2681
- * charset=utf-8 in CGI header.
2682
-
2683
- sample/biofetch.rb | 110 ++++++++++++++++++++++++++++++++++++++++++-----------
2684
- 1 file changed, 87 insertions(+), 23 deletions(-)
2685
-
2686
- commit 114d29d4bdfc328f5e91adee9bea465622248e0d
2687
- Author: Naohisa Goto <ng@bioruby.org>
2688
- Date: Fri Jan 11 09:10:08 2013 +0900
2689
-
2690
- remove excess double quotations in html part
2691
-
2692
- sample/biofetch.rb | 8 ++++----
2693
- 1 file changed, 4 insertions(+), 4 deletions(-)
2694
-
2695
- commit 949311648b92d51a2596f896fdae8d74ac0608a3
2696
- Author: Naohisa Goto <ng@bioruby.org>
2697
- Date: Fri Jan 11 08:59:18 2013 +0900
2698
-
2699
- add magic comment: coding utf-8
2700
-
2701
- sample/biofetch.rb | 1 +
2702
- 1 file changed, 1 insertion(+)
2703
-
2704
- commit 4ae509273134c5deca7910847063ed07c56150db
2705
- Author: Naohisa Goto <ng@bioruby.org>
2706
- Date: Thu Jan 10 23:27:09 2013 +0900
2707
-
2708
- Rewrite to use TogoWS REST API instead of SOAP-based KEGG API.
2709
-
2710
- * Rewrite to use TogoWS REST API instead of deprecated SOAP-based
2711
- KEGG API.
2712
- * Examples are changed to fit with current TogoWS.
2713
- * Now, the script does not depend on any non-standard libraries
2714
- including BioRuby. This means that one can put this script on
2715
- a server without installing BioRuby.
2716
- * New constans SCRIPT_NAME and BASE_URL for easy customizing.
2717
- * Many changes. See "git diff" for details.
2718
-
2719
- sample/biofetch.rb | 265 ++++++++++++++++++++++++++---------------------------
2720
- 1 file changed, 131 insertions(+), 134 deletions(-)
2721
-
2722
- commit bc98bc54c59be98425d66c64b19a3b9612993beb
2723
- Author: Naohisa Goto <ng@bioruby.org>
2724
- Date: Thu Jan 10 15:17:42 2013 +0900
2725
-
2726
- Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
2727
-
2728
- gemfiles/Gemfile.travis-ruby1.9 | 1 +
2729
- 1 file changed, 1 insertion(+)
2730
-
2731
- commit dfe54b2fbe303f56a868404173fe346724b7aa4a
2732
- Author: Naohisa Goto <ng@bioruby.org>
2733
- Date: Thu Jan 10 14:06:45 2013 +0900
2734
-
2735
- Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
2736
-
2737
- gemfiles/Gemfile.travis-jruby1.8 | 1 +
2738
- gemfiles/Gemfile.travis-jruby1.9 | 1 +
2739
- 2 files changed, 2 insertions(+)
2740
-
2741
- commit f07ec6ac326d51c055496983abba54afd00c35d4
2742
- Author: Naohisa Goto <ng@bioruby.org>
2743
- Date: Thu Jan 10 01:38:00 2013 +0900
2744
-
2745
- Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
2746
-
2747
- gemfiles/Gemfile.travis-ruby1.8 | 1 +
2748
- 1 file changed, 1 insertion(+)
2749
-
2750
- commit 4221d52055087f85daa1c23349d10ecdb4d01a31
2751
- Author: Naohisa Goto <ng@bioruby.org>
2752
- Date: Thu Jan 10 01:27:03 2013 +0900
2753
-
2754
- Ruby 2.0 support: Set script encoding to US-ASCII for gff.rb.
2755
-
2756
- lib/bio/db/gff.rb | 1 +
2757
- 1 file changed, 1 insertion(+)
2758
-
2759
- commit 1526df8273e9d2283fd4a921d4cf8c0c664fe71c
2760
- Author: Naohisa Goto <ng@bioruby.org>
2761
- Date: Thu Jan 10 00:45:36 2013 +0900
2762
-
2763
- Convert encoding of the Japanese tutorial files to UTF-8
2764
-
2765
- doc/Tutorial.rd.ja | 1920 +++++++++++++++++++++++------------------------
2766
- doc/Tutorial.rd.ja.html | 1918 +++++++++++++++++++++++-----------------------
2767
- 2 files changed, 1919 insertions(+), 1919 deletions(-)
2768
-
2769
- commit 3215570185a46dd0d6c4cd96d583b2487636b483
2770
- Author: Naohisa Goto <ng@bioruby.org>
2771
- Date: Thu Jan 10 00:41:51 2013 +0900
2772
-
2773
- updated doc/Tutorial.rd.html and doc/Tutorial.rd.ja.html
2774
-
2775
- doc/Tutorial.rd.html | 19 ++---
2776
- doc/Tutorial.rd.ja.html | 202 ++++++++++++++----------------------------------
2777
- 2 files changed, 63 insertions(+), 158 deletions(-)
2778
-
2779
- commit 8db12935a9cc15bae92bdb7183476cfea9e1f819
2780
- Author: Naohisa Goto <ng@bioruby.org>
2781
- Date: Thu Jan 10 00:38:18 2013 +0900
2782
-
2783
- Set html title when generating tutorial html
2784
-
2785
- Rakefile | 3 ++-
2786
- 1 file changed, 2 insertions(+), 1 deletion(-)
2787
-
2788
- commit 644d438decceb072475877a749435fba543ff8ea
2789
- Author: Naohisa Goto <ng@bioruby.org>
2790
- Date: Fri Jan 4 03:19:00 2013 +0900
2791
-
2792
- regenerate bioruby.gemspec with rake regemspec
2793
-
2794
- bioruby.gemspec | 6 ------
2795
- 1 file changed, 6 deletions(-)
2796
-
2797
- commit 54dc9b9f68ee2de9ee005a772ce000277a073d97
2798
- Author: Naohisa Goto <ng@bioruby.org>
2799
- Date: Fri Jan 4 02:35:01 2013 +0900
2800
-
2801
- Remove sample/psortplot_html.rb which depend on Bio::KEGG::API.
2802
-
2803
- * Remove sample/psortplot_html.rb because it strongly depend on
2804
- removed Bio::KEGG::API and discontinued SOAP-based KEGG API.
2805
- It is hard to re-write by using new REST-based KEGG API because
2806
- the new API seems to lack color_pathway_by_objects that returns
2807
- image URL. Moreover, there is no one-by-one API migration guide.
2808
-
2809
- sample/psortplot_html.rb | 214 -----------------------------------------------
2810
- 1 file changed, 214 deletions(-)
2811
- delete mode 100644 sample/psortplot_html.rb
2812
-
2813
- commit dbdf2dad3dec9d10141b891a481b9b05e1561708
2814
- Author: Naohisa Goto <ng@bioruby.org>
2815
- Date: Fri Jan 4 02:34:05 2013 +0900
2816
-
2817
- Remove descriptions about KEGG API and Bio::KEGG::API.
2818
-
2819
- doc/Tutorial.rd | 6 ---
2820
- doc/Tutorial.rd.ja | 106 +----------------------------------------------------
2821
- 2 files changed, 1 insertion(+), 111 deletions(-)
2822
-
2823
- commit 3ca725dc1e07f794344c9fcae43d4972ed2895da
2824
- Author: Naohisa Goto <ng@bioruby.org>
2825
- Date: Fri Jan 4 02:33:09 2013 +0900
2826
-
2827
- Remove description about KEGG API and Bio::KEGG::API.
2828
-
2829
- README.rdoc | 6 ++----
2830
- 1 file changed, 2 insertions(+), 4 deletions(-)
2831
-
2832
- commit d4568788069f2d998a78ad72b1d906aae13e85f4
2833
- Author: Naohisa Goto <ng@bioruby.org>
2834
- Date: Thu Jan 3 23:55:58 2013 +0900
2835
-
2836
- Remove KEGG API plugin of BioRuby Shell, due to the removal of Bio::KEGG::API.
2837
-
2838
- lib/bio/shell.rb | 1 -
2839
- lib/bio/shell/plugin/keggapi.rb | 181 ----------------------------------------
2840
- 2 files changed, 182 deletions(-)
2841
- delete mode 100644 lib/bio/shell/plugin/keggapi.rb
2842
-
2843
- commit 22c8f4945d622f8f22c08b262c6caf81a0261284
2844
- Author: Naohisa Goto <ng@bioruby.org>
2845
- Date: Thu Jan 3 23:52:36 2013 +0900
2846
-
2847
- Delete autoload lines for removed Bio::KEGG::API
2848
-
2849
- lib/bio.rb | 4 ----
2850
- 1 file changed, 4 deletions(-)
2851
-
2852
- commit b56ec0984d5001c3a4d3b4f0ba8fbbbf79835747
2853
- Author: Naohisa Goto <ng@bioruby.org>
2854
- Date: Thu Jan 3 23:51:24 2013 +0900
2855
-
2856
- Remove Bio::KEGG::API and its sample code and documentation files.
2857
-
2858
- * Remove Bio::KEGG::API and its sample code and documentation files.
2859
- * deleted: lib/bio/io/keggapi.rb
2860
- * deleted: doc/KEGG_API.rd
2861
- * deleted: doc/KEGG_API.rd.ja
2862
- * deleted: sample/demo_keggapi.rb
2863
-
2864
- doc/KEGG_API.rd | 1843 ------------------------------------------------
2865
- doc/KEGG_API.rd.ja | 1834 -----------------------------------------------
2866
- lib/bio/io/keggapi.rb | 363 ----------
2867
- sample/demo_keggapi.rb | 502 -------------
2868
- 4 files changed, 4542 deletions(-)
2869
- delete mode 100644 doc/KEGG_API.rd
2870
- delete mode 100644 doc/KEGG_API.rd.ja
2871
- delete mode 100644 lib/bio/io/keggapi.rb
2872
- delete mode 100644 sample/demo_keggapi.rb
2873
-
2874
- commit 63af413c122b4531193153fbfee034deaf0a9606
2875
- Author: Naohisa Goto <ng@bioruby.org>
2876
- Date: Mon Oct 1 21:11:14 2012 +0900
2877
-
2878
- Bug fix: parse error when subject sequence contains spaces
2879
-
2880
- * Bug fix: parse error when subject sequence contains spaces.
2881
- Thanks to Edward Rice who reports the bug. (Bug #3385)
2882
- (https://redmine.open-bio.org/issues/3385)
2883
-
2884
- lib/bio/appl/blast/format0.rb | 38 +++++++++++++++++++-------------------
2885
- 1 file changed, 19 insertions(+), 19 deletions(-)
2886
-
2887
- commit 9f2f682ec6624ff356bea7aca76365ba95d33549
2888
- Author: Naohisa Goto <ng@bioruby.org>
2889
- Date: Fri Sep 7 16:50:44 2012 +0900
2890
-
2891
- add an env line to be recognized in allow_failures
2892
-
2893
- .travis.yml | 1 +
2894
- 1 file changed, 1 insertion(+)
2895
-
2896
- commit fead6dda526081db09c56c2262f111338b7d8cd7
2897
- Author: Naohisa Goto <ng@bioruby.org>
2898
- Date: Fri Sep 7 16:08:57 2012 +0900
2899
-
2900
- environment variable TESTOPTS=-v for verbose output of rake test
2901
-
2902
- .travis.yml | 22 ++++++++++++++--------
2903
- 1 file changed, 14 insertions(+), 8 deletions(-)
2904
-
2905
- commit 3de19895140502898c77fc83d9ad6fae47331763
2906
- Author: Naohisa Goto <ng@bioruby.org>
2907
- Date: Thu Sep 6 18:17:22 2012 +0900
2908
-
2909
- Remove Bio.method_missing because it is broken.
2910
-
2911
- * Bio.method_missing, the hook of undefined methods, providing
2912
- shortcut of Bio::Shell methods, is now removed, because it does
2913
- not work correctly, and because the use of method_missing should
2914
- normally be avoided unless it is really necessary. Alternatively,
2915
- use Bio::Shell.xxxxx (xxxxx is a method name).
2916
-
2917
- lib/bio.rb | 13 -------------
2918
- 1 file changed, 13 deletions(-)
2919
-
2920
- commit a358584c4a76be6a38ab38a18e6dc66840030450
2921
- Author: Naohisa Goto <ng@bioruby.org>
2922
- Date: Thu Sep 6 16:48:51 2012 +0900
2923
-
2924
- Delete autoload line of a removed class Bio::NCBI::SOAP.
2925
-
2926
- lib/bio/io/ncbirest.rb | 1 -
2927
- 1 file changed, 1 deletion(-)
2928
-
2929
- commit 340d665775b862da638e4d12751b84d2ccd83e82
2930
- Author: Naohisa Goto <ng@bioruby.org>
2931
- Date: Thu Sep 6 16:47:03 2012 +0900
2932
-
2933
- Delete autoload lines of removed classes.
2934
-
2935
- lib/bio.rb | 4 ----
2936
- 1 file changed, 4 deletions(-)
2937
-
2938
- commit c7c29a672b38d2182cf4afc9a970b854af1149a7
2939
- Author: Naohisa Goto <ng@bioruby.org>
2940
- Date: Thu Sep 6 16:43:25 2012 +0900
2941
-
2942
- regenerate bioruby.gemspec with rake regemspec
2943
-
2944
- bioruby.gemspec | 3 ---
2945
- 1 file changed, 3 deletions(-)
2946
-
2947
- commit 09bb4b8a8b7e01a36dbe0cf44a5c2a6a6b5750f1
2948
- Author: Naohisa Goto <ng@bioruby.org>
2949
- Date: Thu Sep 6 16:23:17 2012 +0900
2950
-
2951
- Remove Bio::Shell#ncbisoap which uses removed Bio::NCBI::SOAP.
2952
-
2953
- lib/bio/shell/plugin/soap.rb | 9 ---------
2954
- 1 file changed, 9 deletions(-)
2955
-
2956
- commit a5e46acdaf06568bea6cb773200bbf3881b5670e
2957
- Author: Naohisa Goto <ng@bioruby.org>
2958
- Date: Thu Sep 6 16:02:32 2012 +0900
2959
-
2960
- Remove issues about removed classes Bio::NCBI::SOAP and Bio::KEGG::Taxonomy
2961
-
2962
- KNOWN_ISSUES.rdoc | 10 ----------
2963
- 1 file changed, 10 deletions(-)
2964
-
2965
- commit 529815acb1b57486bd506b81eec6be80277cbae7
2966
- Author: Naohisa Goto <ng@bioruby.org>
2967
- Date: Wed Sep 5 11:33:27 2012 +0900
2968
-
2969
- Remove Bio::KEGG::Taxonomy which is old and broken
2970
-
2971
- * Remove Bio::KEGG::Taxonomy because it raises error or the data
2972
- structure in the return value seems to be broken. In addition,
2973
- running the sample script sample/demo_kegg_taxonomy.rb shows
2974
- error or falls into infinite loop. Moreover, KEGG closes public
2975
- FTP site and the target data file of the class ("taxonomy")
2976
- can only be obtained by paid subscribers. From the above reasons,
2977
- it seems there are no users of this class now.
2978
- * Deleted files: lib/bio/db/kegg/taxonomy.rb,
2979
- sample/demo_kegg_taxonomy.rb
2980
-
2981
- lib/bio/db/kegg/taxonomy.rb | 280 -------------------------------------------
2982
- sample/demo_kegg_taxonomy.rb | 92 --------------
2983
- 2 files changed, 372 deletions(-)
2984
- delete mode 100644 lib/bio/db/kegg/taxonomy.rb
2985
- delete mode 100644 sample/demo_kegg_taxonomy.rb
2986
-
2987
- commit dc47fb46e86bba15ba43de31075eaba3cf811fa3
2988
- Author: Naohisa Goto <ng@bioruby.org>
2989
- Date: Wed Sep 5 11:26:00 2012 +0900
2990
-
2991
- Remove Bio::NCBI::SOAP which is broken
2992
-
2993
- * Remove Bio::NCBI::SOAP in lib/bio/io/ncbisoap.rb, because it always
2994
- raises error during the parsing of WSDL files provided by NCBI, both
2995
- with Ruby 1.8.X (with bundled SOAP4R) and Ruby 1.9.X (with
2996
- soap4r-ruby1.9 gem). To solve the error, modifying SOAP4R may be
2997
- needed, that seems very difficult. The alternative is Bio::NCBI::REST,
2998
- REST client class for the NCBI EUtil web services.
2999
-
3000
- lib/bio/io/ncbisoap.rb | 156 -------------------------------------------------
3001
- 1 file changed, 156 deletions(-)
3002
- delete mode 100644 lib/bio/io/ncbisoap.rb
3003
-
3004
- commit 314e06e54603bb238015c391904f414b3da48752
3005
- Author: Naohisa Goto <ng@bioruby.org>
3006
- Date: Tue Sep 4 11:13:47 2012 +0900
3007
-
3008
- regenerate bioruby.gemspec with rake regemspec
3009
-
3010
- bioruby.gemspec | 10 ++++------
3011
- 1 file changed, 4 insertions(+), 6 deletions(-)
3012
-
3013
- commit e929d5d23a9b489ef42f30b33959f059baf1e185
3014
- Author: Naohisa Goto <ng@bioruby.org>
3015
- Date: Tue Sep 4 11:09:36 2012 +0900
3016
-
3017
- Remove issues about removed classes Bio::Ensembl and Bio::DBGET.
3018
-
3019
- KNOWN_ISSUES.rdoc | 16 ----------------
3020
- 1 file changed, 16 deletions(-)
3021
-
3022
- commit 550a5440490012f73b6d38d84238cd498f2ebb02
3023
- Author: Naohisa Goto <ng@bioruby.org>
3024
- Date: Tue Sep 4 10:57:20 2012 +0900
3025
-
3026
- Remove Bio::Ensembl because it does not work
3027
-
3028
- * Remove Bio::Ensembl because it does not work after the renewal of
3029
- the Ensembl web site in 2008.
3030
- * Alternative is io-ensembl gem which supports current Ensembl API.
3031
- http://rubygems.org/gems/bio-ensembl
3032
- * Deleted files: lib/bio/io/ensembl.rb,
3033
- test/network/bio/io/test_ensembl.rb, test/unit/bio/io/test_ensembl.rb.
3034
-
3035
- lib/bio/io/ensembl.rb | 229 -----------------------------------
3036
- test/network/bio/io/test_ensembl.rb | 230 ------------------------------------
3037
- test/unit/bio/io/test_ensembl.rb | 111 -----------------
3038
- 3 files changed, 570 deletions(-)
3039
- delete mode 100644 lib/bio/io/ensembl.rb
3040
- delete mode 100644 test/network/bio/io/test_ensembl.rb
3041
- delete mode 100644 test/unit/bio/io/test_ensembl.rb
3042
-
3043
- commit 61301a8ec252f3623f994edd59f597360f73448b
3044
- Author: Naohisa Goto <ng@bioruby.org>
3045
- Date: Tue Sep 4 10:47:52 2012 +0900
3046
-
3047
- Remove obsolete Bio::DBGET
3048
-
3049
- * Remove Bio::DBGET because it uses old original protocol that was
3050
- discontinued about 8 years ago.
3051
- * Remove lib/bio/io/dbget.rb and sample/dbget.
3052
-
3053
- lib/bio/io/dbget.rb | 194 ----------------------------------------------------
3054
- sample/dbget | 37 ----------
3055
- 2 files changed, 231 deletions(-)
3056
- delete mode 100644 lib/bio/io/dbget.rb
3057
- delete mode 100755 sample/dbget
3058
-
3059
- commit 3c5e288a8685ba3279a3ba73f1b31056c1b6f7a8
3060
- Author: Naohisa Goto <ng@bioruby.org>
3061
- Date: Thu Aug 23 00:25:43 2012 +0900
3062
-
3063
- Refresh ChangeLog, showing changes after 1.4.3 release.
3064
-
3065
- * Refresh to the new ChangeLog, showing changes after 1.4.3 release.
3066
- For the changes before 1.4.3, see doc/ChangeLog-1.4.3.
3067
- For the changes before 1.4.2, see doc/ChangeLog-before-1.4.2.
3068
- For the changes before 1.3.1, see doc/ChangeLog-before-1.3.1.
3069
-
3070
- ChangeLog | 61 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
3071
- 1 file changed, 61 insertions(+)
3072
- create mode 100644 ChangeLog
3073
-
3074
- commit 63c13ad8516b9dcacbe001137666c3468968542b
3075
- Author: Naohisa Goto <ng@bioruby.org>
3076
- Date: Thu Aug 23 00:25:07 2012 +0900
3077
-
3078
- Rakefile: Update hardcoded git tag name for updating of ChangeLog.
3079
-
3080
- Rakefile | 2 +-
3081
- 1 file changed, 1 insertion(+), 1 deletion(-)
3082
-
3083
- commit b10c7ad2db24d88726ffb8c63078baa217aeac43
3084
- Author: Naohisa Goto <ng@bioruby.org>
3085
- Date: Thu Aug 23 00:20:01 2012 +0900
3086
-
3087
- renamed ChangeLog to doc/ChangeLog-1.4.3
3088
-
3089
- ChangeLog => doc/ChangeLog-1.4.3 | 0
3090
- 1 file changed, 0 insertions(+), 0 deletions(-)
3091
- rename ChangeLog => doc/ChangeLog-1.4.3 (100%)
3092
-
3093
- commit 0c20cb62ba6b253098e7198c14de1829f72474f5
3094
- Author: Naohisa Goto <ng@bioruby.org>
3095
- Date: Thu Aug 23 00:18:50 2012 +0900
3096
-
3097
- ChangeLog updated: add log about 1.4.3 release.
3098
-
3099
- ChangeLog | 9 +++++++++
3100
- 1 file changed, 9 insertions(+)
3101
-
3102
- commit 5e88ccbe0fefdd4d57f144aaf9073f5e7d93281c
3103
- Author: Naohisa Goto <ng@bioruby.org>
3104
- Date: Thu Aug 23 00:16:25 2012 +0900
3105
-
3106
- New RELEASE_NOTES.rdoc for the next release version.
3107
-
3108
- RELEASE_NOTES.rdoc | 47 +++++++++++++++++++++++++++++++++++++++++++++++
3109
- 1 file changed, 47 insertions(+)
3110
- create mode 100644 RELEASE_NOTES.rdoc
3111
-
3112
- commit e3d40b90d88ab0d0a91d8e32ebf97c16097f0996
3113
- Author: Naohisa Goto <ng@bioruby.org>
3114
- Date: Thu Aug 23 00:12:40 2012 +0900
3115
-
3116
- Renamed RELEASE_NOTES.rdoc to doc/RELEASE_NOTES-1.4.3.rdoc
3117
-
3118
- RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.4.3.rdoc | 0
3119
- 1 file changed, 0 insertions(+), 0 deletions(-)
3120
- rename RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.4.3.rdoc (100%)
3121
-
3122
- commit 08bcabecccb271385d38a0f807e8c408def5a128
3123
- Author: Naohisa Goto <ng@bioruby.org>
3124
- Date: Thu Aug 23 00:00:15 2012 +0900
3125
-
3126
- Bio::BIORUBY_EXTRA_VERSION set to ".5000" (unstable version).
3127
-
3128
- bioruby.gemspec | 2 +-
3129
- lib/bio/version.rb | 2 +-
3130
- 2 files changed, 2 insertions(+), 2 deletions(-)