bio 1.5.1 → 2.0.2

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Files changed (128) hide show
  1. checksums.yaml +5 -5
  2. data/.travis.yml +35 -36
  3. data/ChangeLog +911 -2554
  4. data/{gemfiles/Gemfile.travis-ruby2.2 → Gemfile} +0 -3
  5. data/KNOWN_ISSUES.rdoc +10 -13
  6. data/LEGAL +0 -10
  7. data/README.rdoc +40 -96
  8. data/README_DEV.rdoc +5 -5
  9. data/RELEASE_NOTES.rdoc +118 -234
  10. data/Rakefile +13 -43
  11. data/appveyor.yml +29 -0
  12. data/bioruby.gemspec +18 -81
  13. data/bioruby.gemspec.erb +8 -28
  14. data/doc/ChangeLog-1.5.0 +2919 -0
  15. data/doc/RELEASE_NOTES-1.5.0.rdoc +285 -0
  16. data/doc/Tutorial.rd +6 -108
  17. data/doc/Tutorial.rd.html +19 -98
  18. data/gemfiles/Gemfile.travis-jruby1.8 +3 -5
  19. data/gemfiles/Gemfile.travis-jruby1.9 +0 -3
  20. data/gemfiles/Gemfile.travis-rbx +0 -3
  21. data/gemfiles/Gemfile.travis-ruby1.8 +3 -5
  22. data/gemfiles/Gemfile.travis-ruby1.9 +0 -3
  23. data/gemfiles/Gemfile.windows +6 -0
  24. data/gemfiles/prepare-gemspec.rb +4 -0
  25. data/lib/bio.rb +0 -10
  26. data/lib/bio/appl/blast/genomenet.rb +4 -4
  27. data/lib/bio/appl/blast/report.rb +40 -8
  28. data/lib/bio/appl/fasta/format10.rb +2 -1
  29. data/lib/bio/command.rb +10 -0
  30. data/lib/bio/data/codontable.rb +99 -3
  31. data/lib/bio/db/aaindex.rb +74 -5
  32. data/lib/bio/db/gff.rb +3 -1
  33. data/lib/bio/db/kegg/common.rb +14 -0
  34. data/lib/bio/db/kegg/genes.rb +26 -0
  35. data/lib/bio/db/kegg/pathway.rb +5 -11
  36. data/lib/bio/db/soft.rb +2 -2
  37. data/lib/bio/io/flatfile/autodetection.rb +5 -0
  38. data/lib/bio/io/togows.rb +5 -5
  39. data/lib/bio/map.rb +4 -4
  40. data/lib/bio/sequence/format.rb +1 -0
  41. data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +1 -1
  42. data/lib/bio/util/sirna.rb +2 -0
  43. data/lib/bio/version.rb +6 -8
  44. data/sample/color_scheme_aa.rb +82 -0
  45. data/sample/color_scheme_na.rb +5 -6
  46. data/sample/fastq2html.cwl +23 -0
  47. data/sample/fastq2html.rb +94 -0
  48. data/sample/fastq2html.testdata.yaml +5 -0
  49. data/sample/na2aa.cwl +23 -0
  50. data/sample/na2aa.rb +11 -25
  51. data/sample/na2aa.testdata.yaml +7 -0
  52. data/sample/rev_comp.cwl +23 -0
  53. data/sample/rev_comp.rb +20 -0
  54. data/sample/rev_comp.testdata.yaml +7 -0
  55. data/sample/test_restriction_enzyme_long.rb +1 -1
  56. data/test/network/bio/db/kegg/test_genes_hsa7422.rb +91 -0
  57. data/test/unit/bio/appl/blast/test_report.rb +4 -4
  58. data/test/unit/bio/data/test_codontable.rb +3 -0
  59. data/test/unit/bio/db/test_gff.rb +5 -0
  60. data/test/unit/bio/test_alignment.rb +2 -2
  61. metadata +20 -77
  62. data/bin/bioruby +0 -47
  63. data/bin/br_biofetch.rb +0 -71
  64. data/bin/br_bioflat.rb +0 -293
  65. data/bin/br_biogetseq.rb +0 -45
  66. data/bin/br_pmfetch.rb +0 -422
  67. data/lib/bio/appl/blast/xmlparser.rb +0 -236
  68. data/lib/bio/db/biosql/biosql_to_biosequence.rb +0 -78
  69. data/lib/bio/db/biosql/sequence.rb +0 -444
  70. data/lib/bio/db/phyloxml/phyloxml.xsd +0 -582
  71. data/lib/bio/db/phyloxml/phyloxml_elements.rb +0 -1197
  72. data/lib/bio/db/phyloxml/phyloxml_parser.rb +0 -1001
  73. data/lib/bio/db/phyloxml/phyloxml_writer.rb +0 -227
  74. data/lib/bio/io/biosql/ar-biosql.rb +0 -257
  75. data/lib/bio/io/biosql/biosql.rb +0 -39
  76. data/lib/bio/io/biosql/config/database.yml +0 -21
  77. data/lib/bio/io/sql.rb +0 -79
  78. data/lib/bio/shell.rb +0 -44
  79. data/lib/bio/shell/core.rb +0 -578
  80. data/lib/bio/shell/demo.rb +0 -146
  81. data/lib/bio/shell/interface.rb +0 -217
  82. data/lib/bio/shell/irb.rb +0 -94
  83. data/lib/bio/shell/object.rb +0 -71
  84. data/lib/bio/shell/plugin/blast.rb +0 -42
  85. data/lib/bio/shell/plugin/codon.rb +0 -218
  86. data/lib/bio/shell/plugin/das.rb +0 -58
  87. data/lib/bio/shell/plugin/emboss.rb +0 -23
  88. data/lib/bio/shell/plugin/entry.rb +0 -137
  89. data/lib/bio/shell/plugin/flatfile.rb +0 -101
  90. data/lib/bio/shell/plugin/midi.rb +0 -430
  91. data/lib/bio/shell/plugin/ncbirest.rb +0 -68
  92. data/lib/bio/shell/plugin/obda.rb +0 -45
  93. data/lib/bio/shell/plugin/psort.rb +0 -56
  94. data/lib/bio/shell/plugin/seq.rb +0 -248
  95. data/lib/bio/shell/plugin/togows.rb +0 -40
  96. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +0 -29
  97. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +0 -4
  98. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +0 -27
  99. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +0 -11
  100. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +0 -4
  101. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +0 -7
  102. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
  103. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
  104. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
  105. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +0 -368
  106. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +0 -47
  107. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +0 -144
  108. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +0 -47
  109. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +0 -8
  110. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +0 -10
  111. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +0 -26
  112. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
  113. data/lib/bio/shell/script.rb +0 -25
  114. data/lib/bio/shell/setup.rb +0 -108
  115. data/lib/bio/shell/web.rb +0 -102
  116. data/sample/test_phyloxml_big.rb +0 -205
  117. data/setup.rb +0 -1600
  118. data/test/data/phyloxml/apaf.xml +0 -666
  119. data/test/data/phyloxml/bcl_2.xml +0 -2097
  120. data/test/data/phyloxml/made_up.xml +0 -144
  121. data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +0 -65
  122. data/test/data/phyloxml/phyloxml_examples.xml +0 -415
  123. data/test/unit/bio/db/biosql/tc_biosql.rb +0 -114
  124. data/test/unit/bio/db/biosql/ts_suite_biosql.rb +0 -8
  125. data/test/unit/bio/db/test_phyloxml.rb +0 -821
  126. data/test/unit/bio/db/test_phyloxml_writer.rb +0 -334
  127. data/test/unit/bio/shell/plugin/test_seq.rb +0 -187
  128. data/test/unit/bio/test_shell.rb +0 -20
@@ -0,0 +1,2919 @@
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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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+
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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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+ 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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+ 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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+ RELEASE_NOTES.rdoc: update many
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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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+ * Bug fix: Bio::UniProtKB#gene_name raised NoMethodError when
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+ gene_names method returns nil. It should return nil.
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+ Thanks to Jose Irizarry who reports and sends suggested fix.
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+ (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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+ 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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+ 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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+ update docs; change recommended Ruby versions
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+ README.rdoc | 9 ++++++---
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+ 1 file changed, 6 insertions(+), 3 deletions(-)
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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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+ delete description about SOAP4R
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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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+ .travis.yml: test/unit no longer bundled with Ruby 2.2
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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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+ .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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+ * Bump up version to 1.5.0-dev (1.5.0.20150630)
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+ * Simplify the versioning rules.
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+ * We will adopt the Semantic Versioning since BioRuby 1.5.1.
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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
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+
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+ * Bug fix: update Bio::Hinv::BASE_URI to follow the server URI change.
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+ * Update official documentation URL.
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+ 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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+ delete $Id:$ line
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+ lib/bio/io/hinv.rb | 1 -
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+ 1 file changed, 1 deletion(-)
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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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+ delete sections about SOAP4R issues
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+ KNOWN_ISSUES.rdoc | 12 ------------
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+ 1 file changed, 12 deletions(-)
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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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+ remove commented-out lines of soap4r-ruby1.9
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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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+ 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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+ .travis.yml: update ruby versions, remove ruby 1.9.2
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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
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+ RELEASE_NOTES.rdoc | 20 ++++++++++++++++++++
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+ 1 file changed, 20 insertions(+)
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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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+ bioruby.gemspec | 6 ------
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+ 1 file changed, 6 deletions(-)
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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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+ not to load deleted file lib/bio/shell/plugin/soap.rb
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+ lib/bio/shell.rb | 1 -
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+ 1 file changed, 1 deletion(-)
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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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+ deleted lib/bio/shell/plugin/soap.rb
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+ * deleted lib/bio/shell/plugin/soap.rb because Bio::SOAPWSDL and
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+ all SOAP client classes in BioRuby are removed.
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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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+ 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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+ not to load removed Bio::EBI::SOAP from lib/bio/io/ebisoap.rb
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+ lib/bio.rb | 4 ----
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+ 1 file changed, 4 deletions(-)
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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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+ remove Bio::EBI::SOAP (lib/bio/io/ebisoap.rb)
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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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+ 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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+ 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
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+
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+ * Bio::SOAPWSDL is removed because SOAP4R (SOAP/WSDL library in Ruby)
312
+ is no longer bundled with Ruby since Ruby 1.9. For Ruby 1.9 or later,
313
+ some gems of SOAP4R are available, but we think they are not
314
+ well-maintained. Moreover, many SOAP servers have been retired
315
+ (see previous commits). So, we give up maintaining Bio::SOAPWSDL.
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+
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+ lib/bio/io/soapwsdl.rb | 119 ----------------------------------
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+ test/network/bio/io/test_soapwsdl.rb | 53 ---------------
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+ test/unit/bio/io/test_soapwsdl.rb | 33 ----------
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+ 3 files changed, 205 deletions(-)
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+ delete mode 100644 lib/bio/io/soapwsdl.rb
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+ 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
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+
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+ RELEASE_NOTES.rdoc | 71 +++++++++++++++++++++++++++++++++++++++++++++++++---
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+ 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
376
+
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+ * extconf.rb is deleted because no native extensions are included in
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+ BioRuby and to avoid potential confusions. Nowadays, extconf.rb is
379
+ 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>
388
+ 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>
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+ Date: Fri May 1 23:42:39 2015 +0900
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+
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+ s.license = "Ruby"
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+
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+ * bioruby.gemspec.erb, bioruby.gemspec: s.license = "Ruby"
402
+ Thanks to Peter Cock who reports a patch.
403
+ (https://github.com/bioruby/bioruby/issues/101 )
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+
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+ bioruby.gemspec | 1 +
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+ 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
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+
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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>
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+ Date: Sat Mar 28 01:51:47 2015 +0900
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+
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+ suppress "character class has duplicated range" warnings
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+
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+ lib/bio/db/gff.rb | 4 ++--
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+ 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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+
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+ 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>
466
+ 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 +-
471
+ 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>
475
+ 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>
484
+ 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 ++++----
489
+ 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>
493
+ 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>
502
+ 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 ++++----
507
+ 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>
511
+ Date: Sat Mar 28 01:20:13 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/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>
520
+ 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>
529
+ 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>
538
+ Date: Sat Mar 28 01:08:04 2015 +0900
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+
540
+ suppress "warning: instance variable @tagsize not initialized"
541
+
542
+ * test/unit/bio/test_db.rb: to suppress "warning: instance variable
543
+ @tagsize not initialized" when executing Bio::TestDB#test_fetch,
544
+ @tagsize is set in setup.
545
+
546
+ test/unit/bio/test_db.rb | 5 ++++-
547
+ 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>
551
+ 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>
560
+ Date: Sat Mar 28 00:57:28 2015 +0900
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+
562
+ 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>
569
+ Date: Sat Mar 28 00:55:25 2015 +0900
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+
571
+ delete obsolete $Id:$ line
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+
573
+ 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>
578
+ Date: Sat Mar 28 00:54:37 2015 +0900
579
+
580
+ suppress warning: instance variable @ipr_ids not initialized
581
+
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+ lib/bio/appl/iprscan/report.rb | 2 +-
583
+ 1 file changed, 1 insertion(+), 1 deletion(-)
584
+
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+ commit 52b6073997c1b26fea9d4aae3154b37575944d4d
586
+ Author: Naohisa Goto <ng@bioruby.org>
587
+ 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
590
+
591
+ lib/bio/db/phyloxml/phyloxml_elements.rb | 46 +++++++++++++++++++++++-------
592
+ 1 file changed, 35 insertions(+), 11 deletions(-)
593
+
594
+ commit 3d2e99fe993d76d5ece5bdbcd2e9541fa098c4dd
595
+ Author: Naohisa Goto <ng@bioruby.org>
596
+ Date: Sat Mar 28 00:36:51 2015 +0900
597
+
598
+ suppress "instance variable @XXX not initialized" warnings
599
+
600
+ lib/bio/db/phyloxml/phyloxml_elements.rb | 88 +++++++++++++++---------------
601
+ 1 file changed, 44 insertions(+), 44 deletions(-)
602
+
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+ commit 02d4f98eae3934d8ad9c950b41132eb14653fe27
604
+ Author: Naohisa Goto <ng@bioruby.org>
605
+ Date: Thu Mar 26 20:33:35 2015 +0900
606
+
607
+ suppress warning: instance variable @uri not initialized
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+
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+ lib/bio/db/phyloxml/phyloxml_elements.rb | 2 +-
610
+ 1 file changed, 1 insertion(+), 1 deletion(-)
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+
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+ commit 94277712e9dd000c2d9bf5b6ebfd84d0f2fc3b59
613
+ Author: Naohisa Goto <ng@bioruby.org>
614
+ Date: Thu Mar 26 01:47:45 2015 +0900
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+
616
+ suppress warning: instance variable @format not initialized
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+
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+ lib/bio/db/fastq.rb | 2 +-
619
+ 1 file changed, 1 insertion(+), 1 deletion(-)
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+
621
+ commit e61e1071e4bb7dd9ee995c3a7f864c2ef4384edd
622
+ Author: Naohisa Goto <ng@bioruby.org>
623
+ Date: Thu Mar 26 01:40:33 2015 +0900
624
+
625
+ suppress "instance variable not initialized" warnings
626
+
627
+ * suppress warning: instance variable @sc_match not initialized
628
+ * suppress warning: instance variable @sc_mismatch not initialized
629
+ * suppress warning: instance variable @gaps not initialized
630
+ * suppress warning: instance variable @hit_frame not initialized
631
+ * suppress warning: instance variable @query_frame not initialized
632
+
633
+ lib/bio/appl/blast/format0.rb | 13 ++++++++++---
634
+ 1 file changed, 10 insertions(+), 3 deletions(-)
635
+
636
+ commit 08c458c74a7a34e340e09053cbc0f9c071e27395
637
+ Author: Naohisa Goto <ng@bioruby.org>
638
+ Date: Thu Mar 26 01:09:16 2015 +0900
639
+
640
+ suppress warning: instance variable @pattern not initialized
641
+
642
+ lib/bio/appl/blast/format0.rb | 8 ++++++--
643
+ 1 file changed, 6 insertions(+), 2 deletions(-)
644
+
645
+ commit 33d7eed180fd601972724f4b992f1a17c689ef62
646
+ Author: Naohisa Goto <ng@bioruby.org>
647
+ Date: Thu Mar 26 00:57:02 2015 +0900
648
+
649
+ Test bug fix: fix typo of test target method
650
+
651
+ test/network/bio/test_command.rb | 2 +-
652
+ 1 file changed, 1 insertion(+), 1 deletion(-)
653
+
654
+ commit 76a98bce1affac03483c08f803d4314b42a0a3d3
655
+ Author: Naohisa Goto <ng@bioruby.org>
656
+ Date: Thu Mar 26 00:32:25 2015 +0900
657
+
658
+ Incompatible Change: Bio::Command.make_cgi_params rejects single String
659
+
660
+ * Incompatible Change: Bio::Command.make_cgi_params no longer accepts a
661
+ single String as a form. Use Hash or Array containing key-value pairs
662
+ as String objects. This change also affects Bio::Command.post_form
663
+ and Bio::Command.http_post_form which internally use this method.
664
+
665
+ lib/bio/command.rb | 2 +-
666
+ test/unit/bio/test_command.rb | 9 +++++----
667
+ 2 files changed, 6 insertions(+), 5 deletions(-)
668
+
669
+ commit b1612545a7516befd850a6d5925aa73bbaa4b4b0
670
+ Author: Naohisa Goto <ng@bioruby.org>
671
+ Date: Wed Mar 25 02:36:41 2015 +0900
672
+
673
+ delete obsolete $Id:$ line
674
+
675
+ lib/bio/io/togows.rb | 1 -
676
+ 1 file changed, 1 deletion(-)
677
+
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+ commit 4d5a419cc78ff2a79cff2812adc6f16f286204e8
679
+ Author: Naohisa Goto <ng@bioruby.org>
680
+ Date: Wed Mar 25 02:35:45 2015 +0900
681
+
682
+ delete obsolete $Id:$ line
683
+
684
+ test/network/bio/io/test_togows.rb | 1 -
685
+ 1 file changed, 1 deletion(-)
686
+
687
+ commit a8d2c4cac665b4bb8140df329a9cc1d6e5e2d02d
688
+ Author: Naohisa Goto <ng@bioruby.org>
689
+ Date: Wed Mar 25 02:35:03 2015 +0900
690
+
691
+ delete obsolete $Id:$ line
692
+
693
+ test/unit/bio/io/test_togows.rb | 1 -
694
+ 1 file changed, 1 deletion(-)
695
+
696
+ commit dd0967db3743789ea5aa48623df8d97f93062694
697
+ Author: Naohisa Goto <ng@bioruby.org>
698
+ Date: Wed Mar 25 02:33:49 2015 +0900
699
+
700
+ test_make_path: add test data using Symbol objects
701
+
702
+ test/unit/bio/io/test_togows.rb | 4 +++-
703
+ 1 file changed, 3 insertions(+), 1 deletion(-)
704
+
705
+ commit e07158a60ca666b5d625408bcf8fa602fd8114a8
706
+ Author: Naohisa Goto <ng@bioruby.org>
707
+ Date: Wed Mar 25 02:22:31 2015 +0900
708
+
709
+ Bio::TogoWS::REST#entry: comma between IDs should NOT be escaped to %2C
710
+
711
+ lib/bio/io/togows.rb | 11 +++++++++--
712
+ 1 file changed, 9 insertions(+), 2 deletions(-)
713
+
714
+ commit 98546289b2f2da2dc7f9586fd5e2942da4d8f3a8
715
+ Author: Naohisa Goto <ng@bioruby.org>
716
+ Date: Wed Mar 25 02:00:17 2015 +0900
717
+
718
+ Bug fix: search with offset did not work due to TogoWS server change
719
+
720
+ * lib/bio/io/togows.rb: Bug fix: Bio::TogoWS::REST#search with offset
721
+ and limit did not work due to TogoWS server change about URI escape.
722
+ For example,
723
+ http://togows.org/search/nuccore/Milnesium+tardigradum/2%2C3 fails,
724
+ http://togows.org/search/nuccore/Milnesium+tardigradum/2,3 works fine.
725
+
726
+ lib/bio/io/togows.rb | 24 +++++++++++++++++++++---
727
+ 1 file changed, 21 insertions(+), 3 deletions(-)
728
+
729
+ commit 7097f80e315a0a6332e7a76a5bb261649e8dcc1a
730
+ Author: Naohisa Goto <ng@bioruby.org>
731
+ Date: Wed Mar 25 01:33:26 2015 +0900
732
+
733
+ Bug fix due to TogoWS convert method spec change
734
+
735
+ * lib/bio/io/togows.rb: Bug fix: Bio::TogoWS::REST#convert did not work
736
+ because of the spec change of TogoWS REST API.
737
+
738
+ lib/bio/io/togows.rb | 7 +++----
739
+ 1 file changed, 3 insertions(+), 4 deletions(-)
740
+
741
+ commit 1a9b1063af4c0b32cd287d4a2c2466343aeddb98
742
+ Author: Naohisa Goto <ng@bioruby.org>
743
+ Date: Wed Mar 25 01:30:34 2015 +0900
744
+
745
+ improve tests for bio/command.rb for methods using http protocol
746
+
747
+ test/network/bio/test_command.rb | 67 ++++++++++++++++++++++++++++++++++++--
748
+ 1 file changed, 65 insertions(+), 2 deletions(-)
749
+
750
+ commit c63920e4d8569e3eaef201d4d60fcddfa15f1f34
751
+ Author: Naohisa Goto <ng@bioruby.org>
752
+ Date: Wed Mar 25 01:30:06 2015 +0900
753
+
754
+ delete obsolete $Id:$ line
755
+
756
+ lib/bio/command.rb | 1 -
757
+ 1 file changed, 1 deletion(-)
758
+
759
+ commit 1683edac0e9ecbf819ffcd332a6db2d25c2d596a
760
+ Author: Naohisa Goto <ng@bioruby.org>
761
+ Date: Wed Mar 25 01:28:28 2015 +0900
762
+
763
+ new methods Bio::Command.http_post and Bio::Command.post to post raw data
764
+
765
+ lib/bio/command.rb | 61 ++++++++++++++++++++++++++++++++++++++++++++++++++++
766
+ 1 file changed, 61 insertions(+)
767
+
768
+ commit a40157205282e148bf3a2e43aed1e08d713fb598
769
+ Author: Naohisa Goto <ng@bioruby.org>
770
+ Date: Tue Mar 24 00:46:23 2015 +0900
771
+
772
+ suppress warnings "instance variable @circular not initialized"
773
+
774
+ lib/bio/util/restriction_enzyme/range/sequence_range.rb | 4 ++--
775
+ 1 file changed, 2 insertions(+), 2 deletions(-)
776
+
777
+ commit abcac8de85c9606f6a1879fe9d2ae559911708c9
778
+ Author: Naohisa Goto <ng@bioruby.org>
779
+ Date: Tue Mar 24 00:29:42 2015 +0900
780
+
781
+ delete obsolete $Id:$ line
782
+
783
+ test/unit/bio/io/flatfile/test_autodetection.rb | 1 -
784
+ 1 file changed, 1 deletion(-)
785
+
786
+ commit 1b5bf586af238b712a9f640087421fd299376c2d
787
+ Author: Naohisa Goto <ng@bioruby.org>
788
+ Date: Tue Mar 24 00:28:38 2015 +0900
789
+
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+ suppress warning: assigned but unused variable - length
791
+
792
+ test/unit/bio/io/flatfile/test_autodetection.rb | 2 +-
793
+ 1 file changed, 1 insertion(+), 1 deletion(-)
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+
795
+ commit 5497068d17c2794ab2b6ef1e603e5478a86537c6
796
+ Author: Naohisa Goto <ng@bioruby.org>
797
+ Date: Tue Mar 24 00:22:54 2015 +0900
798
+
799
+ add/modify assertions to suppress "unused variable" warnings
800
+
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+ test/unit/bio/db/genbank/test_genbank.rb | 12 +++++++++---
802
+ 1 file changed, 9 insertions(+), 3 deletions(-)
803
+
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+ commit d5bafd8b7ee28ab0418b09fd6dd47abcb9eb1ee5
805
+ Author: Naohisa Goto <ng@bioruby.org>
806
+ Date: Mon Mar 23 23:57:56 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/blast.rb | 1 -
811
+ 1 file changed, 1 deletion(-)
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+
813
+ commit bbd60d1aae7c894f914b7265d2de22fea5eb3faf
814
+ Author: Naohisa Goto <ng@bioruby.org>
815
+ Date: Mon Mar 23 23:56:42 2015 +0900
816
+
817
+ suppress warning: assigned but unused variable - dummy
818
+
819
+ lib/bio/appl/blast.rb | 2 +-
820
+ 1 file changed, 1 insertion(+), 1 deletion(-)
821
+
822
+ commit 4a91502ccf14ab8655645144120aa97d0c8313a5
823
+ Author: Naohisa Goto <ng@bioruby.org>
824
+ Date: Mon Mar 23 20:32:59 2015 +0900
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+
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+ delete obsolete $Id:$ line
827
+
828
+ lib/bio/shell/setup.rb | 1 -
829
+ 1 file changed, 1 deletion(-)
830
+
831
+ commit c437a4078ff8e2869b9c1ab3543022db373a93c3
832
+ Author: Naohisa Goto <ng@bioruby.org>
833
+ Date: Mon Mar 23 20:32:20 2015 +0900
834
+
835
+ suppress warning: instance variable @mode not initialized
836
+
837
+ lib/bio/shell/setup.rb | 2 +-
838
+ 1 file changed, 1 insertion(+), 1 deletion(-)
839
+
840
+ commit 8967cf280d5ca8491d57a11e4f3ffab7369c4ea8
841
+ Author: Naohisa Goto <ng@bioruby.org>
842
+ Date: Mon Mar 23 20:28:50 2015 +0900
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+
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+ delete obsolete $Id:$ line
845
+
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+ lib/bio/shell/irb.rb | 1 -
847
+ 1 file changed, 1 deletion(-)
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+
849
+ commit 42b5f030067be4bc9c53ccb4c06ccfc5e8d9df03
850
+ Author: Naohisa Goto <ng@bioruby.org>
851
+ Date: Mon Mar 23 20:28:27 2015 +0900
852
+
853
+ change deprecated method File.exists? to File.exist?
854
+
855
+ lib/bio/shell/irb.rb | 2 +-
856
+ 1 file changed, 1 insertion(+), 1 deletion(-)
857
+
858
+ commit 389ad2f311f161f235db2373aeb2f5500b1ea65f
859
+ Author: Naohisa Goto <ng@bioruby.org>
860
+ Date: Mon Mar 23 20:27:01 2015 +0900
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+
862
+ delete obsolete $Id:$ line
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+
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+ lib/bio/shell/interface.rb | 1 -
865
+ 1 file changed, 1 deletion(-)
866
+
867
+ commit de5949798d66c16d2b5e2cf8ba7192049ec99c5b
868
+ Author: Naohisa Goto <ng@bioruby.org>
869
+ Date: Mon Mar 23 20:26:37 2015 +0900
870
+
871
+ change deprecated method File.exists? to File.exist?
872
+
873
+ lib/bio/shell/interface.rb | 6 +++---
874
+ 1 file changed, 3 insertions(+), 3 deletions(-)
875
+
876
+ commit c8907059a716a8778e333755c8fb53bb2a0c7158
877
+ Author: Naohisa Goto <ng@bioruby.org>
878
+ Date: Mon Mar 23 20:24:58 2015 +0900
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+
880
+ delete obsolete $Id:$ line
881
+
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+ lib/bio/shell/core.rb | 1 -
883
+ 1 file changed, 1 deletion(-)
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+
885
+ commit 1fe5903f8acd8045d203465a099a45218e7e3891
886
+ Author: Naohisa Goto <ng@bioruby.org>
887
+ Date: Mon Mar 23 20:24:25 2015 +0900
888
+
889
+ change deprecated method File.exists? to File.exist?
890
+
891
+ lib/bio/shell/core.rb | 10 +++++-----
892
+ 1 file changed, 5 insertions(+), 5 deletions(-)
893
+
894
+ commit 929207c6f186c81f076fab9b1bbbd23c4b966f4e
895
+ Author: Naohisa Goto <ng@bioruby.org>
896
+ Date: Mon Mar 23 20:20:05 2015 +0900
897
+
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+ delete obsolete $Id:$ line
899
+
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+ test/unit/bio/db/pdb/test_pdb.rb | 1 -
901
+ 1 file changed, 1 deletion(-)
902
+
903
+ commit e75c57fcd7abc56ba6fcbf1996e491aca890f5b1
904
+ Author: Naohisa Goto <ng@bioruby.org>
905
+ Date: Mon Mar 23 20:19:30 2015 +0900
906
+
907
+ suppress "assigned but unused variable" warnings
908
+
909
+ test/unit/bio/db/pdb/test_pdb.rb | 21 ++++++++++++++-------
910
+ 1 file changed, 14 insertions(+), 7 deletions(-)
911
+
912
+ commit b458301f47322c265fce27efd0ed71443c17d9d7
913
+ Author: Naohisa Goto <ng@bioruby.org>
914
+ Date: Mon Mar 23 18:34:12 2015 +0900
915
+
916
+ delete obsolete $Id:$ line
917
+
918
+ lib/bio/shell/plugin/entry.rb | 1 -
919
+ 1 file changed, 1 deletion(-)
920
+
921
+ commit c3f909fe06b82b3cbd4bdcbcdef668fc0727be9d
922
+ Author: Naohisa Goto <ng@bioruby.org>
923
+ Date: Mon Mar 23 18:33:30 2015 +0900
924
+
925
+ change deprecated method File.exists? to File.exist?
926
+
927
+ lib/bio/shell/plugin/entry.rb | 4 ++--
928
+ 1 file changed, 2 insertions(+), 2 deletions(-)
929
+
930
+ commit 7ba6349c2446aa03b843a2a8fb49505c8f63c6ca
931
+ Author: Naohisa Goto <ng@bioruby.org>
932
+ Date: Mon Mar 23 18:20:44 2015 +0900
933
+
934
+ change deprecated method File.exists? to File.exist?
935
+
936
+ lib/bio/appl/meme/mast.rb | 8 ++++----
937
+ 1 file changed, 4 insertions(+), 4 deletions(-)
938
+
939
+ commit e7f78ea3c3fb1b78adcc6ae13f450cf2cda361cd
940
+ Author: Naohisa Goto <ng@bioruby.org>
941
+ Date: Mon Mar 23 18:10:27 2015 +0900
942
+
943
+ delete obsolete $Id:$ line
944
+
945
+ lib/bio/db/phyloxml/phyloxml_writer.rb | 1 -
946
+ 1 file changed, 1 deletion(-)
947
+
948
+ commit b32eae0050a73bd5a2931c17a6694f494ad00bb2
949
+ Author: Naohisa Goto <ng@bioruby.org>
950
+ Date: Mon Mar 23 18:07:54 2015 +0900
951
+
952
+ suppress warning: mismatched indentations at 'end' with 'def' at 166
953
+
954
+ lib/bio/db/phyloxml/phyloxml_writer.rb | 2 +-
955
+ 1 file changed, 1 insertion(+), 1 deletion(-)
956
+
957
+ commit bd735347283ce5d332245d0349186f300800a43f
958
+ Author: Naohisa Goto <ng@bioruby.org>
959
+ Date: Sat Mar 21 12:57:03 2015 +0900
960
+
961
+ remove duplicated line and suppress Ruby 2.2 warning
962
+
963
+ setup.rb | 1 -
964
+ 1 file changed, 1 deletion(-)
965
+
966
+ commit 68ad10e178594691c77ba4b97c2449fecf0ac9de
967
+ Author: Naohisa Goto <ng@bioruby.org>
968
+ Date: Sat Mar 21 12:50:46 2015 +0900
969
+
970
+ Ruby 1.9 support: suppress "shadowing outer local variable" warnings
971
+
972
+ setup.rb | 10 +++++-----
973
+ 1 file changed, 5 insertions(+), 5 deletions(-)
974
+
975
+ commit 2343482078aec8373f7a2eb8ed4d7c44119f809c
976
+ Author: Naohisa Goto <ng@bioruby.org>
977
+ Date: Sat Mar 21 12:16:45 2015 +0900
978
+
979
+ Ruby 2.2 support: Config was renamed to RbConfig
980
+
981
+ setup.rb | 2 +-
982
+ 1 file changed, 1 insertion(+), 1 deletion(-)
983
+
984
+ commit d512712745142d6c6ebe9a6ef51c8c4773bd7c2c
985
+ Author: Naohisa Goto <ng@bioruby.org>
986
+ Date: Sat Mar 21 11:52:47 2015 +0900
987
+
988
+ Ruby 1.9 support: suppress "shadowing outer local variable" warnings
989
+
990
+ lib/bio/db/embl/format_embl.rb | 6 +++---
991
+ 1 file changed, 3 insertions(+), 3 deletions(-)
992
+
993
+ commit bfa75df9047ab6855c931558f6bf9fdbb1c3c288
994
+ Author: Naohisa Goto <ng@bioruby.org>
995
+ Date: Sat Mar 21 11:36:01 2015 +0900
996
+
997
+ delete obsolete $Id:$ line
998
+
999
+ lib/bio/io/flatfile/buffer.rb | 1 -
1000
+ 1 file changed, 1 deletion(-)
1001
+
1002
+ commit d6fbaa0c555117ebadd46e284ae357586856102d
1003
+ Author: Naohisa Goto <ng@bioruby.org>
1004
+ Date: Sat Mar 21 11:35:07 2015 +0900
1005
+
1006
+ Ruby 1.9 support: suppress warning: shadowing outer local variable - fobj
1007
+
1008
+ lib/bio/io/flatfile/buffer.rb | 8 ++++----
1009
+ 1 file changed, 4 insertions(+), 4 deletions(-)
1010
+
1011
+ commit 0083d3284ec181f4bcc3144f76b12f9d52e3eff6
1012
+ Author: Naohisa Goto <ng@bioruby.org>
1013
+ Date: Sat Mar 21 11:29:39 2015 +0900
1014
+
1015
+ delete obsolete $Id:$ line
1016
+
1017
+ lib/bio/io/fastacmd.rb | 1 -
1018
+ 1 file changed, 1 deletion(-)
1019
+
1020
+ commit d4909c0e80e572a639edba07388e430c7f5d6ce8
1021
+ Author: Naohisa Goto <ng@bioruby.org>
1022
+ Date: Sat Mar 21 11:29:01 2015 +0900
1023
+
1024
+ remove old sample script in "if $0 == __FILE__" block
1025
+
1026
+ lib/bio/io/fastacmd.rb | 15 ---------------
1027
+ 1 file changed, 15 deletions(-)
1028
+
1029
+ commit 8171162d0a3991d5f0d9a8bccee57250248d6d3d
1030
+ Author: Naohisa Goto <ng@bioruby.org>
1031
+ Date: Sat Mar 21 11:15:10 2015 +0900
1032
+
1033
+ delete obsolete $Id:$ line
1034
+
1035
+ lib/bio/db/go.rb | 1 -
1036
+ 1 file changed, 1 deletion(-)
1037
+
1038
+ commit ed7c9a5335ef59399f3098311f47b8dec519281a
1039
+ Author: Naohisa Goto <ng@bioruby.org>
1040
+ Date: Sat Mar 21 11:14:19 2015 +0900
1041
+
1042
+ Ruby 1.9 support: suppress warnings: "shadowing outer local variable - goid"
1043
+
1044
+ lib/bio/db/go.rb | 4 ++--
1045
+ 1 file changed, 2 insertions(+), 2 deletions(-)
1046
+
1047
+ commit dd543068b046c9a0c2a40159c830c92b680244f1
1048
+ Author: Naohisa Goto <ng@bioruby.org>
1049
+ Date: Sat Mar 21 11:03:08 2015 +0900
1050
+
1051
+ delete obsolete $Id:$ line
1052
+
1053
+ lib/bio/db/phyloxml/phyloxml_elements.rb | 1 -
1054
+ 1 file changed, 1 deletion(-)
1055
+
1056
+ commit 4c74a6e3aeca30820b0be61e867c9201445542ec
1057
+ Author: Naohisa Goto <ng@bioruby.org>
1058
+ Date: Sat Mar 21 10:24:40 2015 +0900
1059
+
1060
+ suppress warning: mismatched indentations at 'end' with 'class'
1061
+
1062
+ lib/bio/db/phyloxml/phyloxml_elements.rb | 4 ++--
1063
+ 1 file changed, 2 insertions(+), 2 deletions(-)
1064
+
1065
+ commit ee4ffdc748c1f9f45e97ff7f0da8350c5468c333
1066
+ Author: Naohisa Goto <ng@bioruby.org>
1067
+ Date: Sat Mar 21 10:08:30 2015 +0900
1068
+
1069
+ delete obsolete $Id:$ line
1070
+
1071
+ lib/bio/db/phyloxml/phyloxml_parser.rb | 1 -
1072
+ 1 file changed, 1 deletion(-)
1073
+
1074
+ commit 46a4edc8729ff836ae28d11f1503c9923275b9f6
1075
+ Author: Naohisa Goto <ng@bioruby.org>
1076
+ Date: Sat Mar 21 10:00:04 2015 +0900
1077
+
1078
+ Ruby 1.9 support: suppress warning "shadowing outer local variable - flag"
1079
+
1080
+ lib/bio/db/phyloxml/phyloxml_parser.rb | 2 +-
1081
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1082
+
1083
+ commit db3552c683edf79adbfa5ed897f5ef91e8417585
1084
+ Author: Naohisa Goto <ng@bioruby.org>
1085
+ Date: Fri Mar 20 16:33:45 2015 +0900
1086
+
1087
+ Bug fix: Bio::PhyloXML::Parser.open_uri did not return block return value
1088
+
1089
+ * Bug fix: Bio::PhyloXML::Parser.open_uri did not return block
1090
+ return value when giving block.
1091
+ * Suppress warning "assigned but unused variable - ret"
1092
+
1093
+ lib/bio/db/phyloxml/phyloxml_parser.rb | 1 +
1094
+ 1 file changed, 1 insertion(+)
1095
+
1096
+ commit 84c2c4e94352cc9cef982d3b505b4f439617e01e
1097
+ Author: Naohisa Goto <ng@bioruby.org>
1098
+ Date: Fri Mar 20 16:21:49 2015 +0900
1099
+
1100
+ delete obsolete $Id:$ line
1101
+
1102
+ lib/bio/appl/genscan/report.rb | 1 -
1103
+ 1 file changed, 1 deletion(-)
1104
+
1105
+ commit 05c55d0aaf1dc130ac04155622ccebb3394fc3c0
1106
+ Author: Naohisa Goto <ng@bioruby.org>
1107
+ Date: Fri Mar 20 16:21:06 2015 +0900
1108
+
1109
+ Ruby 1.9 support: suppress warning "shadowing outer local variable - i"
1110
+
1111
+ lib/bio/appl/genscan/report.rb | 2 +-
1112
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1113
+
1114
+ commit 5edcc1c97ca7c292fa6551509570daf68ac36837
1115
+ Author: Naohisa Goto <ng@bioruby.org>
1116
+ Date: Fri Mar 20 16:13:57 2015 +0900
1117
+
1118
+ Ruby 1.9 support: suppress warning "shadowing outer local variable - y"
1119
+
1120
+ lib/bio/appl/blast/format0.rb | 2 +-
1121
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1122
+
1123
+ commit 813d53a06258244a47784697e8fc95f1f15db8da
1124
+ Author: Naohisa Goto <ng@bioruby.org>
1125
+ Date: Fri Mar 20 16:03:19 2015 +0900
1126
+
1127
+ delete obsolete $Id:$ line
1128
+
1129
+ lib/bio/io/das.rb | 1 -
1130
+ 1 file changed, 1 deletion(-)
1131
+
1132
+ commit b6ae4a423dd763969c8e18ca6a578fd0600d6159
1133
+ Author: Naohisa Goto <ng@bioruby.org>
1134
+ Date: Fri Mar 20 16:02:20 2015 +0900
1135
+
1136
+ Ruby 1.9 support: suppress "warning: shadowing outer local variable - e"
1137
+
1138
+ lib/bio/io/das.rb | 80 ++++++++++++++++++++++++++---------------------------
1139
+ 1 file changed, 40 insertions(+), 40 deletions(-)
1140
+
1141
+ commit 7fa75a644167dd8c189f681e29c1cf5f1bf2fe0b
1142
+ Author: Naohisa Goto <ng@bioruby.org>
1143
+ Date: Fri Mar 20 15:36:00 2015 +0900
1144
+
1145
+ delete obsolete $Id:$ line
1146
+
1147
+ lib/bio/shell/plugin/seq.rb | 1 -
1148
+ 1 file changed, 1 deletion(-)
1149
+
1150
+ commit 051aba1519d71f1205363c4421feb6c06881ab0c
1151
+ Author: Naohisa Goto <ng@bioruby.org>
1152
+ Date: Fri Mar 20 15:29:02 2015 +0900
1153
+
1154
+ Bug fix: Ruby 1.9 support: did not yield the last part of the string
1155
+
1156
+ * lib/bio/shell/plugin/seq.rb: Bug fix: Ruby 1.9 support:
1157
+ String#step and #skip (extended by bioruby-shell) did not yield
1158
+ the last part of the string due to a change from Ruby 1.8 to 1.9.
1159
+ * Suppress warning message "shadowing outer local variable - i"
1160
+
1161
+ lib/bio/shell/plugin/seq.rb | 12 +++++++-----
1162
+ 1 file changed, 7 insertions(+), 5 deletions(-)
1163
+
1164
+ commit a9f2bff92de58c2ab4cefc67e721d3ad69e9de98
1165
+ Author: Naohisa Goto <ng@bioruby.org>
1166
+ Date: Fri Mar 20 15:09:16 2015 +0900
1167
+
1168
+ Ruby 2.2 support: suppress a "shadowing outer local variable" warning
1169
+
1170
+ lib/bio/alignment.rb | 6 +++---
1171
+ 1 file changed, 3 insertions(+), 3 deletions(-)
1172
+
1173
+ commit d0bcc8766d91eb7cacea2a6d5b32b3e0b3c5ce56
1174
+ Author: Naohisa Goto <ng@bioruby.org>
1175
+ Date: Fri Mar 20 14:31:04 2015 +0900
1176
+
1177
+ delete obsolete $Id:$ line
1178
+
1179
+ test/unit/bio/test_alignment.rb | 1 -
1180
+ 1 file changed, 1 deletion(-)
1181
+
1182
+ commit 0c8fa8fd558088822a98e11b6fa4bec9b37ebec7
1183
+ Author: Naohisa Goto <ng@bioruby.org>
1184
+ Date: Fri Mar 20 14:26:38 2015 +0900
1185
+
1186
+ Ruby 2.2 support: comment out duplicated line to suppress warning
1187
+
1188
+ * Ruby 2.2 support: test/unit/bio/test_alignment.rb:
1189
+ Suppress warning: duplicated key at line 182 ignored: "t"
1190
+
1191
+ test/unit/bio/test_alignment.rb | 2 +-
1192
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1193
+
1194
+ commit ab17c40e1ce492dc924205e8e2f90d31adae4464
1195
+ Author: Naohisa Goto <ng@bioruby.org>
1196
+ Date: Fri Mar 20 14:18:08 2015 +0900
1197
+
1198
+ Ruby 2.2 support: some tests did not run with test-unit gem
1199
+
1200
+ * Ruby 2.2 support: test/unit/bio/db/test_fastq.rb
1201
+ Support for test-unit gem bundled in Ruby 2.2.
1202
+ See commit log b9488a64abb780c5e9b6cd28e8264bad399fa749 for details.
1203
+
1204
+ test/unit/bio/db/test_fastq.rb | 18 ++++++++++++++----
1205
+ 1 file changed, 14 insertions(+), 4 deletions(-)
1206
+
1207
+ commit ea668d73c18e3df33625cba4352ad5f6966e0eb4
1208
+ Author: Naohisa Goto <ng@bioruby.org>
1209
+ Date: Fri Mar 20 14:03:43 2015 +0900
1210
+
1211
+ delete obsolete $Id:$ line
1212
+
1213
+ test/unit/bio/appl/sim4/test_report.rb | 1 -
1214
+ 1 file changed, 1 deletion(-)
1215
+
1216
+ commit 1abb8d362a0f2443b48923bcccba3d7d0caa1f1d
1217
+ Author: Naohisa Goto <ng@bioruby.org>
1218
+ Date: Fri Mar 20 13:57:33 2015 +0900
1219
+
1220
+ Ruby 2.2 support: some tests did not run with test-unit gem
1221
+
1222
+ * Ruby 2.2 support: test/unit/bio/appl/sim4/test_report.rb
1223
+ Support for test-unit gem bundled in Ruby 2.2.
1224
+ See commit log b9488a64abb780c5e9b6cd28e8264bad399fa749 for details.
1225
+
1226
+ test/unit/bio/appl/sim4/test_report.rb | 62 +++++++++++++++++++++++---------
1227
+ 1 file changed, 46 insertions(+), 16 deletions(-)
1228
+
1229
+ commit b9488a64abb780c5e9b6cd28e8264bad399fa749
1230
+ Author: Naohisa Goto <ng@bioruby.org>
1231
+ Date: Fri Mar 20 13:13:28 2015 +0900
1232
+
1233
+ Ruby 2.2 support: some tests did not run with test-unit gem
1234
+
1235
+ * Ruby 2.2 support: test/unit/bio/appl/blast/test_report.rb:
1236
+ With test-unit gem bundled in Ruby 2.2, test methods inherited
1237
+ from a parent class and executed in the parent class do not
1238
+ run in the child class. To avoid the behavior, test methods
1239
+ are moved to modules and test classes are changed to include
1240
+ the modules.
1241
+
1242
+ test/unit/bio/appl/blast/test_report.rb | 156 ++++++++++++++++++++++---------
1243
+ 1 file changed, 110 insertions(+), 46 deletions(-)
1244
+
1245
+ commit febe8bbf614e530f597d7306d33df5f5f4ee6699
1246
+ Author: Naohisa Goto <ng@bioruby.org>
1247
+ Date: Thu Mar 19 00:55:09 2015 +0900
1248
+
1249
+ try to use bio-old-biofetch-emulator gem
1250
+
1251
+ * bin/br_biofetch.rb: try to use bio-old-biofetch-emulator gem.
1252
+ Without bio-old-biofetch-emulator, the program exits with error
1253
+ message when default BioRuby BioFetch server is specified.
1254
+
1255
+ bin/br_biofetch.rb | 19 +++++++++++++++++++
1256
+ 1 file changed, 19 insertions(+)
1257
+
1258
+ commit 08450e0a35cbf5596dd30238d23aa7a7296c8f67
1259
+ Author: Naohisa Goto <ng@bioruby.org>
1260
+ Date: Thu Mar 19 00:36:10 2015 +0900
1261
+
1262
+ do not repeat default_url and another_url
1263
+
1264
+ bin/br_biofetch.rb | 14 ++++++++++----
1265
+ 1 file changed, 10 insertions(+), 4 deletions(-)
1266
+
1267
+ commit 8e39d3411405b09cc6ea55ba31e5206536ebf59d
1268
+ Author: Naohisa Goto <ng@bioruby.org>
1269
+ Date: Wed Mar 18 23:57:59 2015 +0900
1270
+
1271
+ Revert e29fc5fadbe0dae6528cf49637496dc2df3ec0dc
1272
+
1273
+ * bin/br_biofetch.rb: revert e29fc5fadbe0dae6528cf49637496dc2df3ec0dc
1274
+ because the old deprecated bioruby biofetch server can be emulated
1275
+ by bio-old-biofetch-emulator gem package.
1276
+
1277
+ bin/br_biofetch.rb | 15 ++++++++-------
1278
+ 1 file changed, 8 insertions(+), 7 deletions(-)
1279
+
1280
+ commit 849c38931a64b7ff2ba7ec46a495e65a99a869fb
1281
+ Author: Ben J. Woodcroft <donttrustben near gmail.com>
1282
+ Date: Wed Aug 8 09:44:09 2012 +1000
1283
+
1284
+ add FastaFormat#first_name method
1285
+
1286
+ lib/bio/db/fasta.rb | 17 ++++++++++++++++
1287
+ test/unit/bio/db/test_fasta.rb | 42 +++++++++++++++++++++++++++++++++++++++-
1288
+ 2 files changed, 58 insertions(+), 1 deletion(-)
1289
+
1290
+ commit 888a70508c0392cae89021feba5c4a6a62228a11
1291
+ Author: Naohisa Goto <ng@bioruby.org>
1292
+ Date: Fri Nov 14 15:08:35 2014 +0900
1293
+
1294
+ fix typo
1295
+
1296
+ * fix typo. Thanks to Iain Barnett who reported the bug in
1297
+ https://github.com/bioruby/bioruby/pull/93
1298
+ (c4843d65447f6a434da523c9c313f34d025f36f8)
1299
+
1300
+ lib/bio/sequence/compat.rb | 2 +-
1301
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1302
+
1303
+ commit afc6df190109649e8eb11b2af1184ddfcf5327d3
1304
+ Author: Naohisa Goto <ng@bioruby.org>
1305
+ Date: Fri Nov 14 14:29:42 2014 +0900
1306
+
1307
+ add documentation when gc_percent is not enough
1308
+
1309
+ lib/bio/sequence/na.rb | 8 ++++++++
1310
+ 1 file changed, 8 insertions(+)
1311
+
1312
+ commit bb63f67f2dfe6dba5c70ada033ca0cc1ecaa7783
1313
+ Author: Naohisa Goto <ng@bioruby.org>
1314
+ Date: Thu Nov 13 21:43:00 2014 +0900
1315
+
1316
+ Add tests for Bio::PubMed#search, query, pmfetch
1317
+
1318
+ * Add tests for Bio::PubMed#search, query, pmfetch, although
1319
+ they will be deprecated in the future.
1320
+ * This commit and commit bfe4292c51bba5c4032027c36c35e98f28a9605a
1321
+ are inspired by https://github.com/bioruby/bioruby/pull/76
1322
+ (though the pull request have not been merged), and the commits
1323
+ fix the issue https://github.com/bioruby/bioruby/issues/75.
1324
+ Thanks to Paul Leader who reported the issue and the pull request.
1325
+
1326
+ test/network/bio/io/test_pubmed.rb | 49 ++++++++++++++++++++++++++++++++++++
1327
+ 1 file changed, 49 insertions(+)
1328
+
1329
+ commit 74edba100da83c27f2edb7a9edc9ec98265a7cff
1330
+ Author: Naohisa Goto <ng@bioruby.org>
1331
+ Date: Thu Nov 13 12:05:12 2014 +0900
1332
+
1333
+ Change default tool and email values
1334
+
1335
+ * Default "tool" and "email" values are changed to "bioruby" and
1336
+ "staff@bioruby.org" respectively. Now, the author of a script
1337
+ do not need to set his/her email address unless the script makes
1338
+ excess traffic to NCBI.
1339
+ * Update RDoc documentation
1340
+
1341
+ lib/bio/io/ncbirest.rb | 48 +++++++++++++++++++++++++++++++++++++++++++-----
1342
+ 1 file changed, 43 insertions(+), 5 deletions(-)
1343
+
1344
+ commit bfe4292c51bba5c4032027c36c35e98f28a9605a
1345
+ Author: Naohisa Goto <ng@bioruby.org>
1346
+ Date: Thu Nov 13 11:54:53 2014 +0900
1347
+
1348
+ Bug fix: use NCBI E-Utilities instead of old deprecated API
1349
+
1350
+ * Bio::PubMed#search, query, pmfetch: remove old code using deprecated
1351
+ and/or unofficial web API, and change use esearch or efetch methods
1352
+ which use NCBI E-utilities. These methods will be deprecated in the
1353
+ future. To indicate this, show warning message if $VERBOSE is true.
1354
+ * Update RDoc documentation
1355
+
1356
+ lib/bio/io/pubmed.rb | 157 ++++++++++++++++++++++++--------------------------
1357
+ 1 file changed, 76 insertions(+), 81 deletions(-)
1358
+
1359
+ commit d78173a6eb6d8177e733decc0b8137fac067aa82
1360
+ Author: Naohisa Goto <ng@bioruby.org>
1361
+ Date: Tue Nov 11 17:41:32 2014 +0900
1362
+
1363
+ remove unused $Id:$ line
1364
+
1365
+ bin/br_biofetch.rb | 1 -
1366
+ 1 file changed, 1 deletion(-)
1367
+
1368
+ commit e29fc5fadbe0dae6528cf49637496dc2df3ec0dc
1369
+ Author: Naohisa Goto <ng@bioruby.org>
1370
+ Date: Tue Nov 11 17:31:38 2014 +0900
1371
+
1372
+ Change default server to EBI Dbfetch server; remove BioRuby BioFetch server
1373
+
1374
+ * Change default server to EBI Dbfetch server.
1375
+ * The BioRuby BioFetch server is removed. When "-r" option (force to use
1376
+ BioRuby server) is specified, warning message is shown, and the program
1377
+ exits with code 1 (abnormal exit).
1378
+ * Usage message is also changed.
1379
+
1380
+ bin/br_biofetch.rb | 15 +++++++--------
1381
+ 1 file changed, 7 insertions(+), 8 deletions(-)
1382
+
1383
+ commit 94ecac33e87e444d9fe991340c2d8f3709bc6d90
1384
+ Author: Naohisa Goto <ng@bioruby.org>
1385
+ Date: Tue Nov 11 17:19:30 2014 +0900
1386
+
1387
+ fix documentation reflecting recent changes of Bio::Fetch
1388
+
1389
+ lib/bio/io/fetch.rb | 33 ++++++++++++++++++++-------------
1390
+ 1 file changed, 20 insertions(+), 13 deletions(-)
1391
+
1392
+ commit 06a9db014614818ef35108928415ef18e8c8ae2c
1393
+ Author: Naohisa Goto <ng@bioruby.org>
1394
+ Date: Tue Nov 11 16:41:26 2014 +0900
1395
+
1396
+ documentation about incompatible changes of Bio::Fetch
1397
+
1398
+ RELEASE_NOTES.rdoc | 22 ++++++++++++++++++++++
1399
+ 1 file changed, 22 insertions(+)
1400
+
1401
+ commit 6d94e949b6d325f27b45b816a8305f828d049ec6
1402
+ Author: Naohisa Goto <ng@bioruby.org>
1403
+ Date: Tue Nov 11 16:35:50 2014 +0900
1404
+
1405
+ Issue about Bio::Fetch and BioRuby BioFetch server is resolved
1406
+
1407
+ * Issue about Bio::Fetch is resolved by recent commits.
1408
+
1409
+ * The BioRuby BioFetch server is deprecated. There is no hope to restart
1410
+ the service again. EBI Dbfetch server is an alternative.
1411
+
1412
+ KNOWN_ISSUES.rdoc | 9 ---------
1413
+ 1 file changed, 9 deletions(-)
1414
+
1415
+ commit 699cd3ff136310a551d30e0ddd7fbe66e483b5be
1416
+ Author: Naohisa Goto <ng@bioruby.org>
1417
+ Date: Tue Nov 11 15:27:11 2014 +0900
1418
+
1419
+ update RDoc documents for Bio::Fetch
1420
+
1421
+ lib/bio/io/fetch.rb | 61 +++++++++++++++++++++++++++++++++------------------
1422
+ 1 file changed, 40 insertions(+), 21 deletions(-)
1423
+
1424
+ commit c7837f8e5ee2cc1c3085da74567a2b25280bbb8f
1425
+ Author: Naohisa Goto <ng@bioruby.org>
1426
+ Date: Tue Nov 11 14:48:48 2014 +0900
1427
+
1428
+ Incompatibile change: remove Bio::Fetch.query; add Bio::Fetch::EBI.query
1429
+
1430
+ * Incompatible change: remove a class method Bio::Fetch.query because
1431
+ default server URL in Bio::Fetch is deprecated.
1432
+
1433
+ * New class method: Bio::Fetch::EBI.query. This can be used as an
1434
+ alternative method of deprecated Bio::Fetch.query method.
1435
+
1436
+ lib/bio/io/fetch.rb | 35 ++++++++++++++++++-----------------
1437
+ 1 file changed, 18 insertions(+), 17 deletions(-)
1438
+
1439
+ commit f9048684acaff0fcd00b458a946d5f692706325b
1440
+ Author: Naohisa Goto <ng@bioruby.org>
1441
+ Date: Tue Nov 11 14:24:22 2014 +0900
1442
+
1443
+ Incompatible change: Default server in Bio::Fetch.new is deperecated
1444
+
1445
+ * Incompatible change: Default server URL in Bio::Fetch.new is deprecated.
1446
+ Users must explicitly specify the URL. Alternatively, users must change
1447
+ their code to use Bio::Fetch::EBI.
1448
+
1449
+ * New class Bio::Fetch::EBI, EBI Dbfetch client. This acts the same as
1450
+ Bio::Fetch.new(Bio::Fetch::EBI::URL) with default database name
1451
+ "ena_sequence".
1452
+
1453
+ lib/bio/io/fetch.rb | 36 +++++++++++++++++++++++++++++++++---
1454
+ 1 file changed, 33 insertions(+), 3 deletions(-)
1455
+
1456
+ commit e8919f4f57fc545ca194bebb08c11159b36071cb
1457
+ Author: Naohisa Goto <ng@bioruby.org>
1458
+ Date: Tue Nov 11 13:43:28 2014 +0900
1459
+
1460
+ removed unused variables
1461
+
1462
+ lib/bio/io/fetch.rb | 1 -
1463
+ 1 file changed, 1 deletion(-)
1464
+
1465
+ commit faec95656b846a7a17cd6a1dbc633dda63cb5b6e
1466
+ Author: Naohisa Goto <ng@bioruby.org>
1467
+ Date: Tue Nov 11 11:44:00 2014 +0900
1468
+
1469
+ Updated URL of EMBL-EBI Dbfetch
1470
+
1471
+ lib/bio/io/fetch.rb | 2 +-
1472
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1473
+
1474
+ commit 85be893655f68aafbf7e13badd20bf7f26cd7328
1475
+ Author: Jose Irizarry <protechpr@gmail.com>
1476
+ Date: Mon Dec 24 12:30:55 2012 -0400
1477
+
1478
+ Update lib/bio/io/fetch.rb
1479
+
1480
+ Use EBI's dbfetch endpoint as default since BioRuby's endpoint has been disabled for a while now.
1481
+
1482
+ lib/bio/io/fetch.rb | 2 +-
1483
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1484
+
1485
+ commit 163cc06547beed653e19b8c6e71e829d85f2f99c
1486
+ Author: Naohisa Goto <ng@bioruby.org>
1487
+ Date: Tue Oct 21 16:42:30 2014 +0900
1488
+
1489
+ Doc bug fix: wrong sample code
1490
+
1491
+ lib/bio/appl/paml/codeml.rb | 4 ++--
1492
+ 1 file changed, 2 insertions(+), 2 deletions(-)
1493
+
1494
+ commit 97143139d2d4a66366576a8e62518e93fa5afccf
1495
+ Author: Naohisa Goto <ng@bioruby.org>
1496
+ Date: Tue Oct 21 15:47:52 2014 +0900
1497
+
1498
+ Prevent to repeat calculations of total bases
1499
+
1500
+ * Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Prevent to
1501
+ repeat calculations of total bases.
1502
+
1503
+ lib/bio/sequence/na.rb | 20 ++++++++++++--------
1504
+ 1 file changed, 12 insertions(+), 8 deletions(-)
1505
+
1506
+ commit b5dbd882e000842fef65e10290b379bfafdddf06
1507
+ Author: Naohisa Goto <ng@bioruby.org>
1508
+ Date: Tue Oct 21 15:41:13 2014 +0900
1509
+
1510
+ Documentation bug fix: Return value is Rational or Float.
1511
+
1512
+ * Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Return value
1513
+ is Rational or Float in recent versions of Ruby. Documentation added for
1514
+ the treatment of "u" and to return 0.0 if there are no bases.
1515
+ Reported by ctSkennerton (https://github.com/bioruby/bioruby/issues/73 ).
1516
+
1517
+ lib/bio/sequence/na.rb | 47 +++++++++++++++++++++++++++++++++++++++++++----
1518
+ 1 file changed, 43 insertions(+), 4 deletions(-)
1519
+
1520
+ commit 3ba98d52ce57488e604dd7ac388a874e5b40ae9d
1521
+ Author: Naohisa Goto <ng@bioruby.org>
1522
+ Date: Tue Aug 12 00:58:38 2014 +0900
1523
+
1524
+ regenerate bioruby.gemspec with rake regemspec
1525
+
1526
+ bioruby.gemspec | 14 ++++++--------
1527
+ 1 file changed, 6 insertions(+), 8 deletions(-)
1528
+
1529
+ commit a9724d339582952b40c928beccf91376d4e63315
1530
+ Author: Naohisa Goto <ng@bioruby.org>
1531
+ Date: Tue Aug 5 19:20:42 2014 +0900
1532
+
1533
+ Update URIs
1534
+
1535
+ * Update URIs.
1536
+ * Remove links to RubyForge and RAA which have already been closed.
1537
+ * Add some words for Ruby 1.9 or later.
1538
+
1539
+ README.rdoc | 24 +++++++++++-------------
1540
+ 1 file changed, 11 insertions(+), 13 deletions(-)
1541
+
1542
+ commit 5f3569faaf89ebcd2b2cf9cbe6b3c1f0544b2679
1543
+ Author: Iain Barnett <iainspeed@gmail.com>
1544
+ Date: Wed Mar 5 02:11:07 2014 +0000
1545
+
1546
+ Refactor Bio::AminoAcid#weight: Early return clearer and idiomatic.
1547
+
1548
+ lib/bio/data/aa.rb | 26 ++++++++++++--------------
1549
+ 1 file changed, 12 insertions(+), 14 deletions(-)
1550
+
1551
+ commit c229a20887fcb6df9a7ba49ad5a23e175056fa8d
1552
+ Author: Iain Barnett <iainspeed@gmail.com>
1553
+ Date: Wed Mar 5 02:02:45 2014 +0000
1554
+
1555
+ Fixed the stack level too deep errors by using Hash#invert.
1556
+
1557
+ lib/bio/data/aa.rb | 18 +-----------------
1558
+ 1 file changed, 1 insertion(+), 17 deletions(-)
1559
+
1560
+ commit 08dd928df30f5b39c255f9f70dbed8410d395cdf
1561
+ Author: Iain Barnett <iainspeed@gmail.com>
1562
+ Date: Tue Mar 4 01:22:51 2014 +0000
1563
+
1564
+ Refactored to shorten, remove rescues, and clarify.
1565
+
1566
+ lib/bio/alignment.rb | 19 +++++++------------
1567
+ 1 file changed, 7 insertions(+), 12 deletions(-)
1568
+
1569
+ commit 112aa284cb1ebecc1d5de186edf2b385649a7268
1570
+ Author: Naohisa Goto <ng@bioruby.org>
1571
+ Date: Wed Mar 19 14:48:32 2014 +0900
1572
+
1573
+ Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008)
1574
+
1575
+ * Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008).
1576
+ Thanks to a researcher who reports the patch via email.
1577
+
1578
+ lib/bio/db/pdb/pdb.rb | 4 ++--
1579
+ 1 file changed, 2 insertions(+), 2 deletions(-)
1580
+
1581
+ commit ecd5e0c86b04aa918b71c859568425fa39ebbde5
1582
+ Author: Naohisa Goto <ng@bioruby.org>
1583
+ Date: Sat Jan 18 04:22:51 2014 +0900
1584
+
1585
+ suppress "source :rubygems is deprecated" warning
1586
+
1587
+ gemfiles/Gemfile.travis-jruby1.8 | 2 +-
1588
+ gemfiles/Gemfile.travis-jruby1.9 | 2 +-
1589
+ gemfiles/Gemfile.travis-ruby1.8 | 2 +-
1590
+ gemfiles/Gemfile.travis-ruby1.9 | 2 +-
1591
+ 4 files changed, 4 insertions(+), 4 deletions(-)
1592
+
1593
+ commit 4bda345fe3de9cf1b64c26f3dca1cb3727c946d0
1594
+ Author: Naohisa Goto <ng@bioruby.org>
1595
+ Date: Sat Jan 18 04:22:03 2014 +0900
1596
+
1597
+ gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci
1598
+
1599
+ * gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci
1600
+ * .travis.yml is modified to use gemfile/Gemfile.travis-rbx for rbx.
1601
+
1602
+ .travis.yml | 4 ++--
1603
+ gemfiles/Gemfile.travis-rbx | 16 ++++++++++++++++
1604
+ 2 files changed, 18 insertions(+), 2 deletions(-)
1605
+ create mode 100644 gemfiles/Gemfile.travis-rbx
1606
+
1607
+ commit dcff544d6d0a967eb853b97ba9faa30eaa6fd9dc
1608
+ Author: Naohisa Goto <ng@bioruby.org>
1609
+ Date: Sat Jan 18 04:13:50 2014 +0900
1610
+
1611
+ .travis.yml: fix mistakes
1612
+
1613
+ .travis.yml | 8 +-------
1614
+ 1 file changed, 1 insertion(+), 7 deletions(-)
1615
+
1616
+ commit f0f67f295f05a5e1e30c479621c25498e2c8f6f2
1617
+ Author: Naohisa Goto <ng@bioruby.org>
1618
+ Date: Sat Jan 18 03:56:54 2014 +0900
1619
+
1620
+ Ruby 2.1 workaround: Array#uniq does not always choose the first item
1621
+
1622
+ * Ruby 2.1 workaround: Array#uniq does not always choose the first item.
1623
+ Thanks to Andrew Grimm who reported the issue.
1624
+ (https://github.com/bioruby/bioruby/issues/92 )
1625
+ Note that the behavior change is also regarded as a bug in Ruby and
1626
+ is fixed. (https://bugs.ruby-lang.org/issues/9340 )
1627
+
1628
+ test/unit/bio/test_pathway.rb | 35 +++++++++++++++++++++++++----------
1629
+ 1 file changed, 25 insertions(+), 10 deletions(-)
1630
+
1631
+ commit e92e09edf5904f51d3e73e61d13fce4159a543c5
1632
+ Author: Naohisa Goto <ng@bioruby.org>
1633
+ Date: Sat Jan 18 03:32:05 2014 +0900
1634
+
1635
+ .travis.yml: workaround to avoid error in Ruby 1.8.7 and jruby-18mode
1636
+
1637
+ * workaround to avoid error in Ruby 1.8.7 and jruby-18mode
1638
+ (reference: https://github.com/rubygems/rubygems/pull/763 )
1639
+
1640
+ .travis.yml | 2 ++
1641
+ 1 file changed, 2 insertions(+)
1642
+
1643
+ commit 655a675096962710896fb458afcac9b5deb1fa5f
1644
+ Author: Naohisa Goto <ng@bioruby.org>
1645
+ Date: Sat Jan 18 03:22:44 2014 +0900
1646
+
1647
+ .travis.yml: rbx version is changed to 2.2.3
1648
+
1649
+ * rbx version is changed to 2.2.3
1650
+ * add dependent gems for rbx platforms, described in
1651
+ http://docs.travis-ci.com/user/languages/ruby/
1652
+
1653
+ .travis.yml | 7 ++++++-
1654
+ 1 file changed, 6 insertions(+), 1 deletion(-)
1655
+
1656
+ commit d2f5b882d5e2acf35d0c783a56aa47533b9f2bd5
1657
+ Author: Naohisa Goto <ng@bioruby.org>
1658
+ Date: Sat Jan 11 03:46:45 2014 +0900
1659
+
1660
+ .travis.yml: change ruby versions for tar and gem integration tests
1661
+
1662
+ * In tar and gem integration tests, Ruby versions are changed to
1663
+ MRI 2.0.0 and jruby-19mode.
1664
+ * Add jruby-18mode
1665
+ * Add rbx-2.1.1
1666
+
1667
+ .travis.yml | 32 ++++++++++++++++++++++----------
1668
+ 1 file changed, 22 insertions(+), 10 deletions(-)
1669
+
1670
+ commit 71991af394b937d35e2bbbc84a21e65ffba7714d
1671
+ Author: Naohisa Goto <ng@bioruby.org>
1672
+ Date: Thu Jan 9 00:57:25 2014 +0900
1673
+
1674
+ .travis.yml: Add 2.1.0 and 2.0.0, remove rbx-XXmode
1675
+
1676
+ * Add 2.1.0 and 2.0.0
1677
+ * Remove rbx-18mode and rbx-19mode
1678
+ * 1.9.2 is moved from "include" to "rvm".
1679
+ * 1.8.7 is moved from "rvm" to "include", and remove
1680
+ "gemfiles/Gemfile.travis-ruby1.8" line from "gemfile".
1681
+ * Remove "exclude" and simplify build matrix.
1682
+ * Suggested by agrimm in https://github.com/bioruby/bioruby/pull/91
1683
+
1684
+ .travis.yml | 27 +++++----------------------
1685
+ 1 file changed, 5 insertions(+), 22 deletions(-)
1686
+
1687
+ commit 80966bc875cc6e01978b6c9272f6ddd8f344aa62
1688
+ Author: Brynjar Smari Bjarnason <binni@binnisb.com>
1689
+ Date: Mon Dec 9 14:57:42 2013 +0100
1690
+
1691
+ Bug fix: Only do gsub on bio_ref.reference.authors if it exists.
1692
+
1693
+ * Bug fix: Only do gsub on bio_ref.reference.authors if it exists.
1694
+ Fix https://github.com/bioruby/bioruby/issues/89
1695
+
1696
+ lib/bio/db/biosql/sequence.rb | 2 +-
1697
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1698
+
1699
+ commit 3337bbd3be2affcef44202a0c924b3e22dafd856
1700
+ Author: Brynjar Smari Bjarnason <binni@binnisb.com>
1701
+ Date: Mon Dec 9 14:55:24 2013 +0100
1702
+
1703
+ Bug fix: Missing require when generating genbank output for BioSQL sequence
1704
+
1705
+ * Bug fix: Missing require when generating genbank output for BioSQL
1706
+ sequence. Partly fix https://github.com/bioruby/bioruby/issues/89
1707
+
1708
+ lib/bio/db/biosql/biosql_to_biosequence.rb | 1 +
1709
+ 1 file changed, 1 insertion(+)
1710
+
1711
+ commit 1f829ae8e8c89c5c24e7bc7aa8ed5fa25e8ef6c2
1712
+ Author: Naohisa Goto <ng@bioruby.org>
1713
+ Date: Sat Nov 23 18:17:43 2013 +0900
1714
+
1715
+ Benchmark example1-seqnos.aln in addition to example1.aln
1716
+
1717
+ * sample/benchmark_clustalw_report.rb: Benchmark parsing speed of
1718
+ example1-seqnos.aln in addition to example1.aln.
1719
+
1720
+ sample/benchmark_clustalw_report.rb | 28 ++++++++++++++++++++++------
1721
+ 1 file changed, 22 insertions(+), 6 deletions(-)
1722
+
1723
+ commit c5d3e761859fa72c18f9301d84c31070f35e733e
1724
+ Author: Andrew Grimm <andrew.j.grimm@gmail.com>
1725
+ Date: Tue Sep 17 21:15:56 2013 +1000
1726
+
1727
+ Add benchmark script for Bio::ClustalW::Report.
1728
+
1729
+ sample/benchmark_clustalw_report.rb | 31 +++++++++++++++++++++++++++++++
1730
+ 1 file changed, 31 insertions(+)
1731
+ create mode 100644 sample/benchmark_clustalw_report.rb
1732
+
1733
+ commit 07c14e94cdb94cf9ba8a2bf050572ae1cbf24cff
1734
+ Author: Naohisa Goto <ng@bioruby.org>
1735
+ Date: Sat Nov 23 17:49:54 2013 +0900
1736
+
1737
+ Bio::ClustalW::Report#do_parse speed optimization
1738
+
1739
+ * Bio::ClustalW::Report#do_parse speed optimization. Thanks to
1740
+ Andrew Grimm who indicates the optimization point.
1741
+ (https://github.com/bioruby/bioruby/pull/86 )
1742
+ * "$" in the regular expression is changed to "\z". In this context,
1743
+ the "$" was intended to be matched with only the end of the string.
1744
+
1745
+ lib/bio/appl/clustalw/report.rb | 4 +++-
1746
+ 1 file changed, 3 insertions(+), 1 deletion(-)
1747
+
1748
+ commit 6a78028d4f595ecb5b4600d0f238b07a2d80bdd5
1749
+ Author: Naohisa Goto <ng@bioruby.org>
1750
+ Date: Sat Nov 23 15:52:15 2013 +0900
1751
+
1752
+ New test data: ClustalW with -SEQNOS=ON option
1753
+
1754
+ * test/data/clustalw/example1-seqnos.aln: New test data: ClustalW
1755
+ running with -SEQNOS=ON option.
1756
+ * Bio::TestClustalWReport::TestClustalWReportSeqnos: new test class
1757
+ that parses the above data.
1758
+
1759
+ test/data/clustalw/example1-seqnos.aln | 58 ++++++++++++++++++++++++++++
1760
+ test/unit/bio/appl/clustalw/test_report.rb | 11 ++++++
1761
+ 2 files changed, 69 insertions(+)
1762
+ create mode 100644 test/data/clustalw/example1-seqnos.aln
1763
+
1764
+ commit f5da0bbb4b1639616bb8c63ff8c58840e140ef8b
1765
+ Author: Naohisa Goto <ng@bioruby.org>
1766
+ Date: Sat Nov 23 15:35:31 2013 +0900
1767
+
1768
+ Simplify test data path in setup
1769
+
1770
+ * Bio::TestClustalWReport::TestClustalWReport#setup: simplify test data
1771
+ filename path.
1772
+ * Modify indentes and void lines.
1773
+
1774
+ test/unit/bio/appl/clustalw/test_report.rb | 10 +++-------
1775
+ 1 file changed, 3 insertions(+), 7 deletions(-)
1776
+
1777
+ commit 8f0bea1d3252d0de9e2d91dc31ef8a9552c2d758
1778
+ Author: Naohisa Goto <ng@bioruby.org>
1779
+ Date: Sat Nov 23 15:21:38 2013 +0900
1780
+
1781
+ Common test methods are moved to a module
1782
+
1783
+ * New namespace module Bio::TestClustalWReport.
1784
+ * Common test methods are moved to CommonTestMethods,
1785
+ and test classes using the methods include it.
1786
+ * The test_sequences method is split into two methods
1787
+ CommonTestMethods#test_sequence0 and test_sequence1.
1788
+
1789
+ test/unit/bio/appl/clustalw/test_report.rb | 97 +++++++++++++++-------------
1790
+ 1 file changed, 53 insertions(+), 44 deletions(-)
1791
+
1792
+ commit edda65b8fb32c2eee6b0652074981c31aa68b0eb
1793
+ Author: Naohisa Goto <ng@bioruby.org>
1794
+ Date: Fri Aug 23 23:51:59 2013 +0900
1795
+
1796
+ Test bug fix: Read test file with binary mode to avoid encoding error
1797
+
1798
+ * Test bug fix: Read test file with binary mode to avoid string encoding
1799
+ error. Thanks to nieder (github.com/nieder) who reports the bug.
1800
+ (https://github.com/bioruby/bioruby/issues/84)
1801
+
1802
+ test/unit/bio/db/test_phyloxml.rb | 2 +-
1803
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1804
+
1805
+ commit 011d6fe5f016408891c5da3143c83e2564ccbf27
1806
+ Author: meso_cacase <y-naito@dbcls.rois.ac.jp>
1807
+ Date: Fri Apr 5 01:13:27 2013 +0900
1808
+
1809
+ Modified siRNA design rules by Ui-Tei and Reynolds
1810
+
1811
+ * Ui-Tei rule: Avoided contiguous GCs 10 nt or more.
1812
+ * Reynolds rule: Total score of eight criteria is calculated.
1813
+ * Returns numerical score for functional siRNA instead of returning 'true'.
1814
+ * Returns 'false' for non-functional siRNA, as usual.
1815
+ * Unit tests are modified to reflect these changes.
1816
+
1817
+ lib/bio/util/sirna.rb | 92 +++++++++++++++++++++++++++++++-------
1818
+ test/unit/bio/util/test_sirna.rb | 44 +++++++++---------
1819
+ 2 files changed, 98 insertions(+), 38 deletions(-)
1820
+
1821
+ commit b6e7953108ebf34d61bc79ee4bdae1092cfe339f
1822
+ Author: Naohisa Goto <ng@bioruby.org>
1823
+ Date: Fri Jun 28 15:40:57 2013 +0900
1824
+
1825
+ Use Bio::UniProtKB instead of Bio::UniProt
1826
+
1827
+ * Use Bio::UniProtKB instead of Bio::UniProt.
1828
+ * Test class names are also changed from UniProt to UniProtKB.
1829
+
1830
+ test/unit/bio/db/embl/test_uniprotkb_new_part.rb | 22 +++++++++++-----------
1831
+ 1 file changed, 11 insertions(+), 11 deletions(-)
1832
+
1833
+ commit cddd35cf8d64abfff8bd6a8372d019fc4c32848c
1834
+ Author: Naohisa Goto <ng@bioruby.org>
1835
+ Date: Fri Jun 28 15:26:20 2013 +0900
1836
+
1837
+ rename test/unit/bio/db/embl/test_uniprot_new_part.rb to test_uniprotkb_new_part.rb
1838
+
1839
+ test/unit/bio/db/embl/test_uniprot_new_part.rb | 208 ----------------------
1840
+ test/unit/bio/db/embl/test_uniprotkb_new_part.rb | 208 ++++++++++++++++++++++
1841
+ 2 files changed, 208 insertions(+), 208 deletions(-)
1842
+ delete mode 100644 test/unit/bio/db/embl/test_uniprot_new_part.rb
1843
+ create mode 100644 test/unit/bio/db/embl/test_uniprotkb_new_part.rb
1844
+
1845
+ commit 1b51d0940712a6f144f8268dc77048bc7ec7d983
1846
+ Author: Naohisa Goto <ng@bioruby.org>
1847
+ Date: Fri Jun 28 15:21:36 2013 +0900
1848
+
1849
+ Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB.
1850
+
1851
+ * Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB.
1852
+ * Test class names are also changed.
1853
+
1854
+ test/unit/bio/db/embl/test_uniprotkb.rb | 223 +++++++++++++++----------------
1855
+ 1 file changed, 111 insertions(+), 112 deletions(-)
1856
+
1857
+ commit 68494aa862c3495def713e6cad6fc478f223416f
1858
+ Author: Naohisa Goto <ng@bioruby.org>
1859
+ Date: Fri Jun 28 15:01:15 2013 +0900
1860
+
1861
+ test_sptr.rb is renamed to test_uniprotkb.rb
1862
+
1863
+ test/unit/bio/db/embl/test_sptr.rb | 1807 -------------------------------
1864
+ test/unit/bio/db/embl/test_uniprotkb.rb | 1807 +++++++++++++++++++++++++++++++
1865
+ 2 files changed, 1807 insertions(+), 1807 deletions(-)
1866
+ delete mode 100644 test/unit/bio/db/embl/test_sptr.rb
1867
+ create mode 100644 test/unit/bio/db/embl/test_uniprotkb.rb
1868
+
1869
+ commit e1ed7fab4c0350e6866dd420a93e950c53063f38
1870
+ Author: Naohisa Goto <ng@bioruby.org>
1871
+ Date: Fri Jun 28 14:52:08 2013 +0900
1872
+
1873
+ Add autoload of Bio::UniProtKB, and modify comments of deprecated classes.
1874
+
1875
+ lib/bio.rb | 18 ++++++++++--------
1876
+ 1 file changed, 10 insertions(+), 8 deletions(-)
1877
+
1878
+ commit 7c78cb1b275a845e215f9a6da67026836efc5807
1879
+ Author: Naohisa Goto <ng@bioruby.org>
1880
+ Date: Fri Jun 28 14:28:02 2013 +0900
1881
+
1882
+ Bio::SwissProt and Bio::TrEMBL are deprecated
1883
+
1884
+ * Bio::SwissProt and Bio::TrEMBL are deprecated.
1885
+ * Show warning messages when using these classes.
1886
+
1887
+ lib/bio/db/embl/swissprot.rb | 41 ++++++++++++----------------------------
1888
+ lib/bio/db/embl/trembl.rb | 43 +++++++++++++-----------------------------
1889
+ 2 files changed, 25 insertions(+), 59 deletions(-)
1890
+
1891
+ commit b998ad13849ff7f1d69ed0c640a2e1bafe3fc957
1892
+ Author: Naohisa Goto <ng@bioruby.org>
1893
+ Date: Fri Jun 28 14:27:36 2013 +0900
1894
+
1895
+ Bio::UniProt is changed to be an alias of Bio::UniProtKB.
1896
+
1897
+ lib/bio/db/embl/uniprot.rb | 41 ++++++++++++-----------------------------
1898
+ 1 file changed, 12 insertions(+), 29 deletions(-)
1899
+
1900
+ commit f46324e2fb6a2bc3e4680c8064dc0fc3d89e6f24
1901
+ Author: Naohisa Goto <ng@bioruby.org>
1902
+ Date: Fri Jun 28 14:21:56 2013 +0900
1903
+
1904
+ Bio::SPTR is renamed as Bio::UniProtKB and changed to an alias
1905
+
1906
+ * Bio::SPTR is renamed to Bio::UniProtKB.
1907
+ * For older programs which use Bio::SPTR, set Bio::SPTR as an alias of
1908
+ Bio::UniProtKB.
1909
+
1910
+ lib/bio/db/embl/sptr.rb | 20 ++++++
1911
+ lib/bio/db/embl/uniprotkb.rb | 147 +++++++++++++++++++++---------------------
1912
+ 2 files changed, 93 insertions(+), 74 deletions(-)
1913
+ create mode 100644 lib/bio/db/embl/sptr.rb
1914
+
1915
+ commit 70816d90a6ef290c7ca7f50d492e7c4f836aadd8
1916
+ Author: Naohisa Goto <ng@bioruby.org>
1917
+ Date: Thu Jun 27 18:16:38 2013 +0900
1918
+
1919
+ Rename lib/bio/db/embl/sptr.rb to uniprotkb.rb
1920
+
1921
+ lib/bio/db/embl/sptr.rb | 1456 ------------------------------------------
1922
+ lib/bio/db/embl/uniprotkb.rb | 1456 ++++++++++++++++++++++++++++++++++++++++++
1923
+ 2 files changed, 1456 insertions(+), 1456 deletions(-)
1924
+ delete mode 100644 lib/bio/db/embl/sptr.rb
1925
+ create mode 100644 lib/bio/db/embl/uniprotkb.rb
1926
+
1927
+ commit 2a10ded8e1502e0db5ec3b2e060f658ee53aafd0
1928
+ Author: Naohisa Goto <ng@bioruby.org>
1929
+ Date: Thu Jun 27 16:36:58 2013 +0900
1930
+
1931
+ Bio::RefSeq and Bio::DDBJ are deprecated. Show warnings.
1932
+
1933
+ * Bio::RefSeq and Bio::DDBJ are deprecated because they were only
1934
+ an alias of Bio::GenBank. Please use Bio::GenBank instead.
1935
+ * Show warning message when loading the classes and initializing
1936
+ a new instance.
1937
+ * Changed to require genbank.rb only when GenBank is not defined.
1938
+ This might reduce the possibility of circular require.
1939
+
1940
+ lib/bio/db/genbank/ddbj.rb | 11 +++++++++--
1941
+ lib/bio/db/genbank/refseq.rb | 14 +++++++++++---
1942
+ 2 files changed, 20 insertions(+), 5 deletions(-)
1943
+
1944
+ commit 118d0bff58b48f69505eef5dcc2f961ac6e0d9de
1945
+ Author: Naohisa Goto <ng@bioruby.org>
1946
+ Date: Thu Jun 27 16:08:55 2013 +0900
1947
+
1948
+ Remove descriptions about DDBJ Web API (WABI)
1949
+
1950
+ KNOWN_ISSUES.rdoc | 8 --------
1951
+ 1 file changed, 8 deletions(-)
1952
+
1953
+ commit fe8f976c7ced4d525a4eabd728269f71326cf001
1954
+ Author: Naohisa Goto <ng@bioruby.org>
1955
+ Date: Thu Jun 27 13:41:19 2013 +0900
1956
+
1957
+ Remove ddbjsoap method that uses Bio::DDBJ::XML
1958
+
1959
+ lib/bio/shell/plugin/soap.rb | 28 ----------------------------
1960
+ 1 file changed, 28 deletions(-)
1961
+
1962
+ commit 54bef3fc48bb48eb198537a9fba6379f33f036cc
1963
+ Author: Naohisa Goto <ng@bioruby.org>
1964
+ Date: Thu Jun 27 13:39:42 2013 +0900
1965
+
1966
+ Remove Bio::Blast::Remote::DDBJ from the comment line
1967
+
1968
+ test/network/bio/appl/blast/test_remote.rb | 2 +-
1969
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1970
+
1971
+ commit a7c5a656dab1bb8ada6b36ec003a89aec9e26671
1972
+ Author: Naohisa Goto <ng@bioruby.org>
1973
+ Date: Tue Jun 25 18:34:46 2013 +0900
1974
+
1975
+ Delete sample/demo_ddbjxml.rb which uses Bio::DDBJ::XML
1976
+
1977
+ sample/demo_ddbjxml.rb | 212 ------------------------------------------------
1978
+ 1 file changed, 212 deletions(-)
1979
+ delete mode 100644 sample/demo_ddbjxml.rb
1980
+
1981
+ commit e55293b67d305382cfb30b45aa30af82a574b580
1982
+ Author: Naohisa Goto <ng@bioruby.org>
1983
+ Date: Tue Jun 25 18:29:54 2013 +0900
1984
+
1985
+ Remove Bio::Blast::Remote::DDBJ, Bio::Blast.ddbj and related components
1986
+
1987
+ * Remove Bio::Blast::Remote::DDBJ, Bio::Blast.ddbj and related components
1988
+ which use Bio::DDBJ::XML or Bio::DDBJ::REST.
1989
+
1990
+ lib/bio/appl/blast/ddbj.rb | 131 ----------------------------
1991
+ lib/bio/appl/blast/remote.rb | 9 --
1992
+ test/network/bio/appl/blast/test_remote.rb | 14 ---
1993
+ test/network/bio/appl/test_blast.rb | 12 ---
1994
+ 4 files changed, 166 deletions(-)
1995
+ delete mode 100644 lib/bio/appl/blast/ddbj.rb
1996
+
1997
+ commit 19a5c992096a68a26f8684ee2ae128d17f2a49fd
1998
+ Author: Naohisa Goto <ng@bioruby.org>
1999
+ Date: Tue Jun 25 16:52:05 2013 +0900
2000
+
2001
+ Remove Bio::DDBJ::XML and REST due to suspension of DDBJ Web API (WABI)
2002
+
2003
+ * Remove Bio::DDBJ::XML and Bio::DDBJ::REST due to suspension of
2004
+ DDBJ Web API (WABI). DDBJ says that it is now under reconstruction
2005
+ and the API will be completely changed. Thus, I've decided to throw
2006
+ away current API client in Ruby and to implement new one with the new
2007
+ API.
2008
+ * Autoload lines in lib/bio/db/genbank/ddbj.rb are removed.
2009
+ * Tests are also removed.
2010
+
2011
+ lib/bio/db/genbank/ddbj.rb | 3 -
2012
+ lib/bio/io/ddbjrest.rb | 344 -------------------------
2013
+ lib/bio/io/ddbjxml.rb | 458 ----------------------------------
2014
+ test/network/bio/io/test_ddbjrest.rb | 47 ----
2015
+ test/unit/bio/io/test_ddbjxml.rb | 81 ------
2016
+ 5 files changed, 933 deletions(-)
2017
+ delete mode 100644 lib/bio/io/ddbjrest.rb
2018
+ delete mode 100644 lib/bio/io/ddbjxml.rb
2019
+ delete mode 100644 test/network/bio/io/test_ddbjrest.rb
2020
+ delete mode 100644 test/unit/bio/io/test_ddbjxml.rb
2021
+
2022
+ commit 1f852e0bf3c830aaa40dc7fc2bd535418af8dfd1
2023
+ Author: Naohisa Goto <ng@bioruby.org>
2024
+ Date: Sat May 25 03:00:08 2013 +0900
2025
+
2026
+ regenerate bioruby.gemspec with rake regemspec
2027
+
2028
+ bioruby.gemspec | 2 --
2029
+ 1 file changed, 2 deletions(-)
2030
+
2031
+ commit 5b90959ab399f961823a7c4453392c75cf971333
2032
+ Author: Naohisa Goto <ng@bioruby.org>
2033
+ Date: Sat May 25 02:58:50 2013 +0900
2034
+
2035
+ Update files and directories used to create package without git
2036
+
2037
+ bioruby.gemspec.erb | 6 ++++--
2038
+ 1 file changed, 4 insertions(+), 2 deletions(-)
2039
+
2040
+ commit df29f057ded6ac73fbdce7ae04a70ead28f4cc9f
2041
+ Author: Naohisa Goto <ng@bioruby.org>
2042
+ Date: Sat May 25 02:46:32 2013 +0900
2043
+
2044
+ Ruby 2.0 support: not to add ChangeLog and LEGAL to rdoc_files
2045
+
2046
+ * Ruby 2.0 support: not to add ChangeLog and LEGAL to rdoc_files.
2047
+ Because ChangeLog is not rdoc format, rdoc bundled with Ruby 2.0
2048
+ raises error during parsing.
2049
+
2050
+ bioruby.gemspec.erb | 4 ++--
2051
+ 1 file changed, 2 insertions(+), 2 deletions(-)
2052
+
2053
+ commit 930a5fcf5e38ae2bdfeee62eed9a46db1c519fae
2054
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2055
+ Date: Thu Apr 4 17:29:33 2013 +0900
2056
+
2057
+ Remove unused variable in lib/bio/util/contingency_table.rb
2058
+
2059
+ This commit removes below interpreter warning.
2060
+
2061
+ * warning: assigned but unused variable
2062
+
2063
+ lib/bio/util/contingency_table.rb | 2 --
2064
+ 1 file changed, 2 deletions(-)
2065
+
2066
+ commit 490b3f7ca3b987c1a17852b641aad3125fc565cd
2067
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2068
+ Date: Thu Apr 4 17:28:30 2013 +0900
2069
+
2070
+ Rename unused variable in lib/bio/tree.rb
2071
+
2072
+ This commit removes below interpreter warning.
2073
+
2074
+ * warning: assigned but unused variable
2075
+
2076
+ lib/bio/tree.rb | 4 ++--
2077
+ 1 file changed, 2 insertions(+), 2 deletions(-)
2078
+
2079
+ commit c024fb972edb52e213165149273fc7ac4bec2f6e
2080
+ Author: Naohisa Goto <ng@bioruby.org>
2081
+ Date: Thu May 16 21:26:44 2013 +0900
2082
+
2083
+ Refactoring to suppress "warning: assigned but unused variable"
2084
+
2085
+ lib/bio/pathway.rb | 2 +-
2086
+ 1 file changed, 1 insertion(+), 1 deletion(-)
2087
+
2088
+ commit b3b2a268d6118307eed88fce1d805a61c6fb843d
2089
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2090
+ Date: Thu Apr 4 17:18:44 2013 +0900
2091
+
2092
+ Remove unused variable in lib/bio/db/transfac.rb
2093
+
2094
+ This commit removes below interpreter warning.
2095
+
2096
+ * warning: assigned but unused variable
2097
+
2098
+ lib/bio/db/transfac.rb | 2 +-
2099
+ 1 file changed, 1 insertion(+), 1 deletion(-)
2100
+
2101
+ commit dd8abf1f95af4a70cf0b86b0e719e3dcfd8abecf
2102
+ Author: Naohisa Goto <ng@bioruby.org>
2103
+ Date: Thu May 16 21:13:34 2013 +0900
2104
+
2105
+ Refactoring to suppress warnings "assigned but unused variable"
2106
+
2107
+ lib/bio/db/nexus.rb | 5 +++--
2108
+ 1 file changed, 3 insertions(+), 2 deletions(-)
2109
+
2110
+ commit b37512fb8028cf30bb2f813928aed49a5b39dce3
2111
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2112
+ Date: Thu Apr 4 17:15:59 2013 +0900
2113
+
2114
+ Rename unused variable in lib/bio/db/kegg/reaction.rb
2115
+
2116
+ This commit removes below interpreter warning.
2117
+
2118
+ * warning: assigned but unused variable
2119
+
2120
+ lib/bio/db/kegg/reaction.rb | 2 +-
2121
+ 1 file changed, 1 insertion(+), 1 deletion(-)
2122
+
2123
+ commit a81fca3b1247ae4a3e05bfa912c8181efdfca81b
2124
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2125
+ Date: Thu Apr 4 17:15:09 2013 +0900
2126
+
2127
+ Remove unused variable in lib/bio/db/go.rb
2128
+
2129
+ This commit removes below interpreter warning.
2130
+
2131
+ * warning: assigned but unused variable
2132
+
2133
+ lib/bio/db/go.rb | 6 +++---
2134
+ 1 file changed, 3 insertions(+), 3 deletions(-)
2135
+
2136
+ commit 69b0c433e76faffba6a48dfc38dcc2b1444ce2b7
2137
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2138
+ Date: Thu Apr 4 17:13:24 2013 +0900
2139
+
2140
+ Rename unused variable in lib/bio/db/gff.rb
2141
+
2142
+ This commit removes below interpreter warning.
2143
+
2144
+ * warning: assigned but unused variable
2145
+
2146
+ lib/bio/db/gff.rb | 2 +-
2147
+ 1 file changed, 1 insertion(+), 1 deletion(-)
2148
+
2149
+ commit 88c214fe3183c161cda94a3a4cda442b3a769965
2150
+ Author: Naohisa Goto <ng@bioruby.org>
2151
+ Date: Thu May 9 23:46:28 2013 +0900
2152
+
2153
+ add a dummy line to suppress "warning: assigned but unused variable"
2154
+
2155
+ lib/bio/db/embl/sptr.rb | 1 +
2156
+ 1 file changed, 1 insertion(+)
2157
+
2158
+ commit 1ead12f9c951a983c6775f79ca1b6944f95a61b9
2159
+ Author: Naohisa Goto <ng@bioruby.org>
2160
+ Date: Thu May 9 23:41:54 2013 +0900
2161
+
2162
+ Refactoring to suppress warnings "assigned but unused variable"
2163
+
2164
+ lib/bio/db/embl/embl.rb | 7 ++++---
2165
+ 1 file changed, 4 insertions(+), 3 deletions(-)
2166
+
2167
+ commit 8d0eb5105eb2f419f5b4f4fbb191b8fb2032664b
2168
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2169
+ Date: Thu Apr 4 17:01:27 2013 +0900
2170
+
2171
+ Remove unused variable in lib/bio/appl/paml/common
2172
+
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+ This commit removes below interpreter warning.
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+
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+ * warning: assigned but unused variable
2176
+
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+ lib/bio/appl/paml/common.rb | 2 +-
2178
+ 1 file changed, 1 insertion(+), 1 deletion(-)
2179
+
2180
+ commit c6cf0d2e2a3a0b9062f9464dba0e363f460d04e4
2181
+ Author: Naohisa Goto <ng@bioruby.org>
2182
+ Date: Thu May 9 23:27:54 2013 +0900
2183
+
2184
+ suppress warning "assigned but unused variable"
2185
+
2186
+ lib/bio/appl/paml/codeml/report.rb | 1 +
2187
+ 1 file changed, 1 insertion(+)
2188
+
2189
+ commit 8834d50544b03a92a3ca816704b179e4333d1dfc
2190
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2191
+ Date: Thu Apr 4 16:59:18 2013 +0900
2192
+
2193
+ Remove unused variable in lib/bio/appl/meme/mast/report
2194
+
2195
+ This commit removes below interpreter warning.
2196
+
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+ * warning: assigned but unused variable
2198
+
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+ lib/bio/appl/meme/mast/report.rb | 2 +-
2200
+ 1 file changed, 1 insertion(+), 1 deletion(-)
2201
+
2202
+ commit fe51a49ee68c41a3ce0c48c39db6e8a28d1689ee
2203
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2204
+ Date: Thu Apr 4 16:57:44 2013 +0900
2205
+
2206
+ Remove unused variable in lib/bio/appl/blast/report
2207
+
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+ This commit removes below interpreter warning.
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+
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+ * warning: assigned but unused variable
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+
2212
+ lib/bio/appl/blast/report.rb | 2 +-
2213
+ 1 file changed, 1 insertion(+), 1 deletion(-)
2214
+
2215
+ commit 622497ff309412fb986c5315d55d41c3ca48d362
2216
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2217
+ Date: Thu Apr 4 17:25:29 2013 +0900
2218
+
2219
+ Fix indent in lib/bio/map
2220
+
2221
+ This commit removes below interpreter warning.
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+
2223
+ * warning: mismatched indentations at ...
2224
+
2225
+ lib/bio/map.rb | 2 +-
2226
+ 1 file changed, 1 insertion(+), 1 deletion(-)
2227
+
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+ commit 3ea6bcaf229fd1a71a0192253cc47e817bb64b82
2229
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2230
+ Date: Thu Apr 4 18:05:04 2013 +0900
2231
+
2232
+ Remove unused variable in test/unit/bio/appl/blast/test_report
2233
+
2234
+ This commit removes below interpreter warning.
2235
+
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+ * warning: assigned but unused variable
2237
+
2238
+ test/unit/bio/appl/blast/test_report.rb | 2 --
2239
+ 1 file changed, 2 deletions(-)
2240
+
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+ commit 178ca9e5244cc3aa7f0507c7d5528bb57b0858be
2242
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2243
+ Date: Thu Apr 4 18:03:46 2013 +0900
2244
+
2245
+ Remove unused variable in test/unit/bio/appl/bl2seq/test_report
2246
+
2247
+ This commit removes below interpreter warning.
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+
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+ * warning: assigned but unused variable
2250
+
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+ test/unit/bio/appl/bl2seq/test_report.rb | 1 -
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+ 1 file changed, 1 deletion(-)
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+
2254
+ commit b8a5c1cb9f54d9199200b406f77e8152eef96f02
2255
+ Author: Naohisa Goto <ng@bioruby.org>
2256
+ Date: Thu May 9 21:20:10 2013 +0900
2257
+
2258
+ Add assertions and suppress "unused variable" warnings
2259
+
2260
+ * Add assertions to check object id returned by forward_complement
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+ and reverse_complement methods. This change also aims to suppress
2262
+ "assigned but unused variable" warnings.
2263
+
2264
+ test/unit/bio/sequence/test_na.rb | 4 +++-
2265
+ 1 file changed, 3 insertions(+), 1 deletion(-)
2266
+
2267
+ commit bd8fc9b197c54c108d74fea9161c8f0dd3b041fc
2268
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2269
+ Date: Thu Apr 4 17:59:09 2013 +0900
2270
+
2271
+ Remove unused variable in test/unit/bio/io/flatfile/test_splitter
2272
+
2273
+ This commit removes below interpreter warning.
2274
+
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+ * warning: assigned but unused variable
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+
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+ test/unit/bio/io/flatfile/test_splitter.rb | 2 +-
2278
+ 1 file changed, 1 insertion(+), 1 deletion(-)
2279
+
2280
+ commit 0a87c9e265c4560453faf84fc009b60319c75416
2281
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2282
+ Date: Thu Apr 4 17:57:51 2013 +0900
2283
+
2284
+ Remove unused variable in test/unit/bio/db/test_phyloxml_writer
2285
+
2286
+ This commit removes below interpreter warning.
2287
+
2288
+ * warning: assigned but unused variable
2289
+
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+ test/unit/bio/db/test_phyloxml_writer.rb | 4 ++--
2291
+ 1 file changed, 2 insertions(+), 2 deletions(-)
2292
+
2293
+ commit 95b2614eb32eb12428df29360d0c1f146f39a469
2294
+ Author: Naohisa Goto <ng@bioruby.org>
2295
+ Date: Thu May 9 20:56:43 2013 +0900
2296
+
2297
+ Comment out some lines to suppress "unused variable" warnings
2298
+
2299
+ test/unit/bio/db/test_gff.rb | 4 ++--
2300
+ 1 file changed, 2 insertions(+), 2 deletions(-)
2301
+
2302
+ commit b8917841559fbd506c73fdf374a8097f23a1bc37
2303
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2304
+ Date: Thu Apr 4 17:51:11 2013 +0900
2305
+
2306
+ Remove unused variable in test/unit/bio/db/embl/test_sptr.rb
2307
+
2308
+ * Remove warnings "warning: assigned but unused variable"
2309
+ * Note that the sequence in TestSPTRUniProtRel7_6#test_10000aa is
2310
+ a fragment of human p53 protein, and is not related with Q09165.
2311
+
2312
+ test/unit/bio/db/embl/test_sptr.rb | 3 ---
2313
+ 1 file changed, 3 deletions(-)
2314
+
2315
+ commit 6b46d324a545f509bbd238ae7ec009d586469314
2316
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2317
+ Date: Thu Apr 4 17:45:47 2013 +0900
2318
+
2319
+ Remove unused variable in test/unit/bio/db/embl/test_embl_rel89
2320
+
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+ This commit removes below interpreter warning.
2322
+
2323
+ * warning: assigned but unused variable
2324
+
2325
+ test/unit/bio/db/embl/test_embl_rel89.rb | 1 -
2326
+ 1 file changed, 1 deletion(-)
2327
+
2328
+ commit f36eeb0107e7a8315c66888ec8292ed33bd959cc
2329
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2330
+ Date: Thu Apr 4 17:45:21 2013 +0900
2331
+
2332
+ Remove unused variable in test/unit/bio/db/embl/test_embl
2333
+
2334
+ This commit removes below interpreter warning.
2335
+
2336
+ * warning: assigned but unused variable
2337
+
2338
+ test/unit/bio/db/embl/test_embl.rb | 1 -
2339
+ 1 file changed, 1 deletion(-)
2340
+
2341
+ commit a1a2ad9b963d9bb2da8d07ae7b182bd339bea88e
2342
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2343
+ Date: Thu Apr 4 17:36:59 2013 +0900
2344
+
2345
+ Fix indent in test/unit/bio/sequence/test_dblink
2346
+
2347
+ This commit removes below interpreter warning.
2348
+
2349
+ * warning: mismatched indentations at ...
2350
+
2351
+ test/unit/bio/sequence/test_dblink.rb | 2 +-
2352
+ 1 file changed, 1 insertion(+), 1 deletion(-)
2353
+
2354
+ commit 345a8eb4408ca241c13c410a578490c905eb7391
2355
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2356
+ Date: Thu Apr 4 17:36:21 2013 +0900
2357
+
2358
+ Fix indent in test/unit/bio/db/test_phyloxml
2359
+
2360
+ This commit removes below interpreter warning.
2361
+
2362
+ * warning: mismatched indentations at ...
2363
+
2364
+ test/unit/bio/db/test_phyloxml.rb | 58 ++++++++++++++++++-------------------
2365
+ 1 file changed, 29 insertions(+), 29 deletions(-)
2366
+
2367
+ commit ae8c7a6705a30c0c18c57df9869979a968aa63ac
2368
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2369
+ Date: Thu Apr 4 17:35:07 2013 +0900
2370
+
2371
+ Fix indent in test/unit/bio/db/genbank/test_genbank
2372
+
2373
+ This commit removes below interpreter warning.
2374
+
2375
+ * warning: mismatched indentations at ...
2376
+
2377
+ test/unit/bio/db/genbank/test_genbank.rb | 2 +-
2378
+ 1 file changed, 1 insertion(+), 1 deletion(-)
2379
+
2380
+ commit 872d8954e1351251fbace20e331035251ae5f806
2381
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2382
+ Date: Thu Apr 4 17:33:23 2013 +0900
2383
+
2384
+ Fix indent in test/unit/bio/appl/test_blast
2385
+
2386
+ This commit removes below interpreter warning.
2387
+
2388
+ * warning: mismatched indentations at ...
2389
+
2390
+ test/unit/bio/appl/test_blast.rb | 4 ++--
2391
+ 1 file changed, 2 insertions(+), 2 deletions(-)
2392
+
2393
+ commit bd973e084695c4d777c8ecf6d566788838158165
2394
+ Author: Naohisa Goto <ng@bioruby.org>
2395
+ Date: Wed Mar 27 03:03:49 2013 +0900
2396
+
2397
+ .travis.yml: rbx-18mode is moved to allow_failures
2398
+
2399
+ .travis.yml | 8 +++++---
2400
+ 1 file changed, 5 insertions(+), 3 deletions(-)
2401
+
2402
+ commit 63e93faba74a8143a0be9595fdf87329f3015745
2403
+ Author: Andrew Grimm <andrew.j.grimm@gmail.com>
2404
+ Date: Tue Mar 26 20:20:11 2013 +1100
2405
+
2406
+ Squash warning in alignment.rb: assigned but unused variable - oldkeys
2407
+
2408
+ lib/bio/alignment.rb | 1 -
2409
+ 1 file changed, 1 deletion(-)
2410
+
2411
+ commit bd735d6f9d6edfd1550a4279167ac06b372f847a
2412
+ Author: Andrew Grimm <andrew.j.grimm@gmail.com>
2413
+ Date: Tue Mar 26 20:14:46 2013 +1100
2414
+
2415
+ Squash warning in alignment.rb: assigned but unused variable - lines
2416
+
2417
+ lib/bio/alignment.rb | 2 +-
2418
+ 1 file changed, 1 insertion(+), 1 deletion(-)
2419
+
2420
+ commit 3e7b27f96a901a3abfc338572f98d60a9e3be498
2421
+ Author: Andrew Grimm <andrew.j.grimm@gmail.com>
2422
+ Date: Tue Mar 26 19:44:49 2013 +1100
2423
+
2424
+ Squash warning in defline.rb: assigned but unused variable - idtype
2425
+
2426
+ lib/bio/db/fasta/defline.rb | 1 -
2427
+ 1 file changed, 1 deletion(-)
2428
+
2429
+ commit aafc03330fa79243cfa4097d356a7c304ddb7980
2430
+ Author: Kenichi Kamiya <kachick1@gmail.com>
2431
+ Date: Sat Feb 16 21:22:55 2013 +0900
2432
+
2433
+ Simplify some regular expressions
2434
+
2435
+ * /\w/ including /\d/
2436
+ * /\s/ including [/\r/, /\t/, /\n/]
2437
+
2438
+ lib/bio/appl/blast/format0.rb | 2 +-
2439
+ lib/bio/db/embl/common.rb | 2 +-
2440
+ lib/bio/db/embl/embl.rb | 2 +-
2441
+ lib/bio/db/embl/sptr.rb | 2 +-
2442
+ lib/bio/db/gff.rb | 2 +-
2443
+ 5 files changed, 5 insertions(+), 5 deletions(-)
2444
+
2445
+ commit 623ad4011fa8b56f3c9f50a859d1fa26f6570700
2446
+ Author: Naohisa Goto <ng@bioruby.org>
2447
+ Date: Fri Jan 11 16:41:12 2013 +0900
2448
+
2449
+ Improvement of parameter checks and error output
2450
+
2451
+ * Improvement of parameter checks
2452
+ * To avoid potential XSS in old MSIE which ignores content-type,
2453
+ always do CGI.escapeHTML for parameters in error messages
2454
+
2455
+ sample/biofetch.rb | 91 ++++++++++++++++++++++++++++++++++++----------------
2456
+ 1 file changed, 63 insertions(+), 28 deletions(-)
2457
+
2458
+ commit 03d48c43f1de7ebc9104b9aa972f226774a0bf49
2459
+ Author: Naohisa Goto <ng@bioruby.org>
2460
+ Date: Fri Jan 11 15:32:05 2013 +0900
2461
+
2462
+ Add metadata cache
2463
+
2464
+ * Add metadata cache. It caches the list of databases and a list of
2465
+ available formats for each database. Database entries are not cached.
2466
+ * charset=utf-8 in CGI header.
2467
+
2468
+ sample/biofetch.rb | 110 +++++++++++++++++++++++++++++++++++++++++-----------
2469
+ 1 file changed, 87 insertions(+), 23 deletions(-)
2470
+
2471
+ commit 114d29d4bdfc328f5e91adee9bea465622248e0d
2472
+ Author: Naohisa Goto <ng@bioruby.org>
2473
+ Date: Fri Jan 11 09:10:08 2013 +0900
2474
+
2475
+ remove excess double quotations in html part
2476
+
2477
+ sample/biofetch.rb | 8 ++++----
2478
+ 1 file changed, 4 insertions(+), 4 deletions(-)
2479
+
2480
+ commit 949311648b92d51a2596f896fdae8d74ac0608a3
2481
+ Author: Naohisa Goto <ng@bioruby.org>
2482
+ Date: Fri Jan 11 08:59:18 2013 +0900
2483
+
2484
+ add magic comment: coding utf-8
2485
+
2486
+ sample/biofetch.rb | 1 +
2487
+ 1 file changed, 1 insertion(+)
2488
+
2489
+ commit 4ae509273134c5deca7910847063ed07c56150db
2490
+ Author: Naohisa Goto <ng@bioruby.org>
2491
+ Date: Thu Jan 10 23:27:09 2013 +0900
2492
+
2493
+ Rewrite to use TogoWS REST API instead of SOAP-based KEGG API.
2494
+
2495
+ * Rewrite to use TogoWS REST API instead of deprecated SOAP-based
2496
+ KEGG API.
2497
+ * Examples are changed to fit with current TogoWS.
2498
+ * Now, the script does not depend on any non-standard libraries
2499
+ including BioRuby. This means that one can put this script on
2500
+ a server without installing BioRuby.
2501
+ * New constans SCRIPT_NAME and BASE_URL for easy customizing.
2502
+ * Many changes. See "git diff" for details.
2503
+
2504
+ sample/biofetch.rb | 265 ++++++++++++++++++++++++++--------------------------
2505
+ 1 file changed, 131 insertions(+), 134 deletions(-)
2506
+
2507
+ commit bc98bc54c59be98425d66c64b19a3b9612993beb
2508
+ Author: Naohisa Goto <ng@bioruby.org>
2509
+ Date: Thu Jan 10 15:17:42 2013 +0900
2510
+
2511
+ Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
2512
+
2513
+ gemfiles/Gemfile.travis-ruby1.9 | 1 +
2514
+ 1 file changed, 1 insertion(+)
2515
+
2516
+ commit dfe54b2fbe303f56a868404173fe346724b7aa4a
2517
+ Author: Naohisa Goto <ng@bioruby.org>
2518
+ Date: Thu Jan 10 14:06:45 2013 +0900
2519
+
2520
+ Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
2521
+
2522
+ gemfiles/Gemfile.travis-jruby1.8 | 1 +
2523
+ gemfiles/Gemfile.travis-jruby1.9 | 1 +
2524
+ 2 files changed, 2 insertions(+)
2525
+
2526
+ commit f07ec6ac326d51c055496983abba54afd00c35d4
2527
+ Author: Naohisa Goto <ng@bioruby.org>
2528
+ Date: Thu Jan 10 01:38:00 2013 +0900
2529
+
2530
+ Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
2531
+
2532
+ gemfiles/Gemfile.travis-ruby1.8 | 1 +
2533
+ 1 file changed, 1 insertion(+)
2534
+
2535
+ commit 4221d52055087f85daa1c23349d10ecdb4d01a31
2536
+ Author: Naohisa Goto <ng@bioruby.org>
2537
+ Date: Thu Jan 10 01:27:03 2013 +0900
2538
+
2539
+ Ruby 2.0 support: Set script encoding to US-ASCII for gff.rb.
2540
+
2541
+ lib/bio/db/gff.rb | 1 +
2542
+ 1 file changed, 1 insertion(+)
2543
+
2544
+ commit 1526df8273e9d2283fd4a921d4cf8c0c664fe71c
2545
+ Author: Naohisa Goto <ng@bioruby.org>
2546
+ Date: Thu Jan 10 00:45:36 2013 +0900
2547
+
2548
+ Convert encoding of the Japanese tutorial files to UTF-8
2549
+
2550
+ doc/Tutorial.rd.ja | 1920 +++++++++++++++++++++++------------------------
2551
+ doc/Tutorial.rd.ja.html | 1918 +++++++++++++++++++++++-----------------------
2552
+ 2 files changed, 1919 insertions(+), 1919 deletions(-)
2553
+
2554
+ commit 3215570185a46dd0d6c4cd96d583b2487636b483
2555
+ Author: Naohisa Goto <ng@bioruby.org>
2556
+ Date: Thu Jan 10 00:41:51 2013 +0900
2557
+
2558
+ updated doc/Tutorial.rd.html and doc/Tutorial.rd.ja.html
2559
+
2560
+ doc/Tutorial.rd.html | 19 ++---
2561
+ doc/Tutorial.rd.ja.html | 202 +++++++++++++----------------------------------
2562
+ 2 files changed, 63 insertions(+), 158 deletions(-)
2563
+
2564
+ commit 8db12935a9cc15bae92bdb7183476cfea9e1f819
2565
+ Author: Naohisa Goto <ng@bioruby.org>
2566
+ Date: Thu Jan 10 00:38:18 2013 +0900
2567
+
2568
+ Set html title when generating tutorial html
2569
+
2570
+ Rakefile | 3 ++-
2571
+ 1 file changed, 2 insertions(+), 1 deletion(-)
2572
+
2573
+ commit 644d438decceb072475877a749435fba543ff8ea
2574
+ Author: Naohisa Goto <ng@bioruby.org>
2575
+ Date: Fri Jan 4 03:19:00 2013 +0900
2576
+
2577
+ regenerate bioruby.gemspec with rake regemspec
2578
+
2579
+ bioruby.gemspec | 6 ------
2580
+ 1 file changed, 6 deletions(-)
2581
+
2582
+ commit 54dc9b9f68ee2de9ee005a772ce000277a073d97
2583
+ Author: Naohisa Goto <ng@bioruby.org>
2584
+ Date: Fri Jan 4 02:35:01 2013 +0900
2585
+
2586
+ Remove sample/psortplot_html.rb which depend on Bio::KEGG::API.
2587
+
2588
+ * Remove sample/psortplot_html.rb because it strongly depend on
2589
+ removed Bio::KEGG::API and discontinued SOAP-based KEGG API.
2590
+ It is hard to re-write by using new REST-based KEGG API because
2591
+ the new API seems to lack color_pathway_by_objects that returns
2592
+ image URL. Moreover, there is no one-by-one API migration guide.
2593
+
2594
+ sample/psortplot_html.rb | 214 ----------------------------------------------
2595
+ 1 file changed, 214 deletions(-)
2596
+ delete mode 100644 sample/psortplot_html.rb
2597
+
2598
+ commit dbdf2dad3dec9d10141b891a481b9b05e1561708
2599
+ Author: Naohisa Goto <ng@bioruby.org>
2600
+ Date: Fri Jan 4 02:34:05 2013 +0900
2601
+
2602
+ Remove descriptions about KEGG API and Bio::KEGG::API.
2603
+
2604
+ doc/Tutorial.rd | 6 ---
2605
+ doc/Tutorial.rd.ja | 106 +---------------------------------------------------
2606
+ 2 files changed, 1 insertion(+), 111 deletions(-)
2607
+
2608
+ commit 3ca725dc1e07f794344c9fcae43d4972ed2895da
2609
+ Author: Naohisa Goto <ng@bioruby.org>
2610
+ Date: Fri Jan 4 02:33:09 2013 +0900
2611
+
2612
+ Remove description about KEGG API and Bio::KEGG::API.
2613
+
2614
+ README.rdoc | 6 ++----
2615
+ 1 file changed, 2 insertions(+), 4 deletions(-)
2616
+
2617
+ commit d4568788069f2d998a78ad72b1d906aae13e85f4
2618
+ Author: Naohisa Goto <ng@bioruby.org>
2619
+ Date: Thu Jan 3 23:55:58 2013 +0900
2620
+
2621
+ Remove KEGG API plugin of BioRuby Shell, due to the removal of Bio::KEGG::API.
2622
+
2623
+ lib/bio/shell.rb | 1 -
2624
+ lib/bio/shell/plugin/keggapi.rb | 181 ---------------------------------------
2625
+ 2 files changed, 182 deletions(-)
2626
+ delete mode 100644 lib/bio/shell/plugin/keggapi.rb
2627
+
2628
+ commit 22c8f4945d622f8f22c08b262c6caf81a0261284
2629
+ Author: Naohisa Goto <ng@bioruby.org>
2630
+ Date: Thu Jan 3 23:52:36 2013 +0900
2631
+
2632
+ Delete autoload lines for removed Bio::KEGG::API
2633
+
2634
+ lib/bio.rb | 4 ----
2635
+ 1 file changed, 4 deletions(-)
2636
+
2637
+ commit b56ec0984d5001c3a4d3b4f0ba8fbbbf79835747
2638
+ Author: Naohisa Goto <ng@bioruby.org>
2639
+ Date: Thu Jan 3 23:51:24 2013 +0900
2640
+
2641
+ Remove Bio::KEGG::API and its sample code and documentation files.
2642
+
2643
+ * Remove Bio::KEGG::API and its sample code and documentation files.
2644
+ * deleted: lib/bio/io/keggapi.rb
2645
+ * deleted: doc/KEGG_API.rd
2646
+ * deleted: doc/KEGG_API.rd.ja
2647
+ * deleted: sample/demo_keggapi.rb
2648
+
2649
+ doc/KEGG_API.rd | 1843 ------------------------------------------------
2650
+ doc/KEGG_API.rd.ja | 1834 -----------------------------------------------
2651
+ lib/bio/io/keggapi.rb | 363 ----------
2652
+ sample/demo_keggapi.rb | 502 -------------
2653
+ 4 files changed, 4542 deletions(-)
2654
+ delete mode 100644 doc/KEGG_API.rd
2655
+ delete mode 100644 doc/KEGG_API.rd.ja
2656
+ delete mode 100644 lib/bio/io/keggapi.rb
2657
+ delete mode 100644 sample/demo_keggapi.rb
2658
+
2659
+ commit 63af413c122b4531193153fbfee034deaf0a9606
2660
+ Author: Naohisa Goto <ng@bioruby.org>
2661
+ Date: Mon Oct 1 21:11:14 2012 +0900
2662
+
2663
+ Bug fix: parse error when subject sequence contains spaces
2664
+
2665
+ * Bug fix: parse error when subject sequence contains spaces.
2666
+ Thanks to Edward Rice who reports the bug. (Bug #3385)
2667
+ (https://redmine.open-bio.org/issues/3385)
2668
+
2669
+ lib/bio/appl/blast/format0.rb | 38 +++++++++++++++++++-------------------
2670
+ 1 file changed, 19 insertions(+), 19 deletions(-)
2671
+
2672
+ commit 9f2f682ec6624ff356bea7aca76365ba95d33549
2673
+ Author: Naohisa Goto <ng@bioruby.org>
2674
+ Date: Fri Sep 7 16:50:44 2012 +0900
2675
+
2676
+ add an env line to be recognized in allow_failures
2677
+
2678
+ .travis.yml | 1 +
2679
+ 1 file changed, 1 insertion(+)
2680
+
2681
+ commit fead6dda526081db09c56c2262f111338b7d8cd7
2682
+ Author: Naohisa Goto <ng@bioruby.org>
2683
+ Date: Fri Sep 7 16:08:57 2012 +0900
2684
+
2685
+ environment variable TESTOPTS=-v for verbose output of rake test
2686
+
2687
+ .travis.yml | 22 ++++++++++++++--------
2688
+ 1 file changed, 14 insertions(+), 8 deletions(-)
2689
+
2690
+ commit 3de19895140502898c77fc83d9ad6fae47331763
2691
+ Author: Naohisa Goto <ng@bioruby.org>
2692
+ Date: Thu Sep 6 18:17:22 2012 +0900
2693
+
2694
+ Remove Bio.method_missing because it is broken.
2695
+
2696
+ * Bio.method_missing, the hook of undefined methods, providing
2697
+ shortcut of Bio::Shell methods, is now removed, because it does
2698
+ not work correctly, and because the use of method_missing should
2699
+ normally be avoided unless it is really necessary. Alternatively,
2700
+ use Bio::Shell.xxxxx (xxxxx is a method name).
2701
+
2702
+ lib/bio.rb | 13 -------------
2703
+ 1 file changed, 13 deletions(-)
2704
+
2705
+ commit a358584c4a76be6a38ab38a18e6dc66840030450
2706
+ Author: Naohisa Goto <ng@bioruby.org>
2707
+ Date: Thu Sep 6 16:48:51 2012 +0900
2708
+
2709
+ Delete autoload line of a removed class Bio::NCBI::SOAP.
2710
+
2711
+ lib/bio/io/ncbirest.rb | 1 -
2712
+ 1 file changed, 1 deletion(-)
2713
+
2714
+ commit 340d665775b862da638e4d12751b84d2ccd83e82
2715
+ Author: Naohisa Goto <ng@bioruby.org>
2716
+ Date: Thu Sep 6 16:47:03 2012 +0900
2717
+
2718
+ Delete autoload lines of removed classes.
2719
+
2720
+ lib/bio.rb | 4 ----
2721
+ 1 file changed, 4 deletions(-)
2722
+
2723
+ commit c7c29a672b38d2182cf4afc9a970b854af1149a7
2724
+ Author: Naohisa Goto <ng@bioruby.org>
2725
+ Date: Thu Sep 6 16:43:25 2012 +0900
2726
+
2727
+ regenerate bioruby.gemspec with rake regemspec
2728
+
2729
+ bioruby.gemspec | 3 ---
2730
+ 1 file changed, 3 deletions(-)
2731
+
2732
+ commit 09bb4b8a8b7e01a36dbe0cf44a5c2a6a6b5750f1
2733
+ Author: Naohisa Goto <ng@bioruby.org>
2734
+ Date: Thu Sep 6 16:23:17 2012 +0900
2735
+
2736
+ Remove Bio::Shell#ncbisoap which uses removed Bio::NCBI::SOAP.
2737
+
2738
+ lib/bio/shell/plugin/soap.rb | 9 ---------
2739
+ 1 file changed, 9 deletions(-)
2740
+
2741
+ commit a5e46acdaf06568bea6cb773200bbf3881b5670e
2742
+ Author: Naohisa Goto <ng@bioruby.org>
2743
+ Date: Thu Sep 6 16:02:32 2012 +0900
2744
+
2745
+ Remove issues about removed classes Bio::NCBI::SOAP and Bio::KEGG::Taxonomy
2746
+
2747
+ KNOWN_ISSUES.rdoc | 10 ----------
2748
+ 1 file changed, 10 deletions(-)
2749
+
2750
+ commit 529815acb1b57486bd506b81eec6be80277cbae7
2751
+ Author: Naohisa Goto <ng@bioruby.org>
2752
+ Date: Wed Sep 5 11:33:27 2012 +0900
2753
+
2754
+ Remove Bio::KEGG::Taxonomy which is old and broken
2755
+
2756
+ * Remove Bio::KEGG::Taxonomy because it raises error or the data
2757
+ structure in the return value seems to be broken. In addition,
2758
+ running the sample script sample/demo_kegg_taxonomy.rb shows
2759
+ error or falls into infinite loop. Moreover, KEGG closes public
2760
+ FTP site and the target data file of the class ("taxonomy")
2761
+ can only be obtained by paid subscribers. From the above reasons,
2762
+ it seems there are no users of this class now.
2763
+ * Deleted files: lib/bio/db/kegg/taxonomy.rb,
2764
+ sample/demo_kegg_taxonomy.rb
2765
+
2766
+ lib/bio/db/kegg/taxonomy.rb | 280 ------------------------------------------
2767
+ sample/demo_kegg_taxonomy.rb | 92 --------------
2768
+ 2 files changed, 372 deletions(-)
2769
+ delete mode 100644 lib/bio/db/kegg/taxonomy.rb
2770
+ delete mode 100644 sample/demo_kegg_taxonomy.rb
2771
+
2772
+ commit dc47fb46e86bba15ba43de31075eaba3cf811fa3
2773
+ Author: Naohisa Goto <ng@bioruby.org>
2774
+ Date: Wed Sep 5 11:26:00 2012 +0900
2775
+
2776
+ Remove Bio::NCBI::SOAP which is broken
2777
+
2778
+ * Remove Bio::NCBI::SOAP in lib/bio/io/ncbisoap.rb, because it always
2779
+ raises error during the parsing of WSDL files provided by NCBI, both
2780
+ with Ruby 1.8.X (with bundled SOAP4R) and Ruby 1.9.X (with
2781
+ soap4r-ruby1.9 gem). To solve the error, modifying SOAP4R may be
2782
+ needed, that seems very difficult. The alternative is Bio::NCBI::REST,
2783
+ REST client class for the NCBI EUtil web services.
2784
+
2785
+ lib/bio/io/ncbisoap.rb | 156 ------------------------------------------------
2786
+ 1 file changed, 156 deletions(-)
2787
+ delete mode 100644 lib/bio/io/ncbisoap.rb
2788
+
2789
+ commit 314e06e54603bb238015c391904f414b3da48752
2790
+ Author: Naohisa Goto <ng@bioruby.org>
2791
+ Date: Tue Sep 4 11:13:47 2012 +0900
2792
+
2793
+ regenerate bioruby.gemspec with rake regemspec
2794
+
2795
+ bioruby.gemspec | 10 ++++------
2796
+ 1 file changed, 4 insertions(+), 6 deletions(-)
2797
+
2798
+ commit e929d5d23a9b489ef42f30b33959f059baf1e185
2799
+ Author: Naohisa Goto <ng@bioruby.org>
2800
+ Date: Tue Sep 4 11:09:36 2012 +0900
2801
+
2802
+ Remove issues about removed classes Bio::Ensembl and Bio::DBGET.
2803
+
2804
+ KNOWN_ISSUES.rdoc | 16 ----------------
2805
+ 1 file changed, 16 deletions(-)
2806
+
2807
+ commit 550a5440490012f73b6d38d84238cd498f2ebb02
2808
+ Author: Naohisa Goto <ng@bioruby.org>
2809
+ Date: Tue Sep 4 10:57:20 2012 +0900
2810
+
2811
+ Remove Bio::Ensembl because it does not work
2812
+
2813
+ * Remove Bio::Ensembl because it does not work after the renewal of
2814
+ the Ensembl web site in 2008.
2815
+ * Alternative is io-ensembl gem which supports current Ensembl API.
2816
+ http://rubygems.org/gems/bio-ensembl
2817
+ * Deleted files: lib/bio/io/ensembl.rb,
2818
+ test/network/bio/io/test_ensembl.rb, test/unit/bio/io/test_ensembl.rb.
2819
+
2820
+ lib/bio/io/ensembl.rb | 229 ----------------------------------
2821
+ test/network/bio/io/test_ensembl.rb | 230 -----------------------------------
2822
+ test/unit/bio/io/test_ensembl.rb | 111 -----------------
2823
+ 3 files changed, 570 deletions(-)
2824
+ delete mode 100644 lib/bio/io/ensembl.rb
2825
+ delete mode 100644 test/network/bio/io/test_ensembl.rb
2826
+ delete mode 100644 test/unit/bio/io/test_ensembl.rb
2827
+
2828
+ commit 61301a8ec252f3623f994edd59f597360f73448b
2829
+ Author: Naohisa Goto <ng@bioruby.org>
2830
+ Date: Tue Sep 4 10:47:52 2012 +0900
2831
+
2832
+ Remove obsolete Bio::DBGET
2833
+
2834
+ * Remove Bio::DBGET because it uses old original protocol that was
2835
+ discontinued about 8 years ago.
2836
+ * Remove lib/bio/io/dbget.rb and sample/dbget.
2837
+
2838
+ lib/bio/io/dbget.rb | 194 ---------------------------------------------------
2839
+ sample/dbget | 37 ----------
2840
+ 2 files changed, 231 deletions(-)
2841
+ delete mode 100644 lib/bio/io/dbget.rb
2842
+ delete mode 100755 sample/dbget
2843
+
2844
+ commit 3c5e288a8685ba3279a3ba73f1b31056c1b6f7a8
2845
+ Author: Naohisa Goto <ng@bioruby.org>
2846
+ Date: Thu Aug 23 00:25:43 2012 +0900
2847
+
2848
+ Refresh ChangeLog, showing changes after 1.4.3 release.
2849
+
2850
+ * Refresh to the new ChangeLog, showing changes after 1.4.3 release.
2851
+ For the changes before 1.4.3, see doc/ChangeLog-1.4.3.
2852
+ For the changes before 1.4.2, see doc/ChangeLog-before-1.4.2.
2853
+ For the changes before 1.3.1, see doc/ChangeLog-before-1.3.1.
2854
+
2855
+ ChangeLog | 61 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2856
+ 1 file changed, 61 insertions(+)
2857
+ create mode 100644 ChangeLog
2858
+
2859
+ commit 63c13ad8516b9dcacbe001137666c3468968542b
2860
+ Author: Naohisa Goto <ng@bioruby.org>
2861
+ Date: Thu Aug 23 00:25:07 2012 +0900
2862
+
2863
+ Rakefile: Update hardcoded git tag name for updating of ChangeLog.
2864
+
2865
+ Rakefile | 2 +-
2866
+ 1 file changed, 1 insertion(+), 1 deletion(-)
2867
+
2868
+ commit b10c7ad2db24d88726ffb8c63078baa217aeac43
2869
+ Author: Naohisa Goto <ng@bioruby.org>
2870
+ Date: Thu Aug 23 00:20:01 2012 +0900
2871
+
2872
+ renamed ChangeLog to doc/ChangeLog-1.4.3
2873
+
2874
+ ChangeLog | 1478 ---------------------------------------------------
2875
+ doc/ChangeLog-1.4.3 | 1478 +++++++++++++++++++++++++++++++++++++++++++++++++++
2876
+ 2 files changed, 1478 insertions(+), 1478 deletions(-)
2877
+ delete mode 100644 ChangeLog
2878
+ create mode 100644 doc/ChangeLog-1.4.3
2879
+
2880
+ commit 0c20cb62ba6b253098e7198c14de1829f72474f5
2881
+ Author: Naohisa Goto <ng@bioruby.org>
2882
+ Date: Thu Aug 23 00:18:50 2012 +0900
2883
+
2884
+ ChangeLog updated: add log about 1.4.3 release.
2885
+
2886
+ ChangeLog | 9 +++++++++
2887
+ 1 file changed, 9 insertions(+)
2888
+
2889
+ commit 5e88ccbe0fefdd4d57f144aaf9073f5e7d93281c
2890
+ Author: Naohisa Goto <ng@bioruby.org>
2891
+ Date: Thu Aug 23 00:16:25 2012 +0900
2892
+
2893
+ New RELEASE_NOTES.rdoc for the next release version.
2894
+
2895
+ RELEASE_NOTES.rdoc | 47 +++++++++++++++++++++++++++++++++++++++++++++++
2896
+ 1 file changed, 47 insertions(+)
2897
+ create mode 100644 RELEASE_NOTES.rdoc
2898
+
2899
+ commit e3d40b90d88ab0d0a91d8e32ebf97c16097f0996
2900
+ Author: Naohisa Goto <ng@bioruby.org>
2901
+ Date: Thu Aug 23 00:12:40 2012 +0900
2902
+
2903
+ Renamed RELEASE_NOTES.rdoc to doc/RELEASE_NOTES-1.4.3.rdoc
2904
+
2905
+ RELEASE_NOTES.rdoc | 204 ------------------------------------------
2906
+ doc/RELEASE_NOTES-1.4.3.rdoc | 204 ++++++++++++++++++++++++++++++++++++++++++
2907
+ 2 files changed, 204 insertions(+), 204 deletions(-)
2908
+ delete mode 100644 RELEASE_NOTES.rdoc
2909
+ create mode 100644 doc/RELEASE_NOTES-1.4.3.rdoc
2910
+
2911
+ commit 08bcabecccb271385d38a0f807e8c408def5a128
2912
+ Author: Naohisa Goto <ng@bioruby.org>
2913
+ Date: Thu Aug 23 00:00:15 2012 +0900
2914
+
2915
+ Bio::BIORUBY_EXTRA_VERSION set to ".5000" (unstable version).
2916
+
2917
+ bioruby.gemspec | 2 +-
2918
+ lib/bio/version.rb | 2 +-
2919
+ 2 files changed, 2 insertions(+), 2 deletions(-)