bio 1.4.3.0001 → 1.5.0

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Files changed (158) hide show
  1. checksums.yaml +7 -0
  2. data/.travis.yml +39 -33
  3. data/BSDL +22 -0
  4. data/COPYING +2 -2
  5. data/COPYING.ja +36 -36
  6. data/ChangeLog +2404 -1025
  7. data/KNOWN_ISSUES.rdoc +15 -55
  8. data/README.rdoc +17 -23
  9. data/RELEASE_NOTES.rdoc +246 -183
  10. data/Rakefile +3 -2
  11. data/bin/br_biofetch.rb +29 -5
  12. data/bioruby.gemspec +15 -32
  13. data/bioruby.gemspec.erb +10 -20
  14. data/doc/ChangeLog-1.4.3 +1478 -0
  15. data/doc/RELEASE_NOTES-1.4.3.rdoc +204 -0
  16. data/doc/Tutorial.rd +0 -6
  17. data/doc/Tutorial.rd.html +7 -12
  18. data/doc/Tutorial.rd.ja +960 -1064
  19. data/doc/Tutorial.rd.ja.html +977 -1067
  20. data/gemfiles/Gemfile.travis-jruby1.8 +2 -1
  21. data/gemfiles/Gemfile.travis-jruby1.9 +2 -4
  22. data/gemfiles/Gemfile.travis-rbx +13 -0
  23. data/gemfiles/Gemfile.travis-ruby1.8 +2 -1
  24. data/gemfiles/Gemfile.travis-ruby1.9 +2 -4
  25. data/gemfiles/Gemfile.travis-ruby2.2 +9 -0
  26. data/lib/bio.rb +10 -43
  27. data/lib/bio/alignment.rb +8 -14
  28. data/lib/bio/appl/blast.rb +1 -2
  29. data/lib/bio/appl/blast/format0.rb +18 -7
  30. data/lib/bio/appl/blast/remote.rb +0 -9
  31. data/lib/bio/appl/blast/report.rb +1 -1
  32. data/lib/bio/appl/clustalw/report.rb +3 -1
  33. data/lib/bio/appl/genscan/report.rb +1 -2
  34. data/lib/bio/appl/iprscan/report.rb +1 -2
  35. data/lib/bio/appl/meme/mast.rb +4 -4
  36. data/lib/bio/appl/meme/mast/report.rb +1 -1
  37. data/lib/bio/appl/paml/codeml.rb +2 -2
  38. data/lib/bio/appl/paml/codeml/report.rb +1 -0
  39. data/lib/bio/appl/paml/common.rb +1 -1
  40. data/lib/bio/appl/sosui/report.rb +1 -2
  41. data/lib/bio/command.rb +62 -2
  42. data/lib/bio/data/aa.rb +13 -31
  43. data/lib/bio/data/codontable.rb +1 -2
  44. data/lib/bio/db/biosql/biosql_to_biosequence.rb +1 -0
  45. data/lib/bio/db/biosql/sequence.rb +1 -1
  46. data/lib/bio/db/embl/common.rb +1 -1
  47. data/lib/bio/db/embl/embl.rb +5 -4
  48. data/lib/bio/db/embl/format_embl.rb +3 -3
  49. data/lib/bio/db/embl/sptr.rb +9 -1444
  50. data/lib/bio/db/embl/swissprot.rb +12 -29
  51. data/lib/bio/db/embl/trembl.rb +13 -30
  52. data/lib/bio/db/embl/uniprot.rb +12 -29
  53. data/lib/bio/db/embl/uniprotkb.rb +1455 -0
  54. data/lib/bio/db/fasta.rb +17 -0
  55. data/lib/bio/db/fasta/defline.rb +1 -3
  56. data/lib/bio/db/fastq.rb +1 -1
  57. data/lib/bio/db/genbank/ddbj.rb +9 -5
  58. data/lib/bio/db/genbank/refseq.rb +11 -3
  59. data/lib/bio/db/gff.rb +3 -4
  60. data/lib/bio/db/go.rb +5 -6
  61. data/lib/bio/db/kegg/module.rb +4 -5
  62. data/lib/bio/db/kegg/pathway.rb +4 -5
  63. data/lib/bio/db/kegg/reaction.rb +1 -1
  64. data/lib/bio/db/nexus.rb +3 -2
  65. data/lib/bio/db/pdb/pdb.rb +2 -2
  66. data/lib/bio/db/phyloxml/phyloxml_elements.rb +82 -59
  67. data/lib/bio/db/phyloxml/phyloxml_parser.rb +2 -2
  68. data/lib/bio/db/phyloxml/phyloxml_writer.rb +1 -2
  69. data/lib/bio/db/sanger_chromatogram/chromatogram.rb +1 -2
  70. data/lib/bio/db/transfac.rb +1 -1
  71. data/lib/bio/io/das.rb +40 -41
  72. data/lib/bio/io/fastacmd.rb +0 -16
  73. data/lib/bio/io/fetch.rb +111 -55
  74. data/lib/bio/io/flatfile/buffer.rb +4 -5
  75. data/lib/bio/io/hinv.rb +2 -3
  76. data/lib/bio/io/ncbirest.rb +43 -6
  77. data/lib/bio/io/pubmed.rb +76 -81
  78. data/lib/bio/io/togows.rb +33 -10
  79. data/lib/bio/map.rb +1 -1
  80. data/lib/bio/pathway.rb +1 -1
  81. data/lib/bio/sequence/compat.rb +1 -1
  82. data/lib/bio/sequence/na.rb +63 -12
  83. data/lib/bio/shell.rb +0 -2
  84. data/lib/bio/shell/core.rb +5 -6
  85. data/lib/bio/shell/interface.rb +3 -4
  86. data/lib/bio/shell/irb.rb +1 -2
  87. data/lib/bio/shell/plugin/entry.rb +2 -3
  88. data/lib/bio/shell/plugin/seq.rb +7 -6
  89. data/lib/bio/shell/setup.rb +1 -2
  90. data/lib/bio/tree.rb +2 -2
  91. data/lib/bio/util/contingency_table.rb +0 -2
  92. data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +2 -2
  93. data/lib/bio/util/sirna.rb +76 -16
  94. data/lib/bio/version.rb +8 -9
  95. data/sample/benchmark_clustalw_report.rb +47 -0
  96. data/sample/biofetch.rb +248 -151
  97. data/setup.rb +6 -7
  98. data/test/data/clustalw/example1-seqnos.aln +58 -0
  99. data/test/network/bio/appl/blast/test_remote.rb +1 -15
  100. data/test/network/bio/appl/test_blast.rb +0 -12
  101. data/test/network/bio/io/test_pubmed.rb +49 -0
  102. data/test/network/bio/io/test_togows.rb +0 -1
  103. data/test/network/bio/test_command.rb +65 -2
  104. data/test/unit/bio/appl/bl2seq/test_report.rb +0 -1
  105. data/test/unit/bio/appl/blast/test_report.rb +110 -48
  106. data/test/unit/bio/appl/clustalw/test_report.rb +67 -51
  107. data/test/unit/bio/appl/sim4/test_report.rb +46 -17
  108. data/test/unit/bio/appl/test_blast.rb +2 -2
  109. data/test/unit/bio/db/embl/test_embl.rb +0 -1
  110. data/test/unit/bio/db/embl/test_embl_rel89.rb +0 -1
  111. data/test/unit/bio/db/embl/{test_sptr.rb → test_uniprotkb.rb} +111 -115
  112. data/test/unit/bio/db/embl/{test_uniprot_new_part.rb → test_uniprotkb_new_part.rb} +11 -11
  113. data/test/unit/bio/db/genbank/test_genbank.rb +10 -4
  114. data/test/unit/bio/db/pdb/test_pdb.rb +14 -8
  115. data/test/unit/bio/db/test_fasta.rb +41 -1
  116. data/test/unit/bio/db/test_fastq.rb +14 -4
  117. data/test/unit/bio/db/test_gff.rb +2 -2
  118. data/test/unit/bio/db/test_phyloxml.rb +30 -30
  119. data/test/unit/bio/db/test_phyloxml_writer.rb +2 -2
  120. data/test/unit/bio/io/flatfile/test_autodetection.rb +1 -2
  121. data/test/unit/bio/io/flatfile/test_buffer.rb +7 -1
  122. data/test/unit/bio/io/flatfile/test_splitter.rb +1 -1
  123. data/test/unit/bio/io/test_togows.rb +3 -2
  124. data/test/unit/bio/sequence/test_dblink.rb +1 -1
  125. data/test/unit/bio/sequence/test_na.rb +3 -1
  126. data/test/unit/bio/test_alignment.rb +1 -2
  127. data/test/unit/bio/test_command.rb +5 -4
  128. data/test/unit/bio/test_db.rb +4 -2
  129. data/test/unit/bio/test_pathway.rb +25 -10
  130. data/test/unit/bio/util/test_sirna.rb +22 -22
  131. metadata +656 -1430
  132. data/doc/KEGG_API.rd +0 -1843
  133. data/doc/KEGG_API.rd.ja +0 -1834
  134. data/extconf.rb +0 -2
  135. data/lib/bio/appl/blast/ddbj.rb +0 -131
  136. data/lib/bio/db/kegg/taxonomy.rb +0 -280
  137. data/lib/bio/io/dbget.rb +0 -194
  138. data/lib/bio/io/ddbjrest.rb +0 -344
  139. data/lib/bio/io/ddbjxml.rb +0 -458
  140. data/lib/bio/io/ebisoap.rb +0 -158
  141. data/lib/bio/io/ensembl.rb +0 -229
  142. data/lib/bio/io/higet.rb +0 -73
  143. data/lib/bio/io/keggapi.rb +0 -363
  144. data/lib/bio/io/ncbisoap.rb +0 -156
  145. data/lib/bio/io/soapwsdl.rb +0 -119
  146. data/lib/bio/shell/plugin/keggapi.rb +0 -181
  147. data/lib/bio/shell/plugin/soap.rb +0 -87
  148. data/sample/dbget +0 -37
  149. data/sample/demo_ddbjxml.rb +0 -212
  150. data/sample/demo_kegg_taxonomy.rb +0 -92
  151. data/sample/demo_keggapi.rb +0 -502
  152. data/sample/psortplot_html.rb +0 -214
  153. data/test/network/bio/io/test_ddbjrest.rb +0 -47
  154. data/test/network/bio/io/test_ensembl.rb +0 -230
  155. data/test/network/bio/io/test_soapwsdl.rb +0 -53
  156. data/test/unit/bio/io/test_ddbjxml.rb +0 -81
  157. data/test/unit/bio/io/test_ensembl.rb +0 -111
  158. data/test/unit/bio/io/test_soapwsdl.rb +0 -33
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  language: ruby
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  rvm:
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+ - 2.0.0
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  - 1.9.3
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- - 1.8.7
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- - rbx-18mode
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+ env:
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+ - TESTOPTS=-v
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  gemfile:
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  - gemfiles/Gemfile.travis-ruby1.9
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- - gemfiles/Gemfile.travis-ruby1.8
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  before_install:
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+ - gem update --system 2.1.11
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+ - gem --version
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  - mkdir /tmp/bioruby
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  - ruby gemfiles/modify-Gemfile.rb
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- gemfile: gemfiles/Gemfile.travis-ruby1.9
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- - rvm: rbx-19mode
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- gemfile: gemfiles/Gemfile.travis-jruby1.9
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- - rvm: jruby-19mode
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- gemfile: gemfiles/Gemfile.travis-jruby1.9
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- env: TMPDIR=/tmp/bioruby
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- - rvm: 1.9.3
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- gemfile: gemfiles/Gemfile.travis-ruby1.9
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- env: BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test
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- - rvm: 1.9.3
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- gemfile: gemfiles/Gemfile.travis-ruby1.9
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- env: BIORUBY_RAKE_DEFAULT_TASK=gem-test
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- gemfile: gemfiles/Gemfile.travis-jruby1.8
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- env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test
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+ - rvm: 1.8.7
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+ gemfile: gemfiles/Gemfile.travis-ruby1.8
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+ env: TESTOPTS=-v
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+ - rvm: rbx-2.2.3
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+ gemfile: gemfiles/Gemfile.travis-rbx
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+ env: TESTOPTS=-v
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- env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test
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- exclude:
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+ env: TMPDIR=/tmp/bioruby TESTOPTS=-v
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+ - rvm: jruby-19mode
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+ gemfile: gemfiles/Gemfile.travis-jruby1.9
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+ env: TMPDIR=/tmp/bioruby TESTOPTS=-v
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+ - rvm: 2.2.2
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+ env: BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test TESTOPTS=-v
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- allow_failures:
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- gemfile: gemfiles/Gemfile.travis-jruby1.8
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- env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test
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+ env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
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+ allow_failures:
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+ - rvm: rbx-2.2.3
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+ gemfile: gemfiles/Gemfile.travis-rbx
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+ env: TESTOPTS=-v
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- env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test
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-
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+ env: TMPDIR=/tmp/bioruby TESTOPTS=-v
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+ - rvm: jruby-19mode
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+ gemfile: gemfiles/Gemfile.travis-jruby1.9
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+ env: TMPDIR=/tmp/bioruby TESTOPTS=-v
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+ - rvm: jruby-19mode
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+ gemfile: gemfiles/Gemfile.travis-jruby1.9
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+ env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test TESTOPTS=-v
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+ - rvm: jruby-19mode
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+ gemfile: gemfiles/Gemfile.travis-jruby1.9
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+ env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
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data/BSDL ADDED
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+ Copyright (C) 1993-2013 Yukihiro Matsumoto. All rights reserved.
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+
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+ Redistribution and use in source and binary forms, with or without
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+ modification, are permitted provided that the following conditions
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+ are met:
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+ 1. Redistributions of source code must retain the above copyright
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+ notice, this list of conditions and the following disclaimer.
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+ 2. Redistributions in binary form must reproduce the above copyright
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+ notice, this list of conditions and the following disclaimer in the
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+ documentation and/or other materials provided with the distribution.
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+
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+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
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+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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+ ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
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+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
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+ OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
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+ HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
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+ LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
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+ OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
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+ SUCH DAMAGE.
data/COPYING CHANGED
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  BioRuby is copyrighted free software by Toshiaki Katayama <k@bioruby.org>.
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- You can redistribute it and/or modify it under either the terms of the GPL
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- version 2 (see the file GPL), or the conditions below:
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+ You can redistribute it and/or modify it under either the terms of the
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+ 2-clause BSDL (see the file BSDL), or the conditions below:
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  1. You may make and give away verbatim copies of the source form of the
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  software without restriction, provided that you duplicate all of the
data/COPYING.ja CHANGED
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+ 本プログラムはフリーソフトウェアです.2-clause BSDL
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+ または以下に示す条件で本プログラムを再配布できます
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+ 2-clause BSDLについてはBSDLファイルを参照して下さい.
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+ 2. 以下の条件のいずれかを満たす時に本プログラムのソースを
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+ (a) ネットニューズにポストしたり,作者に変更を送付する
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+ (c) 変更点を明示したうえ,ソフトウェアの名前を変更する.
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+ 3. 以下の条件のいずれかを満たす時に本プログラムをコンパイ
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+ ルしたオブジェクトコードや実行形式でも配布できます.
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- $B%k$N%=!<%9%3!<%I$NF~<jK!$rL@<($9$k!%(B
31
+ (c) 変更を行ったバイナリは名前を変更したうえ,オリジナ
32
+ ルのソースコードの入手法を明示する.
33
33
 
34
- (d) $B$=$NB>$NG[I[>r7o$r:n<T$H9g0U$9$k!%(B
34
+ (d) その他の配布条件を作者と合意する.
35
35
 
36
- 4. $BB>$N%W%m%0%i%`$X$N0zMQ$O$$$+$J$kL\E*$G$"$l<+M3$G$9!%$?(B
37
- $B$@$7!$K\%W%m%0%i%`$K4^$^$l$kB>$N:n<T$K$h$k%3!<%I$O!$$=(B
38
- $B$l$>$l$N:n<T$N0U8~$K$h$k@)8B$,2C$($i$l$k>l9g$,$"$j$^$9!%(B
36
+ 4. 他のプログラムへの引用はいかなる目的であれ自由です.た
37
+ だし,本プログラムに含まれる他の作者によるコードは,そ
38
+ れぞれの作者の意向による制限が加えられる場合があります.
39
39
 
40
- $B$=$l$i%U%!%$%k$N0lMw$H$=$l$>$l$NG[I[>r7o$J$I$KIU$$$F$O(B
41
- LEGAL$B%U%!%$%k$r;2>H$7$F$/$@$5$$!%(B
40
+ それらファイルの一覧とそれぞれの配布条件などに付いては
41
+ LEGALファイルを参照してください.
42
42
 
43
- 5. $BK\%W%m%0%i%`$X$NF~NO$H$J$k%9%/%j%W%H$*$h$S!$K\%W%m%0%i(B
44
- $B%`$+$i$N=PNO$N8"Mx$OK\%W%m%0%i%`$N:n<T$G$O$J$/!$$=$l$>(B
45
- $B$l$NF~=PNO$r@8@.$7$??M$KB0$7$^$9!%$^$?!$K\%W%m%0%i%`$K(B
46
- $BAH$_9~$^$l$k$?$a$N3HD%%i%$%V%i%j$K$D$$$F$bF1MM$G$9!%(B
43
+ 5. 本プログラムへの入力となるスクリプトおよび,本プログラ
44
+ ムからの出力の権利は本プログラムの作者ではなく,それぞ
45
+ れの入出力を生成した人に属します.また,本プログラムに
46
+ 組み込まれるための拡張ライブラリについても同様です.
47
47
 
48
- 6. $BK\%W%m%0%i%`$OL5J]>Z$G$9!%:n<T$OK\%W%m%0%i%`$r%5%]!<%H(B
49
- $B$9$k0U;V$O$"$j$^$9$,!$%W%m%0%i%`<+?H$N%P%0$"$k$$$OK\%W(B
50
- $B%m%0%i%`$N<B9T$J$I$+$iH/@8$9$k$$$+$J$kB;32$KBP$7$F$b@U(B
51
- $BG$$r;}$A$^$;$s!%(B
48
+ 6. 本プログラムは無保証です.作者は本プログラムをサポート
49
+ する意志はありますが,プログラム自身のバグあるいは本プ
50
+ ログラムの実行などから発生するいかなる損害に対しても責
51
+ 任を持ちません.
data/ChangeLog CHANGED
@@ -1,1540 +1,2919 @@
1
- commit 960497899e75c0fe36ef662ec4a0159559c836b1
1
+ commit 01ac93ca3b341716c85c571f1194834db0a68e52
2
2
  Author: Naohisa Goto <ng@bioruby.org>
3
- Date: Sat May 25 03:41:51 2013 +0900
3
+ Date: Wed Jul 1 02:21:26 2015 +0900
4
4
 
5
- regenerate bioruby.gemspec with rake regemspec
5
+ update ChangeLog by rake rechangelog
6
6
 
7
- bioruby.gemspec | 4 +---
8
- 1 file changed, 1 insertion(+), 3 deletions(-)
7
+ ChangeLog | 28 ++++++++++++++++++++++++++++
8
+ 1 file changed, 28 insertions(+)
9
9
 
10
- commit e8fa160e158970259d915abc6113cb425537b8d6
10
+ commit cac63ff501df6a71afead77175db9fb491c2985b
11
11
  Author: Naohisa Goto <ng@bioruby.org>
12
- Date: Sat May 25 03:38:17 2013 +0900
12
+ Date: Wed Jul 1 01:31:21 2015 +0900
13
13
 
14
- Bio::BIORUBY_EXTRA_VERSION set to ".0001" (Release version with patches)
14
+ .travis.yml: use Ruby 2.1.6 for tar and gem integration tests
15
15
 
16
- lib/bio/version.rb | 2 +-
17
- 1 file changed, 1 insertion(+), 1 deletion(-)
16
+ .travis.yml | 8 ++++----
17
+ 1 file changed, 4 insertions(+), 4 deletions(-)
18
18
 
19
- commit 9d84d408479aa261b239e3f371f60262782bfb76
19
+ commit 5318c99249f34dacc788b82c658ea0e256770db0
20
20
  Author: Naohisa Goto <ng@bioruby.org>
21
- Date: Sat May 25 03:37:55 2013 +0900
21
+ Date: Wed Jul 1 00:43:39 2015 +0900
22
22
 
23
- Added release notes for 1.4.3.0001 release
23
+ known issues added about new BLAST XML format and BLAST+ text format
24
24
 
25
- RELEASE_NOTES.rdoc | 18 ++++++++++++++++++
26
- 1 file changed, 18 insertions(+)
25
+ KNOWN_ISSUES.rdoc | 11 +++++++++++
26
+ RELEASE_NOTES.rdoc | 11 +++++++++++
27
+ 2 files changed, 22 insertions(+)
27
28
 
28
- commit 1d3530cd1424f2cc0123057424b5c892f45dc93b
29
+ commit b61d8df0300ef366539e1154c9a2dac2f1f4ff18
29
30
  Author: Naohisa Goto <ng@bioruby.org>
30
- Date: Sat May 25 02:46:32 2013 +0900
31
+ Date: Tue Jun 30 23:57:01 2015 +0900
31
32
 
32
- Ruby 2.0 support: not to add ChangeLog and LEGAL to rdoc_files
33
-
34
- * Ruby 2.0 support: not to add ChangeLog and LEGAL to rdoc_files.
35
- Because ChangeLog is not rdoc format, rdoc bundled with Ruby 2.0
36
- raises error during parsing.
33
+ update ChangeLog with rake rechangelog
37
34
 
38
- bioruby.gemspec.erb | 4 ++--
39
- 1 file changed, 2 insertions(+), 2 deletions(-)
35
+ ChangeLog | 47 +++++++++++++++++++++++++++++++++++++++++++++++
36
+ 1 file changed, 47 insertions(+)
40
37
 
41
- commit be72602cb42e6d09d465b9636257335dccb278a4
38
+ commit 75cf6c31c57239b2e39a171e536ad5dddcaec94a
42
39
  Author: Naohisa Goto <ng@bioruby.org>
43
- Date: Thu Jan 10 01:27:03 2013 +0900
40
+ Date: Tue Jun 30 23:56:08 2015 +0900
44
41
 
45
- Ruby 2.0 support: Set script encoding to US-ASCII for gff.rb.
42
+ regenerate bioruby.gemspec with rake regemspec
46
43
 
47
- lib/bio/db/gff.rb | 1 +
44
+ bioruby.gemspec | 1 +
48
45
  1 file changed, 1 insertion(+)
49
46
 
50
- commit 091f6951d23c5ed2418981b2cf94733b1ee7a8b1
47
+ commit 608850beb33f3f7333f05307202b766adb350eb9
51
48
  Author: Naohisa Goto <ng@bioruby.org>
52
- Date: Mon Oct 1 21:11:14 2012 +0900
49
+ Date: Tue Jun 30 23:54:59 2015 +0900
53
50
 
54
- Bug fix: parse error when subject sequence contains spaces
55
-
56
- * Bug fix: parse error when subject sequence contains spaces.
57
- Thanks to Edward Rice who reports the bug. (Bug #3385)
58
- (https://redmine.open-bio.org/issues/3385)
51
+ description about updating of Ruby's License
59
52
 
60
- lib/bio/appl/blast/format0.rb | 38 +++++++++++++++++++-------------------
61
- 1 file changed, 19 insertions(+), 19 deletions(-)
53
+ RELEASE_NOTES.rdoc | 9 +++++++++
54
+ 1 file changed, 9 insertions(+)
62
55
 
63
- commit ad0d7a1712d8b02358763233d38e67a0fff54917
56
+ commit f54bcfc20d20935db4e342e5988c0b7f59c131b3
64
57
  Author: Naohisa Goto <ng@bioruby.org>
65
- Date: Wed Aug 22 00:18:14 2012 +0900
58
+ Date: Tue Jun 30 23:16:51 2015 +0900
66
59
 
67
- BioRuby 1.4.3 is re-released
60
+ BSDL is referred in COPYING and COPYING.ja
68
61
 
69
- ChangeLog | 9 +++++++++
70
- 1 file changed, 9 insertions(+)
62
+ BSDL | 22 ++++++++++++++++++++++
63
+ 1 file changed, 22 insertions(+)
64
+ create mode 100644 BSDL
71
65
 
72
- commit 51ab2dec144c99a14ca9009c7b589b500f1cad5f
66
+ commit d1cbfb699259fd57af02181f4374d562dda3abe1
73
67
  Author: Naohisa Goto <ng@bioruby.org>
74
- Date: Wed Aug 22 00:12:47 2012 +0900
68
+ Date: Tue Jun 30 23:14:42 2015 +0900
75
69
 
76
- Preparation to re-release BioRuby 1.4.3
70
+ changes of Ruby's License is reflected.
77
71
 
78
- ChangeLog | 22 ++++++++++++++++++++++
79
- 1 file changed, 22 insertions(+)
72
+ COPYING | 4 ++--
73
+ COPYING.ja | 72 ++++++++++++++++++++++++++++++------------------------------
74
+ 2 files changed, 38 insertions(+), 38 deletions(-)
80
75
 
81
- commit 5ff159d12252393ff04afe52b59a315d15c63d18
76
+ commit 2d9de9a0e2abe7fa9f193e54af0cbfc24bf2c37b
82
77
  Author: Naohisa Goto <ng@bioruby.org>
83
- Date: Wed Aug 22 00:00:40 2012 +0900
78
+ Date: Tue Jun 30 22:50:37 2015 +0900
84
79
 
85
- Bug fix: bin/bioruby failed to save object
86
-
87
- * Bug fix: bin/bioruby: Failed to save object with error message
88
- "can't convert Symbol into String" on Ruby 1.9.
80
+ ChangeLog is regenerated by using "rake rechangelog"
89
81
 
90
- RELEASE_NOTES.rdoc | 2 ++
91
- lib/bio/shell/core.rb | 1 +
92
- 2 files changed, 3 insertions(+)
82
+ ChangeLog | 2786 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
83
+ 1 file changed, 2780 insertions(+), 6 deletions(-)
93
84
 
94
- commit 74c6ce09413e7ddde1431d74e10cc9c4cdbb95ba
85
+ commit 70665a69a79d569d7bb37ef6d8c238534e6dae3a
95
86
  Author: Naohisa Goto <ng@bioruby.org>
96
- Date: Tue Aug 21 22:35:18 2012 +0900
87
+ Date: Tue Jun 30 22:49:55 2015 +0900
97
88
 
98
- BioRuby 1.4.3 is released.
89
+ KNOWN_ISSUES.rdoc: change ruby versions and add descriptions
99
90
 
100
- ChangeLog | 21 +++++++++++++++++++++
101
- 1 file changed, 21 insertions(+)
91
+ KNOWN_ISSUES.rdoc | 14 +++++++++-----
92
+ 1 file changed, 9 insertions(+), 5 deletions(-)
102
93
 
103
- commit 61af85b6cfc7bb1f3668ed68232113eb0751e7ea
94
+ commit 1054106f93b973b5a92f993c5b83b1444f96fffe
104
95
  Author: Naohisa Goto <ng@bioruby.org>
105
- Date: Tue Aug 21 22:33:30 2012 +0900
96
+ Date: Tue Jun 30 22:48:51 2015 +0900
106
97
 
107
- preparation for BioRuby 1.4.3 release version
98
+ prepare to release BioRuby 1.5.0
108
99
 
109
100
  bioruby.gemspec | 2 +-
110
101
  lib/bio/version.rb | 2 +-
111
102
  2 files changed, 2 insertions(+), 2 deletions(-)
112
103
 
113
- commit 1ec68beac42a06e9ef0a9c953650ef4d599e4e65
104
+ commit 0f150586904f7e423455615313992ccf77d7e123
114
105
  Author: Naohisa Goto <ng@bioruby.org>
115
- Date: Tue Aug 21 20:53:04 2012 +0900
106
+ Date: Tue Jun 30 22:44:58 2015 +0900
116
107
 
117
- ChangeLog modified; release candidate version 1.4.3-rc2
108
+ RELEASE_NOTES.rdoc: update many
118
109
 
119
- ChangeLog | 1353 ++++++++++++++++++++++++++++++++++++++++++++++++++++
120
- bioruby.gemspec | 2 +-
121
- lib/bio/version.rb | 4 +-
122
- 3 files changed, 1356 insertions(+), 3 deletions(-)
110
+ RELEASE_NOTES.rdoc | 151 +++++++++++++++++++++++++++++++++++++++++++++-------
111
+ 1 file changed, 132 insertions(+), 19 deletions(-)
123
112
 
124
- commit e0d570b237a8b96ae0c1e7b1ad72c7333be07c52
113
+ commit 2924ca0b977da13d42f232f880fd2df0b2995677
125
114
  Author: Naohisa Goto <ng@bioruby.org>
126
- Date: Mon Aug 20 20:35:58 2012 +0900
115
+ Date: Tue Jun 30 21:55:52 2015 +0900
127
116
 
128
- version changed to 1.4.3-rc1
117
+ Bug fix: Bio::UniProtKB#gene_name should not raise NoMethodError
118
+
119
+ * Bug fix: Bio::UniProtKB#gene_name raised NoMethodError when
120
+ gene_names method returns nil. It should return nil.
121
+ Thanks to Jose Irizarry who reports and sends suggested fix.
122
+ (https://github.com/bioruby/bioruby/pull/83 )
129
123
 
130
- bioruby.gemspec | 3 ++-
131
- lib/bio/version.rb | 2 +-
132
- 2 files changed, 3 insertions(+), 2 deletions(-)
124
+ lib/bio/db/embl/uniprotkb.rb | 2 +-
125
+ 1 file changed, 1 insertion(+), 1 deletion(-)
133
126
 
134
- commit 511c81ba67f7b8dc9cff85cf68db654d2feaf52e
127
+ commit 9bf9022007a0ff31a870b1ea08e423aebc487c17
135
128
  Author: Naohisa Goto <ng@bioruby.org>
136
- Date: Mon Aug 20 20:17:14 2012 +0900
129
+ Date: Tue Jun 30 18:45:51 2015 +0900
137
130
 
138
- document JRUBY-5678 (resolved) and related issue with the workaround.
131
+ regenerate bioruby.gemspec with rake regemspec
139
132
 
140
- KNOWN_ISSUES.rdoc | 9 +++++++++
141
- RELEASE_NOTES.rdoc | 9 +++++++++
142
- 2 files changed, 18 insertions(+)
133
+ bioruby.gemspec | 1 +
134
+ 1 file changed, 1 insertion(+)
143
135
 
144
- commit 2fdd7a3b3555a33dead31181c9526af22f24916f
136
+ commit a151e51a44b3dd93e5d075d71954f639eaec339e
145
137
  Author: Naohisa Goto <ng@bioruby.org>
146
- Date: Mon Aug 20 19:44:39 2012 +0900
138
+ Date: Tue Jun 30 18:10:55 2015 +0900
147
139
 
148
- update recommended Ruby versions and the year in copyright lines
140
+ update docs; change recommended Ruby versions
149
141
 
150
- README.rdoc | 7 +++----
151
- 1 file changed, 3 insertions(+), 4 deletions(-)
142
+ README.rdoc | 9 ++++++---
143
+ 1 file changed, 6 insertions(+), 3 deletions(-)
152
144
 
153
- commit b156227749e5ada74330e837c9ce48a16e6a6a2f
145
+ commit e86e745c8a6c666c446fe2f9f47818140999e2db
154
146
  Author: Naohisa Goto <ng@bioruby.org>
155
- Date: Mon Aug 20 19:16:25 2012 +0900
147
+ Date: Tue Jun 30 18:08:53 2015 +0900
156
148
 
157
- Bug fix: Bio::EMBL#os raises error, with incompatible change
158
-
159
- * Bug fix: Bio::EMBL#os raises error. The bug is reported by
160
- Marc P. Hoeppner in the BioRuby mailing list
161
- (https://redmine.open-bio.org/issues/3294).
162
- * Incompatible change: Bio::EMBL#os no longer splits the content with
163
- comma, and it no longer raises error even if the OS line is not in
164
- the "Genus species (name)" format. The changes may affect the parsing
165
- of old EMBL files which contain two or more species names in an OS line.
166
- * Unit tests are modified to catch up the above incompatible changes.
149
+ delete description about SOAP4R
167
150
 
168
- RELEASE_NOTES.rdoc | 14 ++++++
169
- lib/bio/db/embl/embl.rb | 74 ++++++++++++++++++++++++++++++
170
- test/unit/bio/db/embl/test_embl.rb | 9 +---
171
- test/unit/bio/db/embl/test_embl_rel89.rb | 9 +---
172
- 4 files changed, 92 insertions(+), 14 deletions(-)
151
+ README.rdoc | 5 -----
152
+ 1 file changed, 5 deletions(-)
173
153
 
174
- commit 31c8b4cb6ce2364aacee8137ddec3aa5f7d2d0d8
154
+ commit 7e4bfb6b3757872691487b080bfd87363a4f9480
175
155
  Author: Naohisa Goto <ng@bioruby.org>
176
- Date: Mon Aug 20 19:04:50 2012 +0900
156
+ Date: Tue Jun 30 03:22:35 2015 +0900
177
157
 
178
- Workaround for jruby-1.7.0.preview2 bugs JRUBY-6195, JRUBY-6818
158
+ .travis.yml: test/unit no longer bundled with Ruby 2.2
179
159
 
180
- * Workaroud for jruby-1.7.0.preview2 bugs JRUBY-6195 and JRUBY-6818.
181
- * Refactoring of call_command_popen: split _call_command_popen_ruby18
182
- and _call_command_popen_ruby19, add _call_command_popen_jruby19.
183
- Note that _call_command_popen_jruby19 will be removed in the future
184
- after the bugs are fixed.
160
+ * For Ruby 2.2, use a new Gemfile named Gemfile.travis-ruby2.2
161
+ that include 'gem "test-unit"' line because test/unit have been
162
+ provided by bundled gem since Ruby 2.2.
185
163
 
186
- lib/bio/command.rb | 98 ++++++++++++++++++++++++++++++++++++++++++++++------
187
- 1 file changed, 88 insertions(+), 10 deletions(-)
164
+ .travis.yml | 7 ++++---
165
+ gemfiles/Gemfile.travis-ruby2.2 | 9 +++++++++
166
+ 2 files changed, 13 insertions(+), 3 deletions(-)
167
+ create mode 100644 gemfiles/Gemfile.travis-ruby2.2
188
168
 
189
- commit 05f51fa2e871e71c2b20559eb05e456768a4f7d6
169
+ commit cac85ca215ed781c80d49a5bf3d5d37d808c783b
190
170
  Author: Naohisa Goto <ng@bioruby.org>
191
- Date: Sat Aug 18 00:32:31 2012 +0900
171
+ Date: Tue Jun 30 02:51:16 2015 +0900
192
172
 
193
- New default etc/bioinformatics/seqdatabase.ini
173
+ bump up version to 1.5.0-dev; simplify the versioning rules
194
174
 
195
- * New default etc/bioinformatics/seqdatabase.ini, with currently
196
- available services.
175
+ * Bump up version to 1.5.0-dev (1.5.0.20150630)
176
+ * Simplify the versioning rules.
177
+ * We will adopt the Semantic Versioning since BioRuby 1.5.1.
197
178
 
198
- etc/bioinformatics/seqdatabase.ini | 27 +++++++++++++++++++++++++++
199
- 1 file changed, 27 insertions(+)
200
- create mode 100644 etc/bioinformatics/seqdatabase.ini
179
+ bioruby.gemspec | 2 +-
180
+ bioruby.gemspec.erb | 21 ++++-----------------
181
+ lib/bio/version.rb | 17 ++++++++---------
182
+ 3 files changed, 13 insertions(+), 27 deletions(-)
201
183
 
202
- commit a4264cc3667b98289c09efc7ccba9c8e86f6d89c
184
+ commit 1a24fb6840932499be833b5ec3bb36184b1334a1
203
185
  Author: Naohisa Goto <ng@bioruby.org>
204
- Date: Sat Aug 18 00:31:10 2012 +0900
186
+ Date: Tue Jun 30 02:14:01 2015 +0900
205
187
 
206
- etc/bioinformatics/seqdatabase.ini is moved to sample/
188
+ Bug fix: update Bio::Hinv::BASE_URI
189
+
190
+ * Bug fix: update Bio::Hinv::BASE_URI to follow the server URI change.
191
+ * Update official documentation URL.
207
192
 
208
- etc/bioinformatics/seqdatabase.ini | 210 ------------------------------------
209
- sample/seqdatabase.ini | 210 ++++++++++++++++++++++++++++++++++++
210
- 2 files changed, 210 insertions(+), 210 deletions(-)
211
- delete mode 100644 etc/bioinformatics/seqdatabase.ini
212
- create mode 100644 sample/seqdatabase.ini
193
+ lib/bio/io/hinv.rb | 4 ++--
194
+ 1 file changed, 2 insertions(+), 2 deletions(-)
213
195
 
214
- commit 04b7a27b557576f5325b3ee420262922ab66ca3b
196
+ commit a9a12fff70ca287aa098d1331a3146e2899cb709
215
197
  Author: Naohisa Goto <ng@bioruby.org>
216
- Date: Sat Aug 18 00:30:38 2012 +0900
198
+ Date: Tue Jun 30 02:08:40 2015 +0900
217
199
 
218
- known issue about http://bioruby.org/cgi-bin/biofetch.rb server down
200
+ delete $Id:$ line
219
201
 
220
- KNOWN_ISSUES.rdoc | 9 +++++++++
221
- 1 file changed, 9 insertions(+)
202
+ lib/bio/io/hinv.rb | 1 -
203
+ 1 file changed, 1 deletion(-)
222
204
 
223
- commit 4a8193f7b91ff703c8f3dc6e6a6ae0c981a404e6
205
+ commit 2bfa0f41969003f17c4b894b5279347616c8f187
224
206
  Author: Naohisa Goto <ng@bioruby.org>
225
- Date: Fri Aug 17 23:45:41 2012 +0900
207
+ Date: Tue Jun 30 01:58:01 2015 +0900
226
208
 
227
- Update descriptions about JRuby and Rubinius bugs
209
+ delete sections about SOAP4R issues
228
210
 
229
- KNOWN_ISSUES.rdoc | 14 ++++++++++----
230
- RELEASE_NOTES.rdoc | 14 ++++++++++----
231
- 2 files changed, 20 insertions(+), 8 deletions(-)
211
+ KNOWN_ISSUES.rdoc | 12 ------------
212
+ 1 file changed, 12 deletions(-)
232
213
 
233
- commit a2d8dd8ccebde84e91f82c59e531cc08fbf0f3fe
214
+ commit 9dbd83aa00acc5f78b5da68f000c305da9f31b66
234
215
  Author: Naohisa Goto <ng@bioruby.org>
235
- Date: Fri Aug 17 17:19:22 2012 +0900
216
+ Date: Tue Jun 30 01:54:16 2015 +0900
236
217
 
237
- Remove the suffix .rb in require, to avoid potential multiple loading.
218
+ remove commented-out lines of soap4r-ruby1.9
238
219
 
239
- test/unit/bio/db/fasta/test_defline.rb | 2 +-
240
- test/unit/bio/db/genbank/test_genpept.rb | 2 +-
241
- test/unit/bio/db/kegg/test_drug.rb | 2 +-
242
- test/unit/bio/db/kegg/test_genome.rb | 2 +-
243
- test/unit/bio/db/kegg/test_glycan.rb | 2 +-
244
- test/unit/bio/util/test_restriction_enzyme.rb | 2 +-
245
- 6 files changed, 6 insertions(+), 6 deletions(-)
220
+ gemfiles/Gemfile.travis-jruby1.9 | 3 ---
221
+ gemfiles/Gemfile.travis-rbx | 3 ---
222
+ gemfiles/Gemfile.travis-ruby1.9 | 3 ---
223
+ 3 files changed, 9 deletions(-)
246
224
 
247
- commit 1d2e8b02db3699c2cd4f4890abc078ffd2b503aa
248
- Author: Ben J. Woodcroft <donttrustben near gmail.com>
249
- Date: Wed Aug 8 09:41:20 2012 +1000
225
+ commit 14d2f3e2fa15f94faeff4d28c957f581461eac82
226
+ Author: Naohisa Goto <ng@bioruby.org>
227
+ Date: Tue Jun 30 01:50:30 2015 +0900
250
228
 
251
- fill in missing piece of documentation in FastaFormat
229
+ .travis.yml: update ruby versions, remove ruby 1.9.2
252
230
 
253
- lib/bio/db/fasta.rb | 2 +-
254
- 1 file changed, 1 insertion(+), 1 deletion(-)
231
+ .travis.yml | 8 ++++----
232
+ 1 file changed, 4 insertions(+), 4 deletions(-)
255
233
 
256
- commit 83bf09d4d81803c8d06e0d45ca25e7c09016161c
234
+ commit 89f9b1fe2332584b5d63b1539b8e470d853478a3
257
235
  Author: Naohisa Goto <ng@bioruby.org>
258
- Date: Wed Aug 8 00:08:26 2012 +0900
236
+ Date: Tue Jun 30 00:36:42 2015 +0900
259
237
 
260
- RELEASE_NOTE.rdoc modified to reflect recent changes
238
+ about removal of Bio::SOAPWSDL, Bio::EBI::SOAP, Bio::HGC::HiGet
261
239
 
262
- RELEASE_NOTES.rdoc | 107 ++++++++++++++++++++++++++++++++++++++++++++--------
263
- 1 file changed, 92 insertions(+), 15 deletions(-)
240
+ RELEASE_NOTES.rdoc | 20 ++++++++++++++++++++
241
+ 1 file changed, 20 insertions(+)
264
242
 
265
- commit c3afb1eb98cf8777ee021624c3d2eab92b3543f2
243
+ commit 29516d3d6d2f907f65822bcf4146e95785773a3a
266
244
  Author: Naohisa Goto <ng@bioruby.org>
267
- Date: Wed Aug 8 00:06:09 2012 +0900
245
+ Date: Tue Jun 30 00:50:47 2015 +0900
268
246
 
269
- Descriptions about JRuby, Rubinius, DDBJ Web API, SOAP4R etc.
247
+ regenerate bioruby.gemspec with rake regemspec
270
248
 
271
- KNOWN_ISSUES.rdoc | 45 +++++++++++++++++++++++++++++++++++++++++++--
272
- 1 file changed, 43 insertions(+), 2 deletions(-)
249
+ bioruby.gemspec | 6 ------
250
+ 1 file changed, 6 deletions(-)
273
251
 
274
- commit 01da7401a011aa519c43a021f89f6e7f769b4649
252
+ commit 357a1afc5ef457326179142c163968aa5cd94864
275
253
  Author: Naohisa Goto <ng@bioruby.org>
276
- Date: Tue Aug 7 23:55:09 2012 +0900
254
+ Date: Tue Jun 30 00:49:42 2015 +0900
277
255
 
278
- regenerate bioruby.gemspec with rake regemspec
256
+ not to load deleted file lib/bio/shell/plugin/soap.rb
279
257
 
280
- bioruby.gemspec | 3 +--
281
- 1 file changed, 1 insertion(+), 2 deletions(-)
258
+ lib/bio/shell.rb | 1 -
259
+ 1 file changed, 1 deletion(-)
282
260
 
283
- commit 9f70c27d9b75408fddae8384a2a09715b959dcb5
261
+ commit 956e475da52ea17f1022493f589489a3e7c06f93
284
262
  Author: Naohisa Goto <ng@bioruby.org>
285
- Date: Tue Aug 7 23:51:56 2012 +0900
263
+ Date: Mon Jun 29 23:43:24 2015 +0900
286
264
 
287
- improve documentation; version changed to 1.4.3-pre1
265
+ deleted lib/bio/shell/plugin/soap.rb
266
+
267
+ * deleted lib/bio/shell/plugin/soap.rb because Bio::SOAPWSDL and
268
+ all SOAP client classes in BioRuby are removed.
288
269
 
289
- lib/bio/version.rb | 13 +++++++++++--
290
- 1 file changed, 11 insertions(+), 2 deletions(-)
270
+ lib/bio/shell/plugin/soap.rb | 50 ------------------------------------------
271
+ 1 file changed, 50 deletions(-)
272
+ delete mode 100644 lib/bio/shell/plugin/soap.rb
291
273
 
292
- commit c11f12c8aa56b8509cd082f3478e96374210e5d7
274
+ commit 00acae3c3a8066891e08dc225eae2c22c3415191
293
275
  Author: Naohisa Goto <ng@bioruby.org>
294
- Date: Tue Aug 7 23:31:41 2012 +0900
276
+ Date: Mon Jun 29 23:41:20 2015 +0900
295
277
 
296
- Remove autorequire which have been deprecated
278
+ not to load removed Bio::EBI::SOAP from lib/bio/io/ebisoap.rb
297
279
 
298
- bioruby.gemspec.erb | 1 -
299
- 1 file changed, 1 deletion(-)
280
+ lib/bio.rb | 4 ----
281
+ 1 file changed, 4 deletions(-)
300
282
 
301
- commit 7792b092033d2c819f2bcad0e206f27608481db5
302
- Author: Ben J Woodcroft <donttrustben@gmail.com>
303
- Date: Mon Aug 6 09:40:55 2012 +1000
283
+ commit d4844b38b5ddaec7ec15b56ef66f6930f0e6cfc0
284
+ Author: Naohisa Goto <ng@bioruby.org>
285
+ Date: Mon Jun 29 23:38:26 2015 +0900
304
286
 
305
- flesh out FastaFormat documentation
287
+ remove Bio::EBI::SOAP (lib/bio/io/ebisoap.rb)
288
+
289
+ * Bio::EBI::SOAP (lib/bio/io/ebisoap.rb) is removed because
290
+ Bio::SOAPWSDL is removed.
306
291
 
307
- lib/bio/db/fasta.rb | 102 ++++++++++++++++++++++++-------------------
308
- lib/bio/db/fasta/defline.rb | 2 +-
309
- 2 files changed, 58 insertions(+), 46 deletions(-)
292
+ lib/bio/io/ebisoap.rb | 158 -------------------------------------------------
293
+ 1 file changed, 158 deletions(-)
294
+ delete mode 100644 lib/bio/io/ebisoap.rb
310
295
 
311
- commit 9a2fe67c247cdc7c9ddc9f8b8de771515ba76ac1
296
+ commit 79b4705bac82fe17b12c649172a629d3de41cbdf
312
297
  Author: Naohisa Goto <ng@bioruby.org>
313
- Date: Fri Aug 3 22:36:12 2012 +0900
298
+ Date: Tue Jun 30 00:12:36 2015 +0900
314
299
 
315
- .travis.yml: restructure matrix, add allow_failures lines
316
-
317
- * Add allow_failures lines
318
- * Restructure matrix: remove many exclude lines and add some
319
- include lines.
320
- * When running jruby, Set TMPDIR to avoid known issue about
321
- FileUtils#remove_entry_secure.
300
+ not to load removed Bio::SOAPWSDL from lib/bio/io/soapwsdl.rb
322
301
 
323
- .travis.yml | 52 ++++++++++++++++++----------------------------------
324
- 1 file changed, 18 insertions(+), 34 deletions(-)
302
+ lib/bio.rb | 1 -
303
+ 1 file changed, 1 deletion(-)
325
304
 
326
- commit 553fd102c533c42675f93895557e3e00d36fd3e7
305
+ commit 03ced6a70973557532517c70dac183775bd11fa7
327
306
  Author: Naohisa Goto <ng@bioruby.org>
328
- Date: Fri Aug 3 22:05:39 2012 +0900
307
+ Date: Mon Jun 29 23:59:28 2015 +0900
329
308
 
330
- Improve tests for BLAST "-m 8" tabular format parser
309
+ remove Bio::SOAPWSDL (lib/bio/io/soapwsdl.rb) and tests
310
+
311
+ * 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.
331
316
 
332
- test/unit/bio/appl/blast/test_report.rb | 119 +++++++++++++++++++++++++++++++
333
- 1 file changed, 119 insertions(+)
317
+ lib/bio/io/soapwsdl.rb | 119 ----------------------------------
318
+ test/network/bio/io/test_soapwsdl.rb | 53 ---------------
319
+ test/unit/bio/io/test_soapwsdl.rb | 33 ----------
320
+ 3 files changed, 205 deletions(-)
321
+ delete mode 100644 lib/bio/io/soapwsdl.rb
322
+ delete mode 100644 test/network/bio/io/test_soapwsdl.rb
323
+ delete mode 100644 test/unit/bio/io/test_soapwsdl.rb
334
324
 
335
- commit 3e1c062dbc168bd558ca8408a6da115aa570f3a7
325
+ commit d927652e9f5d241e3c1b13b7d760f5a190b72e50
336
326
  Author: Naohisa Goto <ng@bioruby.org>
337
- Date: Fri Aug 3 22:05:07 2012 +0900
327
+ Date: Mon Jun 29 23:35:38 2015 +0900
338
328
 
339
- Improve test and suppress warning: assigned but unused variable
329
+ delete old comment-out lines about Bio::DDBJ::XML
340
330
 
341
- test/unit/bio/io/flatfile/test_buffer.rb | 1 +
342
- 1 file changed, 1 insertion(+)
331
+ lib/bio.rb | 5 -----
332
+ 1 file changed, 5 deletions(-)
343
333
 
344
- commit 7e29ce1f050e9e5b23299372d8ddfae781447dc3
334
+ commit b995251bf96b8983def36e77bc94d6f0c0f2c78c
345
335
  Author: Naohisa Goto <ng@bioruby.org>
346
- Date: Fri Aug 3 22:02:21 2012 +0900
336
+ Date: Mon Jun 29 23:29:47 2015 +0900
347
337
 
348
- Improve test and suppress warning: assigned but unused variable
338
+ do not load Bio::HGC::HiGet from deleted lib/bio/io/higet.rb
349
339
 
350
- test/unit/bio/db/test_newick.rb | 2 ++
351
- 1 file changed, 2 insertions(+)
340
+ lib/bio.rb | 4 ----
341
+ 1 file changed, 4 deletions(-)
352
342
 
353
- commit 1053b62069df74f336934e4ed0f3f217e4ad3312
343
+ commit 6191020ed1e150f9e70de687375528a899fcf8ef
354
344
  Author: Naohisa Goto <ng@bioruby.org>
355
- Date: Fri Jul 27 13:56:53 2012 +0900
345
+ Date: Mon Jun 29 23:27:41 2015 +0900
356
346
 
357
- Suppress warnings: shadowing outer local variable
358
-
359
- * Suppress warnings: shadowing outer local variable.
360
- Thanks to Andrew Grimm: https://github.com/bioruby/bioruby/pull/64
347
+ remove lib/bio/io/higet.rb because of the server down for a long time
361
348
 
362
- lib/bio/db/gff.rb | 8 ++++----
363
- 1 file changed, 4 insertions(+), 4 deletions(-)
349
+ lib/bio/io/higet.rb | 73 ---------------------------------------------------
350
+ 1 file changed, 73 deletions(-)
351
+ delete mode 100644 lib/bio/io/higet.rb
364
352
 
365
- commit e55794f65b3fb45c99e61d45220fe42f718426a3
353
+ commit 5a527c5cdd513d72ad5817c66ac87e7613395e26
366
354
  Author: Naohisa Goto <ng@bioruby.org>
367
- Date: Wed Jul 25 23:29:17 2012 +0900
355
+ Date: Sat Jun 27 02:33:46 2015 +0900
368
356
 
369
- Suppress warnings in lib/bio/alignment.rb:2322
370
-
371
- * A space is inserted to suppress warnings in lib/bio/alignment.rb:2322.
372
- * warning: :' after local variable is interpreted as binary operator
373
- * warning: even though it seems like symbol literal
357
+ add/modify about removed features and incompatible changes
374
358
 
375
- lib/bio/alignment.rb | 2 +-
376
- 1 file changed, 1 insertion(+), 1 deletion(-)
359
+ RELEASE_NOTES.rdoc | 71 +++++++++++++++++++++++++++++++++++++++++++++++++---
360
+ 1 file changed, 67 insertions(+), 4 deletions(-)
377
361
 
378
- commit 174a38ea8c4ecea70724bf6ec8e72b2e4259853b
362
+ commit 1886314d2b8dd7d4b3e86c7b93134facd881127a
379
363
  Author: Naohisa Goto <ng@bioruby.org>
380
- Date: Wed Jul 25 23:12:51 2012 +0900
364
+ Date: Sat Jun 27 01:24:36 2015 +0900
381
365
 
382
- Modified to follow changes of GenomeNet BLAST site
366
+ regenerate bioruby.gemspec with rake regemspec
383
367
 
384
- lib/bio/appl/blast/genomenet.rb | 6 +++---
385
- 1 file changed, 3 insertions(+), 3 deletions(-)
368
+ bioruby.gemspec | 1 -
369
+ 1 file changed, 1 deletion(-)
386
370
 
387
- commit 93e24935840dcdec76984313719700134d69daf2
371
+ commit 724e9c1c039dcc7fa19fb15de0313218a87f9868
388
372
  Author: Naohisa Goto <ng@bioruby.org>
389
- Date: Wed Jul 25 15:21:32 2012 +0900
373
+ Date: Thu Jun 25 23:34:44 2015 +0900
390
374
 
391
- suppress warnings: instance variable @comment not initialized
375
+ extconf.rb is deleted because no native extensions are included
376
+
377
+ * extconf.rb is deleted because no native extensions are included in
378
+ BioRuby and to avoid potential confusions. Nowadays, extconf.rb is
379
+ usually used only for building native extensions. Use gem or
380
+ setup.rb to install BioRuby.
392
381
 
393
- lib/bio/db/gff.rb | 6 ++++--
394
- 1 file changed, 4 insertions(+), 2 deletions(-)
382
+ extconf.rb | 2 --
383
+ 1 file changed, 2 deletions(-)
384
+ delete mode 100644 extconf.rb
395
385
 
396
- commit 0ad3818fedb707a26e849877bde1f8dab006b848
386
+ commit d42a1cb1df17e0c11ca0407dc05e1271cd74a0d7
397
387
  Author: Naohisa Goto <ng@bioruby.org>
398
- Date: Wed Jul 25 00:54:02 2012 +0900
388
+ Date: Wed Jun 24 22:29:28 2015 +0900
399
389
 
400
- suppress warnings: URI.escape/URI.unescape is obsolete
390
+ Ruby 2.3 support: IO#close to closed IO object is allowed without error.
401
391
 
402
- lib/bio/db/gff.rb | 39 +++++++++++++++++++++++++++++++++------
403
- 1 file changed, 33 insertions(+), 6 deletions(-)
392
+ test/unit/bio/io/flatfile/test_buffer.rb | 8 +++++++-
393
+ 1 file changed, 7 insertions(+), 1 deletion(-)
404
394
 
405
- commit 1263938742e7eeedb4a877aff7314e304320eca9
395
+ commit 5ea39188ac3cc2609397b2d8864a2019ea6b93d2
406
396
  Author: Naohisa Goto <ng@bioruby.org>
407
- Date: Mon Jul 23 21:15:52 2012 +0900
397
+ Date: Fri May 1 23:42:39 2015 +0900
408
398
 
409
- Added link to blastall options reference
399
+ s.license = "Ruby"
410
400
 
411
- * Added link to blastall options reference.
412
- Thanks to Gareth Rees who sent a pull request.
413
- (https://github.com/bioruby/bioruby/pull/49)
401
+ * 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 )
414
404
 
415
- lib/bio/appl/blast/genomenet.rb | 5 +++++
416
- 1 file changed, 5 insertions(+)
405
+ bioruby.gemspec | 1 +
406
+ bioruby.gemspec.erb | 1 +
407
+ 2 files changed, 2 insertions(+)
417
408
 
418
- commit 2ec5f4fd5abd0db7ec79ab3a9fd4adde7c9384a8
409
+ commit 2b18ae005a592ea4ae7b632f7e658d4bbf153fd8
419
410
  Author: Naohisa Goto <ng@bioruby.org>
420
- Date: Mon Jul 23 17:26:45 2012 +0900
411
+ Date: Fri May 1 23:39:36 2015 +0900
421
412
 
422
- Next bioruby release version will be 1.4.3.
413
+ remove deprecated Gem::Specification#rubyforge_project
423
414
 
424
- RELEASE_NOTES.rdoc | 2 +-
425
- 1 file changed, 1 insertion(+), 1 deletion(-)
415
+ bioruby.gemspec | 2 +-
416
+ bioruby.gemspec.erb | 2 +-
417
+ 2 files changed, 2 insertions(+), 2 deletions(-)
426
418
 
427
- commit 6cf1318507a5d82bb93acdfe33e96723a2e742fc
419
+ commit 3a1d89bde9af44793c850b1cde950e3e3042fb8d
428
420
  Author: Naohisa Goto <ng@bioruby.org>
429
- Date: Mon Jul 23 17:25:35 2012 +0900
421
+ Date: Sat Mar 28 01:52:31 2015 +0900
430
422
 
431
- fix typo
423
+ delete obsolete $Id:$ line
432
424
 
433
- README.rdoc | 2 +-
434
- 1 file changed, 1 insertion(+), 1 deletion(-)
425
+ lib/bio/db/gff.rb | 1 -
426
+ 1 file changed, 1 deletion(-)
435
427
 
436
- commit 2fd71cac315affe6e4d90b03dadac782f11553a5
428
+ commit 165ebf29ba192c7a7e7f1633809d34966c2aeed1
437
429
  Author: Naohisa Goto <ng@bioruby.org>
438
- Date: Mon Jul 23 17:21:57 2012 +0900
430
+ Date: Sat Mar 28 01:51:47 2015 +0900
439
431
 
440
- Bug fix: Genomenet remote blast: catch up changes of the server
432
+ suppress "character class has duplicated range" warnings
441
433
 
442
- lib/bio/appl/blast/genomenet.rb | 33 +++++++++++++++++++++++----------
443
- 1 file changed, 23 insertions(+), 10 deletions(-)
434
+ lib/bio/db/gff.rb | 4 ++--
435
+ 1 file changed, 2 insertions(+), 2 deletions(-)
444
436
 
445
- commit 69d9717da11b2fe81a8f840bbafcc5fbb0dbe688
437
+ commit 715ee5aa3a797737d390365b2c202cc9a0effea5
446
438
  Author: Naohisa Goto <ng@bioruby.org>
447
- Date: Fri Jul 20 11:24:37 2012 +0900
439
+ Date: Sat Mar 28 01:37:35 2015 +0900
448
440
 
449
- regenerate bioruby.gemspec with rake regemspec
441
+ delete obsolete $Id:$ line
450
442
 
451
- bioruby.gemspec | 2 ++
452
- 1 file changed, 2 insertions(+)
443
+ lib/bio/appl/sosui/report.rb | 1 -
444
+ 1 file changed, 1 deletion(-)
453
445
 
454
- commit 9683da186579dbfa5da1bb1a32edc49cfdc026b8
446
+ commit 71e34938f1228911657ebf00720712a17bc89ea9
455
447
  Author: Naohisa Goto <ng@bioruby.org>
456
- Date: Wed Jul 18 23:19:33 2012 +0900
448
+ Date: Sat Mar 28 01:36:44 2015 +0900
457
449
 
458
- Incompatible changes in Bio::KEGG::KGML are documented.
459
-
460
- * Incompatible changes in Bio::KEGG::KGML are documented.
461
- * Next BioRuby release version will be 1.4.3.
450
+ comment out a line to suppress warning: assigned but unused variable - tmh
462
451
 
463
- RELEASE_NOTES.rdoc | 44 +++++++++++++++++++++++++++++++++++++++++---
464
- 1 file changed, 41 insertions(+), 3 deletions(-)
452
+ lib/bio/appl/sosui/report.rb | 2 +-
453
+ 1 file changed, 1 insertion(+), 1 deletion(-)
465
454
 
466
- commit 6cab377ae760d1abfda06caafe4a04ecd549e21d
455
+ commit fc518f3826bf60d70ebdbd70acdba512f1462c6f
467
456
  Author: Naohisa Goto <ng@bioruby.org>
468
- Date: Wed Jul 18 22:56:00 2012 +0900
457
+ Date: Sat Mar 28 01:34:22 2015 +0900
469
458
 
470
- Incompatible changes: Bio::KEGG::KGML::Reaction#substrates, products
471
-
472
- * Incompatible changes: Bio::KEGG::KGML::Reaction#substrates and
473
- Bio::KEGG::KGML::Reaction#products are changed to return an array
474
- containing Bio::KEGG::KGML::Substrate and Bio::KEGG::KGML::Product
475
- objects, respectively. The aim of these changes are to store ID
476
- of substrates and products that were thrown away in the previous
477
- versions.
459
+ delete obsolete $Id:$ line
478
460
 
479
- lib/bio/db/kegg/kgml.rb | 48 ++++++++++++++---
480
- test/unit/bio/db/kegg/test_kgml.rb | 104 +++++++++++++++++++++++++++++++++++-
481
- 2 files changed, 144 insertions(+), 8 deletions(-)
461
+ lib/bio/db/sanger_chromatogram/chromatogram.rb | 1 -
462
+ 1 file changed, 1 deletion(-)
482
463
 
483
- commit 3cb1e09709d3c6b934028e28f9cafed149c9c751
464
+ commit 516c467dfb245d99c4f7f77e251c77ffc5d274ca
484
465
  Author: Naohisa Goto <ng@bioruby.org>
485
- Date: Wed Jul 18 22:16:46 2012 +0900
466
+ Date: Sat Mar 28 01:33:19 2015 +0900
486
467
 
487
- Bio::KEGG::KGML#parse_* :use new attribute names
488
-
489
- * In Bio::KEGG::KGML#parse_* (private methods) new attribute method
490
- names should be used instead of deprecated old names.
468
+ suppress warning: instance variable @aqual not initialized
491
469
 
492
- lib/bio/db/kegg/kgml.rb | 18 +++++++++---------
493
- 1 file changed, 9 insertions(+), 9 deletions(-)
470
+ lib/bio/db/sanger_chromatogram/chromatogram.rb | 2 +-
471
+ 1 file changed, 1 insertion(+), 1 deletion(-)
494
472
 
495
- commit c5ef981db6add98dc6778cd9809aff38a7071593
473
+ commit 56d2e472196ba03ba6aa2a2bdf8d3de81272fa15
496
474
  Author: Naohisa Goto <ng@bioruby.org>
497
- Date: Wed Jul 18 22:14:33 2012 +0900
475
+ Date: Sat Mar 28 01:30:26 2015 +0900
498
476
 
499
- modified documentation for Bio::KEGG::KGML
477
+ delete obsolete $Id:$ line
500
478
 
501
- lib/bio/db/kegg/kgml.rb | 73 +++++++++++++++++++++++++++--------------------
502
- 1 file changed, 42 insertions(+), 31 deletions(-)
479
+ lib/bio/db/kegg/module.rb | 1 -
480
+ 1 file changed, 1 deletion(-)
503
481
 
504
- commit 5416b84eaa37b5abf15f905586a5eee65c4026f0
482
+ commit fb6b9b6578d08a87c1974e58f6d1f231b4ad52c0
505
483
  Author: Naohisa Goto <ng@bioruby.org>
506
- Date: Wed Jul 18 15:01:58 2012 +0900
484
+ Date: Sat Mar 28 01:28:05 2015 +0900
507
485
 
508
- New class Bio::KEGG::KGML::Graphics with tests for Bio::KEGG::KGML
509
-
510
- * New class Bio::KEGG::KGML::Graphics for storing a graphics element.
511
- This fixes https://github.com/bioruby/bioruby/issues/51.
512
- * Unit tests for Bio::KEGG::KGML are added with mock test data.
513
- * Improve rdoc documentation for Bio::KEGG::KGML.
514
- * New method Bio::KEGG::KGML::Reaction#id
515
- * Attribute methods that were different from the KGML attribute
516
- names are renamed to the names of the KGML attribute names.
517
- Old method names are deprecated and are changed to aliases
518
- and will be removed in the future.
519
- * Bio::KEGG::KGML::Entry#id (old name: entry_id)
520
- * Bio::KEGG::KGML::Entry#type (old name: category)
521
- * Bio::KEGG::KGML::Entry#entry1 (old name: node1)
522
- * Bio::KEGG::KGML::Entry#entry2 (old name: node2)
523
- * Bio::KEGG::KGML::Entry#type (old name: rel)
524
- * Bio::KEGG::KGML::Reaction#name (old name: entry_id)
525
- * Bio::KEGG::KGML::Reaction#type (old name: direction)
526
- * Following attribute methods are deprecated because two or more
527
- graphics elements may exist in an entry element. They will be
528
- removed in the future.
529
- * Bio::KEGG::KGML::Entry#label
530
- * Bio::KEGG::KGML::Entry#shape
531
- * Bio::KEGG::KGML::Entry#x
532
- * Bio::KEGG::KGML::Entry#y
533
- * Bio::KEGG::KGML::Entry#width
534
- * Bio::KEGG::KGML::Entry#height
535
- * Bio::KEGG::KGML::Entry#fgcolor
536
- * Bio::KEGG::KGML::Entry#bgcolor
486
+ suppress "instance variable @XXX not initialized" warnings
537
487
 
538
- lib/bio/db/kegg/kgml.rb | 321 ++++++++++---
539
- test/data/KEGG/test.kgml | 37 ++
540
- test/unit/bio/db/kegg/test_kgml.rb | 922 ++++++++++++++++++++++++++++++++++++
541
- 3 files changed, 1223 insertions(+), 57 deletions(-)
542
- create mode 100644 test/data/KEGG/test.kgml
543
- create mode 100644 test/unit/bio/db/kegg/test_kgml.rb
488
+ lib/bio/db/kegg/module.rb | 8 ++++----
489
+ 1 file changed, 4 insertions(+), 4 deletions(-)
544
490
 
545
- commit e5478363ef6969ec14c4e09c2bd7c6d27c12cf5b
491
+ commit 9f70b8d54abd9adbd50d46a3176f23f51af01cc7
546
492
  Author: Naohisa Goto <ng@bioruby.org>
547
- Date: Tue Jul 17 22:23:28 2012 +0900
493
+ Date: Sat Mar 28 01:25:50 2015 +0900
548
494
 
549
- rdoc documentation for Bio::KEGG::KGML
495
+ delete obsolete $Id:$ line
550
496
 
551
- lib/bio/db/kegg/kgml.rb | 166 ++++++++++++++++++++++++++++++++++++++++++++---
552
- 1 file changed, 157 insertions(+), 9 deletions(-)
497
+ lib/bio/db/kegg/pathway.rb | 1 -
498
+ 1 file changed, 1 deletion(-)
553
499
 
554
- commit 4a97e7034cae835b3bbc8ef918b9c6c48910dec5
500
+ commit 3844b9bb69e1f657c9b85bb20a4d209828b78b12
555
501
  Author: Naohisa Goto <ng@bioruby.org>
556
- Date: Wed Jul 11 15:16:49 2012 +0900
502
+ Date: Sat Mar 28 01:25:03 2015 +0900
557
503
 
558
- autoload should not be used for libraries outside bio
504
+ suppress "instance variable @XXX not initialized" warnings
559
505
 
560
- lib/bio/db/kegg/kgml.rb | 3 +--
561
- 1 file changed, 1 insertion(+), 2 deletions(-)
506
+ lib/bio/db/kegg/pathway.rb | 8 ++++----
507
+ 1 file changed, 4 insertions(+), 4 deletions(-)
562
508
 
563
- commit 338d4cd9913d70041349c5201f80f7a65e7135a6
509
+ commit 8d857e246eacb6c9f8fbbceaa2fba7f1211e2b86
564
510
  Author: Naohisa Goto <ng@bioruby.org>
565
- Date: Fri Jul 6 00:50:01 2012 +0900
511
+ Date: Sat Mar 28 01:20:13 2015 +0900
566
512
 
567
- remove unnecessary require "bio/db" in lib/bio/db/pdb.rb
513
+ delete obsolete $Id:$ line
568
514
 
569
- lib/bio/db/pdb.rb | 5 +----
570
- 1 file changed, 1 insertion(+), 4 deletions(-)
515
+ lib/bio/db/fasta/defline.rb | 1 -
516
+ 1 file changed, 1 deletion(-)
571
517
 
572
- commit 87c806a480fcacb0fc610c9669de19e4cb661a9c
518
+ commit aadf285bc9e618b7813b42fd39e0b1966a04385c
573
519
  Author: Naohisa Goto <ng@bioruby.org>
574
- Date: Fri Jul 6 00:47:20 2012 +0900
520
+ Date: Sat Mar 28 01:18:43 2015 +0900
575
521
 
576
- workaround to avoid circular require about Bio::PDB
522
+ suppress defline.rb:393: warning: character class has duplicated range
577
523
 
578
- lib/bio/db/pdb/atom.rb | 5 +++--
579
- lib/bio/db/pdb/chain.rb | 5 ++---
580
- lib/bio/db/pdb/chemicalcomponent.rb | 5 +++--
581
- lib/bio/db/pdb/model.rb | 4 ++--
582
- lib/bio/db/pdb/pdb.rb | 3 ++-
583
- lib/bio/db/pdb/residue.rb | 4 ++--
584
- lib/bio/db/pdb/utils.rb | 11 +++++++----
585
- 7 files changed, 21 insertions(+), 16 deletions(-)
524
+ lib/bio/db/fasta/defline.rb | 2 +-
525
+ 1 file changed, 1 insertion(+), 1 deletion(-)
586
526
 
587
- commit 874f35c3930506fa029b419aa84677d1fea6681a
527
+ commit 5297db11eb165885c4f15b914c2132c4122ae5a9
588
528
  Author: Naohisa Goto <ng@bioruby.org>
589
- Date: Fri Jul 6 00:24:24 2012 +0900
529
+ Date: Sat Mar 28 01:11:43 2015 +0900
590
530
 
591
- regenerate bioruby.gemspec with rake regemspec
531
+ delete obsolete $Id:$ line
592
532
 
593
- bioruby.gemspec | 1 +
594
- 1 file changed, 1 insertion(+)
533
+ test/unit/bio/test_db.rb | 1 -
534
+ 1 file changed, 1 deletion(-)
595
535
 
596
- commit 090d4edb5698135f87df450a963ef35a307349c4
536
+ commit 20381ad45c674c0844a92891cb8ae71edaa6e333
597
537
  Author: Naohisa Goto <ng@bioruby.org>
598
- Date: Fri Jul 6 00:19:54 2012 +0900
538
+ Date: Sat Mar 28 01:08:04 2015 +0900
599
539
 
600
- Tree output (formatter) methods moved to lib/bio/tree/output.rb
540
+ suppress "warning: instance variable @tagsize not initialized"
601
541
 
602
- * To avoid circular require about bio/tree, phylogenetic tree output
603
- (formatter) methods are moved to lib/bio/tree/output.rb.
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.
604
545
 
605
- lib/bio/db/newick.rb | 244 --------------------------------------------
606
- lib/bio/tree.rb | 3 +-
607
- lib/bio/tree/output.rb | 264 ++++++++++++++++++++++++++++++++++++++++++++++++
608
- 3 files changed, 265 insertions(+), 246 deletions(-)
609
- create mode 100644 lib/bio/tree/output.rb
546
+ test/unit/bio/test_db.rb | 5 ++++-
547
+ 1 file changed, 4 insertions(+), 1 deletion(-)
610
548
 
611
- commit b3d12b63097a5141b029bbfb3690870cd1935a60
549
+ commit d194edfc68bc10fde11f2cf014a59113ddc63b24
612
550
  Author: Naohisa Goto <ng@bioruby.org>
613
- Date: Fri Jul 6 00:18:44 2012 +0900
551
+ Date: Sat Mar 28 00:59:21 2015 +0900
614
552
 
615
- Workaround to avoid circular require for Bio::Blast
553
+ delete obsolete $Id:$ line
616
554
 
617
- lib/bio/appl/bl2seq/report.rb | 6 +++---
618
- lib/bio/appl/blast/ddbj.rb | 3 ---
619
- lib/bio/appl/blast/format0.rb | 3 +++
620
- lib/bio/appl/blast/genomenet.rb | 2 --
621
- lib/bio/appl/blast/ncbioptions.rb | 11 ++++++++---
622
- lib/bio/appl/blast/remote.rb | 11 ++++++-----
623
- lib/bio/appl/blast/report.rb | 16 ++++++++++------
624
- lib/bio/appl/blast/rpsblast.rb | 5 +++--
625
- lib/bio/appl/blast/wublast.rb | 6 +++---
626
- 9 files changed, 36 insertions(+), 27 deletions(-)
555
+ lib/bio/data/codontable.rb | 1 -
556
+ 1 file changed, 1 deletion(-)
627
557
 
628
- commit 8f6c906c7b0d65b93ebf0a1e1307259e6eab8465
558
+ commit fac51f540dc7b33cd3ec51f97b5cb1ea587a461e
629
559
  Author: Naohisa Goto <ng@bioruby.org>
630
- Date: Thu Jul 5 23:29:42 2012 +0900
560
+ Date: Sat Mar 28 00:57:28 2015 +0900
631
561
 
632
- remove old require lines that are commented out
562
+ suppress warning: instance variable @reverse not initialized
633
563
 
634
- lib/bio/appl/blast/format0.rb | 5 -----
635
- 1 file changed, 5 deletions(-)
564
+ lib/bio/data/codontable.rb | 2 +-
565
+ 1 file changed, 1 insertion(+), 1 deletion(-)
636
566
 
637
- commit c632fbf2d0320860eadfacb196d51d80ed3a2b34
567
+ commit 4e85315f03e374157f832c8435d0d2f43cd969af
638
568
  Author: Naohisa Goto <ng@bioruby.org>
639
- Date: Thu Jul 5 23:16:49 2012 +0900
569
+ Date: Sat Mar 28 00:55:25 2015 +0900
640
570
 
641
- Remove old workaround of strscan.so for Ruby 1.7 or earlier
571
+ delete obsolete $Id:$ line
642
572
 
643
- lib/bio/appl/blast/format0.rb | 18 +-----------------
644
- 1 file changed, 1 insertion(+), 17 deletions(-)
573
+ lib/bio/appl/iprscan/report.rb | 1 -
574
+ 1 file changed, 1 deletion(-)
645
575
 
646
- commit c81dce87f53d3ea7c7d2335e077fa609f2737779
576
+ commit dafa7ce62378ff1605a295f8c620eb3a0a4a3c57
647
577
  Author: Naohisa Goto <ng@bioruby.org>
648
- Date: Thu Jul 5 23:03:40 2012 +0900
578
+ Date: Sat Mar 28 00:54:37 2015 +0900
649
579
 
650
- .travis.yml: include ruby 1.9.2 test
580
+ suppress warning: instance variable @ipr_ids not initialized
651
581
 
652
- .travis.yml | 2 ++
653
- 1 file changed, 2 insertions(+)
582
+ lib/bio/appl/iprscan/report.rb | 2 +-
583
+ 1 file changed, 1 insertion(+), 1 deletion(-)
654
584
 
655
- commit 34709d114089c722b5da796028ffb91021761fdd
585
+ commit 52b6073997c1b26fea9d4aae3154b37575944d4d
656
586
  Author: Naohisa Goto <ng@bioruby.org>
657
- Date: Thu Jul 5 23:00:37 2012 +0900
587
+ Date: Sat Mar 28 00:50:43 2015 +0900
658
588
 
659
- Remove old comment lines
589
+ suppress "method redefined" warnings and fill RDoc for some methods
660
590
 
661
- lib/bio/sequence/format.rb | 6 ------
662
- 1 file changed, 6 deletions(-)
591
+ lib/bio/db/phyloxml/phyloxml_elements.rb | 46 +++++++++++++++++++++++-------
592
+ 1 file changed, 35 insertions(+), 11 deletions(-)
663
593
 
664
- commit e0d5ed61e0101e2e72ad024dccd58c8c90def2b9
594
+ commit 3d2e99fe993d76d5ece5bdbcd2e9541fa098c4dd
665
595
  Author: Naohisa Goto <ng@bioruby.org>
666
- Date: Thu Jul 5 22:42:17 2012 +0900
596
+ Date: Sat Mar 28 00:36:51 2015 +0900
667
597
 
668
- Finalizer for Bio::Command::Tmpdir is changed to suppress test failure
669
-
670
- * New class Bio::Command::Tmpdir::Remover for removing temporary
671
- directory in finilizer. This class is BioRuby internal use only.
672
- Users should not use this class.
673
- * Finalizer for Bio::Command::Tmpdir is changed from a Proc object
674
- to an instance of the Remover class.
675
- * Test failure fix: In some environment, with Ruby 1.9.2,
676
- test_output_embl(Bio::FuncTestSequenceOutputEMBL) was failed with
677
- "<#<ArgumentError: wrong number of arguments (1 for 0)>" that was
678
- raised in the finalizer callback of Bio::Command::Tmpdir. This
679
- commit fixes the problem.
598
+ suppress "instance variable @XXX not initialized" warnings
680
599
 
681
- lib/bio/command.rb | 56 ++++++++++++++++++++++++++++------------------------
682
- 1 file changed, 30 insertions(+), 26 deletions(-)
600
+ lib/bio/db/phyloxml/phyloxml_elements.rb | 88 +++++++++++++++---------------
601
+ 1 file changed, 44 insertions(+), 44 deletions(-)
683
602
 
684
- commit cca98d1378ce66d6db84cc9c1beadd39ed0e0fee
603
+ commit 02d4f98eae3934d8ad9c950b41132eb14653fe27
685
604
  Author: Naohisa Goto <ng@bioruby.org>
686
- Date: Thu Jul 5 22:21:34 2012 +0900
605
+ Date: Thu Mar 26 20:33:35 2015 +0900
687
606
 
688
- Workaround to avoid circular require and JRuby autoload bug
689
-
690
- * "require" lines are modified to avoid circular require.
691
- * In files that would be required directly from outside bio/sequence
692
- (aa.rb, adapter.rb, common.rb, compat.rb, dblink.rb, generic.rb,
693
- na.rb, quality_score.rb, sequence_masker.rb), because of avoiding
694
- potential mismatch of superclass and/or lack of some methods,
695
- bio/sequence.rb is required when Bio::Sequence is not defined.
696
- * workaround to avoid JRuby autoload bug
607
+ suppress warning: instance variable @uri not initialized
697
608
 
698
- lib/bio/sequence.rb | 10 ++++++----
699
- lib/bio/sequence/aa.rb | 8 +++-----
700
- lib/bio/sequence/adapter.rb | 12 ++++++------
701
- lib/bio/sequence/common.rb | 2 ++
702
- lib/bio/sequence/compat.rb | 9 ++-------
703
- lib/bio/sequence/dblink.rb | 11 ++++++-----
704
- lib/bio/sequence/generic.rb | 7 +++----
705
- lib/bio/sequence/na.rb | 10 ++++------
706
- lib/bio/sequence/quality_score.rb | 2 ++
707
- lib/bio/sequence/sequence_masker.rb | 3 +++
708
- 10 files changed, 37 insertions(+), 37 deletions(-)
609
+ lib/bio/db/phyloxml/phyloxml_elements.rb | 2 +-
610
+ 1 file changed, 1 insertion(+), 1 deletion(-)
709
611
 
710
- commit d2915c33ae7f330837688195a58c1e60fe78402a
612
+ commit 94277712e9dd000c2d9bf5b6ebfd84d0f2fc3b59
711
613
  Author: Naohisa Goto <ng@bioruby.org>
712
- Date: Thu Jul 5 21:04:28 2012 +0900
614
+ Date: Thu Mar 26 01:47:45 2015 +0900
713
615
 
714
- workaround to avoid circular require in Bio::RestrictionEnzyme
715
-
716
- * Workaround to avoid circular require in Bio::RestrictionEnzyme
717
- * Special care was needed for Bio::RestrictionEnzyme::Analysis
718
- because its method definitions are divided into two files:
719
- analysis.rb, analysis_basic.rb.
616
+ suppress warning: instance variable @format not initialized
720
617
 
721
- lib/bio/util/restriction_enzyme/analysis.rb | 13 ++++++++-----
722
- lib/bio/util/restriction_enzyme/analysis_basic.rb | 7 ++++---
723
- lib/bio/util/restriction_enzyme/cut_symbol.rb | 5 +++--
724
- lib/bio/util/restriction_enzyme/dense_int_array.rb | 3 +++
725
- lib/bio/util/restriction_enzyme/double_stranded.rb | 7 +++----
726
- .../restriction_enzyme/double_stranded/aligned_strands.rb | 7 +++----
727
- .../double_stranded/cut_location_pair.rb | 7 +++----
728
- .../cut_location_pair_in_enzyme_notation.rb | 7 +++----
729
- .../restriction_enzyme/double_stranded/cut_locations.rb | 7 +++----
730
- .../double_stranded/cut_locations_in_enzyme_notation.rb | 7 +++----
731
- lib/bio/util/restriction_enzyme/range/cut_range.rb | 7 +++----
732
- lib/bio/util/restriction_enzyme/range/cut_ranges.rb | 7 +++----
733
- .../util/restriction_enzyme/range/horizontal_cut_range.rb | 7 +++----
734
- lib/bio/util/restriction_enzyme/range/sequence_range.rb | 7 +++----
735
- .../range/sequence_range/calculated_cuts.rb | 7 +++----
736
- .../restriction_enzyme/range/sequence_range/fragment.rb | 7 +++----
737
- .../restriction_enzyme/range/sequence_range/fragments.rb | 7 +++----
738
- .../util/restriction_enzyme/range/vertical_cut_range.rb | 7 +++----
739
- lib/bio/util/restriction_enzyme/single_strand.rb | 6 +++---
740
- .../single_strand/cut_locations_in_enzyme_notation.rb | 7 +++----
741
- .../util/restriction_enzyme/single_strand_complement.rb | 7 +++----
742
- lib/bio/util/restriction_enzyme/sorted_num_array.rb | 3 +++
743
- lib/bio/util/restriction_enzyme/string_formatting.rb | 7 +++----
744
- 23 files changed, 75 insertions(+), 81 deletions(-)
618
+ lib/bio/db/fastq.rb | 2 +-
619
+ 1 file changed, 1 insertion(+), 1 deletion(-)
745
620
 
746
- commit 7df4843288ffde6d7132a5651fe978301f8ebd2b
621
+ commit e61e1071e4bb7dd9ee995c3a7f864c2ef4384edd
747
622
  Author: Naohisa Goto <ng@bioruby.org>
748
- Date: Thu Jul 5 20:18:08 2012 +0900
623
+ Date: Thu Mar 26 01:40:33 2015 +0900
749
624
 
750
- workaround to avoid JRuby autoload bug
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
751
632
 
752
- lib/bio/util/restriction_enzyme.rb | 4 +---
753
- 1 file changed, 1 insertion(+), 3 deletions(-)
633
+ lib/bio/appl/blast/format0.rb | 13 ++++++++++---
634
+ 1 file changed, 10 insertions(+), 3 deletions(-)
754
635
 
755
- commit 97d95f2b400006d4229a7ce69d7d8a5cdce42764
636
+ commit 08c458c74a7a34e340e09053cbc0f9c071e27395
756
637
  Author: Naohisa Goto <ng@bioruby.org>
757
- Date: Wed Jul 4 22:00:27 2012 +0900
638
+ Date: Thu Mar 26 01:09:16 2015 +0900
758
639
 
759
- changed require to autoload for the workaround of JRuby autoload bug
640
+ suppress warning: instance variable @pattern not initialized
760
641
 
761
- lib/bio/feature.rb | 5 ++---
762
- 1 file changed, 2 insertions(+), 3 deletions(-)
642
+ lib/bio/appl/blast/format0.rb | 8 ++++++--
643
+ 1 file changed, 6 insertions(+), 2 deletions(-)
763
644
 
764
- commit 530b82a45731c2a71a110826341be425de1271e0
645
+ commit 33d7eed180fd601972724f4b992f1a17c689ef62
765
646
  Author: Naohisa Goto <ng@bioruby.org>
766
- Date: Wed Jul 4 22:00:06 2012 +0900
647
+ Date: Thu Mar 26 00:57:02 2015 +0900
767
648
 
768
- workaround to avoid JRuby autoload bug
649
+ Test bug fix: fix typo of test target method
769
650
 
770
- lib/bio/sequence/common.rb | 4 +---
771
- 1 file changed, 1 insertion(+), 3 deletions(-)
651
+ test/network/bio/test_command.rb | 2 +-
652
+ 1 file changed, 1 insertion(+), 1 deletion(-)
772
653
 
773
- commit 8614f31b36fb93d6e49d109268d646ff3032cd1a
654
+ commit 76a98bce1affac03483c08f803d4314b42a0a3d3
774
655
  Author: Naohisa Goto <ng@bioruby.org>
775
- Date: Wed Jul 4 21:28:52 2012 +0900
656
+ Date: Thu Mar 26 00:32:25 2015 +0900
776
657
 
777
- workaround to avoid JRuby autoload bug
658
+ Incompatible Change: Bio::Command.make_cgi_params rejects single String
778
659
 
779
- * Workaround to avoid JRuby autoload bug.
780
- * Changed to require bio/db.rb because it is always loaded.
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.
781
664
 
782
- lib/bio/db/kegg/genes.rb | 6 +++---
783
- 1 file changed, 3 insertions(+), 3 deletions(-)
665
+ lib/bio/command.rb | 2 +-
666
+ test/unit/bio/test_command.rb | 9 +++++----
667
+ 2 files changed, 6 insertions(+), 5 deletions(-)
784
668
 
785
- commit ea500006ed56857139c858bdfeb98773e5ca541e
669
+ commit b1612545a7516befd850a6d5925aa73bbaa4b4b0
786
670
  Author: Naohisa Goto <ng@bioruby.org>
787
- Date: Thu Jun 28 21:36:35 2012 +0900
671
+ Date: Wed Mar 25 02:36:41 2015 +0900
788
672
 
789
- Rakefile: use own mktmpdir
673
+ delete obsolete $Id:$ line
790
674
 
791
- Rakefile | 59 +++++++++++++++++++++++++++++++++++++++++++----------------
792
- 1 file changed, 43 insertions(+), 16 deletions(-)
675
+ lib/bio/io/togows.rb | 1 -
676
+ 1 file changed, 1 deletion(-)
793
677
 
794
- commit 452fadcab61083dcb9d01ee05d300eae5cb23fee
678
+ commit 4d5a419cc78ff2a79cff2812adc6f16f286204e8
795
679
  Author: Naohisa Goto <ng@bioruby.org>
796
- Date: Thu Jun 28 20:37:59 2012 +0900
680
+ Date: Wed Mar 25 02:35:45 2015 +0900
797
681
 
798
- .travis.yml: remove "rake regemspec" from after_install
682
+ delete obsolete $Id:$ line
799
683
 
800
- .travis.yml | 2 --
801
- 1 file changed, 2 deletions(-)
684
+ test/network/bio/io/test_togows.rb | 1 -
685
+ 1 file changed, 1 deletion(-)
802
686
 
803
- commit 3fad822af3d7e558a58b71fd8ec2a7061b49f9f2
687
+ commit a8d2c4cac665b4bb8140df329a9cc1d6e5e2d02d
804
688
  Author: Naohisa Goto <ng@bioruby.org>
805
- Date: Thu Jun 28 20:36:59 2012 +0900
689
+ Date: Wed Mar 25 02:35:03 2015 +0900
806
690
 
807
- regenerate bioruby.gemspec with rake regemspec
691
+ delete obsolete $Id:$ line
808
692
 
809
- bioruby.gemspec | 2 ++
810
- 1 file changed, 2 insertions(+)
693
+ test/unit/bio/io/test_togows.rb | 1 -
694
+ 1 file changed, 1 deletion(-)
811
695
 
812
- commit ea6e96fc654c797664b118a6326a84e4f9b1a8a3
696
+ commit dd0967db3743789ea5aa48623df8d97f93062694
813
697
  Author: Naohisa Goto <ng@bioruby.org>
814
- Date: Thu Jun 28 20:35:49 2012 +0900
698
+ Date: Wed Mar 25 02:33:49 2015 +0900
815
699
 
816
- print message when doing Dir.chdir
700
+ test_make_path: add test data using Symbol objects
817
701
 
818
- Rakefile | 17 +++++++++++------
819
- 1 file changed, 11 insertions(+), 6 deletions(-)
702
+ test/unit/bio/io/test_togows.rb | 4 +++-
703
+ 1 file changed, 3 insertions(+), 1 deletion(-)
820
704
 
821
- commit c2fcd5e8cc71da38dc3c6d1f8c8d0233e47398b3
705
+ commit e07158a60ca666b5d625408bcf8fa602fd8114a8
822
706
  Author: Naohisa Goto <ng@bioruby.org>
823
- Date: Thu Jun 28 20:28:41 2012 +0900
707
+ Date: Wed Mar 25 02:22:31 2015 +0900
824
708
 
825
- In tar-install, removed dependency to regemspec
709
+ Bio::TogoWS::REST#entry: comma between IDs should NOT be escaped to %2C
826
710
 
827
- Rakefile | 2 +-
828
- 1 file changed, 1 insertion(+), 1 deletion(-)
711
+ lib/bio/io/togows.rb | 11 +++++++++--
712
+ 1 file changed, 9 insertions(+), 2 deletions(-)
829
713
 
830
- commit 67a7e83d516aab5d60f8263525b359be8b0ffc0b
714
+ commit 98546289b2f2da2dc7f9586fd5e2942da4d8f3a8
831
715
  Author: Naohisa Goto <ng@bioruby.org>
832
- Date: Thu Jun 28 20:23:24 2012 +0900
716
+ Date: Wed Mar 25 02:00:17 2015 +0900
833
717
 
834
- Rakefile: give up using Dir.mktmpdir because of JRuby's behavior
718
+ Bug fix: search with offset did not work due to TogoWS server change
835
719
 
836
- * Rakefile: give up using Dir.mktmpdir because of JRuby's behavior
837
- that may be related with http://jira.codehaus.org/browse/JRUBY-5678
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.
838
725
 
839
- Rakefile | 61 ++++++++++++++++++++++++++++++++++++++++++++++---------------
840
- 1 file changed, 46 insertions(+), 15 deletions(-)
726
+ lib/bio/io/togows.rb | 24 +++++++++++++++++++++---
727
+ 1 file changed, 21 insertions(+), 3 deletions(-)
841
728
 
842
- commit cff098034a338bbe9579d6c7b4380c7132a38ef5
729
+ commit 7097f80e315a0a6332e7a76a5bb261649e8dcc1a
843
730
  Author: Naohisa Goto <ng@bioruby.org>
844
- Date: Thu Jun 28 19:23:57 2012 +0900
731
+ Date: Wed Mar 25 01:33:26 2015 +0900
845
732
 
846
- gem-integration-test, gem-install and gem-install-nodoc are removed
733
+ Bug fix due to TogoWS convert method spec change
847
734
 
848
- * gem-integration-test, gem-install and gem-install-nodoc are removed
849
- because they are useless with Bundler
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.
850
737
 
851
- Rakefile | 13 -------------
852
- 1 file changed, 13 deletions(-)
738
+ lib/bio/io/togows.rb | 7 +++----
739
+ 1 file changed, 3 insertions(+), 4 deletions(-)
853
740
 
854
- commit d5c054265af4f80318cbfa5a5bbdee6125219de2
741
+ commit 1a9b1063af4c0b32cd287d4a2c2466343aeddb98
855
742
  Author: Naohisa Goto <ng@bioruby.org>
856
- Date: Thu Jun 28 18:10:05 2012 +0900
743
+ Date: Wed Mar 25 01:30:34 2015 +0900
857
744
 
858
- .travis.yml: .gemspec is needed to install local gem
745
+ improve tests for bio/command.rb for methods using http protocol
859
746
 
860
- .travis.yml | 1 +
861
- gemfiles/prepare-gemspec.rb | 25 +++++++++++++++++++++++++
862
- 2 files changed, 26 insertions(+)
863
- create mode 100644 gemfiles/prepare-gemspec.rb
747
+ test/network/bio/test_command.rb | 67 ++++++++++++++++++++++++++++++++++++--
748
+ 1 file changed, 65 insertions(+), 2 deletions(-)
864
749
 
865
- commit 05b6172123f42a1d8d46668d8a3d5f698c371704
750
+ commit c63920e4d8569e3eaef201d4d60fcddfa15f1f34
866
751
  Author: Naohisa Goto <ng@bioruby.org>
867
- Date: Thu Jun 28 17:51:43 2012 +0900
752
+ Date: Wed Mar 25 01:30:06 2015 +0900
868
753
 
869
- remove 1.9.2; add tar/gem integration tests
870
-
871
- * Remove ruby version 1.9.2 from matrix for reducing builds
872
- * Add tar/gem integration tests
873
- * Add a new helper script gemfiles/modify-Gemfile.rb,
874
- modifying gemfile when running gem integration test.
875
- * Remove jruby version comments
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
876
764
 
877
- .travis.yml | 26 +++++++++++++++++---------
878
- gemfiles/modify-Gemfile.rb | 28 ++++++++++++++++++++++++++++
879
- 2 files changed, 45 insertions(+), 9 deletions(-)
880
- create mode 100644 gemfiles/modify-Gemfile.rb
765
+ lib/bio/command.rb | 61 ++++++++++++++++++++++++++++++++++++++++++++++++++++
766
+ 1 file changed, 61 insertions(+)
881
767
 
882
- commit 6813f91893e7ddc3000047357c9ed2dafb32a722
768
+ commit a40157205282e148bf3a2e43aed1e08d713fb598
883
769
  Author: Naohisa Goto <ng@bioruby.org>
884
- Date: Thu Jun 28 17:06:28 2012 +0900
770
+ Date: Tue Mar 24 00:46:23 2015 +0900
885
771
 
886
- descriptions are modified for danger operations
772
+ suppress warnings "instance variable @circular not initialized"
887
773
 
888
- Rakefile | 4 ++--
774
+ lib/bio/util/restriction_enzyme/range/sequence_range.rb | 4 ++--
889
775
  1 file changed, 2 insertions(+), 2 deletions(-)
890
776
 
891
- commit a209688952c922d9ba45c227874990bccd3da7c0
777
+ commit abcac8de85c9606f6a1879fe9d2ae559911708c9
892
778
  Author: Naohisa Goto <ng@bioruby.org>
893
- Date: Mon Jun 25 23:25:51 2012 +0900
779
+ Date: Tue Mar 24 00:29:42 2015 +0900
894
780
 
895
- regenerate bioruby.gemspec with rake regemspec
781
+ delete obsolete $Id:$ line
896
782
 
897
- bioruby.gemspec | 5 +++++
898
- 1 file changed, 5 insertions(+)
783
+ test/unit/bio/io/flatfile/test_autodetection.rb | 1 -
784
+ 1 file changed, 1 deletion(-)
899
785
 
900
- commit 8f6459497be0e9ca7dc3eb2eb9606e42d97ad60c
786
+ commit 1b5bf586af238b712a9f640087421fd299376c2d
901
787
  Author: Naohisa Goto <ng@bioruby.org>
902
- Date: Mon Jun 25 21:01:06 2012 +0900
788
+ Date: Tue Mar 24 00:28:38 2015 +0900
903
789
 
904
- rake tasks added and default task is changed
905
-
906
- * New tasks:
907
- * gem-install: build gem and install it
908
- * gem-install-nodoc: build gem and install it with --no-ri --no-rdoc.
909
- * gem-test: test installed bioruby gem installed with gem-install
910
- (or gem-install-nodoc)
911
- * gem-integration-test: build gem, install and run test (with --no-ri
912
- --no-rdoc)
913
- * tar-install: DANGER: build tar and install by using setup.rb
914
- * installed-test: test installed bioruby
915
- * tar-integration-test: DANGER: build tar, install and run test
916
- * see-env: see BIORUBY_RAKE_DEFAULT_TASK environment variable and
917
- invoke the specified task. If the variable did not exist, it
918
- invokes "test" which is previously the default task. It is added
919
- for selecting task on Travis-ci. It is not recommended to invoke
920
- the task explicitly by hand.
921
- * Default task is changed from "test" to "see-env".
790
+ suppress warning: assigned but unused variable - length
922
791
 
923
- Rakefile | 110 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++--
924
- 1 file changed, 107 insertions(+), 3 deletions(-)
792
+ test/unit/bio/io/flatfile/test_autodetection.rb | 2 +-
793
+ 1 file changed, 1 insertion(+), 1 deletion(-)
925
794
 
926
- commit 3b400042cd361e1ab6d0fb0d8c8cce14a6c2ae10
795
+ commit 5497068d17c2794ab2b6ef1e603e5478a86537c6
927
796
  Author: Naohisa Goto <ng@bioruby.org>
928
- Date: Mon Jun 25 20:58:13 2012 +0900
797
+ Date: Tue Mar 24 00:22:54 2015 +0900
929
798
 
930
- BIORUBY_TEST_LIB is always added on the top of $LOAD_PATH
931
-
932
- * When BIORUBY_TEST_LIB is specified, the specified directory name
933
- is always added on the top of $LOAD_PATH even if it is already
934
- included in the middle of $LOAD_PATH.
799
+ add/modify assertions to suppress "unused variable" warnings
935
800
 
936
- test/bioruby_test_helper.rb | 4 ++--
937
- 1 file changed, 2 insertions(+), 2 deletions(-)
801
+ test/unit/bio/db/genbank/test_genbank.rb | 12 +++++++++---
802
+ 1 file changed, 9 insertions(+), 3 deletions(-)
938
803
 
939
- commit 848304b6f90310f8fa15c80ba06655ae5cae5053
804
+ commit d5bafd8b7ee28ab0418b09fd6dd47abcb9eb1ee5
940
805
  Author: Naohisa Goto <ng@bioruby.org>
941
- Date: Mon Jun 25 20:42:07 2012 +0900
806
+ Date: Mon Mar 23 23:57:56 2015 +0900
942
807
 
943
- New env BIORUBY_TEST_GEM and BIORUBY_TEST_LIB behavior changed
944
-
945
- * New environment variable BIORUBY_TEST_GEM for testing installed
946
- bio-X.X.X gem. Version number can be specified.
947
- Example with version number:
948
- % env BIORUBY_TEST_GEM=1.4.2.5000 ruby test/runner.rb
949
- Example without version number:
950
- % env BIORUBY_TEST_GEM="" ruby test/runner.rb
951
- * When BIORUBY_TEST_LIB is empty, it no longer add an empty string to
952
- $LOAD_PATH. Moreover, when BIORUBY_TEST_GEM is set, the variable is
953
- ignored.
808
+ delete obsolete $Id:$ line
954
809
 
955
- test/bioruby_test_helper.rb | 49 ++++++++++++++++++++++++++++++++-----------
956
- 1 file changed, 37 insertions(+), 12 deletions(-)
810
+ lib/bio/appl/blast.rb | 1 -
811
+ 1 file changed, 1 deletion(-)
957
812
 
958
- commit 9453a6773c24f866698370195fd8e767443a38b9
959
- Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>
960
- Date: Fri Jun 1 18:06:40 2012 +0900
813
+ commit bbd60d1aae7c894f914b7265d2de22fea5eb3faf
814
+ Author: Naohisa Goto <ng@bioruby.org>
815
+ Date: Mon Mar 23 23:56:42 2015 +0900
961
816
 
962
- broader FASTQ file recognition
963
-
964
- * Because PacBio RS sequencer may produce kilobases long reads and
965
- read buffer size (default 31 lines) for file format detection
966
- may not be sufficient to find the second id line starting with "+",
967
- the regular expression for FASTQ is truncated only to check the
968
- first id line starting with "@".
969
- * Test code is added.
817
+ suppress warning: assigned but unused variable - dummy
970
818
 
971
- lib/bio/io/flatfile/autodetection.rb | 2 +-
972
- test/unit/bio/io/flatfile/test_autodetection.rb | 6 ++++++
973
- 2 files changed, 7 insertions(+), 1 deletion(-)
819
+ lib/bio/appl/blast.rb | 2 +-
820
+ 1 file changed, 1 insertion(+), 1 deletion(-)
974
821
 
975
- commit 120e780c023cba06b83899c2f8a17c8fc1de4faa
822
+ commit 4a91502ccf14ab8655645144120aa97d0c8313a5
976
823
  Author: Naohisa Goto <ng@bioruby.org>
977
- Date: Fri Jun 8 15:36:29 2012 +0900
824
+ Date: Mon Mar 23 20:32:59 2015 +0900
978
825
 
979
- Retry sequence randomize test up to 10 times when fails
980
-
981
- * To suppress rare failure of chi-square equiprobability tests for
982
- Bio::Sequence::Common#randomize, test code changed to retry
983
- up to 10 times if the chi-square test fails. The assertion fails
984
- if the chi-square test fails 10 consecutive times, and this
985
- strongly suggests bugs in codes or in the random number generator.
986
- * The chi-square equiprobability tests are separated into a new
987
- test class.
826
+ delete obsolete $Id:$ line
988
827
 
989
- test/unit/bio/sequence/test_common.rb | 40 +++++++++++++++++++++++++++++----
990
- 1 file changed, 36 insertions(+), 4 deletions(-)
828
+ lib/bio/shell/setup.rb | 1 -
829
+ 1 file changed, 1 deletion(-)
991
830
 
992
- commit 20dde52f7da784d4d9ac551957700cd96e842ef6
831
+ commit c437a4078ff8e2869b9c1ab3543022db373a93c3
993
832
  Author: Naohisa Goto <ng@bioruby.org>
994
- Date: Sat May 19 18:14:19 2012 +0900
833
+ Date: Mon Mar 23 20:32:20 2015 +0900
995
834
 
996
- libxml-ruby is disabled because of build error on Travis-ci
835
+ suppress warning: instance variable @mode not initialized
997
836
 
998
- gemfiles/Gemfile.travis-jruby1.8 | 3 ++-
999
- gemfiles/Gemfile.travis-jruby1.9 | 3 ++-
1000
- 2 files changed, 4 insertions(+), 2 deletions(-)
837
+ lib/bio/shell/setup.rb | 2 +-
838
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1001
839
 
1002
- commit 3c5c1cc277d30737815c7e44a2abbb308f5324b0
1003
- Author: Clayton Wheeler <cswh@umich.edu>
1004
- Date: Mon May 14 21:48:41 2012 -0400
840
+ commit 8967cf280d5ca8491d57a11e4f3ffab7369c4ea8
841
+ Author: Naohisa Goto <ng@bioruby.org>
842
+ Date: Mon Mar 23 20:28:50 2015 +0900
1005
843
 
1006
- Use libxml-ruby instead of libxml-jruby to fix JRuby test failures.
1007
-
1008
- The travis-ci Gemfiles currently call for libxml-jruby; this appears
1009
- not to support the same API as libxml-ruby, resulting in several tests
1010
- in test/unit/bio/db/test_phyloxml.rb failing with "NameError:
1011
- uninitialized constant LibXMLJRuby::XML::Parser::Options". Switching
1012
- to the C libxml-ruby library allows these tests to pass under JRuby in
1013
- 1.8 mode.
1014
-
1015
- JRuby in 1.9 mode still fails a few PhyloXML tests due to
1016
- https://jira.codehaus.org/browse/JRUBY-6662.
844
+ delete obsolete $Id:$ line
1017
845
 
1018
- gemfiles/Gemfile.travis-jruby1.8 | 2 +-
1019
- gemfiles/Gemfile.travis-jruby1.9 | 2 +-
1020
- 2 files changed, 2 insertions(+), 2 deletions(-)
846
+ lib/bio/shell/irb.rb | 1 -
847
+ 1 file changed, 1 deletion(-)
1021
848
 
1022
- commit 01a618242d67f0d00fe681dfd85e68bb393513fc
1023
- Author: Clayton Wheeler <cswh@umich.edu>
1024
- Date: Thu May 10 23:13:56 2012 -0400
849
+ commit 42b5f030067be4bc9c53ccb4c06ccfc5e8d9df03
850
+ Author: Naohisa Goto <ng@bioruby.org>
851
+ Date: Mon Mar 23 20:28:27 2015 +0900
1025
852
 
1026
- test_tree.rb: to use %f instead of %g to prevent odd behavior.
853
+ change deprecated method File.exists? to File.exist?
1027
854
 
1028
- test/unit/bio/test_tree.rb | 22 +++++++++++-----------
1029
- 1 file changed, 11 insertions(+), 11 deletions(-)
855
+ lib/bio/shell/irb.rb | 2 +-
856
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1030
857
 
1031
- commit 5e80e4394bf2a5e4ee472fe84ab76239b293e1b5
1032
- Author: Clayton Wheeler <cswh@umich.edu>
1033
- Date: Thu May 10 23:04:55 2012 -0400
858
+ commit 389ad2f311f161f235db2373aeb2f5500b1ea65f
859
+ Author: Naohisa Goto <ng@bioruby.org>
860
+ Date: Mon Mar 23 20:27:01 2015 +0900
1034
861
 
1035
- Fixed spurious JRuby failures in test_tree.rb due to floating point differences.
862
+ delete obsolete $Id:$ line
1036
863
 
1037
- test/unit/bio/test_tree.rb | 14 +++++++-------
1038
- 1 file changed, 7 insertions(+), 7 deletions(-)
864
+ lib/bio/shell/interface.rb | 1 -
865
+ 1 file changed, 1 deletion(-)
1039
866
 
1040
- commit 459d4da894e9a9b9db0d793e3711dc45bae2089b
1041
- Author: Artem Tarasov <lomereiter@gmail.com>
1042
- Date: Thu May 10 16:23:13 2012 +0400
867
+ commit de5949798d66c16d2b5e2cf8ba7192049ec99c5b
868
+ Author: Naohisa Goto <ng@bioruby.org>
869
+ Date: Mon Mar 23 20:26:37 2015 +0900
1043
870
 
1044
- Test bug fix: order of hash keys are not guaranteed
1045
-
1046
- * Test bug fix: Bio::TestSOFT#test_dataset: order of hash keys are
1047
- not guaranteed.
871
+ change deprecated method File.exists? to File.exist?
1048
872
 
1049
- test/unit/bio/db/test_soft.rb | 2 +-
1050
- 1 file changed, 1 insertion(+), 1 deletion(-)
873
+ lib/bio/shell/interface.rb | 6 +++---
874
+ 1 file changed, 3 insertions(+), 3 deletions(-)
1051
875
 
1052
- commit 7e730691d6ec597a610dc0d4665db3598fcfde59
876
+ commit c8907059a716a8778e333755c8fb53bb2a0c7158
1053
877
  Author: Naohisa Goto <ng@bioruby.org>
1054
- Date: Thu May 10 00:06:19 2012 +0900
878
+ Date: Mon Mar 23 20:24:58 2015 +0900
1055
879
 
1056
- removed potential circular require about Bio::Sequence::Format
880
+ delete obsolete $Id:$ line
1057
881
 
1058
- lib/bio/db/embl/format_embl.rb | 4 ----
1059
- lib/bio/db/fasta/format_fasta.rb | 4 ----
1060
- lib/bio/db/fasta/format_qual.rb | 5 -----
1061
- lib/bio/db/fastq/format_fastq.rb | 1 -
1062
- lib/bio/db/genbank/format_genbank.rb | 4 ----
1063
- lib/bio/sequence/format_raw.rb | 4 ----
1064
- 6 files changed, 22 deletions(-)
882
+ lib/bio/shell/core.rb | 1 -
883
+ 1 file changed, 1 deletion(-)
1065
884
 
1066
- commit f1c398fdc3488bd18bd13ac864920ce6db4dab9e
885
+ commit 1fe5903f8acd8045d203465a099a45218e7e3891
1067
886
  Author: Naohisa Goto <ng@bioruby.org>
1068
- Date: Wed May 9 15:54:20 2012 +0900
887
+ Date: Mon Mar 23 20:24:25 2015 +0900
1069
888
 
1070
- .travis.yml: comment out apt-get lines
1071
-
1072
- * .travis.yml: comment out apt-get lines because libxml2-dev
1073
- and libexpat1-dev are already installed.
889
+ change deprecated method File.exists? to File.exist?
1074
890
 
1075
- .travis.yml | 6 +++---
1076
- 1 file changed, 3 insertions(+), 3 deletions(-)
891
+ lib/bio/shell/core.rb | 10 +++++-----
892
+ 1 file changed, 5 insertions(+), 5 deletions(-)
1077
893
 
1078
- commit bc5ef4959e51f4a199d9f740b07812e9b8216255
894
+ commit 929207c6f186c81f076fab9b1bbbd23c4b966f4e
1079
895
  Author: Naohisa Goto <ng@bioruby.org>
1080
- Date: Wed May 9 15:47:11 2012 +0900
896
+ Date: Mon Mar 23 20:20:05 2015 +0900
1081
897
 
1082
- travis-ci: comment out soap4r-ruby1.9 in Gemfile because of error
1083
-
1084
- * travis-ci: soap4r-ruby1.9 gem in Gemfile.travis-ruby1.9 and
1085
- Gemfile.travis-jruby1.9 is commented out because of an error
1086
- "uninitialized constant XML::SaxParser".
898
+ delete obsolete $Id:$ line
1087
899
 
1088
- gemfiles/Gemfile.travis-jruby1.9 | 4 +++-
1089
- gemfiles/Gemfile.travis-ruby1.9 | 4 +++-
1090
- 2 files changed, 6 insertions(+), 2 deletions(-)
900
+ test/unit/bio/db/pdb/test_pdb.rb | 1 -
901
+ 1 file changed, 1 deletion(-)
1091
902
 
1092
- commit 7e8153c09660c31d6286c1924680b8c5073a10b6
903
+ commit e75c57fcd7abc56ba6fcbf1996e491aca890f5b1
1093
904
  Author: Naohisa Goto <ng@bioruby.org>
1094
- Date: Tue May 1 18:11:09 2012 +0900
905
+ Date: Mon Mar 23 20:19:30 2015 +0900
1095
906
 
1096
- config files for Travis CI continuous integration service
907
+ suppress "assigned but unused variable" warnings
1097
908
 
1098
- .travis.yml | 73 ++++++++++++++++++++++++++++++++++++++
1099
- gemfiles/Gemfile.travis-jruby1.8 | 6 ++++
1100
- gemfiles/Gemfile.travis-jruby1.9 | 7 ++++
1101
- gemfiles/Gemfile.travis-ruby1.8 | 7 ++++
1102
- gemfiles/Gemfile.travis-ruby1.9 | 8 +++++
1103
- 5 files changed, 101 insertions(+)
1104
- create mode 100644 .travis.yml
1105
- create mode 100644 gemfiles/Gemfile.travis-jruby1.8
1106
- create mode 100644 gemfiles/Gemfile.travis-jruby1.9
1107
- create mode 100644 gemfiles/Gemfile.travis-ruby1.8
1108
- create mode 100644 gemfiles/Gemfile.travis-ruby1.9
909
+ test/unit/bio/db/pdb/test_pdb.rb | 21 ++++++++++++++-------
910
+ 1 file changed, 14 insertions(+), 7 deletions(-)
1109
911
 
1110
- commit f1ecae7763648cb735a885ddb6c46d71c59b0694
912
+ commit b458301f47322c265fce27efd0ed71443c17d9d7
1111
913
  Author: Naohisa Goto <ng@bioruby.org>
1112
- Date: Fri Mar 23 01:36:59 2012 +0900
914
+ Date: Mon Mar 23 18:34:12 2015 +0900
1113
915
 
1114
- Test bug fix: tests affected by the bug of Bio::NucleicAcid.to_re("s")
916
+ delete obsolete $Id:$ line
1115
917
 
1116
- test/unit/bio/data/test_na.rb | 2 +-
1117
- test/unit/bio/sequence/test_na.rb | 2 +-
1118
- test/unit/bio/test_sequence.rb | 4 ++--
1119
- 3 files changed, 4 insertions(+), 4 deletions(-)
918
+ lib/bio/shell/plugin/entry.rb | 1 -
919
+ 1 file changed, 1 deletion(-)
1120
920
 
1121
- commit 3fd9384b1b59140a929c81dcc4b07cb3c2e47525
1122
- Author: Trevor Wennblom <trevor@well.com>
1123
- Date: Sat Feb 25 15:26:27 2012 -0600
921
+ commit c3f909fe06b82b3cbd4bdcbcdef668fc0727be9d
922
+ Author: Naohisa Goto <ng@bioruby.org>
923
+ Date: Mon Mar 23 18:33:30 2015 +0900
1124
924
 
1125
- Bug fix: Bio::NucleicAcid.to_re("s") typo
925
+ change deprecated method File.exists? to File.exist?
1126
926
 
1127
- lib/bio/data/na.rb | 2 +-
1128
- 1 file changed, 1 insertion(+), 1 deletion(-)
927
+ lib/bio/shell/plugin/entry.rb | 4 ++--
928
+ 1 file changed, 2 insertions(+), 2 deletions(-)
1129
929
 
1130
- commit c552aa3a6773139b14ae95e79e0fb43a2f91c6fb
930
+ commit 7ba6349c2446aa03b843a2a8fb49505c8f63c6ca
1131
931
  Author: Naohisa Goto <ng@bioruby.org>
1132
- Date: Thu Jan 12 22:24:37 2012 +0900
932
+ Date: Mon Mar 23 18:20:44 2015 +0900
1133
933
 
1134
- Bug fix: GenomeNet BLAST server URI changed.
1135
-
1136
- * Bug fix: GenomeNet BLAST server URI changed.
1137
- Reported by joaocardoso via GitHub.
1138
- ( https://github.com/bioruby/bioruby/issues/44 )
934
+ change deprecated method File.exists? to File.exist?
1139
935
 
1140
- lib/bio/appl/blast/genomenet.rb | 3 ++-
1141
- 1 file changed, 2 insertions(+), 1 deletion(-)
936
+ lib/bio/appl/meme/mast.rb | 8 ++++----
937
+ 1 file changed, 4 insertions(+), 4 deletions(-)
1142
938
 
1143
- commit f33abf9bbd90c3c1e320f06447fdb54ffd094c5d
1144
- Author: peterjc <p.j.a.cock@googlemail.com>
1145
- Date: Fri Nov 25 11:20:08 2011 +0000
939
+ commit e7f78ea3c3fb1b78adcc6ae13f450cf2cda361cd
940
+ Author: Naohisa Goto <ng@bioruby.org>
941
+ Date: Mon Mar 23 18:10:27 2015 +0900
1146
942
 
1147
- Mark echoarg2.bat and echoarg2.sh as world executable
943
+ delete obsolete $Id:$ line
1148
944
 
1149
- 0 files changed
1150
- mode change 100644 => 100755 test/data/command/echoarg2.bat
1151
- mode change 100644 => 100755 test/data/command/echoarg2.sh
945
+ lib/bio/db/phyloxml/phyloxml_writer.rb | 1 -
946
+ 1 file changed, 1 deletion(-)
1152
947
 
1153
- commit d2d66f833d0b20647e8d761d2a240b99b206eaa8
948
+ commit b32eae0050a73bd5a2931c17a6694f494ad00bb2
1154
949
  Author: Naohisa Goto <ng@bioruby.org>
1155
- Date: Thu Nov 24 13:32:37 2011 +0900
950
+ Date: Mon Mar 23 18:07:54 2015 +0900
1156
951
 
1157
- Bug fix: rake aborted without git
952
+ suppress warning: mismatched indentations at 'end' with 'def' at 166
1158
953
 
1159
- bioruby.gemspec.erb | 2 +-
954
+ lib/bio/db/phyloxml/phyloxml_writer.rb | 2 +-
1160
955
  1 file changed, 1 insertion(+), 1 deletion(-)
1161
956
 
1162
- commit c2139739988ef731d61bf1a8cdba2dc5c48393bd
957
+ commit bd735347283ce5d332245d0349186f300800a43f
1163
958
  Author: Naohisa Goto <ng@bioruby.org>
1164
- Date: Thu Nov 24 13:07:10 2011 +0900
959
+ Date: Sat Mar 21 12:57:03 2015 +0900
1165
960
 
1166
- regenerate bioruby.gemspec with rake regemspec.
961
+ remove duplicated line and suppress Ruby 2.2 warning
1167
962
 
1168
- bioruby.gemspec | 18 ++++++++++--------
1169
- 1 file changed, 10 insertions(+), 8 deletions(-)
963
+ setup.rb | 1 -
964
+ 1 file changed, 1 deletion(-)
1170
965
 
1171
- commit 6213b45d28bfea2cc8c838813b524d48c369266b
966
+ commit 68ad10e178594691c77ba4b97c2449fecf0ac9de
1172
967
  Author: Naohisa Goto <ng@bioruby.org>
1173
- Date: Thu Nov 24 13:05:07 2011 +0900
968
+ Date: Sat Mar 21 12:50:46 2015 +0900
1174
969
 
1175
- Added workaround for changes of a module name and file names to require.
970
+ Ruby 1.9 support: suppress "shadowing outer local variable" warnings
1176
971
 
1177
- Rakefile | 21 +++++++++++++++++++--
1178
- 1 file changed, 19 insertions(+), 2 deletions(-)
972
+ setup.rb | 10 +++++-----
973
+ 1 file changed, 5 insertions(+), 5 deletions(-)
1179
974
 
1180
- commit 39f847cf8d453476275361078b831da43d400816
975
+ commit 2343482078aec8373f7a2eb8ed4d7c44119f809c
1181
976
  Author: Naohisa Goto <ng@bioruby.org>
1182
- Date: Thu Nov 24 12:08:47 2011 +0900
977
+ Date: Sat Mar 21 12:16:45 2015 +0900
1183
978
 
1184
- Use binary mode to open files.
979
+ Ruby 2.2 support: Config was renamed to RbConfig
1185
980
 
1186
- Rakefile | 6 ++++--
1187
- 1 file changed, 4 insertions(+), 2 deletions(-)
981
+ setup.rb | 2 +-
982
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1188
983
 
1189
- commit 688779e71a27e861fb01e07f816384561b8cfe45
984
+ commit d512712745142d6c6ebe9a6ef51c8c4773bd7c2c
1190
985
  Author: Naohisa Goto <ng@bioruby.org>
1191
- Date: Thu Nov 24 11:49:30 2011 +0900
986
+ Date: Sat Mar 21 11:52:47 2015 +0900
1192
987
 
1193
- Rakefile: new tasks: test-all to run all tests, etc.
1194
-
1195
- * Rakefile: new tasks: test-all to run all tests, and test-network
1196
- to run tests in test/network.
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(-)
1197
992
 
1198
- Rakefile | 10 ++++++++++
1199
- 1 file changed, 10 insertions(+)
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(-)
1200
1001
 
1201
- commit 53719535defcb0fefb3cf8bebe3fad6716bf7de2
1002
+ commit d6fbaa0c555117ebadd46e284ae357586856102d
1202
1003
  Author: Naohisa Goto <ng@bioruby.org>
1203
- Date: Thu Nov 24 11:28:38 2011 +0900
1004
+ Date: Sat Mar 21 11:35:07 2015 +0900
1204
1005
 
1205
- test/runner.rb: Run tests only in test/unit and test/functional.
1006
+ Ruby 1.9 support: suppress warning: shadowing outer local variable - fobj
1206
1007
 
1207
- test/runner.rb | 22 ++++++++++++++++------
1208
- 1 file changed, 16 insertions(+), 6 deletions(-)
1008
+ lib/bio/io/flatfile/buffer.rb | 8 ++++----
1009
+ 1 file changed, 4 insertions(+), 4 deletions(-)
1209
1010
 
1210
- commit fb9ee403db6b447aee73ebb7f12ff5a5b73d6c52
1011
+ commit 0083d3284ec181f4bcc3144f76b12f9d52e3eff6
1211
1012
  Author: Naohisa Goto <ng@bioruby.org>
1212
- Date: Wed Nov 23 20:36:36 2011 +0900
1013
+ Date: Sat Mar 21 11:29:39 2015 +0900
1213
1014
 
1214
- A test class using network connection is moved under test/network/.
1015
+ delete obsolete $Id:$ line
1215
1016
 
1216
- test/functional/bio/test_command.rb | 16 ----------------
1217
- test/network/bio/test_command.rb | 35 +++++++++++++++++++++++++++++++++++
1218
- 2 files changed, 35 insertions(+), 16 deletions(-)
1219
- create mode 100644 test/network/bio/test_command.rb
1017
+ lib/bio/io/fastacmd.rb | 1 -
1018
+ 1 file changed, 1 deletion(-)
1220
1019
 
1221
- commit a6dda2215aa686a9ca4af7484aa190f726d51e69
1020
+ commit d4909c0e80e572a639edba07388e430c7f5d6ce8
1222
1021
  Author: Naohisa Goto <ng@bioruby.org>
1223
- Date: Wed Nov 23 20:28:58 2011 +0900
1022
+ Date: Sat Mar 21 11:29:01 2015 +0900
1224
1023
 
1225
- Tests using network connections are moved to test/network/
1226
-
1227
- * Tests using network connections are moved to test/network/.
1228
- * renamed: test/functional/bio/appl -> test/network/bio/appl
1229
- * renamed: test/functional/bio/io -> test/network/bio/io
1024
+ remove old sample script in "if $0 == __FILE__" block
1230
1025
 
1231
- test/functional/bio/appl/blast/test_remote.rb | 93 ---------
1232
- test/functional/bio/appl/test_blast.rb | 61 ------
1233
- test/functional/bio/appl/test_pts1.rb | 117 -----------
1234
- test/functional/bio/io/test_ddbjrest.rb | 47 -----
1235
- test/functional/bio/io/test_ensembl.rb | 230 ---------------------
1236
- test/functional/bio/io/test_pubmed.rb | 135 -------------
1237
- test/functional/bio/io/test_soapwsdl.rb | 53 -----
1238
- test/functional/bio/io/test_togows.rb | 268 -------------------------
1239
- test/network/bio/appl/blast/test_remote.rb | 93 +++++++++
1240
- test/network/bio/appl/test_blast.rb | 61 ++++++
1241
- test/network/bio/appl/test_pts1.rb | 117 +++++++++++
1242
- test/network/bio/io/test_ddbjrest.rb | 47 +++++
1243
- test/network/bio/io/test_ensembl.rb | 230 +++++++++++++++++++++
1244
- test/network/bio/io/test_pubmed.rb | 135 +++++++++++++
1245
- test/network/bio/io/test_soapwsdl.rb | 53 +++++
1246
- test/network/bio/io/test_togows.rb | 268 +++++++++++++++++++++++++
1247
- 16 files changed, 1004 insertions(+), 1004 deletions(-)
1248
- delete mode 100644 test/functional/bio/appl/blast/test_remote.rb
1249
- delete mode 100644 test/functional/bio/appl/test_blast.rb
1250
- delete mode 100644 test/functional/bio/appl/test_pts1.rb
1251
- delete mode 100644 test/functional/bio/io/test_ddbjrest.rb
1252
- delete mode 100644 test/functional/bio/io/test_ensembl.rb
1253
- delete mode 100644 test/functional/bio/io/test_pubmed.rb
1254
- delete mode 100644 test/functional/bio/io/test_soapwsdl.rb
1255
- delete mode 100644 test/functional/bio/io/test_togows.rb
1256
- create mode 100644 test/network/bio/appl/blast/test_remote.rb
1257
- create mode 100644 test/network/bio/appl/test_blast.rb
1258
- create mode 100644 test/network/bio/appl/test_pts1.rb
1259
- create mode 100644 test/network/bio/io/test_ddbjrest.rb
1260
- create mode 100644 test/network/bio/io/test_ensembl.rb
1261
- create mode 100644 test/network/bio/io/test_pubmed.rb
1262
- create mode 100644 test/network/bio/io/test_soapwsdl.rb
1263
- create mode 100644 test/network/bio/io/test_togows.rb
1026
+ lib/bio/io/fastacmd.rb | 15 ---------------
1027
+ 1 file changed, 15 deletions(-)
1264
1028
 
1265
- commit ec747aa33d06e08a6469dfd330360161d1b0f8e2
1029
+ commit 8171162d0a3991d5f0d9a8bccee57250248d6d3d
1266
1030
  Author: Naohisa Goto <ng@bioruby.org>
1267
- Date: Wed Nov 23 15:03:08 2011 +0900
1031
+ Date: Sat Mar 21 11:15:10 2015 +0900
1268
1032
 
1269
- Test bug fix: use binmode to disable CR/LF conversion (fail on Windows)
1033
+ delete obsolete $Id:$ line
1270
1034
 
1271
- test/unit/bio/appl/blast/test_rpsblast.rb | 1 +
1272
- test/unit/bio/io/flatfile/test_buffer.rb | 1 +
1273
- 2 files changed, 2 insertions(+)
1035
+ lib/bio/db/go.rb | 1 -
1036
+ 1 file changed, 1 deletion(-)
1274
1037
 
1275
- commit 07ce32da009baa2c4e81f6d96f45e3dac49da183
1038
+ commit ed7c9a5335ef59399f3098311f47b8dec519281a
1276
1039
  Author: Naohisa Goto <ng@bioruby.org>
1277
- Date: Wed Nov 23 14:47:33 2011 +0900
1040
+ Date: Sat Mar 21 11:14:19 2015 +0900
1278
1041
 
1279
- Test bug fix: Read Sanger chromatogram files with binary mode
1280
-
1281
- * Test bug fix: Read Sanger chromatogram files with binary mode.
1282
- Fix error/failure on Windows due to default text mode reading.
1042
+ Ruby 1.9 support: suppress warnings: "shadowing outer local variable - goid"
1283
1043
 
1284
- test/unit/bio/db/sanger_chromatogram/test_abif.rb | 3 ++-
1285
- test/unit/bio/db/sanger_chromatogram/test_scf.rb | 6 ++++--
1286
- 2 files changed, 6 insertions(+), 3 deletions(-)
1044
+ lib/bio/db/go.rb | 4 ++--
1045
+ 1 file changed, 2 insertions(+), 2 deletions(-)
1287
1046
 
1288
- commit 20d9068643214e3482d18c36028e50b3c9109755
1047
+ commit dd543068b046c9a0c2a40159c830c92b680244f1
1289
1048
  Author: Naohisa Goto <ng@bioruby.org>
1290
- Date: Wed Nov 23 14:17:25 2011 +0900
1049
+ Date: Sat Mar 21 11:03:08 2015 +0900
1291
1050
 
1292
- Incompatible change: Bio::FlatFile.open and auto use binary mode
1293
-
1294
- * Incompatible change: Bio::FlatFile.open and auto use binary mode
1295
- (binmode) unless text mode option is explicitly given.
1051
+ delete obsolete $Id:$ line
1296
1052
 
1297
- RELEASE_NOTES.rdoc | 7 ++
1298
- lib/bio/io/flatfile/buffer.rb | 84 ++++++++++++++++++
1299
- test/unit/bio/io/flatfile/test_buffer.rb | 139 ++++++++++++++++++++++++++++++
1300
- 3 files changed, 230 insertions(+)
1053
+ lib/bio/db/phyloxml/phyloxml_elements.rb | 1 -
1054
+ 1 file changed, 1 deletion(-)
1301
1055
 
1302
- commit 48bd150a6180d59879872bd85dd95c7ddf1a19c0
1056
+ commit 4c74a6e3aeca30820b0be61e867c9201445542ec
1303
1057
  Author: Naohisa Goto <ng@bioruby.org>
1304
- Date: Tue Nov 22 17:32:23 2011 +0900
1058
+ Date: Sat Mar 21 10:24:40 2015 +0900
1305
1059
 
1306
- Test bug fix: fixed incomplete Windows platform detection.
1060
+ suppress warning: mismatched indentations at 'end' with 'class'
1307
1061
 
1308
- test/unit/bio/test_command.rb | 13 +++++++++----
1309
- 1 file changed, 9 insertions(+), 4 deletions(-)
1062
+ lib/bio/db/phyloxml/phyloxml_elements.rb | 4 ++--
1063
+ 1 file changed, 2 insertions(+), 2 deletions(-)
1310
1064
 
1311
- commit d499bcee7956b1a0a4c04aeb106e50a0839167b0
1065
+ commit ee4ffdc748c1f9f45e97ff7f0da8350c5468c333
1312
1066
  Author: Naohisa Goto <ng@bioruby.org>
1313
- Date: Tue Nov 22 16:15:05 2011 +0900
1067
+ Date: Sat Mar 21 10:08:30 2015 +0900
1314
1068
 
1315
- FuncTestCommandCall is changed to test various command-lines.
1316
-
1317
- * New file test/data/command/echoarg2.sh shell script, which acts
1318
- like echoarg2.bat for Windows.
1319
- * FuncTestCommandCall is changed to test various command-lines.
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"
1320
1079
 
1321
- test/data/command/echoarg2.sh | 4 ++
1322
- test/functional/bio/test_command.rb | 70 +++++++++++++++++++++++++++++------
1323
- 2 files changed, 62 insertions(+), 12 deletions(-)
1324
- create mode 100644 test/data/command/echoarg2.sh
1080
+ lib/bio/db/phyloxml/phyloxml_parser.rb | 2 +-
1081
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1325
1082
 
1326
- commit d45e311c09ad2f4116770dd903f81e652a63ca2a
1083
+ commit db3552c683edf79adbfa5ed897f5ef91e8417585
1327
1084
  Author: Naohisa Goto <ng@bioruby.org>
1328
- Date: Tue Nov 22 14:21:34 2011 +0900
1085
+ Date: Fri Mar 20 16:33:45 2015 +0900
1329
1086
 
1330
- Test bug fix: Opened files should be closed.
1087
+ Bug fix: Bio::PhyloXML::Parser.open_uri did not return block return value
1331
1088
 
1332
- * Test bug fix: Opened files should be closed. When finalizing writer
1333
- tests, temporary files are not properly closed after verify reading,
1334
- and removing the temporary files raise erro on Windows.
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"
1335
1092
 
1336
- test/unit/bio/db/test_phyloxml_writer.rb | 24 +++++++++++++++---------
1337
- 1 file changed, 15 insertions(+), 9 deletions(-)
1093
+ lib/bio/db/phyloxml/phyloxml_parser.rb | 1 +
1094
+ 1 file changed, 1 insertion(+)
1338
1095
 
1339
- commit a9022c61b98746e98a83f1cfd902e0e6b11c7bbb
1096
+ commit 84c2c4e94352cc9cef982d3b505b4f439617e01e
1340
1097
  Author: Naohisa Goto <ng@bioruby.org>
1341
- Date: Tue Nov 22 13:55:15 2011 +0900
1098
+ Date: Fri Mar 20 16:21:49 2015 +0900
1342
1099
 
1343
- New method Bio::PhyloXML::Parser#closed?, and Bio::PhyloXML::Parser.open with block.
1344
-
1345
- * New method Bio::PhyloXML::Parser#closed? to check if it is closed
1346
- or not.
1347
- * Bio::PhyloXML::Parser.open and open_uri now can get a block.
1348
- When a block is given, a Bio::PhyloXML::Parser object is passed
1349
- to the block as an argument. When the block terminates, the object
1350
- is closed.
1351
- * Added tests about the above changes.
1100
+ delete obsolete $Id:$ line
1352
1101
 
1353
- lib/bio/db/phyloxml/phyloxml_parser.rb | 57 +++++++++++++++++++++++++++++---
1354
- test/unit/bio/db/test_phyloxml.rb | 56 +++++++++++++++++++++++++++++--
1355
- 2 files changed, 106 insertions(+), 7 deletions(-)
1102
+ lib/bio/appl/genscan/report.rb | 1 -
1103
+ 1 file changed, 1 deletion(-)
1356
1104
 
1357
- commit 893cbe6ca993eca08427074059c2ba03621ea889
1105
+ commit 05c55d0aaf1dc130ac04155622ccebb3394fc3c0
1358
1106
  Author: Naohisa Goto <ng@bioruby.org>
1359
- Date: Sat Nov 5 00:49:10 2011 +0900
1107
+ Date: Fri Mar 20 16:21:06 2015 +0900
1360
1108
 
1361
- Ruby 1.9 should be fully supported, and optional requirements are revised.
1109
+ Ruby 1.9 support: suppress warning "shadowing outer local variable - i"
1362
1110
 
1363
- README.rdoc | 48 +++++++++++++++++++++++++++++++++---------------
1364
- 1 file changed, 33 insertions(+), 15 deletions(-)
1111
+ lib/bio/appl/genscan/report.rb | 2 +-
1112
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1365
1113
 
1366
- commit 38b1715c2d6bad39560e0846781ca903b1c16eda
1114
+ commit 5edcc1c97ca7c292fa6551509570daf68ac36837
1367
1115
  Author: Naohisa Goto <ng@bioruby.org>
1368
- Date: Fri Nov 4 22:12:38 2011 +0900
1116
+ Date: Fri Mar 20 16:13:57 2015 +0900
1369
1117
 
1370
- Added REFERENCE.
1118
+ Ruby 1.9 support: suppress warning "shadowing outer local variable - y"
1371
1119
 
1372
- README.rdoc | 12 ++++++++++++
1373
- 1 file changed, 12 insertions(+)
1120
+ lib/bio/appl/blast/format0.rb | 2 +-
1121
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1374
1122
 
1375
- commit 9a766cd17236bbe1e28d6972001dd5e3ed596123
1123
+ commit 813d53a06258244a47784697e8fc95f1f15db8da
1376
1124
  Author: Naohisa Goto <ng@bioruby.org>
1377
- Date: Fri Nov 4 21:39:20 2011 +0900
1125
+ Date: Fri Mar 20 16:03:19 2015 +0900
1378
1126
 
1379
- Removed "setup.rb test" and added about running tests.
1127
+ delete obsolete $Id:$ line
1380
1128
 
1381
- README.rdoc | 39 ++++++++++++++++++++++++++++++++++-----
1382
- 1 file changed, 34 insertions(+), 5 deletions(-)
1129
+ lib/bio/io/das.rb | 1 -
1130
+ 1 file changed, 1 deletion(-)
1383
1131
 
1384
- commit 39737179b06366e1d5acf2e5ac930e41b3a4ee38
1385
- Author: Pjotr Prins <pjotr.public01@thebird.nl>
1386
- Date: Fri Oct 14 08:58:01 2011 +0200
1132
+ commit b6ae4a423dd763969c8e18ca6a578fd0600d6159
1133
+ Author: Naohisa Goto <ng@bioruby.org>
1134
+ Date: Fri Mar 20 16:02:20 2015 +0900
1387
1135
 
1388
- Tutorial: added info on biogems
1136
+ Ruby 1.9 support: suppress "warning: shadowing outer local variable - e"
1389
1137
 
1390
- doc/Tutorial.rd | 16 ++++++++++++++++
1391
- doc/Tutorial.rd.html | 23 +++++++++++++++--------
1392
- 2 files changed, 31 insertions(+), 8 deletions(-)
1138
+ lib/bio/io/das.rb | 80 ++++++++++++++++++++++++++---------------------------
1139
+ 1 file changed, 40 insertions(+), 40 deletions(-)
1393
1140
 
1394
- commit e84400c5e9e94d95d6a8d3c4b72388b94d204766
1395
- Author: Pjotr Prins <pjotr.public01@thebird.nl>
1396
- Date: Fri Oct 14 08:49:41 2011 +0200
1141
+ commit 7fa75a644167dd8c189f681e29c1cf5f1bf2fe0b
1142
+ Author: Naohisa Goto <ng@bioruby.org>
1143
+ Date: Fri Mar 20 15:36:00 2015 +0900
1397
1144
 
1398
- Tutorial: small updates
1145
+ delete obsolete $Id:$ line
1399
1146
 
1400
- doc/Tutorial.rd | 8 +++++---
1401
- doc/Tutorial.rd.html | 9 +++++----
1402
- 2 files changed, 10 insertions(+), 7 deletions(-)
1147
+ lib/bio/shell/plugin/seq.rb | 1 -
1148
+ 1 file changed, 1 deletion(-)
1403
1149
 
1404
- commit 9fe07345b3b7be890d5baad9a51f0752af5e0ac4
1150
+ commit 051aba1519d71f1205363c4421feb6c06881ab0c
1405
1151
  Author: Naohisa Goto <ng@bioruby.org>
1406
- Date: Tue Sep 13 23:05:39 2011 +0900
1152
+ Date: Fri Mar 20 15:29:02 2015 +0900
1407
1153
 
1408
- README_DEV.rdoc: added git tips and policies, etc.
1154
+ Bug fix: Ruby 1.9 support: did not yield the last part of the string
1409
1155
 
1410
- * Added Git tips about sending a patch or a pull request.
1411
- * Added Git management policies for the blessed repository.
1412
- * Added some coding styles.
1413
- * Added descriptions about Ruby versions and OS.
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"
1414
1160
 
1415
- README_DEV.rdoc | 95 +++++++++++++++++++++++++++++++++++++++++++++++++++++--
1416
- 1 file changed, 93 insertions(+), 2 deletions(-)
1161
+ lib/bio/shell/plugin/seq.rb | 12 +++++++-----
1162
+ 1 file changed, 7 insertions(+), 5 deletions(-)
1417
1163
 
1418
- commit 3c952c4a782501b21f36ece5bcab672dab12fc6d
1164
+ commit a9f2bff92de58c2ab4cefc67e721d3ad69e9de98
1419
1165
  Author: Naohisa Goto <ng@bioruby.org>
1420
- Date: Tue Sep 13 13:21:20 2011 +0900
1166
+ Date: Fri Mar 20 15:09:16 2015 +0900
1421
1167
 
1422
- README.rdoc: for release notes and changelog, about sample files.
1168
+ Ruby 2.2 support: suppress a "shadowing outer local variable" warning
1423
1169
 
1424
- README.rdoc | 10 +++++++++-
1425
- 1 file changed, 9 insertions(+), 1 deletion(-)
1170
+ lib/bio/alignment.rb | 6 +++---
1171
+ 1 file changed, 3 insertions(+), 3 deletions(-)
1426
1172
 
1427
- commit fba9a6c0f1f79dd567ca54ba085b6258ac8efb31
1173
+ commit d0bcc8766d91eb7cacea2a6d5b32b3e0b3c5ce56
1428
1174
  Author: Naohisa Goto <ng@bioruby.org>
1429
- Date: Tue Sep 13 13:20:05 2011 +0900
1175
+ Date: Fri Mar 20 14:31:04 2015 +0900
1430
1176
 
1431
- RELEASE_NOTES.rdoc: mentioned about removal of rdoc.zsh.
1177
+ delete obsolete $Id:$ line
1432
1178
 
1433
- RELEASE_NOTES.rdoc | 6 +++++-
1434
- 1 file changed, 5 insertions(+), 1 deletion(-)
1179
+ test/unit/bio/test_alignment.rb | 1 -
1180
+ 1 file changed, 1 deletion(-)
1435
1181
 
1436
- commit 685b6bb7b98083e1b50e73baf4e7fa71bc9a39fa
1182
+ commit 0c8fa8fd558088822a98e11b6fa4bec9b37ebec7
1437
1183
  Author: Naohisa Goto <ng@bioruby.org>
1438
- Date: Mon Sep 12 21:23:34 2011 +0900
1184
+ Date: Fri Mar 20 14:26:38 2015 +0900
1439
1185
 
1440
- bioruby.gemspec.erb: LEGAL is added to rdoc files
1186
+ Ruby 2.2 support: comment out duplicated line to suppress warning
1441
1187
 
1442
- * bioruby.gemspec.erb: LEGAL is added to rdoc files.
1443
- * bioruby.gemspec is updated by "rake regemspec".
1188
+ * Ruby 2.2 support: test/unit/bio/test_alignment.rb:
1189
+ Suppress warning: duplicated key at line 182 ignored: "t"
1444
1190
 
1445
- bioruby.gemspec | 9 ++++++---
1446
- bioruby.gemspec.erb | 6 +++++-
1447
- 2 files changed, 11 insertions(+), 4 deletions(-)
1191
+ test/unit/bio/test_alignment.rb | 2 +-
1192
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1448
1193
 
1449
- commit 414a6331f40fc99f554042e9a031689ea6d76da4
1194
+ commit ab17c40e1ce492dc924205e8e2f90d31adae4464
1450
1195
  Author: Naohisa Goto <ng@bioruby.org>
1451
- Date: Mon Sep 12 20:54:06 2011 +0900
1196
+ Date: Fri Mar 20 14:18:08 2015 +0900
1452
1197
 
1453
- deleted rdoc.zsh which is obsolete and unused
1198
+ Ruby 2.2 support: some tests did not run with test-unit gem
1454
1199
 
1455
- * Deleted rdoc.zsh which is obsolete and unused.
1456
- To generate rdoc html, "rake rdoc" or "rake rerdoc".
1457
- See "rake -T" for more information.
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.
1458
1203
 
1459
- rdoc.zsh | 8 --------
1460
- 1 file changed, 8 deletions(-)
1461
- delete mode 100644 rdoc.zsh
1204
+ test/unit/bio/db/test_fastq.rb | 18 ++++++++++++++----
1205
+ 1 file changed, 14 insertions(+), 4 deletions(-)
1462
1206
 
1463
- commit 272d9106cec43b0f219edd92a6f7bd3f9875a761
1207
+ commit ea668d73c18e3df33625cba4352ad5f6966e0eb4
1464
1208
  Author: Naohisa Goto <ng@bioruby.org>
1465
- Date: Mon Sep 12 20:35:47 2011 +0900
1209
+ Date: Fri Mar 20 14:03:43 2015 +0900
1466
1210
 
1467
- Added new ChangeLog, showing changes after 1.4.2 release.
1468
-
1469
- * Added new ChangeLog, showing changes after 1.4.2 release.
1470
- For the changes before 1.4.2, see doc/ChangeLog-before-1.4.2.
1471
- For the changes before 1.3.1, see doc/ChangeLog-before-1.3.1.
1211
+ delete obsolete $Id:$ line
1472
1212
 
1473
- ChangeLog | 64 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
1474
- 1 file changed, 64 insertions(+)
1475
- create mode 100644 ChangeLog
1213
+ test/unit/bio/appl/sim4/test_report.rb | 1 -
1214
+ 1 file changed, 1 deletion(-)
1476
1215
 
1477
- commit 941493378f9884978c81d5f63ee4ed5c175d4bea
1216
+ commit 1abb8d362a0f2443b48923bcccba3d7d0caa1f1d
1478
1217
  Author: Naohisa Goto <ng@bioruby.org>
1479
- Date: Mon Sep 12 20:28:28 2011 +0900
1218
+ Date: Fri Mar 20 13:57:33 2015 +0900
1480
1219
 
1481
- Rakefile: add new task :rechangelog to update ChangeLog using git log.
1220
+ Ruby 2.2 support: some tests did not run with test-unit gem
1482
1221
 
1483
- * Rakefile: add new task :rechangelog to update ChangeLog using
1484
- git log. Note that the tag name (currently 1.4.2) is hardcoded
1485
- in Rakefile.
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.
1486
1225
 
1487
- Rakefile | 9 +++++++++
1488
- 1 file changed, 9 insertions(+)
1226
+ test/unit/bio/appl/sim4/test_report.rb | 62 +++++++++++++++++++++++---------
1227
+ 1 file changed, 46 insertions(+), 16 deletions(-)
1489
1228
 
1490
- commit 1c89e6546223c3c05ea79b8ade4b493580851efa
1229
+ commit b9488a64abb780c5e9b6cd28e8264bad399fa749
1491
1230
  Author: Naohisa Goto <ng@bioruby.org>
1492
- Date: Mon Sep 12 20:24:49 2011 +0900
1231
+ Date: Fri Mar 20 13:13:28 2015 +0900
1493
1232
 
1494
- renamed ChangeLog to doc/ChangeLog-before-1.4.2
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.
1495
1241
 
1496
- ChangeLog | 5013 --------------------------------------------
1497
- doc/ChangeLog-before-1.4.2 | 5013 ++++++++++++++++++++++++++++++++++++++++++++
1498
- 2 files changed, 5013 insertions(+), 5013 deletions(-)
1499
- delete mode 100644 ChangeLog
1500
- create mode 100644 doc/ChangeLog-before-1.4.2
1242
+ test/unit/bio/appl/blast/test_report.rb | 156 ++++++++++++++++++++++---------
1243
+ 1 file changed, 110 insertions(+), 46 deletions(-)
1501
1244
 
1502
- commit 2233fbada55034bd16fb5b9c642292b4b6ccca83
1245
+ commit febe8bbf614e530f597d7306d33df5f5f4ee6699
1503
1246
  Author: Naohisa Goto <ng@bioruby.org>
1504
- Date: Mon Sep 12 20:22:49 2011 +0900
1247
+ Date: Thu Mar 19 00:55:09 2015 +0900
1505
1248
 
1506
- ChangeLog updated: add log about 1.4.2 release
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.
1507
1254
 
1508
- ChangeLog | 9 +++++++++
1509
- 1 file changed, 9 insertions(+)
1255
+ bin/br_biofetch.rb | 19 +++++++++++++++++++
1256
+ 1 file changed, 19 insertions(+)
1510
1257
 
1511
- commit 1c02ab0488e4097a2cf5c16180c3179c78e3d572
1258
+ commit 08450e0a35cbf5596dd30238d23aa7a7296c8f67
1512
1259
  Author: Naohisa Goto <ng@bioruby.org>
1513
- Date: Mon Sep 12 19:40:54 2011 +0900
1260
+ Date: Thu Mar 19 00:36:10 2015 +0900
1514
1261
 
1515
- New RELEASE_NOTES.rdoc for next release version.
1262
+ do not repeat default_url and another_url
1516
1263
 
1517
- RELEASE_NOTES.rdoc | 47 +++++++++++++++++++++++++++++++++++++++++++++++
1518
- 1 file changed, 47 insertions(+)
1519
- create mode 100644 RELEASE_NOTES.rdoc
1264
+ bin/br_biofetch.rb | 14 ++++++++++----
1265
+ 1 file changed, 10 insertions(+), 4 deletions(-)
1520
1266
 
1521
- commit 4e63e69e98c0c440ec476ef3407fcc8fd2411056
1267
+ commit 8e39d3411405b09cc6ea55ba31e5206536ebf59d
1522
1268
  Author: Naohisa Goto <ng@bioruby.org>
1523
- Date: Mon Sep 12 19:32:48 2011 +0900
1269
+ Date: Wed Mar 18 23:57:59 2015 +0900
1524
1270
 
1525
- renamed RELEASE_NOTES.rdoc to doc/RELEASE_NOTES-1.4.2.rdoc
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.
1526
1276
 
1527
- RELEASE_NOTES.rdoc | 132 ------------------------------------------
1528
- doc/RELEASE_NOTES-1.4.2.rdoc | 132 ++++++++++++++++++++++++++++++++++++++++++
1529
- 2 files changed, 132 insertions(+), 132 deletions(-)
1530
- delete mode 100644 RELEASE_NOTES.rdoc
1531
- create mode 100644 doc/RELEASE_NOTES-1.4.2.rdoc
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
1532
1283
 
1533
- commit 9c5c8cafc3ec372ef80aa20d01d13034f94d5af2
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
1534
1291
  Author: Naohisa Goto <ng@bioruby.org>
1535
- Date: Fri Sep 2 12:02:41 2011 +0900
1292
+ Date: Fri Nov 14 15:08:35 2014 +0900
1536
1293
 
1537
- Bio::BIORUBY_EXTRA_VERSION set to ".5000" (unstable version).
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)
1538
1299
 
1539
- lib/bio/version.rb | 2 +-
1300
+ lib/bio/sequence/compat.rb | 2 +-
1540
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
+
2173
+ This commit removes below interpreter warning.
2174
+
2175
+ * warning: assigned but unused variable
2176
+
2177
+ 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
+
2197
+ * warning: assigned but unused variable
2198
+
2199
+ 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
+
2208
+ This commit removes below interpreter warning.
2209
+
2210
+ * warning: assigned but unused variable
2211
+
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.
2222
+
2223
+ * warning: mismatched indentations at ...
2224
+
2225
+ lib/bio/map.rb | 2 +-
2226
+ 1 file changed, 1 insertion(+), 1 deletion(-)
2227
+
2228
+ 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
+
2236
+ * warning: assigned but unused variable
2237
+
2238
+ test/unit/bio/appl/blast/test_report.rb | 2 --
2239
+ 1 file changed, 2 deletions(-)
2240
+
2241
+ 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.
2248
+
2249
+ * warning: assigned but unused variable
2250
+
2251
+ test/unit/bio/appl/bl2seq/test_report.rb | 1 -
2252
+ 1 file changed, 1 deletion(-)
2253
+
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
2261
+ 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
+
2275
+ * warning: assigned but unused variable
2276
+
2277
+ 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
+
2290
+ 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
+
2321
+ 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(-)