bio 1.5.2 → 1.6.0.pre.20181210

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (93) hide show
  1. checksums.yaml +5 -5
  2. data/.travis.yml +12 -11
  3. data/ChangeLog +14 -3106
  4. data/{gemfiles/Gemfile.travis-ruby2.2 → Gemfile} +0 -1
  5. data/KNOWN_ISSUES.rdoc +0 -5
  6. data/README.rdoc +11 -18
  7. data/RELEASE_NOTES.rdoc +34 -291
  8. data/Rakefile +13 -9
  9. data/appveyor.yml +21 -0
  10. data/bioruby.gemspec +7 -78
  11. data/bioruby.gemspec.erb +8 -27
  12. data/doc/ChangeLog-1.5.0 +2919 -0
  13. data/doc/RELEASE_NOTES-1.5.0.rdoc +285 -0
  14. data/doc/Tutorial.rd +6 -108
  15. data/doc/Tutorial.rd.html +19 -98
  16. data/gemfiles/Gemfile.travis-jruby1.8 +3 -5
  17. data/gemfiles/Gemfile.travis-jruby1.9 +0 -3
  18. data/gemfiles/Gemfile.travis-rbx +0 -1
  19. data/gemfiles/Gemfile.travis-ruby1.8 +4 -4
  20. data/gemfiles/Gemfile.travis-ruby1.9 +0 -1
  21. data/gemfiles/prepare-gemspec.rb +4 -0
  22. data/lib/bio.rb +0 -10
  23. data/lib/bio/data/codontable.rb +99 -3
  24. data/lib/bio/io/togows.rb +5 -5
  25. data/lib/bio/version.rb +6 -8
  26. data/sample/test_restriction_enzyme_long.rb +1 -1
  27. data/test/unit/bio/data/test_codontable.rb +3 -0
  28. metadata +11 -77
  29. data/bin/bioruby +0 -47
  30. data/bin/br_biofetch.rb +0 -71
  31. data/bin/br_bioflat.rb +0 -293
  32. data/bin/br_biogetseq.rb +0 -45
  33. data/bin/br_pmfetch.rb +0 -422
  34. data/lib/bio/db/biosql/biosql_to_biosequence.rb +0 -78
  35. data/lib/bio/db/biosql/sequence.rb +0 -444
  36. data/lib/bio/db/phyloxml/phyloxml.xsd +0 -582
  37. data/lib/bio/db/phyloxml/phyloxml_elements.rb +0 -1197
  38. data/lib/bio/db/phyloxml/phyloxml_parser.rb +0 -1001
  39. data/lib/bio/db/phyloxml/phyloxml_writer.rb +0 -227
  40. data/lib/bio/io/biosql/ar-biosql.rb +0 -257
  41. data/lib/bio/io/biosql/biosql.rb +0 -39
  42. data/lib/bio/io/biosql/config/database.yml +0 -21
  43. data/lib/bio/io/sql.rb +0 -79
  44. data/lib/bio/shell.rb +0 -44
  45. data/lib/bio/shell/core.rb +0 -578
  46. data/lib/bio/shell/demo.rb +0 -146
  47. data/lib/bio/shell/interface.rb +0 -217
  48. data/lib/bio/shell/irb.rb +0 -94
  49. data/lib/bio/shell/object.rb +0 -71
  50. data/lib/bio/shell/plugin/blast.rb +0 -42
  51. data/lib/bio/shell/plugin/codon.rb +0 -218
  52. data/lib/bio/shell/plugin/das.rb +0 -58
  53. data/lib/bio/shell/plugin/emboss.rb +0 -23
  54. data/lib/bio/shell/plugin/entry.rb +0 -137
  55. data/lib/bio/shell/plugin/flatfile.rb +0 -101
  56. data/lib/bio/shell/plugin/midi.rb +0 -430
  57. data/lib/bio/shell/plugin/ncbirest.rb +0 -68
  58. data/lib/bio/shell/plugin/obda.rb +0 -45
  59. data/lib/bio/shell/plugin/psort.rb +0 -56
  60. data/lib/bio/shell/plugin/seq.rb +0 -248
  61. data/lib/bio/shell/plugin/togows.rb +0 -40
  62. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +0 -29
  63. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +0 -4
  64. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +0 -27
  65. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +0 -11
  66. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +0 -4
  67. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +0 -7
  68. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
  69. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
  70. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
  71. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +0 -368
  72. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +0 -47
  73. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +0 -144
  74. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +0 -47
  75. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +0 -8
  76. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +0 -10
  77. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +0 -26
  78. data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
  79. data/lib/bio/shell/script.rb +0 -25
  80. data/lib/bio/shell/setup.rb +0 -108
  81. data/lib/bio/shell/web.rb +0 -102
  82. data/sample/test_phyloxml_big.rb +0 -205
  83. data/test/data/phyloxml/apaf.xml +0 -666
  84. data/test/data/phyloxml/bcl_2.xml +0 -2097
  85. data/test/data/phyloxml/made_up.xml +0 -144
  86. data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +0 -65
  87. data/test/data/phyloxml/phyloxml_examples.xml +0 -415
  88. data/test/unit/bio/db/biosql/tc_biosql.rb +0 -114
  89. data/test/unit/bio/db/biosql/ts_suite_biosql.rb +0 -8
  90. data/test/unit/bio/db/test_phyloxml.rb +0 -821
  91. data/test/unit/bio/db/test_phyloxml_writer.rb +0 -334
  92. data/test/unit/bio/shell/plugin/test_seq.rb +0 -187
  93. data/test/unit/bio/test_shell.rb +0 -20
data/test/unit/bio/test_shell.rb DELETED
@@ -1,20 +0,0 @@
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- #
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- # test/unit/bio/test_shell.rb - Unit test for Bio::Shell
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- #
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- # Copyright:: Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
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- # License:: The Ruby License
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- #
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- # $Id:$
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- #
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-
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- # loading helper routine for testing bioruby
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- require 'pathname'
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- load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
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- 'bioruby_test_helper.rb')).cleanpath.to_s
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-
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- # libraries needed for the tests
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- require 'test/unit'
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- require 'bio/shell'
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-
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- module Bio
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- end