BioDSL 1.0.1 → 1.0.2

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 (186) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +1 -0
  3. data/BioDSL.gemspec +1 -1
  4. data/Gemfile +6 -0
  5. data/README.md +289 -155
  6. data/Rakefile +18 -16
  7. data/lib/BioDSL.rb +1 -1
  8. data/lib/BioDSL/cary.rb +78 -53
  9. data/lib/BioDSL/command.rb +2 -2
  10. data/lib/BioDSL/commands.rb +1 -1
  11. data/lib/BioDSL/commands/add_key.rb +1 -1
  12. data/lib/BioDSL/commands/align_seq_mothur.rb +4 -4
  13. data/lib/BioDSL/commands/analyze_residue_distribution.rb +5 -5
  14. data/lib/BioDSL/commands/assemble_pairs.rb +13 -13
  15. data/lib/BioDSL/commands/assemble_seq_idba.rb +7 -9
  16. data/lib/BioDSL/commands/assemble_seq_ray.rb +13 -13
  17. data/lib/BioDSL/commands/assemble_seq_spades.rb +4 -4
  18. data/lib/BioDSL/commands/classify_seq.rb +8 -8
  19. data/lib/BioDSL/commands/classify_seq_mothur.rb +5 -5
  20. data/lib/BioDSL/commands/clip_primer.rb +7 -7
  21. data/lib/BioDSL/commands/cluster_otus.rb +5 -5
  22. data/lib/BioDSL/commands/collapse_otus.rb +2 -2
  23. data/lib/BioDSL/commands/collect_otus.rb +2 -2
  24. data/lib/BioDSL/commands/complement_seq.rb +4 -4
  25. data/lib/BioDSL/commands/count.rb +1 -1
  26. data/lib/BioDSL/commands/count_values.rb +2 -2
  27. data/lib/BioDSL/commands/degap_seq.rb +6 -7
  28. data/lib/BioDSL/commands/dereplicate_seq.rb +1 -1
  29. data/lib/BioDSL/commands/dump.rb +2 -2
  30. data/lib/BioDSL/commands/filter_rrna.rb +4 -4
  31. data/lib/BioDSL/commands/genecall.rb +7 -7
  32. data/lib/BioDSL/commands/grab.rb +1 -1
  33. data/lib/BioDSL/commands/index_taxonomy.rb +3 -3
  34. data/lib/BioDSL/commands/mask_seq.rb +4 -4
  35. data/lib/BioDSL/commands/mean_scores.rb +2 -2
  36. data/lib/BioDSL/commands/merge_pair_seq.rb +3 -3
  37. data/lib/BioDSL/commands/merge_table.rb +1 -1
  38. data/lib/BioDSL/commands/merge_values.rb +1 -1
  39. data/lib/BioDSL/commands/plot_heatmap.rb +4 -5
  40. data/lib/BioDSL/commands/plot_histogram.rb +4 -4
  41. data/lib/BioDSL/commands/plot_matches.rb +5 -5
  42. data/lib/BioDSL/commands/plot_residue_distribution.rb +6 -6
  43. data/lib/BioDSL/commands/plot_scores.rb +7 -7
  44. data/lib/BioDSL/commands/random.rb +1 -1
  45. data/lib/BioDSL/commands/read_fasta.rb +9 -9
  46. data/lib/BioDSL/commands/read_fastq.rb +16 -16
  47. data/lib/BioDSL/commands/read_table.rb +2 -3
  48. data/lib/BioDSL/commands/reverse_seq.rb +4 -4
  49. data/lib/BioDSL/commands/slice_align.rb +4 -4
  50. data/lib/BioDSL/commands/slice_seq.rb +3 -3
  51. data/lib/BioDSL/commands/sort.rb +1 -1
  52. data/lib/BioDSL/commands/split_pair_seq.rb +6 -7
  53. data/lib/BioDSL/commands/split_values.rb +2 -2
  54. data/lib/BioDSL/commands/trim_primer.rb +13 -8
  55. data/lib/BioDSL/commands/trim_seq.rb +5 -5
  56. data/lib/BioDSL/commands/uchime_ref.rb +6 -6
  57. data/lib/BioDSL/commands/uclust.rb +5 -5
  58. data/lib/BioDSL/commands/unique_values.rb +1 -1
  59. data/lib/BioDSL/commands/usearch_global.rb +2 -2
  60. data/lib/BioDSL/commands/usearch_local.rb +2 -2
  61. data/lib/BioDSL/commands/write_fasta.rb +7 -9
  62. data/lib/BioDSL/commands/write_fastq.rb +4 -4
  63. data/lib/BioDSL/commands/write_table.rb +3 -3
  64. data/lib/BioDSL/commands/write_tree.rb +2 -3
  65. data/lib/BioDSL/config.rb +2 -2
  66. data/lib/BioDSL/csv.rb +8 -10
  67. data/lib/BioDSL/debug.rb +1 -1
  68. data/lib/BioDSL/fasta.rb +54 -40
  69. data/lib/BioDSL/fastq.rb +35 -32
  70. data/lib/BioDSL/filesys.rb +56 -47
  71. data/lib/BioDSL/fork.rb +1 -1
  72. data/lib/BioDSL/hamming.rb +1 -1
  73. data/lib/BioDSL/helpers.rb +1 -1
  74. data/lib/BioDSL/helpers/aux_helper.rb +1 -1
  75. data/lib/BioDSL/helpers/email_helper.rb +1 -1
  76. data/lib/BioDSL/helpers/history_helper.rb +1 -1
  77. data/lib/BioDSL/helpers/log_helper.rb +1 -1
  78. data/lib/BioDSL/helpers/options_helper.rb +1 -1
  79. data/lib/BioDSL/helpers/status_helper.rb +1 -1
  80. data/lib/BioDSL/html_report.rb +1 -1
  81. data/lib/BioDSL/math.rb +1 -1
  82. data/lib/BioDSL/mummer.rb +1 -1
  83. data/lib/BioDSL/pipeline.rb +1 -1
  84. data/lib/BioDSL/seq.rb +240 -231
  85. data/lib/BioDSL/seq/ambiguity.rb +1 -1
  86. data/lib/BioDSL/seq/assemble.rb +1 -1
  87. data/lib/BioDSL/seq/backtrack.rb +93 -76
  88. data/lib/BioDSL/seq/digest.rb +1 -1
  89. data/lib/BioDSL/seq/dynamic.rb +43 -55
  90. data/lib/BioDSL/seq/homopolymer.rb +34 -36
  91. data/lib/BioDSL/seq/kmer.rb +67 -50
  92. data/lib/BioDSL/seq/levenshtein.rb +35 -40
  93. data/lib/BioDSL/seq/translate.rb +64 -55
  94. data/lib/BioDSL/seq/trim.rb +60 -50
  95. data/lib/BioDSL/serializer.rb +1 -1
  96. data/lib/BioDSL/stream.rb +1 -1
  97. data/lib/BioDSL/taxonomy.rb +1 -1
  98. data/lib/BioDSL/test.rb +1 -1
  99. data/lib/BioDSL/tmp_dir.rb +1 -1
  100. data/lib/BioDSL/usearch.rb +1 -1
  101. data/lib/BioDSL/verbose.rb +1 -1
  102. data/lib/BioDSL/version.rb +2 -2
  103. data/test/BioDSL/commands/test_add_key.rb +1 -1
  104. data/test/BioDSL/commands/test_align_seq_mothur.rb +1 -1
  105. data/test/BioDSL/commands/test_analyze_residue_distribution.rb +1 -1
  106. data/test/BioDSL/commands/test_assemble_pairs.rb +1 -1
  107. data/test/BioDSL/commands/test_assemble_seq_idba.rb +1 -1
  108. data/test/BioDSL/commands/test_assemble_seq_ray.rb +1 -1
  109. data/test/BioDSL/commands/test_assemble_seq_spades.rb +1 -1
  110. data/test/BioDSL/commands/test_classify_seq.rb +1 -1
  111. data/test/BioDSL/commands/test_classify_seq_mothur.rb +1 -1
  112. data/test/BioDSL/commands/test_clip_primer.rb +1 -1
  113. data/test/BioDSL/commands/test_cluster_otus.rb +1 -1
  114. data/test/BioDSL/commands/test_collapse_otus.rb +1 -1
  115. data/test/BioDSL/commands/test_collect_otus.rb +1 -1
  116. data/test/BioDSL/commands/test_complement_seq.rb +1 -1
  117. data/test/BioDSL/commands/test_count.rb +1 -1
  118. data/test/BioDSL/commands/test_count_values.rb +1 -1
  119. data/test/BioDSL/commands/test_degap_seq.rb +1 -1
  120. data/test/BioDSL/commands/test_dereplicate_seq.rb +1 -1
  121. data/test/BioDSL/commands/test_dump.rb +1 -1
  122. data/test/BioDSL/commands/test_filter_rrna.rb +1 -1
  123. data/test/BioDSL/commands/test_genecall.rb +1 -1
  124. data/test/BioDSL/commands/test_grab.rb +1 -1
  125. data/test/BioDSL/commands/test_index_taxonomy.rb +1 -1
  126. data/test/BioDSL/commands/test_mask_seq.rb +1 -1
  127. data/test/BioDSL/commands/test_mean_scores.rb +1 -1
  128. data/test/BioDSL/commands/test_merge_pair_seq.rb +1 -1
  129. data/test/BioDSL/commands/test_merge_table.rb +1 -1
  130. data/test/BioDSL/commands/test_merge_values.rb +1 -1
  131. data/test/BioDSL/commands/test_plot_heatmap.rb +1 -1
  132. data/test/BioDSL/commands/test_plot_histogram.rb +1 -1
  133. data/test/BioDSL/commands/test_plot_matches.rb +1 -1
  134. data/test/BioDSL/commands/test_plot_residue_distribution.rb +1 -1
  135. data/test/BioDSL/commands/test_plot_scores.rb +1 -1
  136. data/test/BioDSL/commands/test_random.rb +1 -1
  137. data/test/BioDSL/commands/test_read_fasta.rb +1 -1
  138. data/test/BioDSL/commands/test_read_fastq.rb +1 -1
  139. data/test/BioDSL/commands/test_read_table.rb +1 -1
  140. data/test/BioDSL/commands/test_reverse_seq.rb +1 -1
  141. data/test/BioDSL/commands/test_slice_align.rb +1 -1
  142. data/test/BioDSL/commands/test_slice_seq.rb +1 -1
  143. data/test/BioDSL/commands/test_sort.rb +1 -1
  144. data/test/BioDSL/commands/test_split_pair_seq.rb +1 -1
  145. data/test/BioDSL/commands/test_split_values.rb +1 -1
  146. data/test/BioDSL/commands/test_trim_primer.rb +1 -1
  147. data/test/BioDSL/commands/test_trim_seq.rb +1 -1
  148. data/test/BioDSL/commands/test_uchime_ref.rb +1 -1
  149. data/test/BioDSL/commands/test_uclust.rb +1 -1
  150. data/test/BioDSL/commands/test_unique_values.rb +1 -1
  151. data/test/BioDSL/commands/test_usearch_global.rb +1 -1
  152. data/test/BioDSL/commands/test_usearch_local.rb +1 -1
  153. data/test/BioDSL/commands/test_write_fasta.rb +1 -1
  154. data/test/BioDSL/commands/test_write_fastq.rb +1 -1
  155. data/test/BioDSL/commands/test_write_table.rb +1 -1
  156. data/test/BioDSL/commands/test_write_tree.rb +1 -1
  157. data/test/BioDSL/helpers/test_options_helper.rb +3 -3
  158. data/test/BioDSL/seq/test_assemble.rb +58 -56
  159. data/test/BioDSL/seq/test_backtrack.rb +83 -81
  160. data/test/BioDSL/seq/test_digest.rb +47 -45
  161. data/test/BioDSL/seq/test_dynamic.rb +66 -64
  162. data/test/BioDSL/seq/test_homopolymer.rb +35 -33
  163. data/test/BioDSL/seq/test_kmer.rb +29 -28
  164. data/test/BioDSL/seq/test_translate.rb +44 -42
  165. data/test/BioDSL/seq/test_trim.rb +59 -57
  166. data/test/BioDSL/test_cary.rb +1 -1
  167. data/test/BioDSL/test_command.rb +2 -2
  168. data/test/BioDSL/test_csv.rb +34 -31
  169. data/test/BioDSL/test_debug.rb +31 -31
  170. data/test/BioDSL/test_fasta.rb +30 -29
  171. data/test/BioDSL/test_fastq.rb +27 -26
  172. data/test/BioDSL/test_filesys.rb +28 -27
  173. data/test/BioDSL/test_fork.rb +29 -28
  174. data/test/BioDSL/test_math.rb +31 -30
  175. data/test/BioDSL/test_mummer.rb +1 -1
  176. data/test/BioDSL/test_pipeline.rb +1 -1
  177. data/test/BioDSL/test_seq.rb +42 -41
  178. data/test/BioDSL/test_serializer.rb +35 -33
  179. data/test/BioDSL/test_stream.rb +28 -27
  180. data/test/BioDSL/test_taxonomy.rb +38 -37
  181. data/test/BioDSL/test_test.rb +32 -31
  182. data/test/BioDSL/test_tmp_dir.rb +1 -1
  183. data/test/BioDSL/test_usearch.rb +28 -27
  184. data/test/BioDSL/test_verbose.rb +32 -31
  185. data/test/helper.rb +34 -31
  186. metadata +3 -2
data/test/BioDSL/test_tmp_dir.rb CHANGED
@@ -24,7 +24,7 @@ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..')
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  # #
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  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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  # #
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- # This software is part of BioDSL (www.github.com/maasha/BioDSL). #
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+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
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  # #
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  # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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data/test/BioDSL/test_usearch.rb CHANGED
@@ -1,33 +1,34 @@
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  #!/usr/bin/env ruby
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- $:.unshift File.join(File.dirname(__FILE__), '..', '..')
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+ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..')
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- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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- # #
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- # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
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- # #
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- # This program is free software; you can redistribute it and/or #
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- # modify it under the terms of the GNU General Public License #
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- # as published by the Free Software Foundation; either version 2 #
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- # of the License, or (at your option) any later version. #
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- # #
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- # This program is distributed in the hope that it will be useful, #
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- # but WITHOUT ANY WARRANTY; without even the implied warranty of #
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- # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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- # GNU General Public License for more details. #
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- # #
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- # You should have received a copy of the GNU General Public License #
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- # along with this program; if not, write to the Free Software #
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- # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
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- # #
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- # http://www.gnu.org/copyleft/gpl.html #
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- # #
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- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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- # #
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- # This software is part of BioDSL (www.BioDSL.org). #
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- # #
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- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ # #
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+ # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
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+ # #
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+ # This program is free software; you can redistribute it and/or #
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+ # modify it under the terms of the GNU General Public License #
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+ # as published by the Free Software Foundation; either version 2 #
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+ # of the License, or (at your option) any later version. #
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+ # #
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+ # This program is distributed in the hope that it will be useful, #
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+ # but WITHOUT ANY WARRANTY; without even the implied warranty of #
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+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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+ # GNU General Public License for more details. #
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+ # #
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+ # You should have received a copy of the GNU General Public License #
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+ # along with this program; if not, write to the Free Software #
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+ # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, #
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+ # USA. #
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+ # #
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+ # http://www.gnu.org/copyleft/gpl.html #
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+ # #
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+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ # #
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+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
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+ # #
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+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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30
 
30
31
  require 'test/helper'
31
32
 
32
- class TestUsearch < Test::Unit::TestCase
33
+ class TestUsearch < Test::Unit::TestCase
33
34
  end
data/test/BioDSL/test_verbose.rb CHANGED
@@ -1,42 +1,43 @@
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  #!/usr/bin/env ruby
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- $:.unshift File.join(File.dirname(__FILE__), '..', '..')
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+ $LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..')
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- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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- # #
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- # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
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- # #
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- # This program is free software; you can redistribute it and/or #
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- # modify it under the terms of the GNU General Public License #
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- # as published by the Free Software Foundation; either version 2 #
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- # of the License, or (at your option) any later version. #
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- # #
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- # This program is distributed in the hope that it will be useful, #
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- # but WITHOUT ANY WARRANTY; without even the implied warranty of #
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- # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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- # GNU General Public License for more details. #
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- # #
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- # You should have received a copy of the GNU General Public License #
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- # along with this program; if not, write to the Free Software #
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- # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
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- # #
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- # http://www.gnu.org/copyleft/gpl.html #
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- # #
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- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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- # #
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- # This software is part of BioDSL (www.BioDSL.org). #
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- # #
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- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ # #
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+ # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
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+ # #
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+ # This program is free software; you can redistribute it and/or #
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+ # modify it under the terms of the GNU General Public License #
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+ # as published by the Free Software Foundation; either version 2 #
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+ # of the License, or (at your option) any later version. #
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+ # #
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+ # This program is distributed in the hope that it will be useful, #
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+ # but WITHOUT ANY WARRANTY; without even the implied warranty of #
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+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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+ # GNU General Public License for more details. #
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+ # #
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+ # You should have received a copy of the GNU General Public License #
19
+ # along with this program; if not, write to the Free Software #
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+ # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, #
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+ # USA. #
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+ # #
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+ # http://www.gnu.org/copyleft/gpl.html #
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+ # #
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+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ # #
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+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
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+ # #
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+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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30
 
30
31
  require 'test/helper'
31
32
 
33
+ # Test class for Verbose.
32
34
  class VerboseTest < Test::Unit::TestCase
33
35
  def teardown
34
- BioDSL::verbose = false
36
+ BioDSL.verbose = false
35
37
  end
36
38
 
37
- test "BioDSL::verbose returns correctly" do
38
- BioDSL::verbose = true
39
- assert_equal(true, BioDSL::verbose)
39
+ test 'BioDSL::verbose returns correctly' do
40
+ BioDSL.verbose = true
41
+ assert_equal(true, BioDSL.verbose)
40
42
  end
41
43
  end
42
-
data/test/helper.rb CHANGED
@@ -1,34 +1,36 @@
1
- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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- # #
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- # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
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- # #
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- # This program is free software; you can redistribute it and/or #
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- # modify it under the terms of the GNU General Public License #
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- # as published by the Free Software Foundation; either version 2 #
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- # of the License, or (at your option) any later version. #
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- # #
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- # This program is distributed in the hope that it will be useful, #
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- # but WITHOUT ANY WARRANTY; without even the implied warranty of #
12
- # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
13
- # GNU General Public License for more details. #
14
- # #
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- # You should have received a copy of the GNU General Public License #
16
- # along with this program; if not, write to the Free Software #
17
- # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
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- # #
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- # http://www.gnu.org/copyleft/gpl.html #
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- # #
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- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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- # #
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- # This software is part of the BioDSL framework (www.BioDSL.org). #
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- # #
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- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ # #
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+ # Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk). #
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+ # #
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+ # This program is free software; you can redistribute it and/or #
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+ # modify it under the terms of the GNU General Public License #
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+ # as published by the Free Software Foundation; either version 2 #
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+ # of the License, or (at your option) any later version. #
9
+ # #
10
+ # This program is distributed in the hope that it will be useful, #
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+ # but WITHOUT ANY WARRANTY; without even the implied warranty of #
12
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
13
+ # GNU General Public License for more details. #
14
+ # #
15
+ # You should have received a copy of the GNU General Public License #
16
+ # along with this program; if not, write to the Free Software #
17
+ # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, #
18
+ # USA. #
19
+ # #
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+ # http://www.gnu.org/copyleft/gpl.html #
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+ # #
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+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
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+ # #
24
+ # This software is part of BioDSL (http://maasha.github.io/BioDSL). #
25
+ # #
26
+ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
26
27
 
27
28
  require 'simplecov'
29
+ require 'English'
28
30
 
29
31
  if ENV['SIMPLECOV']
30
32
  SimpleCov.start do
31
- add_filter "/test/"
33
+ add_filter '/test/'
32
34
  end
33
35
 
34
36
  SimpleCov.command_name 'test:units'
@@ -41,8 +43,9 @@ require 'BioDSL'
41
43
  require 'test/unit'
42
44
  require 'mocha/test_unit'
43
45
 
44
- ENV['BD_TEST'] = "true"
46
+ ENV['BD_TEST'] = 'true'
45
47
 
48
+ # Kernel namespace
46
49
  module Kernel
47
50
  def capture_stdout
48
51
  out = StringIO.new
@@ -63,20 +66,20 @@ module Kernel
63
66
  end
64
67
  end
65
68
 
69
+ # Patching TestCase
66
70
  class Test::Unit::TestCase
67
71
  # Ruby 2.2 have omit, < 2.2 have skip
68
- alias :omit :skip if ! self.instance_methods.include? :omit
72
+ alias_method :omit, :skip unless instance_methods.include? :omit
69
73
 
70
74
  def self.test(desc, &impl)
71
75
  define_method("test #{desc}", &impl)
72
76
  end
73
77
 
74
78
  def collect_result
75
- @input2.each_with_object('') { |e, a| a << "#{e}#{$/}" }
79
+ @input2.each_with_object('') { |e, a| a << "#{e}#{$RS}" }
76
80
  end
77
81
 
78
82
  def collect_sorted_result
79
- @input2.sort_by { |a| a.to_s }.
80
- each_with_object('') { |e, a| a << "#{e}#{$/}" }
83
+ @input2.sort_by(&:to_s).each_with_object('') { |e, a| a << "#{e}#{$RS}" }
81
84
  end
82
85
  end
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: BioDSL
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.0.1
4
+ version: 1.0.2
5
5
  platform: ruby
6
6
  authors:
7
7
  - Martin A. Hansen
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2015-11-11 00:00:00.000000000 Z
11
+ date: 2015-11-18 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: haml
@@ -200,6 +200,7 @@ extra_rdoc_files: []
200
200
  files:
201
201
  - ".gitignore"
202
202
  - BioDSL.gemspec
203
+ - Gemfile
203
204
  - LICENSE
204
205
  - README.md
205
206
  - Rakefile