bio 1.6.0.pre.20181210 → 2.0.3

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Files changed (48) hide show
  1. checksums.yaml +4 -4
  2. data/.travis.yml +32 -34
  3. data/ChangeLog +1462 -8
  4. data/Gemfile +0 -2
  5. data/KNOWN_ISSUES.rdoc +4 -10
  6. data/LEGAL +0 -10
  7. data/README.rdoc +31 -80
  8. data/README_DEV.rdoc +5 -5
  9. data/RELEASE_NOTES.rdoc +171 -18
  10. data/Rakefile +0 -34
  11. data/appveyor.yml +15 -7
  12. data/bioruby.gemspec +13 -4
  13. data/bioruby.gemspec.erb +0 -1
  14. data/gemfiles/Gemfile.travis-rbx +0 -2
  15. data/gemfiles/Gemfile.travis-ruby1.8 +0 -2
  16. data/gemfiles/Gemfile.travis-ruby1.9 +0 -2
  17. data/gemfiles/Gemfile.windows +6 -0
  18. data/lib/bio/appl/blast/report.rb +40 -8
  19. data/lib/bio/appl/iprscan/report.rb +3 -3
  20. data/lib/bio/appl/sosui/report.rb +1 -1
  21. data/lib/bio/db/embl/uniprotkb.rb +1 -1
  22. data/lib/bio/db/gff.rb +3 -1
  23. data/lib/bio/db/go.rb +2 -2
  24. data/lib/bio/db/kegg/common.rb +14 -0
  25. data/lib/bio/db/kegg/genes.rb +26 -0
  26. data/lib/bio/db/kegg/pathway.rb +5 -11
  27. data/lib/bio/sequence/common.rb +112 -0
  28. data/lib/bio/sequence/format.rb +1 -0
  29. data/lib/bio/tree.rb +1 -1
  30. data/lib/bio/version.rb +3 -3
  31. data/sample/color_scheme_aa.rb +82 -0
  32. data/sample/color_scheme_na.rb +5 -6
  33. data/sample/fastq2html.cwl +23 -0
  34. data/sample/fastq2html.rb +94 -0
  35. data/sample/fastq2html.testdata.yaml +5 -0
  36. data/sample/na2aa.cwl +23 -0
  37. data/sample/na2aa.rb +11 -25
  38. data/sample/na2aa.testdata.yaml +7 -0
  39. data/sample/rev_comp.cwl +23 -0
  40. data/sample/rev_comp.rb +20 -0
  41. data/sample/rev_comp.testdata.yaml +7 -0
  42. data/test/network/bio/db/kegg/test_genes_hsa7422.rb +91 -0
  43. data/test/unit/bio/appl/blast/test_report.rb +4 -4
  44. data/test/unit/bio/db/test_gff.rb +5 -0
  45. data/test/unit/bio/sequence/test_ruby3.rb +462 -0
  46. metadata +17 -8
  47. data/lib/bio/appl/blast/xmlparser.rb +0 -236
  48. data/setup.rb +0 -1600
data/ChangeLog CHANGED
@@ -1,14 +1,1468 @@
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+ commit c16e230d15cf30478a3739563b4e4745dc57ef82
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Nov 5 23:44:45 2021 +0900
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+
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+ regenerate bioruby.gemspec with rake regemspec
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+
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+ bioruby.gemspec | 3 ++-
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+ 1 file changed, 2 insertions(+), 1 deletion(-)
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+
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+ commit 1a8c44dc5b8d24342550273a594e5f75e41f41df
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Nov 5 23:41:29 2021 +0900
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+
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+ prepare for BioRuby 2.0.3 release
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+
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+ lib/bio/version.rb | 2 +-
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+ 1 file changed, 1 insertion(+), 1 deletion(-)
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+
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+ commit 863242cdb9a748ba9efb3be3b39f92c17ed3ea84
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Nov 5 23:36:27 2021 +0900
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+
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+ update release notes for upcoming BioRuby 2.0.3
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+
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+ RELEASE_NOTES.rdoc | 26 ++++++++++++++++++++++++++
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+ 1 file changed, 26 insertions(+)
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+
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+ commit b97794d632c73dc45639cec000fb11238740eb30
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Nov 5 23:26:20 2021 +0900
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+
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+ Ruby 3.0 compatibility fix: Bio::Sequence::*#partition, #rpartiton
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+
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+ * Behaviors of Bio::Sequence::*#partition and #rpartition in Ruby 3.0
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+ are changed to mimic those in Ruby 2.x.
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+
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+ lib/bio/sequence/common.rb | 17 +++++++
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+ test/unit/bio/sequence/test_ruby3.rb | 94 ++++++++++++++++++++++++++++++++++++
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+ 2 files changed, 111 insertions(+)
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+
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+ commit 7ff79cd449ee03e0063120fb9abec50d9b08e979
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Nov 5 22:24:16 2021 +0900
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+
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+ remove resolved Ruby 3.0 issue
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+
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+ KNOWN_ISSUES.rdoc | 8 --------
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+ 1 file changed, 8 deletions(-)
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+
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+ commit 24bb3c3cf417837ad63a27913db7237aef1414c6
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Nov 5 21:24:26 2021 +0900
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+
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+ Bio::Sequence::NA,AA,Generic: workaround for Ruby 3.0.0 incompatible change
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+
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+ * Since Ruby 3.0.0, over 30 methods in subclass of String class are
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+ changed to return/yield String instance instead of the subclass
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+ instance. (https://github.com/ruby/ruby/blob/v3_0_0/NEWS.md )
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+
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+ * In this commit, workaround is made for the following methods:
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+ * *
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+ * capitalize
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+ * center
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+ * chomp
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+ * chop
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+ * delete
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+ * delete_prefix
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+ * delete_suffix
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+ * downcase
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+ * each_char
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+ * each_grapheme_cluster
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+ * each_line
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+ * gsub
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+ * gsub!
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+ * ljust
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+ * lstrip
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+ * revserse
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+ * rjust
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+ * rstrip
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+ * slice!
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+ * slice / []
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+ * split
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+ * squeeze
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+ * strip
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+ * sub
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+ * sub!
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+ * succ / next
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+ * swapcase
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+ * tr
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+ * tr_s
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+ * upcase
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+ * Note: sub! and gsub! are not described in the NEWS.md
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+ but are also affected by this Ruby 3.0.0 incompatible changes.
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+
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+ * The following methods are not patched i.e. they return/yield
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+ String instances.
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+ * dump
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+ * partition
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+ * rpartition
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+ * scrub
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+ * Note: In Ruby 2.7 or earlier, Bio::Sequence::NA#partition
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+ and #rpartition methods return an array that may contain
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+ mixture of Bio::Sequence::NA instances and String instances.
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+
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+ * test/unit/bio/sequence/test_ruby3.rb: unit tests for the
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+ above methods.
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+
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+ * Close https://github.com/bioruby/bioruby/issues/137
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+
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+ lib/bio/sequence/common.rb | 95 +++++++++
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+ test/unit/bio/sequence/test_ruby3.rb | 368 +++++++++++++++++++++++++++++++++++
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+ 2 files changed, 463 insertions(+)
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+ create mode 100644 test/unit/bio/sequence/test_ruby3.rb
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+
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+ commit 0efc0a54685d43645daa9c53d7140bfb81577777
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+ Author: kojix2 <2xijok@gmail.com>
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+ Date: Tue Aug 31 19:39:25 2021 +0900
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+
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+ Fix typos: Retrun -> Return
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+
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+ lib/bio/appl/iprscan/report.rb | 6 +++---
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+ lib/bio/appl/sosui/report.rb | 2 +-
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+ lib/bio/db/embl/uniprotkb.rb | 2 +-
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+ lib/bio/db/go.rb | 4 ++--
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+ lib/bio/tree.rb | 2 +-
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+ 5 files changed, 8 insertions(+), 8 deletions(-)
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+
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+ commit a291b5a72da12a5cc8b006d1dd63d002fda5dff3
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Dec 31 23:52:54 2020 +0900
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+
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+ BioRuby 2.0.2 is released
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+
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+ ChangeLog | 98 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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+ 1 file changed, 98 insertions(+)
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+
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+ commit fd420b713ca364e677ef3551919ec907791df86d
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Dec 31 23:51:08 2020 +0900
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+
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+ RELEASE_NOTES.rdoc: change some description
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+
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+ RELEASE_NOTES.rdoc | 2 +-
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+ 1 file changed, 1 insertion(+), 1 deletion(-)
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+
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+ commit 0ed9b37f38fa1b00dcc1d422914e4cbdbbc5f6ab
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Dec 31 23:46:46 2020 +0900
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+
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+ regenerate bioruby.gemspec with rake regemspec
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+
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+ bioruby.gemspec | 2 +-
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+ 1 file changed, 1 insertion(+), 1 deletion(-)
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+
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+ commit fa84b8fac653c26b9f8db429321ef49202554a69
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Dec 31 23:45:38 2020 +0900
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+
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+ prepare for BioRuby 2.0.2 release
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+
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+ lib/bio/version.rb | 2 +-
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+ 1 file changed, 1 insertion(+), 1 deletion(-)
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+
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+ commit 32c5efccbad4e0d3440726383f863520ee242cc5
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Dec 31 23:39:18 2020 +0900
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+
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+ update release notes for upcoming BioRuby 2.0.2
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+
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+ RELEASE_NOTES.rdoc | 19 +++++++++++++++++++
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+ 1 file changed, 19 insertions(+)
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+
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+ commit c2f6e62ab64bc532f442bccc0d76ced5380664ec
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Dec 31 23:38:43 2020 +0900
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+
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+ add a known issue about Ruby 3.0
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+
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+ KNOWN_ISSUES.rdoc | 10 +++++++++-
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+ 1 file changed, 9 insertions(+), 1 deletion(-)
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+
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+ commit a733c0816da7c97ca0c23016b473b004fb755f54
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Dec 31 23:04:55 2020 +0900
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+
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+ remove deprecation warning of Gem::Specification#has_rdoc=
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+
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+ Gem::Specification#has_rdoc= have been deprecated since RubyGems 1.3.3
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+ in 2009. (https://blog.rubygems.org/2009/05/04/1.3.3-released.html )
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+ RDoc is always generated regardless of the value, and the line is
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+ safely removed.
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+
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+ This fixes https://github.com/bioruby/bioruby/issues/138 .
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+ Thanks to @jaysonvirissimo for reporting the issue.
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+
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+ bioruby.gemspec | 1 -
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+ bioruby.gemspec.erb | 1 -
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+ 2 files changed, 2 deletions(-)
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+
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+ commit bed6746ce62059795996eeb6e5ac65655bab12b5
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Dec 31 22:51:56 2020 +0900
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+
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+ require ruby's date library to avoid NameError for Date
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+
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+ In Bio::Sequence#output(:embl), NameError (uninitialized constant
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+ Bio::Sequence::Format::INSDFeatureHelper::Date) is observed.
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+ The error message is misleading because Date is provided by Ruby's
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+ standard date library.
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+
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+ This fixes https://github.com/bioruby/bioruby/issues/135 .
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+ Thanks to Dr. Mark Wilkinson for reporting the issue.
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+
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+ lib/bio/sequence/format.rb | 1 +
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+ 1 file changed, 1 insertion(+)
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+
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+ commit 5f3aa79fdaf6dd5551d51663ca2e9b6f5e56d855
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Nov 6 17:45:12 2020 +0900
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+
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+ fix mistaken URLs
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+
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+ README.rdoc | 6 +++---
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+ 1 file changed, 3 insertions(+), 3 deletions(-)
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+
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+ commit d5e1670ee4863cc60d3aa08432a7ee3b1e445439
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Sep 6 15:48:45 2019 +0900
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+
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+ BioRuby 2.0.1 is released
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+
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+ ChangeLog | 185 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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+ 1 file changed, 185 insertions(+)
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+
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+ commit 21bf51a1ec8c18c9cdf8528ffc3c59c503cef042
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Sep 6 15:45:47 2019 +0900
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+
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+ RELEASE_NOTES.rdoc: describe notable changes since 2.0.0
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+
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+ RELEASE_NOTES.rdoc | 40 ++++++++++++++++++++++++++++++++++++++++
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+ 1 file changed, 40 insertions(+)
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+
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+ commit 9092a629e0e28b416ee7288d349fb9d73dd2b961
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Sep 6 15:06:11 2019 +0900
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+
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+ regenerate bioruby.gemspec with rake regemspec
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+
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+ bioruby.gemspec | 11 ++++++++++-
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+ 1 file changed, 10 insertions(+), 1 deletion(-)
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+
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+ commit 59e24b6e55d2c9a8887e8e01a91999d33a008042
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Sep 6 15:04:33 2019 +0900
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+
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+ prepare for BioRuby 2.0.1 release
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+
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+ lib/bio/version.rb | 2 +-
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+ 1 file changed, 1 insertion(+), 1 deletion(-)
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+
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+ commit 9635a38a158db434fd2b6aff7a2ee75622ddecef
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Sep 6 14:51:23 2019 +0900
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+
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+ sample/fastq2html.rb: A html visualization of FASTQ sequences
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+
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+ * sample/fastq2html: A html visualization of FASTQ sequences.
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+ Each sequence is colored with the quality score.
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+ * sample/fastq2html.cwl: CWL workflow for the above sample script
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+ * sample/fastq2html.testdata.yaml: Test data for the above workflow
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+
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+ sample/fastq2html.cwl | 23 ++++++++++
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+ sample/fastq2html.rb | 94 +++++++++++++++++++++++++++++++++++++++++
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+ sample/fastq2html.testdata.yaml | 5 +++
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+ 3 files changed, 122 insertions(+)
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+ create mode 100644 sample/fastq2html.cwl
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+ create mode 100644 sample/fastq2html.rb
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+ create mode 100644 sample/fastq2html.testdata.yaml
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+
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+ commit 6bbcf8b66310c225d686f2c59359680a0bc0b4b6
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Sep 6 14:42:19 2019 +0900
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+
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+ sample/rev_comp.rb: Generates reverse-complement sequences
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+
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+ * sample/rev_comp.rb: Generates reverse-complement sequences of
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+ the given nucleotide sequences.
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+ * sample/rev_comp.cwl: CWL cowkflow for the sample script
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+ * sample/rev_comp.testdata.yaml: Test data for the above CWL workflow
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+
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+ sample/rev_comp.cwl | 23 +++++++++++++++++++++++
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+ sample/rev_comp.rb | 20 ++++++++++++++++++++
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+ sample/rev_comp.testdata.yaml | 7 +++++++
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+ 3 files changed, 50 insertions(+)
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+ create mode 100644 sample/rev_comp.cwl
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+ create mode 100644 sample/rev_comp.rb
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+ create mode 100644 sample/rev_comp.testdata.yaml
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+
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+ commit ff0e6c3c6b6f1b56d81b5a4b579a6d0984bfc607
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Sep 6 14:40:45 2019 +0900
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+
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+ sample/color_scheme_(na|aa).rb: use String#each_char instead of each_byte
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+
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+ sample/color_scheme_aa.rb | 6 +++---
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+ sample/color_scheme_na.rb | 6 +++---
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+ 2 files changed, 6 insertions(+), 6 deletions(-)
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+
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+ commit 6f7c1be09aa3d6cdb76fd029fc0f84efda31c907
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Sep 5 17:32:07 2019 +0900
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+
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+ sample/color_scheme_aa.rb: new sample based on color_scheme_na.rb
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+
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+ sample/color_scheme_aa.rb | 82 +++++++++++++++++++++++++++++++++++++++++++++++
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+ 1 file changed, 82 insertions(+)
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+ create mode 100644 sample/color_scheme_aa.rb
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+
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+ commit 51864c3857178f58133b759f7608b8d6d8991c44
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Sep 5 17:13:20 2019 +0900
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+
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+ sample/color_scheme_na.rb: use const_get instead of eval
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+
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+ sample/color_scheme_na.rb | 2 +-
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+ 1 file changed, 1 insertion(+), 1 deletion(-)
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+
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+ commit ba0b554971a9a387a54fc04c5002853d91357347
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Sep 5 17:02:20 2019 +0900
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+
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+ sample/na2aa.cwl: inputBinding position -1 for the script
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+
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+ * sample/na2aa.cwl: inputBinding position -1 is used for the script
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+ to emphasize that the argument is the first one.
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+
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+ sample/na2aa.cwl | 2 +-
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+ 1 file changed, 1 insertion(+), 1 deletion(-)
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+
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+ commit 26a27ec261e2251f3ff3a85007147d33682778d0
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Sep 5 16:56:08 2019 +0900
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+
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+ sample/color_scheme_na.rb: Supports more file formats
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+
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+ * sample/color_scheme_na.rb: Supports more file formats other than
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+ fasta format, by using Bio::Flatfile.
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+
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+ sample/color_scheme_na.rb | 3 +--
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+ 1 file changed, 1 insertion(+), 2 deletions(-)
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+
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+ commit 5c053a606382bb578a2b6884ee639805154433e5
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Sep 5 12:32:00 2019 +0900
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+
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+ sample/na2aa.cwl: use inputBinding
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+
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+ sample/na2aa.cwl | 5 ++++-
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+ 1 file changed, 4 insertions(+), 1 deletion(-)
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+
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+ commit 6a3c3e02f08549d47dda00dca92d55bbadfc468f
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Wed Sep 4 22:59:21 2019 +0900
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+
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+ Sample CWL workflow to run sample/na2aa.rb
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+
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+ * na2aa.cwl: A sample CWL workflow to run na2aa.rb in sample/ dir
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+ * na2aa.testdata.yaml: Test data for the workflow
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+
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+ sample/na2aa.cwl | 20 ++++++++++++++++++++
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+ sample/na2aa.testdata.yaml | 7 +++++++
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+ 2 files changed, 27 insertions(+)
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+ create mode 100644 sample/na2aa.cwl
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+ create mode 100644 sample/na2aa.testdata.yaml
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+
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+ commit 960b885036f549863e3cfe9c693c90f9bef27d3d
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Wed Sep 4 21:00:50 2019 +0900
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+
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+ LEGAL: na2aa.rb is now Ruby's License
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+
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+ LEGAL | 1 -
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+ 1 file changed, 1 deletion(-)
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+
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+ commit 7af9e81988939007eb36dab6b102a7422e8196d8
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Wed Sep 4 14:34:05 2019 +0900
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+
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+ sample/na2aa.rb: Completely rewritten
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+
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+ * sample/na2aa.rb: Completely rewritten. License is changed because
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+ old code is completely wiped out. Note that the old code always
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+ raises error due to a bug in the code.
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+ * The old code was trying to replace 'X' (any) to '-' (gap) but
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+ the new code does not modify translated sequences anymore.
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+
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+ sample/na2aa.rb | 36 +++++++++++-------------------------
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+ 1 file changed, 11 insertions(+), 25 deletions(-)
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+
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+ commit cf8cac5e32db42b6683c1a837adc9e1c04994062
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Mon Sep 2 17:11:08 2019 +0900
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+
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+ Bug fix: Bio::GFF::GFF2::Record.parse did not return correct object
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+
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+ lib/bio/db/gff.rb | 4 +++-
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+ test/unit/bio/db/test_gff.rb | 5 +++++
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+ 2 files changed, 8 insertions(+), 1 deletion(-)
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+
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+ commit 80b387e7e2bb8570d9204e389b6c5d90c6ea31de
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Jun 14 14:33:19 2019 +0900
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+
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+ BioRuby 2.0.0 is released
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+
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+ ChangeLog | 1051 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
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+ 1 file changed, 1043 insertions(+), 8 deletions(-)
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+
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+ commit 2e4046517fd8ee1c105ef53131e69f787d790099
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Jun 14 14:23:19 2019 +0900
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+
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+ Add "Recommended Plugins" section and description is moved to it
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+
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+ README.rdoc | 22 +++++++++++++++-------
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+ 1 file changed, 15 insertions(+), 7 deletions(-)
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+
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+ commit 7a533e4f57edcebb5dfe15fdddc9fbc986d2b7ec
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Jun 14 14:17:08 2019 +0900
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+
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+ fix directory name
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+
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+ README.rdoc | 2 +-
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+ 1 file changed, 1 insertion(+), 1 deletion(-)
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+
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+ commit 805266c9c900903156efd0baa8c1e6ee524a8147
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Jun 14 14:14:52 2019 +0900
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+
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+ add description about recommended plugins
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+
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+ README.rdoc | 11 +++++++++++
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+ 1 file changed, 11 insertions(+)
446
+
447
+ commit 02b7d8b9bc5dcd56f501a15e5e820f450153aa1c
448
+ Author: Naohisa Goto <ng@bioruby.org>
449
+ Date: Fri Jun 14 13:33:30 2019 +0900
450
+
451
+ prepare to release BioRuby 2.0.0
452
+
453
+ lib/bio/version.rb | 4 ++--
454
+ 1 file changed, 2 insertions(+), 2 deletions(-)
455
+
456
+ commit f1fed8dacb425d19c12abec5d4faeb733827f80f
457
+ Author: Naohisa Goto <ng@bioruby.org>
458
+ Date: Fri Jun 14 13:31:08 2019 +0900
459
+
460
+ regenerate bioruby.gemspec with rake regemspec
461
+
462
+ bioruby.gemspec | 6 +++---
463
+ 1 file changed, 3 insertions(+), 3 deletions(-)
464
+
465
+ commit 3952ec9d5ce1e3ceea9734f667d36595808c4989
466
+ Author: Naohisa Goto <ng@bioruby.org>
467
+ Date: Fri Jun 14 13:28:19 2019 +0900
468
+
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+ Remove xmlparser dependency from Gemfile and gemfiles/Gemfile.*
470
+
471
+ Gemfile | 2 --
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+ gemfiles/Gemfile.travis-rbx | 2 --
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+ gemfiles/Gemfile.travis-ruby1.8 | 2 --
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+ gemfiles/Gemfile.travis-ruby1.9 | 2 --
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+ gemfiles/Gemfile.windows | 2 --
476
+ 5 files changed, 10 deletions(-)
477
+
478
+ commit d4a8ee7ae3d3b13a8be4c57c1f8db5b29f2c4a13
479
+ Author: Naohisa Goto <ng@bioruby.org>
480
+ Date: Fri Jun 14 12:34:45 2019 +0900
481
+
482
+ RELEASE_NOTES.rdoc: update aboue new features and improvements
483
+
484
+ RELEASE_NOTES.rdoc | 15 +++++++++++++--
485
+ 1 file changed, 13 insertions(+), 2 deletions(-)
486
+
487
+ commit 2d4170a2a0262f5d75cef5a54b5d6f3da298f145
488
+ Author: Naohisa Goto <ng@bioruby.org>
489
+ Date: Fri Jun 14 12:24:12 2019 +0900
490
+
491
+ Tests added in the previous commit is moved and modified
492
+
493
+ * test/network/bio/db/kegg/test_genes_hsa7422.rb: tests added in the
494
+ previous commit is moved to the file and modified to get data
495
+ from the internet for avoiding KEGG data license issue.
496
+ Note that some of the tests might be fail in the near future due to
497
+ the database entry updates.
498
+
499
+ test/network/bio/db/kegg/test_genes_hsa7422.rb | 91 ++++++++++++++++++++++++++
500
+ test/unit/bio/db/kegg/test_genes.rb | 51 ---------------
501
+ 2 files changed, 91 insertions(+), 51 deletions(-)
502
+ create mode 100644 test/network/bio/db/kegg/test_genes_hsa7422.rb
503
+
504
+ commit 67f8105acf22e88a7624305743ad13802ffed124
505
+ Author: kojix2 <2xijok@gmail.com>
506
+ Date: Mon Oct 22 00:46:31 2018 +0900
507
+
508
+ add DiseasesAsHash to KEGG/Common
509
+
510
+ lib/bio/db/kegg/common.rb | 14 ++++++++++
511
+ lib/bio/db/kegg/genes.rb | 26 +++++++++++++++++++
512
+ lib/bio/db/kegg/pathway.rb | 16 ++++--------
513
+ test/unit/bio/db/kegg/test_genes.rb | 51 +++++++++++++++++++++++++++++++++++++
514
+ 4 files changed, 96 insertions(+), 11 deletions(-)
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+
516
+ commit 9dbb655e1c3ec7460b77f1d0ea475531ac3a9361
517
+ Author: Naohisa Goto <ng@bioruby.org>
518
+ Date: Fri Jun 14 11:37:11 2019 +0900
519
+
520
+ update documents for upcoming new release
521
+
522
+ KNOWN_ISSUES.rdoc | 14 +++-----
523
+ LEGAL | 9 ------
524
+ README.rdoc | 92 +++++++----------------------------------------------
525
+ README_DEV.rdoc | 10 +++---
526
+ RELEASE_NOTES.rdoc | 93 +++++++++++++++++++++++++++++++++++++++++++-----------
527
+ 5 files changed, 96 insertions(+), 122 deletions(-)
528
+
529
+ commit 6f388019a035a41a8867c6a03ef7e2707d1edce4
530
+ Author: Naohisa Goto <ng@bioruby.org>
531
+ Date: Fri Jun 14 11:32:40 2019 +0900
532
+
533
+ .travis.yml: move 1.8.7 and 1.9.3 to allow_failures; update ruby versions
534
+
535
+ .travis.yml | 23 ++++++++++++-----------
536
+ 1 file changed, 12 insertions(+), 11 deletions(-)
537
+
538
+ commit f2cbe9db9b78df653d774a7676e00f6f1a212b23
539
+ Author: Naohisa Goto <ng@bioruby.org>
540
+ Date: Fri Jun 14 11:18:27 2019 +0900
541
+
542
+ .travis.yml: Remove jobs using "tar-integration-test"
543
+
544
+ .travis.yml | 9 ---------
545
+ 1 file changed, 9 deletions(-)
546
+
547
+ commit 68f28e81e3fa566843b548f1899549adcad5225a
548
+ Author: Naohisa Goto <ng@bioruby.org>
549
+ Date: Fri Jun 14 11:10:18 2019 +0900
550
+
551
+ remove "rake tar-install" and "rake tar-integration-test" tasks
552
+
553
+ * Rakefile: Remove "tar-install" and "tar-integration-test" tasks
554
+ because they use setup.rb that is removed from the repository.
555
+
556
+ Rakefile | 34 ----------------------------------
557
+ 1 file changed, 34 deletions(-)
558
+
559
+ commit 0cbdb4586f2231a68579105dbc7f0fb413b38a96
560
+ Author: Naohisa Goto <ng@bioruby.org>
561
+ Date: Fri Jun 14 10:48:15 2019 +0900
562
+
563
+ next bioruby version will be 2.0.0
564
+
565
+ lib/bio/version.rb | 2 +-
566
+ 1 file changed, 1 insertion(+), 1 deletion(-)
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+
568
+ commit 300d10b9791b7f0c0eff1d0544cae63fecc3b31a
569
+ Author: Naohisa Goto <ng@bioruby.org>
570
+ Date: Fri Jun 14 10:41:12 2019 +0900
571
+
572
+ Remove setup.rb. Use RubyGems to install BioRuby.
573
+
574
+ setup.rb | 1600 --------------------------------------------------------------
575
+ 1 file changed, 1600 deletions(-)
576
+ delete mode 100644 setup.rb
577
+
578
+ commit a74683d9acfc16d0d715b020839839afc8b43350
579
+ Author: Naohisa Goto <ng@bioruby.org>
580
+ Date: Fri Jun 14 02:28:31 2019 +0900
581
+
582
+ try to require "bio-blast-xmlparser" provided by separete gem
583
+
584
+ lib/bio/appl/blast/report.rb | 8 ++++++++
585
+ 1 file changed, 8 insertions(+)
586
+
587
+ commit de1c1e33aed392d4e2265a028b8acb50501f56bd
588
+ Author: Naohisa Goto <ng@bioruby.org>
589
+ Date: Sat Sep 16 04:49:21 2017 +0900
590
+
591
+ check existance of a private method instead of XMLParser constant
592
+
593
+ test/unit/bio/appl/blast/test_report.rb | 8 ++++----
594
+ 1 file changed, 4 insertions(+), 4 deletions(-)
595
+
596
+ commit 3f54d19c44411e845b32c522fc0deca4288dcf07
597
+ Author: Naohisa Goto <ng@bioruby.org>
598
+ Date: Sat Sep 16 04:39:19 2017 +0900
599
+
600
+ xml_set_parameter is moved from xmlparser.rb etc.
601
+
602
+ * The method xml_set_parameter is moved from
603
+ lib/bio/appl/blast/xmlparser.rb because it is used by
604
+ the REXML parser.
605
+ * The method Bio::Blast::Report.xmlparser is move to
606
+ lib/bio/appl/blast/xmlparser.rb in the separate repo.
607
+ * Use "defined? xmlparser_parse" for checking existance of
608
+ the blast xmlparser component.
609
+ * Removed line to require bio/appl/blast/xmlparser.
610
+
611
+ lib/bio/appl/blast/report.rb | 40 ++++++++++++++++++++++++++++++++--------
612
+ 1 file changed, 32 insertions(+), 8 deletions(-)
613
+
614
+ commit b19cd507c432739c5aaac700e222e6e4ecc63ddc
615
+ Author: Naohisa Goto <ng@bioruby.org>
616
+ Date: Sat Sep 16 03:32:54 2017 +0900
617
+
618
+ lib/bio/appl/blast/xmlparser.rb is removed and moved to separate gem
619
+
620
+ * lib/bio/appl/blast/xmlparser.rb is removed and moved to separate gem
621
+ to eliminate dependency to xmlparser that includes native extension.
622
+
623
+ lib/bio/appl/blast/xmlparser.rb | 236 ----------------------------------------
624
+ 1 file changed, 236 deletions(-)
625
+ delete mode 100644 lib/bio/appl/blast/xmlparser.rb
626
+
627
+ commit 525d3450ad3440bfbbe3a1540fe60d83c3845ec7
628
+ Author: Naohisa Goto <ng@bioruby.org>
629
+ Date: Sat Dec 15 11:33:08 2018 +0900
630
+
631
+ .travis.yml: remove jruby-18mode and jruby-19mode; add jruby and truffleruby
632
+
633
+ .travis.yml | 24 ++++++++++++------------
634
+ 1 file changed, 12 insertions(+), 12 deletions(-)
635
+
636
+ commit 5bc0042b7fc39c62222534e0e4129d3f9794fd8c
637
+ Author: Naohisa Goto <ng@bioruby.org>
638
+ Date: Fri Dec 14 22:46:08 2018 +0900
639
+
640
+ appveyor.yml: regenerate bioruby.gemspec before creating gem
641
+
642
+ appveyor.yml | 1 +
643
+ 1 file changed, 1 insertion(+)
644
+
645
+ commit 5582dc1db60ffc812211d9803d5adce9c0dd70d3
646
+ Author: Naohisa Goto <ng@bioruby.org>
647
+ Date: Fri Dec 14 22:39:35 2018 +0900
648
+
649
+ appveyor.yml: modify gemfile/Gemfile.windows after bundle install
650
+
651
+ appveyor.yml | 1 +
652
+ 1 file changed, 1 insertion(+)
653
+
654
+ commit 09031bcae0a42fe93d07b46eb489ffbabc8c1319
655
+ Author: Naohisa Goto <ng@bioruby.org>
656
+ Date: Fri Dec 14 22:30:09 2018 +0900
657
+
658
+ appveyor.yml: give up using vendor/bundle; set BUNDLE_GEMFILE
659
+
660
+ appveyor.yml | 6 ++----
661
+ 1 file changed, 2 insertions(+), 4 deletions(-)
662
+
663
+ commit 44fb6c67aef1b0311d32ac806fc9a62f09d401d5
664
+ Author: Naohisa Goto <ng@bioruby.org>
665
+ Date: Fri Dec 14 21:59:44 2018 +0900
666
+
667
+ appveyor.yml: Specify gemfiles/Gemfile.windows
668
+
669
+ * appveyor.yml: Specify gemfiles/Gemfile.windows in which xmlparser gem
670
+ is excluded because of build failure of the xmlparser gem on Windows.
671
+ * gemfiles/Gemfile.windows: Gemfile for Appveyor, running on Microsoft
672
+ Windows.
673
+
674
+ appveyor.yml | 2 +-
675
+ gemfiles/Gemfile.windows | 8 ++++++++
676
+ 2 files changed, 9 insertions(+), 1 deletion(-)
677
+ create mode 100644 gemfiles/Gemfile.windows
678
+
679
+ commit fe55e52b42660dda1d21749bf714e989e7db754e
680
+ Author: Naohisa Goto <ng@bioruby.org>
681
+ Date: Fri Dec 14 21:48:06 2018 +0900
682
+
683
+ appveyor.yml: update ruby versions and test procedure
684
+
685
+ appveyor.yml | 22 +++++++++++++++-------
686
+ 1 file changed, 15 insertions(+), 7 deletions(-)
687
+
688
+ commit 739f5c9a512074a7de25d87e8104ed15bdb28b5d
689
+ Author: Naohisa Goto <ng@bioruby.org>
690
+ Date: Fri Dec 14 11:57:43 2018 +0900
691
+
692
+ .travis.yml: change default Gemfile
693
+
694
+ * Change default Gemfile to Gemfile
695
+ * Move old Ruby versions to "include" matrix.
696
+ * Change ruby version for gem-integration-test and tar-integration-test
697
+
698
+ .travis.yml | 22 ++++++++++++----------
699
+ 1 file changed, 12 insertions(+), 10 deletions(-)
700
+
701
+ commit 2f54a9cbf8fb6d8580d488b20007d5ce4562e5e9
702
+ Author: Naohisa Goto <ng@bioruby.org>
703
+ Date: Fri Dec 14 11:42:58 2018 +0900
704
+
705
+ .travis.yml: No more limit to master branch. Instead, add blocklist.
706
+
707
+ .travis.yml | 7 ++++---
708
+ 1 file changed, 4 insertions(+), 3 deletions(-)
709
+
710
+ commit 9ac3e44318c67fd4415a2118dd5631902e784e12
711
+ Author: Kozo Nishida <knishida@riken.jp>
712
+ Date: Thu Dec 13 22:47:54 2018 +0900
713
+
714
+ ci(travis): Add rvm versions
715
+
716
+ .travis.yml | 5 ++++-
717
+ 1 file changed, 4 insertions(+), 1 deletion(-)
718
+
719
+ commit 258dd67c9d65f1247e56d5c5228cc6f9c019d133
720
+ Author: Naohisa Goto <ng@bioruby.org>
721
+ Date: Mon Dec 10 21:56:16 2018 +0900
722
+
723
+ regenerate bioruby.gemspec with rake regemspec
724
+
725
+ bioruby.gemspec | 2 +-
726
+ 1 file changed, 1 insertion(+), 1 deletion(-)
727
+
728
+ commit 3920483d6b5a3759e6c610d7ee9fb1a63dcc9ce4
729
+ Author: Naohisa Goto <ng@bioruby.org>
730
+ Date: Mon Dec 10 21:55:19 2018 +0900
731
+
732
+ Simplify version number processing
733
+
734
+ bioruby.gemspec.erb | 14 +++++++-------
735
+ lib/bio/version.rb | 12 +++++-------
736
+ 2 files changed, 12 insertions(+), 14 deletions(-)
737
+
738
+ commit 80949a10ea5e4f88d21d893905b720925f5a9e7b
739
+ Author: Naohisa Goto <ng@bioruby.org>
740
+ Date: Mon Dec 10 18:54:00 2018 +0900
741
+
742
+ next bioruby version will be 1.6.0
743
+
744
+ lib/bio/version.rb | 2 +-
745
+ 1 file changed, 1 insertion(+), 1 deletion(-)
746
+
747
+ commit 2b542865a4d4af2684ace41f79e273ebceb51807
748
+ Merge: 02a96424 d71e07a0
749
+ Author: Toshiaki Katayama <k@bioruby.org>
750
+ Date: Fri Oct 19 06:45:49 2018 +0900
751
+
752
+ Merge pull request #125 from kojix2/master
753
+
754
+ update TogoWS documentation. genbank -> ncbi-nucleotide
755
+
756
+ commit d71e07a0cb1cc441241be91273bd44e3717b8773
757
+ Author: kojix2 <2xijok@gmail.com>
758
+ Date: Thu Oct 18 19:10:29 2018 +0900
759
+
760
+ update TogoWS documentation. genbank -> ncbi-nucleotide
761
+
762
+ lib/bio/io/togows.rb | 10 +++++-----
763
+ sample/test_restriction_enzyme_long.rb | 2 +-
764
+ 2 files changed, 6 insertions(+), 6 deletions(-)
765
+
766
+ commit 02a964241b79e2307d0a00473427ea6bc2ea6932
767
+ Author: Naohisa Goto <ng@bioruby.org>
768
+ Date: Thu Sep 20 07:06:08 2018 +0900
769
+
770
+ Improvement documentation
771
+
772
+ * Improve documentation.
773
+ * Close https://github.com/bioruby/bioruby/pull/120 .
774
+
775
+ lib/bio/db/aaindex.rb | 79 +++++++++++++++++++++++++++++++++++++++++++++++----
776
+ 1 file changed, 74 insertions(+), 5 deletions(-)
777
+
778
+ commit 6bfef40ae87099565371abf94cf2cc8bfac76b12
779
+ Author: Naohisa Goto <ng@bioruby.org>
780
+ Date: Thu Sep 20 05:01:12 2018 +0900
781
+
782
+ Bug fix: Bio::Command.new_https should support proxy
783
+
784
+ lib/bio/command.rb | 18 +++++++-----------
785
+ 1 file changed, 7 insertions(+), 11 deletions(-)
786
+
787
+ commit 4e3251d2172f58239f103e7edf8f4c351140f378
788
+ Author: Naohisa Goto <ng@bioruby.org>
789
+ Date: Thu Sep 20 04:58:56 2018 +0900
790
+
791
+ https support for Bio::Blast::Remote::GenomeNet::Information
792
+
793
+ lib/bio/appl/blast/genomenet.rb | 6 +++---
794
+ 1 file changed, 3 insertions(+), 3 deletions(-)
795
+
796
+ commit 6dd1f9fb8c2b4ba95086eab7bffc01583feccf3a
797
+ Author: ramadis <rramiro.o@hotmail.com>
798
+ Date: Sat Jul 7 15:12:33 2018 -0300
799
+
800
+ Add https requests in command. Fix genomenet query by allowing https requests.
801
+
802
+ lib/bio/appl/blast/genomenet.rb | 2 +-
803
+ lib/bio/command.rb | 14 ++++++++++++++
804
+ 2 files changed, 15 insertions(+), 1 deletion(-)
805
+
806
+ commit 4b6f87c9fd2dc62418ddfc4b57bcc4b73287a603
807
+ Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>
808
+ Date: Sat Mar 31 13:08:07 2018 +0900
809
+
810
+ directly refer to the given hash
811
+
812
+ lib/bio/data/codontable.rb | 2 +-
813
+ 1 file changed, 1 insertion(+), 1 deletion(-)
814
+
815
+ commit 25636ffa08c6ea9a9e4d1b451a456bc1f482ad40
816
+ Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>
817
+ Date: Sat Jun 2 15:10:12 2018 +0900
818
+
819
+ precalculated ambiguity codontable
820
+
821
+ lib/bio/data/codontable.rb | 55 +++++++++++++++++++++++++++++++++++++++++++---
822
+ 1 file changed, 52 insertions(+), 3 deletions(-)
823
+
824
+ commit b2d924045202ec3aa4e1b79341fd939a881d4c2e
825
+ Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>
826
+ Date: Sat Mar 31 11:55:57 2018 +0900
827
+
828
+ construct ambiguity nucleotide to amino acid table
829
+
830
+ lib/bio/data/codontable.rb | 49 ++++++++++++++++++++++++++++++++++-
831
+ test/unit/bio/data/test_codontable.rb | 3 +++
832
+ 2 files changed, 51 insertions(+), 1 deletion(-)
833
+
834
+ commit a7378b6b269ea1c0391e259dd8e4868f03b064ea
835
+ Author: markwilkinson <markw@illuminae.com>
836
+ Date: Tue Dec 12 14:13:51 2017 +0100
837
+
838
+ fixing Fasta Report parser for fasta36 -m10
839
+
840
+ lib/bio/appl/fasta/format10.rb | 3 ++-
841
+ 1 file changed, 2 insertions(+), 1 deletion(-)
842
+
843
+ commit c89c40c29c3c92f8e548c79d2d04698123559007
844
+ Author: Naohisa Goto <ng@bioruby.org>
845
+ Date: Fri Sep 15 16:33:19 2017 +0900
846
+
847
+ Remove settings about executables
848
+
849
+ * Definitions and settings about executables are removed because
850
+ all files in bin/ have been moved to separate gem packages
851
+ (bio-shell and bio-executables).
852
+
853
+ bioruby.gemspec | 13 -------------
854
+ bioruby.gemspec.erb | 21 +--------------------
855
+ 2 files changed, 1 insertion(+), 33 deletions(-)
856
+
857
+ commit b5a8d385da8f2c1b6e1caf77295e590f55595944
858
+ Author: Naohisa Goto <ng@bioruby.org>
859
+ Date: Fri Sep 15 16:20:03 2017 +0900
860
+
861
+ bin/br_*.rb is moved to bio-executables gem
862
+
863
+ * The following executable files are moved to "bio-executables" gem.
864
+ * bin/br_biofetch.rb
865
+ * bin/br_bioflat.rb
866
+ * bin/br_biogetseq.rb
867
+ * bin/br_pmfetch.rb
868
+
869
+ bin/br_biofetch.rb | 71 ---------
870
+ bin/br_bioflat.rb | 293 ------------------------------------
871
+ bin/br_biogetseq.rb | 45 ------
872
+ bin/br_pmfetch.rb | 422 ----------------------------------------------------
873
+ 4 files changed, 831 deletions(-)
874
+ delete mode 100755 bin/br_biofetch.rb
875
+ delete mode 100755 bin/br_bioflat.rb
876
+ delete mode 100755 bin/br_biogetseq.rb
877
+ delete mode 100755 bin/br_pmfetch.rb
878
+
879
+ commit eb61d89a366437570a0590a629cb75718866b236
880
+ Author: Naohisa Goto <ng@bioruby.org>
881
+ Date: Fri Sep 15 09:31:14 2017 +0900
882
+
883
+ regenerate bioruby.gemspec with rake regemspec
884
+
885
+ bioruby.gemspec | 44 +-------------------------------------------
886
+ 1 file changed, 1 insertion(+), 43 deletions(-)
887
+
888
+ commit 6d40721d039fdb6b77af656f32ccabeabc427409
889
+ Author: Naohisa Goto <ng@bioruby.org>
890
+ Date: Fri Sep 15 09:29:33 2017 +0900
891
+
892
+ Remove BioRuby Shell files that are released as independent gem package
893
+
894
+ bin/bioruby | 47 --
895
+ lib/bio/shell.rb | 44 --
896
+ lib/bio/shell/core.rb | 578 ---------------------
897
+ lib/bio/shell/demo.rb | 146 ------
898
+ lib/bio/shell/interface.rb | 217 --------
899
+ lib/bio/shell/irb.rb | 94 ----
900
+ lib/bio/shell/object.rb | 71 ---
901
+ lib/bio/shell/plugin/blast.rb | 42 --
902
+ lib/bio/shell/plugin/codon.rb | 218 --------
903
+ lib/bio/shell/plugin/das.rb | 58 ---
904
+ lib/bio/shell/plugin/emboss.rb | 23 -
905
+ lib/bio/shell/plugin/entry.rb | 137 -----
906
+ lib/bio/shell/plugin/flatfile.rb | 101 ----
907
+ lib/bio/shell/plugin/midi.rb | 430 ---------------
908
+ lib/bio/shell/plugin/ncbirest.rb | 68 ---
909
+ lib/bio/shell/plugin/obda.rb | 45 --
910
+ lib/bio/shell/plugin/psort.rb | 56 --
911
+ lib/bio/shell/plugin/seq.rb | 248 ---------
912
+ lib/bio/shell/plugin/togows.rb | 40 --
913
+ .../generators/bioruby/bioruby_generator.rb | 29 --
914
+ .../generators/bioruby/templates/_classes.rhtml | 4 -
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+ .../generators/bioruby/templates/_log.rhtml | 27 -
916
+ .../generators/bioruby/templates/_methods.rhtml | 11 -
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+ .../generators/bioruby/templates/_modules.rhtml | 4 -
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+ .../generators/bioruby/templates/_variables.rhtml | 7 -
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+ .../generators/bioruby/templates/bioruby-bg.gif | Bin 1431 -> 0 bytes
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+ .../generators/bioruby/templates/bioruby-gem.png | Bin 6951 -> 0 bytes
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+ .../generators/bioruby/templates/bioruby-link.gif | Bin 2758 -> 0 bytes
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+ .../generators/bioruby/templates/bioruby.css | 368 -------------
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+ .../generators/bioruby/templates/bioruby.rhtml | 47 --
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+ .../bioruby/templates/bioruby_controller.rb | 144 -----
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+ .../generators/bioruby/templates/bioruby_helper.rb | 47 --
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+ .../generators/bioruby/templates/commands.rhtml | 8 -
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+ .../generators/bioruby/templates/history.rhtml | 10 -
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+ .../generators/bioruby/templates/index.rhtml | 26 -
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+ .../generators/bioruby/templates/spinner.gif | Bin 1542 -> 0 bytes
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+ lib/bio/shell/script.rb | 25 -
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+ lib/bio/shell/setup.rb | 108 ----
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+ lib/bio/shell/web.rb | 102 ----
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+ test/unit/bio/shell/plugin/test_seq.rb | 187 -------
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+ test/unit/bio/test_shell.rb | 20 -
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+ 41 files changed, 3837 deletions(-)
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+ delete mode 100755 bin/bioruby
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+ delete mode 100644 lib/bio/shell.rb
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+ delete mode 100644 lib/bio/shell/core.rb
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+ delete mode 100644 lib/bio/shell/demo.rb
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+ delete mode 100644 lib/bio/shell/interface.rb
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+ delete mode 100644 lib/bio/shell/irb.rb
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+ delete mode 100644 lib/bio/shell/object.rb
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+ delete mode 100644 lib/bio/shell/plugin/blast.rb
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+ delete mode 100644 lib/bio/shell/plugin/codon.rb
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+ delete mode 100644 lib/bio/shell/plugin/das.rb
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+ delete mode 100644 lib/bio/shell/plugin/emboss.rb
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+ delete mode 100644 lib/bio/shell/plugin/entry.rb
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+ delete mode 100644 lib/bio/shell/plugin/flatfile.rb
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+ delete mode 100644 lib/bio/shell/plugin/midi.rb
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+ delete mode 100644 lib/bio/shell/plugin/ncbirest.rb
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+ delete mode 100644 lib/bio/shell/plugin/obda.rb
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+ delete mode 100644 lib/bio/shell/plugin/psort.rb
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+ delete mode 100644 lib/bio/shell/plugin/seq.rb
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+ delete mode 100644 lib/bio/shell/plugin/togows.rb
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml
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+ delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif
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+ delete mode 100644 lib/bio/shell/script.rb
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+ delete mode 100644 lib/bio/shell/setup.rb
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+ delete mode 100644 lib/bio/shell/web.rb
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+ delete mode 100644 test/unit/bio/shell/plugin/test_seq.rb
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+ delete mode 100644 test/unit/bio/test_shell.rb
977
+
978
+ commit ab9feb6f1f495a2b3ca350005c6162c51178aecb
979
+ Author: Naohisa Goto <ng@bioruby.org>
980
+ Date: Wed Sep 13 22:13:59 2017 +0900
981
+
982
+ Suppress warning "assigned but unused variable"
983
+
984
+ lib/bio/io/flatfile/autodetection.rb | 5 +++++
985
+ 1 file changed, 5 insertions(+)
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+
987
+ commit cf486e327c253482f54e59b2e18f73db27641135
988
+ Author: Naohisa Goto <ng@bioruby.org>
989
+ Date: Wed Sep 13 22:10:53 2017 +0900
990
+
991
+ Suppress warning: "instance variable @top_strand not initialized"
992
+
993
+ * Suppress warning: "instance variable @top_strand not initialized".
994
+ To do so, force to raise NoMethodError when @top_strand is not
995
+ initialized or is nil. This should be changed to appropriate
996
+ exception in the future.
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+
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+ lib/bio/util/sirna.rb | 2 ++
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+ 1 file changed, 2 insertions(+)
1000
+
1001
+ commit 88477698f0e1b5a74f9682f26e97c5f90f6912b4
1002
+ Author: Naohisa Goto <ng@bioruby.org>
1003
+ Date: Wed Sep 13 21:31:38 2017 +0900
1004
+
1005
+ Suppress warning in Ruby 2.4: "constant ::Fixnum is deprecated"
1006
+
1007
+ lib/bio/db/soft.rb | 4 ++--
1008
+ .../util/restriction_enzyme/range/sequence_range/calculated_cuts.rb | 2 +-
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+ test/unit/bio/test_alignment.rb | 4 ++--
1010
+ 3 files changed, 5 insertions(+), 5 deletions(-)
1011
+
1012
+ commit f8cff14179cfeea0d685f4df756db71ceb6d5fab
1013
+ Author: Naohisa Goto <ng@bioruby.org>
1014
+ Date: Wed Sep 13 21:19:12 2017 +0900
1015
+
1016
+ Suppress warning "parentheses after method name is interpreted as an argument list, not a decomposed argument" in Ruby 2.4
1017
+
1018
+ lib/bio/map.rb | 8 ++++----
1019
+ 1 file changed, 4 insertions(+), 4 deletions(-)
1020
+
1021
+ commit ddb25c2bf3872c6306a91e407d95caa2e136cee9
1022
+ Author: Jun Aruga <jaruga@redhat.com>
1023
+ Date: Fri Nov 18 11:14:38 2016 +0100
1024
+
1025
+ Gemfile for local development.
1026
+
1027
+ .travis.yml | 8 ++++----
1028
+ gemfiles/Gemfile.travis-ruby2.2 => Gemfile | 0
1029
+ bioruby.gemspec | 2 +-
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+ 3 files changed, 5 insertions(+), 5 deletions(-)
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+ rename gemfiles/Gemfile.travis-ruby2.2 => Gemfile (100%)
1032
+
1033
+ commit 16faf6473b74eb172716b713ab757cb2ab2bcacc
1034
+ Author: Jun Aruga <jaruga@redhat.com>
1035
+ Date: Thu Nov 17 17:50:40 2016 +0100
1036
+
1037
+ Fixes ruby1.8 Travis failure that is because rdoc 4.3.0 requires Ruby >= 1.9.3.
1038
+
1039
+ gemfiles/Gemfile.travis-jruby1.8 | 3 ++-
1040
+ gemfiles/Gemfile.travis-ruby1.8 | 3 ++-
1041
+ 2 files changed, 4 insertions(+), 2 deletions(-)
1042
+
1043
+ commit 146fd66b3a14972bcfd0e9bf8ec007d38c55ac39
1044
+ Author: Naohisa Goto <ng@bioruby.org>
1045
+ Date: Sat Aug 13 08:22:22 2016 +0900
1046
+
1047
+ Update URLs and use https for NCBI REST web services
1048
+
1049
+ lib/bio/io/ncbirest.rb | 50 ++++++++++++++++++++++++++------------------------
1050
+ 1 file changed, 26 insertions(+), 24 deletions(-)
1051
+
1052
+ commit 7abd46f058a17ac34b263714449756383622012d
1053
+ Author: Naohisa Goto <ng@bioruby.org>
1054
+ Date: Sat Aug 13 08:12:08 2016 +0900
1055
+
1056
+ New method Bio::Command#start_http_uri(uri) with tests
1057
+
1058
+ * lib/bio/command.rb: New method Bio::Command#start_http_uri(uri)
1059
+ that supports HTTPS. Note that this method is intended to be
1060
+ called only from BioRuby internals.
1061
+ * lib/bio/command.rb: Bio::Command#post and #post_form are changed
1062
+ to use the start_http_uri().
1063
+ * test/network/bio/test_command.rb: tests for start_http_uri().
1064
+
1065
+ lib/bio/command.rb | 42 ++++++++++++++++++++++++++++++++++++++--
1066
+ test/network/bio/test_command.rb | 17 ++++++++++++++++
1067
+ 2 files changed, 57 insertions(+), 2 deletions(-)
1068
+
1069
+ commit 11c680f6d64a60bdc0f4248951bf2d2ebafbc433
1070
+ Author: Naohisa Goto <ng@bioruby.org>
1071
+ Date: Fri Jun 17 20:40:41 2016 +0900
1072
+
1073
+ gemfiles/Gemfile.*: remove dependency on libxml-ruby
1074
+
1075
+ * gemfiles/Gemfile.*: remove dependency on libxml-ruby.
1076
+ Bio::PhyloXML required libxml-ruby but was already removed.
1077
+
1078
+ gemfiles/Gemfile.travis-jruby1.8 | 3 ---
1079
+ gemfiles/Gemfile.travis-jruby1.9 | 3 ---
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+ gemfiles/Gemfile.travis-rbx | 1 -
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+ gemfiles/Gemfile.travis-ruby1.8 | 1 -
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+ gemfiles/Gemfile.travis-ruby1.9 | 1 -
1083
+ gemfiles/Gemfile.travis-ruby2.2 | 1 -
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+ 6 files changed, 10 deletions(-)
1085
+
1086
+ commit 09fa57f987445e8654de6a0d0cf7c45f7625600c
1087
+ Author: Naohisa Goto <ng@bioruby.org>
1088
+ Date: Fri Jun 17 16:16:40 2016 +0900
1089
+
1090
+ regenerate bioruby.gemspec with rake regemspec
1091
+
1092
+ bioruby.gemspec | 10 +---------
1093
+ 1 file changed, 1 insertion(+), 9 deletions(-)
1094
+
1095
+ commit 87812d119820bf66767c7767cfec7554d7a00f3b
1096
+ Author: Naohisa Goto <ng@bioruby.org>
1097
+ Date: Fri Jun 17 15:45:46 2016 +0900
1098
+
1099
+ README.rdoc: about bioruby-phyloxml and bio-biosql
1100
+
1101
+ README.rdoc | 10 ++++++++++
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+ 1 file changed, 10 insertions(+)
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+
1104
+ commit 2294f255f5f05f9f629a1e88c0e1f59bb74b32bc
1105
+ Author: Naohisa Goto <ng@bioruby.org>
1106
+ Date: Fri Jun 17 15:42:46 2016 +0900
1107
+
1108
+ KNOWN_ISSUES.rdoc: remove descriptions about Bio::SQL
1109
+
1110
+ KNOWN_ISSUES.rdoc | 5 -----
1111
+ 1 file changed, 5 deletions(-)
1112
+
1113
+ commit 35a6f761dc5fa493b8311747dde7f2a54d8aee75
1114
+ Author: Naohisa Goto <ng@bioruby.org>
1115
+ Date: Fri Jun 17 15:40:57 2016 +0900
1116
+
1117
+ README.rdoc: remove descriptions about Bio::SQL
1118
+
1119
+ README.rdoc | 13 +------------
1120
+ 1 file changed, 1 insertion(+), 12 deletions(-)
1121
+
1122
+ commit 46a5bf7acdc803b7e75225c41b23396c4619f25d
1123
+ Author: Naohisa Goto <ng@bioruby.org>
1124
+ Date: Fri Jun 17 14:59:41 2016 +0900
1125
+
1126
+ remove autoload of Bio::SQL
1127
+
1128
+ lib/bio.rb | 1 -
1129
+ 1 file changed, 1 deletion(-)
1130
+
1131
+ commit 57bf535da34715beafccb902404cf1bb35b18af4
1132
+ Author: Naohisa Goto <ng@bioruby.org>
1133
+ Date: Fri Jun 17 14:48:46 2016 +0900
1134
+
1135
+ Removed Bio::SQL that have been moved to separate repository
1136
+
1137
+ * Bio::SQL is moved to https://github.com/bioruby/bioruby-biosql
1138
+ and removed from this repository.
1139
+
1140
+ * List of deleted files:
1141
+ * deleted: lib/bio/db/biosql/biosql_to_biosequence.rb
1142
+ * deleted: lib/bio/db/biosql/sequence.rb
1143
+ * deleted: lib/bio/io/biosql/ar-biosql.rb
1144
+ * deleted: lib/bio/io/biosql/biosql.rb
1145
+ * deleted: lib/bio/io/biosql/config/database.yml
1146
+ * deleted: lib/bio/io/sql.rb
1147
+ * deleted: test/unit/bio/db/biosql/tc_biosql.rb
1148
+ * deleted: test/unit/bio/db/biosql/ts_suite_biosql.rb
1149
+
1150
+ lib/bio/db/biosql/biosql_to_biosequence.rb | 78 -----
1151
+ lib/bio/db/biosql/sequence.rb | 444 -----------------------------
1152
+ lib/bio/io/biosql/ar-biosql.rb | 257 -----------------
1153
+ lib/bio/io/biosql/biosql.rb | 39 ---
1154
+ lib/bio/io/biosql/config/database.yml | 21 --
1155
+ lib/bio/io/sql.rb | 79 -----
1156
+ test/unit/bio/db/biosql/tc_biosql.rb | 114 --------
1157
+ test/unit/bio/db/biosql/ts_suite_biosql.rb | 8 -
1158
+ 8 files changed, 1040 deletions(-)
1159
+ delete mode 100644 lib/bio/db/biosql/biosql_to_biosequence.rb
1160
+ delete mode 100644 lib/bio/db/biosql/sequence.rb
1161
+ delete mode 100644 lib/bio/io/biosql/ar-biosql.rb
1162
+ delete mode 100644 lib/bio/io/biosql/biosql.rb
1163
+ delete mode 100644 lib/bio/io/biosql/config/database.yml
1164
+ delete mode 100644 lib/bio/io/sql.rb
1165
+ delete mode 100644 test/unit/bio/db/biosql/tc_biosql.rb
1166
+ delete mode 100644 test/unit/bio/db/biosql/ts_suite_biosql.rb
1167
+
1168
+ commit 476dcdbe2b21cd5adb641952ee3da92c2d593121
1169
+ Author: Naohisa Goto <ng@bioruby.org>
1170
+ Date: Wed Jun 8 12:38:22 2016 +0900
1171
+
1172
+ appveyor.yml: eliminate old Ruby versions and add Ruby 2.3
1173
+
1174
+ appveyor.yml | 5 ++---
1175
+ 1 file changed, 2 insertions(+), 3 deletions(-)
1176
+
1177
+ commit c26e2b77b75b5505a274822f53c6c5a8f842f6c0
1178
+ Author: Naohisa Goto <ng@bioruby.org>
1179
+ Date: Wed Jun 8 01:50:19 2016 +0900
1180
+
1181
+ .travis.yml: fix to use rbx-3.29
1182
+
1183
+ .travis.yml | 2 +-
1184
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1185
+
1186
+ commit b524abedac9c85d4f8259191b973bc38a9fc557c
1187
+ Author: Naohisa Goto <ng@bioruby.org>
1188
+ Date: Wed Jun 8 01:45:48 2016 +0900
1189
+
1190
+ gemfiles/Gemfile.travis-jruby1.8: use old gem versions supporting Ruby 1.8
1191
+
1192
+ gemfiles/Gemfile.travis-jruby1.8 | 6 +++---
1193
+ 1 file changed, 3 insertions(+), 3 deletions(-)
1194
+
1195
+ commit c5df9268b77f1d4dc2b29e7cfb7baf3c528c1558
1196
+ Author: Naohisa Goto <ng@bioruby.org>
1197
+ Date: Wed Jun 8 01:42:40 2016 +0900
1198
+
1199
+ .travis.yml: use rbx-3.29 instead of rbx-3
1200
+
1201
+ .travis.yml | 2 +-
1202
+ 1 file changed, 1 insertion(+), 1 deletion(-)
1203
+
1204
+ commit b51b54894ca2d76d9c13680fd72b87951a10a1df
1205
+ Author: Naohisa Goto <ng@bioruby.org>
1206
+ Date: Wed Jun 8 01:25:18 2016 +0900
1207
+
1208
+ Workaround to avoid bug in old versions of Bundler
1209
+
1210
+ * gemfiles/prepare-gemspec.rb: execute "gem update bundler" to avoid
1211
+ "NoMethodError: undefined method `spec' for nil:NilClass"
1212
+ during "bundle install". This error may be due to a bug of Bundler
1213
+ and the bug seems to be fixed in the latest version of Budler.
1214
+
1215
+ gemfiles/prepare-gemspec.rb | 4 ++++
1216
+ 1 file changed, 4 insertions(+)
1217
+
1218
+ commit a82424b4864e243ebf1f8cc7f181044798b34b5a
1219
+ Author: Naohisa Goto <ng@bioruby.org>
1220
+ Date: Wed Jun 8 01:20:15 2016 +0900
1221
+
1222
+ .travis.yml: add Ruby 2.3.1; use Ruby 2.2.5 instead of 2.2
1223
+
1224
+ .travis.yml | 8 +++++---
1225
+ 1 file changed, 5 insertions(+), 3 deletions(-)
1226
+
1227
+ commit ae927514a5c2853d3839750af86bfcc1fc53e4f1
1228
+ Author: Naohisa Goto <ng@bioruby.org>
1229
+ Date: Wed Jun 8 00:54:22 2016 +0900
1230
+
1231
+ .travis.yml: add "sudo: false" for faster testing
1232
+
1233
+ .travis.yml | 1 +
1234
+ 1 file changed, 1 insertion(+)
1235
+
1236
+ commit 832c4dd94a5602a9deadf599ce1778fac870ac81
1237
+ Author: Naohisa Goto <ng@bioruby.org>
1238
+ Date: Wed Jun 8 00:46:26 2016 +0900
1239
+
1240
+ gemfiles/Gemfile.travis-ruby1.8: use old gem versions supporting Ruby 1.8
1241
+
1242
+ gemfiles/Gemfile.travis-ruby1.8 | 8 ++++----
1243
+ 1 file changed, 4 insertions(+), 4 deletions(-)
1244
+
1245
+ commit 6cf0ab84cd67aab0f6f4012438c1852a19f3ac7a
1246
+ Author: Naohisa Goto <ng@bioruby.org>
1247
+ Date: Wed Jun 8 00:04:36 2016 +0900
1248
+
1249
+ regenerate bioruby.gemspec with rake regemspec
1250
+
1251
+ bioruby.gemspec | 3 ++-
1252
+ 1 file changed, 2 insertions(+), 1 deletion(-)
1253
+
1254
+ commit 8e986984892d661b4f09a06158a634554d931718
1255
+ Author: Naohisa Goto <ng@bioruby.org>
1256
+ Date: Tue Jun 7 23:59:35 2016 +0900
1257
+
1258
+ .travis.yml: Update ruby versions and remove temporary workaround
1259
+
1260
+ * Update Ruby versions to 2.2, 2.1.10, and rbx-3.
1261
+ * Remove temporary workaround about RubyGems introduced in
1262
+ e92e09edf5904f51d3e73e61d13fce4159a543c5.
1263
+
1264
+ .travis.yml | 18 ++++++++----------
1265
+ 1 file changed, 8 insertions(+), 10 deletions(-)
1266
+
1267
+ commit 90e678d6d74d86c45631128c0f16181679f0d599
1268
+ Author: Naohisa Goto <ng@bioruby.org>
1269
+ Date: Tue Jun 7 23:37:45 2016 +0900
1270
+
1271
+ Test bug: fix gem version mismatch error on Travis-CI
1272
+
1273
+ * Rakefile: prefer to use spec read from existing bioruby.gemspec file
1274
+ instead of that of generated from bioruby.gemspec.erb.
1275
+ This fixes "can't activate bio (= 1.5.1.2016XXXX), already activated
1276
+ bio-1.5.1.2015NNNN" occurred on Travis-CI during gem integration tests.
1277
+
1278
+ Rakefile | 20 ++++++++++++--------
1279
+ 1 file changed, 12 insertions(+), 8 deletions(-)
1280
+
1281
+ commit bdb33fe752b7dddcb35f57d826f85dbdd512c3c1
1282
+ Author: Kozo Nishida <knishida@riken.jp>
1283
+ Date: Wed Nov 4 12:08:24 2015 +0900
1284
+
1285
+ add appveyor.yml
1286
+
1287
+ appveyor.yml | 22 ++++++++++++++++++++++
1288
+ 1 file changed, 22 insertions(+)
1289
+ create mode 100644 appveyor.yml
1290
+
1291
+ commit 8b0fa73c57232a6a86d2d6fd0711f51bc50aa333
1292
+ Author: Naohisa Goto <ng@bioruby.org>
1293
+ Date: Thu Sep 17 23:34:34 2015 +0900
1294
+
1295
+ regenerate bioruby.gemspec with rake regemspec
1296
+
1297
+ bioruby.gemspec | 14 +-------------
1298
+ 1 file changed, 1 insertion(+), 13 deletions(-)
1299
+
1300
+ commit 813fc808e9a235e03ed2d5bad2d15f74946bd65a
1301
+ Author: Naohisa Goto <ng@bioruby.org>
1302
+ Date: Thu Sep 17 23:30:46 2015 +0900
1303
+
1304
+ Tutorial.rd.html is regenerated by rake retutorial2html
1305
+
1306
+ doc/Tutorial.rd.html | 117 +++++++++------------------------------------------
1307
+ 1 file changed, 19 insertions(+), 98 deletions(-)
1308
+
1309
+ commit 756f14122a45973289172a88241490a1bcc0054a
1310
+ Author: Naohisa Goto <ng@bioruby.org>
1311
+ Date: Thu Sep 17 23:25:07 2015 +0900
1312
+
1313
+ Delete Bio::PhyloXML tutorial
1314
+
1315
+ * Tutorial for Bio::PhyloXML is deleted from BioRuby core.
1316
+ It is now moved to bio-phyloxml gem. New tutorial for
1317
+ Bio::PhyloXML is available at:
1318
+ https://github.com/bioruby/bioruby-phyloxml/blob/master/doc/Tutorial.rd
1319
+
1320
+ doc/Tutorial.rd | 114 +++-----------------------------------------------------
1321
+ 1 file changed, 6 insertions(+), 108 deletions(-)
1322
+
1323
+ commit bb42efdd2eec380c99cbd3e505577a550dda8ce7
1324
+ Author: Naohisa Goto <ng@bioruby.org>
1325
+ Date: Thu Sep 17 23:20:50 2015 +0900
1326
+
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+ Delete description of Bio::PhyloXML and its dependency libxml-ruby.
1328
+
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+ README.rdoc | 6 ------
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+ 1 file changed, 6 deletions(-)
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+
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+ commit 4202ae936baf0f4c8a722af240a6613f4e8a8cee
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Sep 17 22:48:23 2015 +0900
1335
+
1336
+ Remove PhyloXML (split out bio-phyloxml gem)
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+
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+ * Bio::PhyloXML is removed from BioRuby core.
1339
+ It will soon be released as separate bio-phyloxml gem.
1340
+ The development repository of the new Bio::PhyloXML is
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+ https://github.com/bioruby/bioruby-phyloxml
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+
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+ lib/bio/db/phyloxml/phyloxml.xsd | 582 ------
1344
+ lib/bio/db/phyloxml/phyloxml_elements.rb | 1194 -----------
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+ lib/bio/db/phyloxml/phyloxml_parser.rb | 1001 ----------
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+ lib/bio/db/phyloxml/phyloxml_writer.rb | 227 ---
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+ sample/test_phyloxml_big.rb | 205 --
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+ test/data/phyloxml/apaf.xml | 666 -------
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+ test/data/phyloxml/bcl_2.xml | 2097 --------------------
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+ test/data/phyloxml/made_up.xml | 144 --
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+ .../data/phyloxml/ncbi_taxonomy_mollusca_short.xml | 65 -
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+ test/data/phyloxml/phyloxml_examples.xml | 415 ----
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+ test/unit/bio/db/test_phyloxml.rb | 821 --------
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+ test/unit/bio/db/test_phyloxml_writer.rb | 334 ----
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+ 12 files changed, 7751 deletions(-)
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+ delete mode 100644 lib/bio/db/phyloxml/phyloxml.xsd
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+ delete mode 100644 lib/bio/db/phyloxml/phyloxml_elements.rb
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+ delete mode 100644 lib/bio/db/phyloxml/phyloxml_parser.rb
1359
+ delete mode 100644 lib/bio/db/phyloxml/phyloxml_writer.rb
1360
+ delete mode 100644 sample/test_phyloxml_big.rb
1361
+ delete mode 100644 test/data/phyloxml/apaf.xml
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+ delete mode 100644 test/data/phyloxml/bcl_2.xml
1363
+ delete mode 100644 test/data/phyloxml/made_up.xml
1364
+ delete mode 100644 test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml
1365
+ delete mode 100644 test/data/phyloxml/phyloxml_examples.xml
1366
+ delete mode 100644 test/unit/bio/db/test_phyloxml.rb
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+ delete mode 100644 test/unit/bio/db/test_phyloxml_writer.rb
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+
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+ commit e3a85ad9eb6d258e79fdfbe600711a5296a20e8c
1370
+ Author: Naohisa Goto <ng@bioruby.org>
1371
+ Date: Thu Sep 17 22:45:32 2015 +0900
1372
+
1373
+ Delete autoload of Bio::PhyloXML
1374
+
1375
+ * Delete autoload of Bio::PhyloXML, for preparation of spliting
1376
+ out Bio::PhyloXML.
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+
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+ lib/bio.rb | 7 -------
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+ 1 file changed, 7 deletions(-)
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+
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+ commit 422ffe6fedecf41d83327c01f7a55ebce4afd70d
1382
+ Author: Naohisa Goto <ng@bioruby.org>
1383
+ Date: Tue Sep 15 22:33:14 2015 +0900
1384
+
1385
+ Incompatible change about deprecated Bio::Taxonomy is described.
1386
+
1387
+ RELEASE_NOTES.rdoc | 21 +++++++++++++++++++++
1388
+ 1 file changed, 21 insertions(+)
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+
1390
+ commit 3ea10d73340d8ad571ab6ca386cffca18ec725d1
1391
+ Author: Naohisa Goto <ng@bioruby.org>
1392
+ Date: Tue Sep 15 21:06:29 2015 +0900
1393
+
1394
+ Bio::Taxonomy is removed and merged to Bio::PhyloXML::Taxonomy
1395
+
1396
+ * Bio::Taxonomy in lib/bio/db/phyloxml/phyloxml_elements.rb was
1397
+ written for PhyloXML, but it was intended to become general
1398
+ taxonomy data class in BioRuby. However, no efforts have been
1399
+ made to improve the Bio::Taxonomy class, and it still remains
1400
+ to be a PhyloXML specific class. As the first step to split out
1401
+ Bio::PhyloXML to a new Gem (Biogem) package, we now decide to
1402
+ remove Bio::Taxonomy and merge it to Bio::PhyloXML::Taxonomy.
1403
+
1404
+ * Codes using Bio::Taxonomy should be modified. Changing
1405
+ Bio::Taxonomy to Bio::PhyloXML::Taxonomy, or adding the
1406
+ following monkey patch is needed.
1407
+
1408
+ module Bio
1409
+ unless defined? Taxonomy
1410
+ Taxonomy = Bio::PhyloXML::Taxonomy
1411
+ end
1412
+ end
1413
+
1414
+ lib/bio.rb | 2 --
1415
+ lib/bio/db/phyloxml/phyloxml_elements.rb | 21 +++++++++------------
1416
+ 2 files changed, 9 insertions(+), 14 deletions(-)
1417
+
1418
+ commit f89f49223f7d6ed74a8fc50aa2355fb5912c885f
1419
+ Author: Naohisa Goto <ng@bioruby.org>
1420
+ Date: Mon Sep 14 15:15:56 2015 +0900
1421
+
1422
+ regenerate bioruby.gemspec with rake regemspec
1423
+
1424
+ bioruby.gemspec | 7 +++++--
1425
+ 1 file changed, 5 insertions(+), 2 deletions(-)
1426
+
1427
+ commit 809e190d710caceee1c213da1aa067dee87e6ebd
1428
+ Author: Naohisa Goto <ng@bioruby.org>
1429
+ Date: Mon Sep 14 15:14:05 2015 +0900
1430
+
1431
+ New RELEASE_NOTES.rdoc for the next release version
1432
+
1433
+ RELEASE_NOTES.rdoc | 47 +++++++++++++++++++++++++++++++++++++++++++++++
1434
+ 1 file changed, 47 insertions(+)
1435
+ create mode 100644 RELEASE_NOTES.rdoc
1436
+
1437
+ commit a44257e933165509f3d2b164ea547ed8fba18ea5
1438
+ Author: Naohisa Goto <ng@bioruby.org>
1439
+ Date: Mon Sep 14 15:10:42 2015 +0900
1440
+
1441
+ move RELEASE_NOTES.rdoc to doc/RELEASE_NOTES-1.5.0.rdoc
1442
+
1443
+ RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.5.0.rdoc | 0
1444
+ 1 file changed, 0 insertions(+), 0 deletions(-)
1445
+ rename RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.5.0.rdoc (100%)
1446
+
1447
+ commit 4d53755b0181255e2ee69193a5a3b064ef4f4b77
1448
+ Author: Naohisa Goto <ng@bioruby.org>
1449
+ Date: Thu Jul 2 22:19:03 2015 +0900
1450
+
1451
+ ChangeLog since 1.5.0 release
1452
+
1453
+ ChangeLog | 38 ++++++++++++++++++++++++++++++++++++++
1454
+ 1 file changed, 38 insertions(+)
1455
+ create mode 100644 ChangeLog
1456
+
1
1457
  commit e066e3c8bcf0c6b7eadd3573576d4550aca77cc5
2
1458
  Author: Naohisa Goto <ng@bioruby.org>
3
1459
  Date: Thu Jul 2 22:17:06 2015 +0900
4
1460
 
5
1461
  ChangeLog is moved to doc/ChangeLog-1.5.0
6
1462
 
7
- ChangeLog | 2919 ---------------------------------------------------
8
- doc/ChangeLog-1.5.0 | 2919 +++++++++++++++++++++++++++++++++++++++++++++++++++
9
- 2 files changed, 2919 insertions(+), 2919 deletions(-)
10
- delete mode 100644 ChangeLog
11
- create mode 100644 doc/ChangeLog-1.5.0
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+ ChangeLog => doc/ChangeLog-1.5.0 | 0
1464
+ 1 file changed, 0 insertions(+), 0 deletions(-)
1465
+ rename ChangeLog => doc/ChangeLog-1.5.0 (100%)
12
1466
 
13
1467
  commit dd53e885c1baa765bc094897d53309af7b15497b
14
1468
  Author: Naohisa Goto <ng@bioruby.org>
@@ -16,7 +1470,7 @@ Date: Thu Jul 2 22:09:26 2015 +0900
16
1470
 
17
1471
  change version for generating ChangeLog to 1.5.0
18
1472
 
19
- Rakefile | 2 +-
1473
+ Rakefile | 2 +-
20
1474
  1 file changed, 1 insertion(+), 1 deletion(-)
21
1475
 
22
1476
  commit 7a5d897ebc45d9ec5357918a42eb2980decf01e4
@@ -25,7 +1479,7 @@ Date: Thu Jul 2 21:52:17 2015 +0900
25
1479
 
26
1480
  version changed to 1.5.1-dev (pre-release version of 1.5.1)
27
1481
 
28
- lib/bio/version.rb | 4 ++--
1482
+ lib/bio/version.rb | 4 ++--
29
1483
  1 file changed, 2 insertions(+), 2 deletions(-)
30
1484
 
31
1485
  commit 8fc4d6c64f6958a352c36b171b00d1f1ff2a2354
@@ -34,5 +1488,5 @@ Date: Thu Jul 2 21:47:28 2015 +0900
34
1488
 
35
1489
  fix English syntax and unexpected word insertion
36
1490
 
37
- RELEASE_NOTES.rdoc | 4 ++--
1491
+ RELEASE_NOTES.rdoc | 4 ++--
38
1492
  1 file changed, 2 insertions(+), 2 deletions(-)