ChangeLog in bio-2.0.2 vs ChangeLog in bio-2.0.3

- old
+ new

@@ -1,4 +1,140 @@ +commit c16e230d15cf30478a3739563b4e4745dc57ef82 +Author: Naohisa Goto <ng@bioruby.org> +Date: Fri Nov 5 23:44:45 2021 +0900 + + regenerate bioruby.gemspec with rake regemspec + + bioruby.gemspec | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +commit 1a8c44dc5b8d24342550273a594e5f75e41f41df +Author: Naohisa Goto <ng@bioruby.org> +Date: Fri Nov 5 23:41:29 2021 +0900 + + prepare for BioRuby 2.0.3 release + + lib/bio/version.rb | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +commit 863242cdb9a748ba9efb3be3b39f92c17ed3ea84 +Author: Naohisa Goto <ng@bioruby.org> +Date: Fri Nov 5 23:36:27 2021 +0900 + + update release notes for upcoming BioRuby 2.0.3 + + RELEASE_NOTES.rdoc | 26 ++++++++++++++++++++++++++ + 1 file changed, 26 insertions(+) + +commit b97794d632c73dc45639cec000fb11238740eb30 +Author: Naohisa Goto <ng@bioruby.org> +Date: Fri Nov 5 23:26:20 2021 +0900 + + Ruby 3.0 compatibility fix: Bio::Sequence::*#partition, #rpartiton + + * Behaviors of Bio::Sequence::*#partition and #rpartition in Ruby 3.0 + are changed to mimic those in Ruby 2.x. + + lib/bio/sequence/common.rb | 17 +++++++ + test/unit/bio/sequence/test_ruby3.rb | 94 ++++++++++++++++++++++++++++++++++++ + 2 files changed, 111 insertions(+) + +commit 7ff79cd449ee03e0063120fb9abec50d9b08e979 +Author: Naohisa Goto <ng@bioruby.org> +Date: Fri Nov 5 22:24:16 2021 +0900 + + remove resolved Ruby 3.0 issue + + KNOWN_ISSUES.rdoc | 8 -------- + 1 file changed, 8 deletions(-) + +commit 24bb3c3cf417837ad63a27913db7237aef1414c6 +Author: Naohisa Goto <ng@bioruby.org> +Date: Fri Nov 5 21:24:26 2021 +0900 + + Bio::Sequence::NA,AA,Generic: workaround for Ruby 3.0.0 incompatible change + + * Since Ruby 3.0.0, over 30 methods in subclass of String class are + changed to return/yield String instance instead of the subclass + instance. (https://github.com/ruby/ruby/blob/v3_0_0/NEWS.md ) + + * In this commit, workaround is made for the following methods: + * * + * capitalize + * center + * chomp + * chop + * delete + * delete_prefix + * delete_suffix + * downcase + * each_char + * each_grapheme_cluster + * each_line + * gsub + * gsub! + * ljust + * lstrip + * revserse + * rjust + * rstrip + * slice! + * slice / [] + * split + * squeeze + * strip + * sub + * sub! + * succ / next + * swapcase + * tr + * tr_s + * upcase + * Note: sub! and gsub! are not described in the NEWS.md + but are also affected by this Ruby 3.0.0 incompatible changes. + + * The following methods are not patched i.e. they return/yield + String instances. + * dump + * partition + * rpartition + * scrub + * Note: In Ruby 2.7 or earlier, Bio::Sequence::NA#partition + and #rpartition methods return an array that may contain + mixture of Bio::Sequence::NA instances and String instances. + + * test/unit/bio/sequence/test_ruby3.rb: unit tests for the + above methods. + + * Close https://github.com/bioruby/bioruby/issues/137 + + lib/bio/sequence/common.rb | 95 +++++++++ + test/unit/bio/sequence/test_ruby3.rb | 368 +++++++++++++++++++++++++++++++++++ + 2 files changed, 463 insertions(+) + create mode 100644 test/unit/bio/sequence/test_ruby3.rb + +commit 0efc0a54685d43645daa9c53d7140bfb81577777 +Author: kojix2 <2xijok@gmail.com> +Date: Tue Aug 31 19:39:25 2021 +0900 + + Fix typos: Retrun -> Return + + lib/bio/appl/iprscan/report.rb | 6 +++--- + lib/bio/appl/sosui/report.rb | 2 +- + lib/bio/db/embl/uniprotkb.rb | 2 +- + lib/bio/db/go.rb | 4 ++-- + lib/bio/tree.rb | 2 +- + 5 files changed, 8 insertions(+), 8 deletions(-) + +commit a291b5a72da12a5cc8b006d1dd63d002fda5dff3 +Author: Naohisa Goto <ng@bioruby.org> +Date: Thu Dec 31 23:52:54 2020 +0900 + + BioRuby 2.0.2 is released + + ChangeLog | 98 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + 1 file changed, 98 insertions(+) + commit fd420b713ca364e677ef3551919ec907791df86d Author: Naohisa Goto <ng@bioruby.org> Date: Thu Dec 31 23:51:08 2020 +0900 RELEASE_NOTES.rdoc: change some description