ChangeLog in bio-2.0.4 vs ChangeLog in bio-2.0.5

- old
+ new

@@ -1,4 +1,291 @@ +commit 1bf3a415b694e34f112ed082184c5bdf21157d3b +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Sep 27 22:54:17 2023 +0900 + + update release notes for upcoming BioRuby 2.0.5 + + RELEASE_NOTES.rdoc | 36 ++++++++++++++++++++++++++++++++++++ + 1 file changed, 36 insertions(+) + +commit e7cd12319f207da77cfcde822bfc7e158897a42b +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Sep 27 22:18:54 2023 +0900 + + README.rdoc: change recommended Ruby versions + + README.rdoc | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +commit 631f2546ca5fa9e499d55bd20053e81bb3efa206 +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Sep 27 21:58:24 2023 +0900 + + PTS1 site seems to be migrated to https + + lib/bio/appl/pts1.rb | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +commit f31fbbaa27532cd29c2f7303e729a97a6843b297 +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Sep 27 21:40:26 2023 +0900 + + POST path seems to be changed in remote BLAST in genome.jp (GenomeNet) + + lib/bio/appl/blast/genomenet.rb | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +commit 9013c2f8b90fc1f56d410d78007dc500af87ee45 +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Sep 27 18:41:32 2023 +0900 + + regenerate bioruby.gemspec with rake regemspec + + bioruby.gemspec | 17 +++++++---------- + 1 file changed, 7 insertions(+), 10 deletions(-) + +commit 6681c10f947290fc90b410c7620968164d777c85 +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Sep 27 18:29:40 2023 +0900 + + appveyor.yml: disable 31-x64 because of stringio 3.0.8 build failure + + appveyor.yml | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +commit 002227f52b05144668214b5c460055d002d865a1 +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Sep 27 18:11:53 2023 +0900 + + remove files/dirs only used from older appveyor.yml + + gemfiles/Gemfile.windows | 6 ------ + 1 file changed, 6 deletions(-) + delete mode 100644 gemfiles/Gemfile.windows + +commit e47f4dc8026cf78ab9daaa59e023512081aa88a1 +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Sep 27 18:01:26 2023 +0900 + + update appveyor.yml + + * Visual Studio 2019 image is specified + * Branch "incoming" is added + * Not to use customized Gemfile + * Not to build and install gem but only to execute rake normally + * Update ruby versions + * Add installation retry and caching, copied from jekyll repository + * References: + * https://www.appveyor.com/docs/lang/ruby/ + * https://github.com/jekyll/jekyll/blob/master/appveyor.yml + + appveyor.yml | 27 ++++++++++++++------------- + 1 file changed, 14 insertions(+), 13 deletions(-) + +commit b3977e58cde42f0c56fd3dccd6847d162dc349e8 +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Sep 27 17:03:33 2023 +0900 + + remove files only used for Travis-CI, mentioned in .travis.yml + + gemfiles/Gemfile.travis-jruby1.8 | 6 ------ + gemfiles/Gemfile.travis-jruby1.9 | 5 ----- + gemfiles/Gemfile.travis-rbx | 10 ---------- + gemfiles/Gemfile.travis-ruby1.8 | 6 ------ + gemfiles/Gemfile.travis-ruby1.9 | 5 ----- + gemfiles/modify-Gemfile.rb | 28 ---------------------------- + gemfiles/prepare-gemspec.rb | 29 ----------------------------- + 7 files changed, 89 deletions(-) + delete mode 100644 gemfiles/Gemfile.travis-jruby1.8 + delete mode 100644 gemfiles/Gemfile.travis-jruby1.9 + delete mode 100644 gemfiles/Gemfile.travis-rbx + delete mode 100644 gemfiles/Gemfile.travis-ruby1.8 + delete mode 100644 gemfiles/Gemfile.travis-ruby1.9 + delete mode 100644 gemfiles/modify-Gemfile.rb + delete mode 100644 gemfiles/prepare-gemspec.rb + +commit f7a2063353351f1b7341e98857f25e182c41adaa +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Sep 27 16:44:58 2023 +0900 + + remove .travis.yml + + * Also remove webhook for Travis-CI in GitHub settings + * Thanks to Travis-CI to run CI for a long time. + * Thanks to Open Bioinformatics Foundation for funding to + automatic testing of pull requests for a long time. + (https://www.open-bio.org/2012/07/30/travis-ci-for-testing/ ). + + .travis.yml | 71 ------------------------------------------------------------- + 1 file changed, 71 deletions(-) + delete mode 100644 .travis.yml + +commit 3ea8ecdd482ca2b5c8525959f37ed8f0f9a881e6 +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Sep 27 16:10:15 2023 +0900 + + ruby.yml: add "incoming" branch + + .github/workflows/ruby.yml | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +commit 350587b2b16532078e8bd5f303df96a5dc5a0d70 +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Sep 27 16:04:48 2023 +0900 + + ruby.yml: add ruby 3.1 and 3.2 + + .github/workflows/ruby.yml | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +commit 6a0de6744b7324a3a04e5c3d7468d5aec84608b1 +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Sep 27 15:43:27 2023 +0900 + + prepare for BioRuby 2.0.5 release + + lib/bio/version.rb | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +commit 1c77ef24514e87f98be72792646910285be8498f +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Sep 27 14:42:57 2023 +0900 + + Create ruby.yml + + Create ruby.yml from the template by GitHub + + .github/workflows/ruby.yml | 38 ++++++++++++++++++++++++++++++++++++++ + 1 file changed, 38 insertions(+) + create mode 100644 .github/workflows/ruby.yml + +commit 22b7217c5c830013cb53cb297e6a07e940d60ddc +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Sep 27 13:55:50 2023 +0900 + + add .gitignore + + * References: + * https://www.gitignore.io/api/ruby + * https://github.com/github/gitignore/blob/main/Ruby.gitignore + + .gitignore | 32 ++++++++++++++++++++++++++++++++ + 1 file changed, 32 insertions(+) + create mode 100644 .gitignore + +commit 1244da434f1a46d85a3204f9ba74d038c9535631 +Author: Naohisa Goto <ng@bioruby.org> +Date: Wed Sep 27 11:06:49 2023 +0900 + + added gems that are no longer "default" gems in recent Ruby versions + + * Added gems that are no longer the default gems: + * "rexml" -- since Ruby 3.0 + * "matrix" -- since Ruby 3.1 + + Gemfile | 3 +++ + 1 file changed, 3 insertions(+) + +commit bd77c7a25eca7681f0176c2425d84415461bcc61 +Author: Naohisa Goto <ng@bioruby.org> +Date: Tue Sep 26 17:52:03 2023 +0900 + + update tests to reflect changes of hsa:7422 (KEGG GENES) + + test/network/bio/db/kegg/test_genes_hsa7422.rb | 38 ++++++++++++++++++-------- + 1 file changed, 26 insertions(+), 12 deletions(-) + +commit 0eca7bba8ee26f2bc4db86b10053e291cd1ab8a9 +Author: Naohisa Goto <ng@bioruby.org> +Date: Tue Sep 26 17:50:31 2023 +0900 + + add assertions to suppress warnings when ruby -v + + test/functional/bio/test_command.rb | 2 ++ + 1 file changed, 2 insertions(+) + +commit 34f56a39baadd5247423588579330f279ab220f5 +Author: Naohisa Goto <ng@bioruby.org> +Date: Tue Sep 26 17:48:24 2023 +0900 + + update test/data/uniprot/P49144.uniprot and change related tests + + test/data/uniprot/P49144.uniprot | 13 +++++++++---- + test/unit/bio/db/embl/test_uniprotkb_P49144.rb | 4 ++-- + 2 files changed, 11 insertions(+), 6 deletions(-) + +commit 2a9f6b0b0bf10a376dff48da58b74eecb40e8553 +Author: Naohisa Goto <ng@bioruby.org> +Date: Tue Sep 26 17:34:23 2023 +0900 + + Bug fix: Bio::UniProtKB#oh: OH lines parser error occurred for P03589 + + lib/bio/db/embl/uniprotkb.rb | 51 +++++++++++++++++++++++++++++++------------- + 1 file changed, 36 insertions(+), 15 deletions(-) + +commit 5a644566891b274cc9532b926d4380899b7725af +Author: Naohisa Goto <ng@bioruby.org> +Date: Tue Sep 26 17:28:54 2023 +0900 + + Add a test class to parse UniProtKB P03589 with the data + + LEGAL | 1 + + test/data/uniprot/P03589.uniprot | 127 +++++++++ + test/unit/bio/db/embl/test_uniprotkb_P03589.rb | 378 +++++++++++++++++++++++++ + 3 files changed, 506 insertions(+) + create mode 100644 test/data/uniprot/P03589.uniprot + create mode 100644 test/unit/bio/db/embl/test_uniprotkb_P03589.rb + +commit 3273d1e9f7fa625fa1120ab17b85a222f9142cff +Author: Naohisa Goto <ng@bioruby.org> +Date: Thu Oct 6 23:17:17 2022 +0900 + + Bug fix: suppress NoMethodError when parsing CC lines + + * Bio::UniProtKB#cc: When parsing a nonexistent CC topic, + "NoMethodError: undefined method `join' for nil:NilClass" + was raised. To suppress the error, changed to return nil + if the given data is nil. + + lib/bio/db/embl/uniprotkb.rb | 8 ++++++++ + 1 file changed, 8 insertions(+) + +commit c426a71de2ed6bb58cd097cecc221f12c0a0ab8a +Author: Naohisa Goto <ng@bioruby.org> +Date: Thu Oct 6 23:10:42 2022 +0900 + + Another tests for the FT lines format change since UniProt release 2019_11 + + LEGAL | 1 + + test/data/uniprot/P49144.uniprot | 227 ++++++++++++++++ + test/unit/bio/db/embl/test_uniprotkb_P49144.rb | 359 +++++++++++++++++++++++++ + 3 files changed, 587 insertions(+) + create mode 100644 test/data/uniprot/P49144.uniprot + create mode 100644 test/unit/bio/db/embl/test_uniprotkb_P49144.rb + +commit a9af82b3c61ebaa4351c7dfdfa3d1a1c09581b73 +Author: Naohisa Goto <ng@bioruby.org> +Date: Thu Oct 6 23:00:37 2022 +0900 + + more fix for FT lines format change since UniProt release 2019_11 + + * Bio::UniProtKB#ft: When the end position is empty, end position + is regarded as the same as start position. + This fix the bug: + https://github.com/bioruby/bioruby/issues/147#issuecomment-1246458688 + + lib/bio/db/embl/uniprotkb.rb | 12 ++++++++---- + 1 file changed, 8 insertions(+), 4 deletions(-) + +commit 5d1cc85ff9e028f4663d6a4ac1e312b50eb50c72 +Author: Naohisa Goto <ng@bioruby.org> +Date: Tue Sep 13 21:20:12 2022 +0900 + + BioRuby 2.0.4 is released + + ChangeLog | 79 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + 1 file changed, 79 insertions(+) + commit 1bc877e557e165b42eea992d89f19a63996cb586 Author: Naohisa Goto <ng@bioruby.org> Date: Tue Sep 13 21:19:01 2022 +0900 regenerate bioruby.gemspec with rake regemspec