Skip to content

Commit

Permalink
BioRuby 2.0.5 is released
Browse files Browse the repository at this point in the history
  • Loading branch information
@ngoto
ngoto committed Sep 27, 2023
1 parent 1bf3a41 commit 7a1809f
Showing 1 changed file with 287 additions and 0 deletions.
287 changes: 287 additions & 0 deletions ChangeLog
View file
Original file line number Diff line number Diff line change
@@ -1,3 +1,290 @@
commit 1bf3a415b694e34f112ed082184c5bdf21157d3b
Author: Naohisa Goto <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date: Tue Sep 13 21:19:01 2022 +0900
Expand Down

0 comments on commit 7a1809f

Please sign in to comment.