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ChangeLog
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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
bioruby.gemspec | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
commit 190e4751b84cc45cbce636c4414482a8169b08df
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Sep 13 21:18:06 2022 +0900
prepare for BioRuby 2.0.4 release
lib/bio/version.rb | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit a666639e0393e96b2de0bbcb447c13f8a14ad06d
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Sep 13 21:17:11 2022 +0900
update release notes for upcoming BioRuby 2.0.4
RELEASE_NOTES.rdoc | 14 ++++++++++++++
1 file changed, 14 insertions(+)
commit c0d197343dd7fd8999d04083c9e8f24fa37a2f93
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Sep 13 21:13:40 2022 +0900
License of UniProt data is CC BY 4.0
LEGAL | 9 +++++++++
1 file changed, 9 insertions(+)
commit e670102e6d4deb04c1fcae62459cc02861132d25
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Sep 13 21:01:50 2022 +0900
Bug fix: Bio::UniProtKB#protein_name and #synonyms may raise error
* Bug fix: Bio::UniProtKB#protein_name and #synonyms may raise error
after calling Bio::UniProtKB#de method.
lib/bio/db/embl/uniprotkb.rb | 25 ++++++++++++++++++-------
test/unit/bio/db/embl/test_uniprotkb_P28907.rb | 11 +++++++++++
2 files changed, 29 insertions(+), 7 deletions(-)
commit 9c04e08e8d1316ffd7fc15ab311cea5dd6937d36
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Sep 13 20:44:46 2022 +0900
Supports format change of FT lines since UniProt release 2019_11
* Bio::UniProtKB#ft: Supports text format change of FT lines since
UniProt release 2019_11. (Details of the format changes:
https://www.uniprot.org/release-notes/2019-12-18-release#text%5Fft )
This closes https://github.com/bioruby/bioruby/issues/147 .
* Tests are added with a new test data
lib/bio/db/embl/uniprotkb.rb | 122 +++++-
test/data/uniprot/P28907.uniprot | 551 +++++++++++++++++++++++++
test/unit/bio/db/embl/test_uniprotkb_P28907.rb | 314 ++++++++++++++
3 files changed, 983 insertions(+), 4 deletions(-)
create mode 100644 test/data/uniprot/P28907.uniprot
create mode 100644 test/unit/bio/db/embl/test_uniprotkb_P28907.rb
commit b18ee463d4328b5ef619733b46f568b18459be7a
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Nov 5 23:49:18 2021 +0900
BioRuby 2.0.3 is released
ChangeLog | 136 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 136 insertions(+)
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
RELEASE_NOTES.rdoc | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit 0ed9b37f38fa1b00dcc1d422914e4cbdbbc5f6ab
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Dec 31 23:46:46 2020 +0900
regenerate bioruby.gemspec with rake regemspec
bioruby.gemspec | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit fa84b8fac653c26b9f8db429321ef49202554a69
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Dec 31 23:45:38 2020 +0900
prepare for BioRuby 2.0.2 release
lib/bio/version.rb | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit 32c5efccbad4e0d3440726383f863520ee242cc5
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Dec 31 23:39:18 2020 +0900
update release notes for upcoming BioRuby 2.0.2
RELEASE_NOTES.rdoc | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
commit c2f6e62ab64bc532f442bccc0d76ced5380664ec
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Dec 31 23:38:43 2020 +0900
add a known issue about Ruby 3.0
KNOWN_ISSUES.rdoc | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
commit a733c0816da7c97ca0c23016b473b004fb755f54
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Dec 31 23:04:55 2020 +0900
remove deprecation warning of Gem::Specification#has_rdoc=
Gem::Specification#has_rdoc= have been deprecated since RubyGems 1.3.3
in 2009. (https://blog.rubygems.org/2009/05/04/1.3.3-released.html )
RDoc is always generated regardless of the value, and the line is
safely removed.
This fixes https://github.com/bioruby/bioruby/issues/138 .
Thanks to @jaysonvirissimo for reporting the issue.
bioruby.gemspec | 1 -
bioruby.gemspec.erb | 1 -
2 files changed, 2 deletions(-)
commit bed6746ce62059795996eeb6e5ac65655bab12b5
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Dec 31 22:51:56 2020 +0900
require ruby's date library to avoid NameError for Date
In Bio::Sequence#output(:embl), NameError (uninitialized constant
Bio::Sequence::Format::INSDFeatureHelper::Date) is observed.
The error message is misleading because Date is provided by Ruby's
standard date library.
This fixes https://github.com/bioruby/bioruby/issues/135 .
Thanks to Dr. Mark Wilkinson for reporting the issue.
lib/bio/sequence/format.rb | 1 +
1 file changed, 1 insertion(+)
commit 5f3aa79fdaf6dd5551d51663ca2e9b6f5e56d855
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Nov 6 17:45:12 2020 +0900
fix mistaken URLs
README.rdoc | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
commit d5e1670ee4863cc60d3aa08432a7ee3b1e445439
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Sep 6 15:48:45 2019 +0900
BioRuby 2.0.1 is released
ChangeLog | 185 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 185 insertions(+)
commit 21bf51a1ec8c18c9cdf8528ffc3c59c503cef042
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Sep 6 15:45:47 2019 +0900
RELEASE_NOTES.rdoc: describe notable changes since 2.0.0
RELEASE_NOTES.rdoc | 40 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
commit 9092a629e0e28b416ee7288d349fb9d73dd2b961
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Sep 6 15:06:11 2019 +0900
regenerate bioruby.gemspec with rake regemspec
bioruby.gemspec | 11 ++++++++++-
1 file changed, 10 insertions(+), 1 deletion(-)
commit 59e24b6e55d2c9a8887e8e01a91999d33a008042
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Sep 6 15:04:33 2019 +0900
prepare for BioRuby 2.0.1 release
lib/bio/version.rb | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit 9635a38a158db434fd2b6aff7a2ee75622ddecef
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Sep 6 14:51:23 2019 +0900
sample/fastq2html.rb: A html visualization of FASTQ sequences
* sample/fastq2html: A html visualization of FASTQ sequences.
Each sequence is colored with the quality score.
* sample/fastq2html.cwl: CWL workflow for the above sample script
* sample/fastq2html.testdata.yaml: Test data for the above workflow
sample/fastq2html.cwl | 23 ++++++++++
sample/fastq2html.rb | 94 +++++++++++++++++++++++++++++++++++++++++
sample/fastq2html.testdata.yaml | 5 +++
3 files changed, 122 insertions(+)
create mode 100644 sample/fastq2html.cwl
create mode 100644 sample/fastq2html.rb
create mode 100644 sample/fastq2html.testdata.yaml
commit 6bbcf8b66310c225d686f2c59359680a0bc0b4b6
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Sep 6 14:42:19 2019 +0900
sample/rev_comp.rb: Generates reverse-complement sequences
* sample/rev_comp.rb: Generates reverse-complement sequences of
the given nucleotide sequences.
* sample/rev_comp.cwl: CWL cowkflow for the sample script
* sample/rev_comp.testdata.yaml: Test data for the above CWL workflow
sample/rev_comp.cwl | 23 +++++++++++++++++++++++
sample/rev_comp.rb | 20 ++++++++++++++++++++
sample/rev_comp.testdata.yaml | 7 +++++++
3 files changed, 50 insertions(+)
create mode 100644 sample/rev_comp.cwl
create mode 100644 sample/rev_comp.rb
create mode 100644 sample/rev_comp.testdata.yaml
commit ff0e6c3c6b6f1b56d81b5a4b579a6d0984bfc607
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Sep 6 14:40:45 2019 +0900
sample/color_scheme_(na|aa).rb: use String#each_char instead of each_byte
sample/color_scheme_aa.rb | 6 +++---
sample/color_scheme_na.rb | 6 +++---
2 files changed, 6 insertions(+), 6 deletions(-)
commit 6f7c1be09aa3d6cdb76fd029fc0f84efda31c907
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Sep 5 17:32:07 2019 +0900
sample/color_scheme_aa.rb: new sample based on color_scheme_na.rb
sample/color_scheme_aa.rb | 82 +++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 82 insertions(+)
create mode 100644 sample/color_scheme_aa.rb
commit 51864c3857178f58133b759f7608b8d6d8991c44
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Sep 5 17:13:20 2019 +0900
sample/color_scheme_na.rb: use const_get instead of eval
sample/color_scheme_na.rb | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit ba0b554971a9a387a54fc04c5002853d91357347
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Sep 5 17:02:20 2019 +0900
sample/na2aa.cwl: inputBinding position -1 for the script
* sample/na2aa.cwl: inputBinding position -1 is used for the script
to emphasize that the argument is the first one.
sample/na2aa.cwl | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit 26a27ec261e2251f3ff3a85007147d33682778d0
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Sep 5 16:56:08 2019 +0900
sample/color_scheme_na.rb: Supports more file formats
* sample/color_scheme_na.rb: Supports more file formats other than
fasta format, by using Bio::Flatfile.
sample/color_scheme_na.rb | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
commit 5c053a606382bb578a2b6884ee639805154433e5
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Sep 5 12:32:00 2019 +0900
sample/na2aa.cwl: use inputBinding
sample/na2aa.cwl | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
commit 6a3c3e02f08549d47dda00dca92d55bbadfc468f
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Sep 4 22:59:21 2019 +0900
Sample CWL workflow to run sample/na2aa.rb
* na2aa.cwl: A sample CWL workflow to run na2aa.rb in sample/ dir
* na2aa.testdata.yaml: Test data for the workflow
sample/na2aa.cwl | 20 ++++++++++++++++++++
sample/na2aa.testdata.yaml | 7 +++++++
2 files changed, 27 insertions(+)
create mode 100644 sample/na2aa.cwl
create mode 100644 sample/na2aa.testdata.yaml
commit 960b885036f549863e3cfe9c693c90f9bef27d3d
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Sep 4 21:00:50 2019 +0900
LEGAL: na2aa.rb is now Ruby's License
LEGAL | 1 -
1 file changed, 1 deletion(-)
commit 7af9e81988939007eb36dab6b102a7422e8196d8
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Sep 4 14:34:05 2019 +0900
sample/na2aa.rb: Completely rewritten
* sample/na2aa.rb: Completely rewritten. License is changed because
old code is completely wiped out. Note that the old code always
raises error due to a bug in the code.
* The old code was trying to replace 'X' (any) to '-' (gap) but
the new code does not modify translated sequences anymore.
sample/na2aa.rb | 36 +++++++++++-------------------------
1 file changed, 11 insertions(+), 25 deletions(-)
commit cf8cac5e32db42b6683c1a837adc9e1c04994062
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Sep 2 17:11:08 2019 +0900
Bug fix: Bio::GFF::GFF2::Record.parse did not return correct object
lib/bio/db/gff.rb | 4 +++-
test/unit/bio/db/test_gff.rb | 5 +++++
2 files changed, 8 insertions(+), 1 deletion(-)
commit 80b387e7e2bb8570d9204e389b6c5d90c6ea31de
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 14 14:33:19 2019 +0900
BioRuby 2.0.0 is released
ChangeLog | 1051 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
1 file changed, 1043 insertions(+), 8 deletions(-)
commit 2e4046517fd8ee1c105ef53131e69f787d790099
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 14 14:23:19 2019 +0900
Add "Recommended Plugins" section and description is moved to it
README.rdoc | 22 +++++++++++++++-------
1 file changed, 15 insertions(+), 7 deletions(-)
commit 7a533e4f57edcebb5dfe15fdddc9fbc986d2b7ec
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 14 14:17:08 2019 +0900
fix directory name
README.rdoc | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit 805266c9c900903156efd0baa8c1e6ee524a8147
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 14 14:14:52 2019 +0900
add description about recommended plugins
README.rdoc | 11 +++++++++++
1 file changed, 11 insertions(+)
commit 02b7d8b9bc5dcd56f501a15e5e820f450153aa1c
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 14 13:33:30 2019 +0900
prepare to release BioRuby 2.0.0
lib/bio/version.rb | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
commit f1fed8dacb425d19c12abec5d4faeb733827f80f
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 14 13:31:08 2019 +0900
regenerate bioruby.gemspec with rake regemspec
bioruby.gemspec | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
commit 3952ec9d5ce1e3ceea9734f667d36595808c4989
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 14 13:28:19 2019 +0900
Remove xmlparser dependency from Gemfile and gemfiles/Gemfile.*
Gemfile | 2 --
gemfiles/Gemfile.travis-rbx | 2 --
gemfiles/Gemfile.travis-ruby1.8 | 2 --
gemfiles/Gemfile.travis-ruby1.9 | 2 --
gemfiles/Gemfile.windows | 2 --
5 files changed, 10 deletions(-)
commit d4a8ee7ae3d3b13a8be4c57c1f8db5b29f2c4a13
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 14 12:34:45 2019 +0900
RELEASE_NOTES.rdoc: update aboue new features and improvements
RELEASE_NOTES.rdoc | 15 +++++++++++++--
1 file changed, 13 insertions(+), 2 deletions(-)
commit 2d4170a2a0262f5d75cef5a54b5d6f3da298f145
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 14 12:24:12 2019 +0900
Tests added in the previous commit is moved and modified
* test/network/bio/db/kegg/test_genes_hsa7422.rb: tests added in the
previous commit is moved to the file and modified to get data
from the internet for avoiding KEGG data license issue.
Note that some of the tests might be fail in the near future due to
the database entry updates.
test/network/bio/db/kegg/test_genes_hsa7422.rb | 91 ++++++++++++++++++++++++++
test/unit/bio/db/kegg/test_genes.rb | 51 ---------------
2 files changed, 91 insertions(+), 51 deletions(-)
create mode 100644 test/network/bio/db/kegg/test_genes_hsa7422.rb
commit 67f8105acf22e88a7624305743ad13802ffed124
Author: kojix2 <2xijok@gmail.com>
Date: Mon Oct 22 00:46:31 2018 +0900
add DiseasesAsHash to KEGG/Common
lib/bio/db/kegg/common.rb | 14 ++++++++++
lib/bio/db/kegg/genes.rb | 26 +++++++++++++++++++
lib/bio/db/kegg/pathway.rb | 16 ++++--------
test/unit/bio/db/kegg/test_genes.rb | 51 +++++++++++++++++++++++++++++++++++++
4 files changed, 96 insertions(+), 11 deletions(-)
commit 9dbb655e1c3ec7460b77f1d0ea475531ac3a9361
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 14 11:37:11 2019 +0900
update documents for upcoming new release
KNOWN_ISSUES.rdoc | 14 +++-----
LEGAL | 9 ------
README.rdoc | 92 +++++++----------------------------------------------
README_DEV.rdoc | 10 +++---
RELEASE_NOTES.rdoc | 93 +++++++++++++++++++++++++++++++++++++++++++-----------
5 files changed, 96 insertions(+), 122 deletions(-)
commit 6f388019a035a41a8867c6a03ef7e2707d1edce4
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 14 11:32:40 2019 +0900
.travis.yml: move 1.8.7 and 1.9.3 to allow_failures; update ruby versions
.travis.yml | 23 ++++++++++++-----------
1 file changed, 12 insertions(+), 11 deletions(-)
commit f2cbe9db9b78df653d774a7676e00f6f1a212b23
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 14 11:18:27 2019 +0900
.travis.yml: Remove jobs using "tar-integration-test"
.travis.yml | 9 ---------
1 file changed, 9 deletions(-)
commit 68f28e81e3fa566843b548f1899549adcad5225a
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 14 11:10:18 2019 +0900
remove "rake tar-install" and "rake tar-integration-test" tasks
* Rakefile: Remove "tar-install" and "tar-integration-test" tasks
because they use setup.rb that is removed from the repository.
Rakefile | 34 ----------------------------------
1 file changed, 34 deletions(-)
commit 0cbdb4586f2231a68579105dbc7f0fb413b38a96
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 14 10:48:15 2019 +0900
next bioruby version will be 2.0.0
lib/bio/version.rb | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit 300d10b9791b7f0c0eff1d0544cae63fecc3b31a
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 14 10:41:12 2019 +0900
Remove setup.rb. Use RubyGems to install BioRuby.
setup.rb | 1600 --------------------------------------------------------------
1 file changed, 1600 deletions(-)
delete mode 100644 setup.rb
commit a74683d9acfc16d0d715b020839839afc8b43350
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 14 02:28:31 2019 +0900
try to require "bio-blast-xmlparser" provided by separete gem
lib/bio/appl/blast/report.rb | 8 ++++++++
1 file changed, 8 insertions(+)
commit de1c1e33aed392d4e2265a028b8acb50501f56bd
Author: Naohisa Goto <ng@bioruby.org>
Date: Sat Sep 16 04:49:21 2017 +0900
check existance of a private method instead of XMLParser constant
test/unit/bio/appl/blast/test_report.rb | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
commit 3f54d19c44411e845b32c522fc0deca4288dcf07
Author: Naohisa Goto <ng@bioruby.org>
Date: Sat Sep 16 04:39:19 2017 +0900
xml_set_parameter is moved from xmlparser.rb etc.
* The method xml_set_parameter is moved from
lib/bio/appl/blast/xmlparser.rb because it is used by
the REXML parser.
* The method Bio::Blast::Report.xmlparser is move to
lib/bio/appl/blast/xmlparser.rb in the separate repo.
* Use "defined? xmlparser_parse" for checking existance of
the blast xmlparser component.
* Removed line to require bio/appl/blast/xmlparser.
lib/bio/appl/blast/report.rb | 40 ++++++++++++++++++++++++++++++++--------
1 file changed, 32 insertions(+), 8 deletions(-)
commit b19cd507c432739c5aaac700e222e6e4ecc63ddc
Author: Naohisa Goto <ng@bioruby.org>
Date: Sat Sep 16 03:32:54 2017 +0900
lib/bio/appl/blast/xmlparser.rb is removed and moved to separate gem
* lib/bio/appl/blast/xmlparser.rb is removed and moved to separate gem
to eliminate dependency to xmlparser that includes native extension.
lib/bio/appl/blast/xmlparser.rb | 236 ----------------------------------------
1 file changed, 236 deletions(-)
delete mode 100644 lib/bio/appl/blast/xmlparser.rb
commit 525d3450ad3440bfbbe3a1540fe60d83c3845ec7
Author: Naohisa Goto <ng@bioruby.org>
Date: Sat Dec 15 11:33:08 2018 +0900
.travis.yml: remove jruby-18mode and jruby-19mode; add jruby and truffleruby
.travis.yml | 24 ++++++++++++------------
1 file changed, 12 insertions(+), 12 deletions(-)