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ChangeLog
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ChangeLog
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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(-)
commit 5bc0042b7fc39c62222534e0e4129d3f9794fd8c
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Dec 14 22:46:08 2018 +0900
appveyor.yml: regenerate bioruby.gemspec before creating gem
appveyor.yml | 1 +
1 file changed, 1 insertion(+)
commit 5582dc1db60ffc812211d9803d5adce9c0dd70d3
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Dec 14 22:39:35 2018 +0900
appveyor.yml: modify gemfile/Gemfile.windows after bundle install
appveyor.yml | 1 +
1 file changed, 1 insertion(+)
commit 09031bcae0a42fe93d07b46eb489ffbabc8c1319
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Dec 14 22:30:09 2018 +0900
appveyor.yml: give up using vendor/bundle; set BUNDLE_GEMFILE
appveyor.yml | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
commit 44fb6c67aef1b0311d32ac806fc9a62f09d401d5
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Dec 14 21:59:44 2018 +0900
appveyor.yml: Specify gemfiles/Gemfile.windows
* appveyor.yml: Specify gemfiles/Gemfile.windows in which xmlparser gem
is excluded because of build failure of the xmlparser gem on Windows.
* gemfiles/Gemfile.windows: Gemfile for Appveyor, running on Microsoft
Windows.
appveyor.yml | 2 +-
gemfiles/Gemfile.windows | 8 ++++++++
2 files changed, 9 insertions(+), 1 deletion(-)
create mode 100644 gemfiles/Gemfile.windows
commit fe55e52b42660dda1d21749bf714e989e7db754e
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Dec 14 21:48:06 2018 +0900
appveyor.yml: update ruby versions and test procedure
appveyor.yml | 22 +++++++++++++++-------
1 file changed, 15 insertions(+), 7 deletions(-)
commit 739f5c9a512074a7de25d87e8104ed15bdb28b5d
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Dec 14 11:57:43 2018 +0900
.travis.yml: change default Gemfile
* Change default Gemfile to Gemfile
* Move old Ruby versions to "include" matrix.
* Change ruby version for gem-integration-test and tar-integration-test
.travis.yml | 22 ++++++++++++----------
1 file changed, 12 insertions(+), 10 deletions(-)
commit 2f54a9cbf8fb6d8580d488b20007d5ce4562e5e9
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Dec 14 11:42:58 2018 +0900
.travis.yml: No more limit to master branch. Instead, add blocklist.
.travis.yml | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
commit 9ac3e44318c67fd4415a2118dd5631902e784e12
Author: Kozo Nishida <knishida@riken.jp>
Date: Thu Dec 13 22:47:54 2018 +0900
ci(travis): Add rvm versions
.travis.yml | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
commit 258dd67c9d65f1247e56d5c5228cc6f9c019d133
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Dec 10 21:56:16 2018 +0900
regenerate bioruby.gemspec with rake regemspec
bioruby.gemspec | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit 3920483d6b5a3759e6c610d7ee9fb1a63dcc9ce4
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Dec 10 21:55:19 2018 +0900
Simplify version number processing
bioruby.gemspec.erb | 14 +++++++-------
lib/bio/version.rb | 12 +++++-------
2 files changed, 12 insertions(+), 14 deletions(-)
commit 80949a10ea5e4f88d21d893905b720925f5a9e7b
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Dec 10 18:54:00 2018 +0900
next bioruby version will be 1.6.0
lib/bio/version.rb | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit 2b542865a4d4af2684ace41f79e273ebceb51807
Merge: 02a96424 d71e07a0
Author: Toshiaki Katayama <k@bioruby.org>
Date: Fri Oct 19 06:45:49 2018 +0900
Merge pull request #125 from kojix2/master
update TogoWS documentation. genbank -> ncbi-nucleotide
commit d71e07a0cb1cc441241be91273bd44e3717b8773
Author: kojix2 <2xijok@gmail.com>
Date: Thu Oct 18 19:10:29 2018 +0900
update TogoWS documentation. genbank -> ncbi-nucleotide
lib/bio/io/togows.rb | 10 +++++-----
sample/test_restriction_enzyme_long.rb | 2 +-
2 files changed, 6 insertions(+), 6 deletions(-)
commit 02a964241b79e2307d0a00473427ea6bc2ea6932
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Sep 20 07:06:08 2018 +0900
Improvement documentation
* Improve documentation.
* Close https://github.com/bioruby/bioruby/pull/120 .
lib/bio/db/aaindex.rb | 79 +++++++++++++++++++++++++++++++++++++++++++++++----
1 file changed, 74 insertions(+), 5 deletions(-)
commit 6bfef40ae87099565371abf94cf2cc8bfac76b12
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Sep 20 05:01:12 2018 +0900
Bug fix: Bio::Command.new_https should support proxy
lib/bio/command.rb | 18 +++++++-----------
1 file changed, 7 insertions(+), 11 deletions(-)
commit 4e3251d2172f58239f103e7edf8f4c351140f378
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Sep 20 04:58:56 2018 +0900
https support for Bio::Blast::Remote::GenomeNet::Information
lib/bio/appl/blast/genomenet.rb | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
commit 6dd1f9fb8c2b4ba95086eab7bffc01583feccf3a
Author: ramadis <rramiro.o@hotmail.com>
Date: Sat Jul 7 15:12:33 2018 -0300
Add https requests in command. Fix genomenet query by allowing https requests.
lib/bio/appl/blast/genomenet.rb | 2 +-
lib/bio/command.rb | 14 ++++++++++++++
2 files changed, 15 insertions(+), 1 deletion(-)
commit 4b6f87c9fd2dc62418ddfc4b57bcc4b73287a603
Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>
Date: Sat Mar 31 13:08:07 2018 +0900
directly refer to the given hash
lib/bio/data/codontable.rb | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit 25636ffa08c6ea9a9e4d1b451a456bc1f482ad40
Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>
Date: Sat Jun 2 15:10:12 2018 +0900
precalculated ambiguity codontable
lib/bio/data/codontable.rb | 55 +++++++++++++++++++++++++++++++++++++++++++---
1 file changed, 52 insertions(+), 3 deletions(-)
commit b2d924045202ec3aa4e1b79341fd939a881d4c2e
Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>
Date: Sat Mar 31 11:55:57 2018 +0900
construct ambiguity nucleotide to amino acid table
lib/bio/data/codontable.rb | 49 ++++++++++++++++++++++++++++++++++-
test/unit/bio/data/test_codontable.rb | 3 +++
2 files changed, 51 insertions(+), 1 deletion(-)
commit a7378b6b269ea1c0391e259dd8e4868f03b064ea
Author: markwilkinson <markw@illuminae.com>
Date: Tue Dec 12 14:13:51 2017 +0100
fixing Fasta Report parser for fasta36 -m10
lib/bio/appl/fasta/format10.rb | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
commit c89c40c29c3c92f8e548c79d2d04698123559007
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Sep 15 16:33:19 2017 +0900
Remove settings about executables
* Definitions and settings about executables are removed because
all files in bin/ have been moved to separate gem packages
(bio-shell and bio-executables).
bioruby.gemspec | 13 -------------
bioruby.gemspec.erb | 21 +--------------------
2 files changed, 1 insertion(+), 33 deletions(-)
commit b5a8d385da8f2c1b6e1caf77295e590f55595944
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Sep 15 16:20:03 2017 +0900
bin/br_*.rb is moved to bio-executables gem
* The following executable files are moved to "bio-executables" gem.
* bin/br_biofetch.rb
* bin/br_bioflat.rb
* bin/br_biogetseq.rb
* bin/br_pmfetch.rb
bin/br_biofetch.rb | 71 ---------
bin/br_bioflat.rb | 293 ------------------------------------
bin/br_biogetseq.rb | 45 ------
bin/br_pmfetch.rb | 422 ----------------------------------------------------
4 files changed, 831 deletions(-)
delete mode 100755 bin/br_biofetch.rb
delete mode 100755 bin/br_bioflat.rb
delete mode 100755 bin/br_biogetseq.rb
delete mode 100755 bin/br_pmfetch.rb
commit eb61d89a366437570a0590a629cb75718866b236
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Sep 15 09:31:14 2017 +0900
regenerate bioruby.gemspec with rake regemspec
bioruby.gemspec | 44 +-------------------------------------------
1 file changed, 1 insertion(+), 43 deletions(-)
commit 6d40721d039fdb6b77af656f32ccabeabc427409
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Sep 15 09:29:33 2017 +0900
Remove BioRuby Shell files that are released as independent gem package
bin/bioruby | 47 --
lib/bio/shell.rb | 44 --
lib/bio/shell/core.rb | 578 ---------------------
lib/bio/shell/demo.rb | 146 ------
lib/bio/shell/interface.rb | 217 --------
lib/bio/shell/irb.rb | 94 ----
lib/bio/shell/object.rb | 71 ---
lib/bio/shell/plugin/blast.rb | 42 --
lib/bio/shell/plugin/codon.rb | 218 --------
lib/bio/shell/plugin/das.rb | 58 ---
lib/bio/shell/plugin/emboss.rb | 23 -
lib/bio/shell/plugin/entry.rb | 137 -----
lib/bio/shell/plugin/flatfile.rb | 101 ----
lib/bio/shell/plugin/midi.rb | 430 ---------------
lib/bio/shell/plugin/ncbirest.rb | 68 ---
lib/bio/shell/plugin/obda.rb | 45 --
lib/bio/shell/plugin/psort.rb | 56 --
lib/bio/shell/plugin/seq.rb | 248 ---------
lib/bio/shell/plugin/togows.rb | 40 --
.../generators/bioruby/bioruby_generator.rb | 29 --
.../generators/bioruby/templates/_classes.rhtml | 4 -
.../generators/bioruby/templates/_log.rhtml | 27 -
.../generators/bioruby/templates/_methods.rhtml | 11 -
.../generators/bioruby/templates/_modules.rhtml | 4 -
.../generators/bioruby/templates/_variables.rhtml | 7 -
.../generators/bioruby/templates/bioruby-bg.gif | Bin 1431 -> 0 bytes
.../generators/bioruby/templates/bioruby-gem.png | Bin 6951 -> 0 bytes
.../generators/bioruby/templates/bioruby-link.gif | Bin 2758 -> 0 bytes
.../generators/bioruby/templates/bioruby.css | 368 -------------
.../generators/bioruby/templates/bioruby.rhtml | 47 --
.../bioruby/templates/bioruby_controller.rb | 144 -----
.../generators/bioruby/templates/bioruby_helper.rb | 47 --
.../generators/bioruby/templates/commands.rhtml | 8 -
.../generators/bioruby/templates/history.rhtml | 10 -
.../generators/bioruby/templates/index.rhtml | 26 -
.../generators/bioruby/templates/spinner.gif | Bin 1542 -> 0 bytes
lib/bio/shell/script.rb | 25 -
lib/bio/shell/setup.rb | 108 ----
lib/bio/shell/web.rb | 102 ----
test/unit/bio/shell/plugin/test_seq.rb | 187 -------
test/unit/bio/test_shell.rb | 20 -
41 files changed, 3837 deletions(-)
delete mode 100755 bin/bioruby
delete mode 100644 lib/bio/shell.rb
delete mode 100644 lib/bio/shell/core.rb
delete mode 100644 lib/bio/shell/demo.rb
delete mode 100644 lib/bio/shell/interface.rb
delete mode 100644 lib/bio/shell/irb.rb
delete mode 100644 lib/bio/shell/object.rb
delete mode 100644 lib/bio/shell/plugin/blast.rb
delete mode 100644 lib/bio/shell/plugin/codon.rb
delete mode 100644 lib/bio/shell/plugin/das.rb
delete mode 100644 lib/bio/shell/plugin/emboss.rb
delete mode 100644 lib/bio/shell/plugin/entry.rb
delete mode 100644 lib/bio/shell/plugin/flatfile.rb
delete mode 100644 lib/bio/shell/plugin/midi.rb
delete mode 100644 lib/bio/shell/plugin/ncbirest.rb
delete mode 100644 lib/bio/shell/plugin/obda.rb
delete mode 100644 lib/bio/shell/plugin/psort.rb
delete mode 100644 lib/bio/shell/plugin/seq.rb
delete mode 100644 lib/bio/shell/plugin/togows.rb
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif
delete mode 100644 lib/bio/shell/script.rb
delete mode 100644 lib/bio/shell/setup.rb
delete mode 100644 lib/bio/shell/web.rb
delete mode 100644 test/unit/bio/shell/plugin/test_seq.rb
delete mode 100644 test/unit/bio/test_shell.rb
commit ab9feb6f1f495a2b3ca350005c6162c51178aecb
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Sep 13 22:13:59 2017 +0900
Suppress warning "assigned but unused variable"
lib/bio/io/flatfile/autodetection.rb | 5 +++++
1 file changed, 5 insertions(+)
commit cf486e327c253482f54e59b2e18f73db27641135
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Sep 13 22:10:53 2017 +0900
Suppress warning: "instance variable @top_strand not initialized"
* Suppress warning: "instance variable @top_strand not initialized".
To do so, force to raise NoMethodError when @top_strand is not
initialized or is nil. This should be changed to appropriate
exception in the future.
lib/bio/util/sirna.rb | 2 ++
1 file changed, 2 insertions(+)
commit 88477698f0e1b5a74f9682f26e97c5f90f6912b4
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Sep 13 21:31:38 2017 +0900
Suppress warning in Ruby 2.4: "constant ::Fixnum is deprecated"
lib/bio/db/soft.rb | 4 ++--
.../util/restriction_enzyme/range/sequence_range/calculated_cuts.rb | 2 +-
test/unit/bio/test_alignment.rb | 4 ++--
3 files changed, 5 insertions(+), 5 deletions(-)
commit f8cff14179cfeea0d685f4df756db71ceb6d5fab
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Sep 13 21:19:12 2017 +0900
Suppress warning "parentheses after method name is interpreted as an argument list, not a decomposed argument" in Ruby 2.4
lib/bio/map.rb | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
commit ddb25c2bf3872c6306a91e407d95caa2e136cee9
Author: Jun Aruga <jaruga@redhat.com>
Date: Fri Nov 18 11:14:38 2016 +0100
Gemfile for local development.
.travis.yml | 8 ++++----
gemfiles/Gemfile.travis-ruby2.2 => Gemfile | 0
bioruby.gemspec | 2 +-
3 files changed, 5 insertions(+), 5 deletions(-)
rename gemfiles/Gemfile.travis-ruby2.2 => Gemfile (100%)
commit 16faf6473b74eb172716b713ab757cb2ab2bcacc
Author: Jun Aruga <jaruga@redhat.com>
Date: Thu Nov 17 17:50:40 2016 +0100
Fixes ruby1.8 Travis failure that is because rdoc 4.3.0 requires Ruby >= 1.9.3.
gemfiles/Gemfile.travis-jruby1.8 | 3 ++-
gemfiles/Gemfile.travis-ruby1.8 | 3 ++-
2 files changed, 4 insertions(+), 2 deletions(-)
commit 146fd66b3a14972bcfd0e9bf8ec007d38c55ac39
Author: Naohisa Goto <ng@bioruby.org>
Date: Sat Aug 13 08:22:22 2016 +0900
Update URLs and use https for NCBI REST web services
lib/bio/io/ncbirest.rb | 50 ++++++++++++++++++++++++++------------------------
1 file changed, 26 insertions(+), 24 deletions(-)
commit 7abd46f058a17ac34b263714449756383622012d
Author: Naohisa Goto <ng@bioruby.org>
Date: Sat Aug 13 08:12:08 2016 +0900
New method Bio::Command#start_http_uri(uri) with tests
* lib/bio/command.rb: New method Bio::Command#start_http_uri(uri)
that supports HTTPS. Note that this method is intended to be
called only from BioRuby internals.
* lib/bio/command.rb: Bio::Command#post and #post_form are changed
to use the start_http_uri().
* test/network/bio/test_command.rb: tests for start_http_uri().
lib/bio/command.rb | 42 ++++++++++++++++++++++++++++++++++++++--
test/network/bio/test_command.rb | 17 ++++++++++++++++
2 files changed, 57 insertions(+), 2 deletions(-)
commit 11c680f6d64a60bdc0f4248951bf2d2ebafbc433
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 17 20:40:41 2016 +0900
gemfiles/Gemfile.*: remove dependency on libxml-ruby
* gemfiles/Gemfile.*: remove dependency on libxml-ruby.
Bio::PhyloXML required libxml-ruby but was already removed.
gemfiles/Gemfile.travis-jruby1.8 | 3 ---
gemfiles/Gemfile.travis-jruby1.9 | 3 ---
gemfiles/Gemfile.travis-rbx | 1 -
gemfiles/Gemfile.travis-ruby1.8 | 1 -
gemfiles/Gemfile.travis-ruby1.9 | 1 -
gemfiles/Gemfile.travis-ruby2.2 | 1 -
6 files changed, 10 deletions(-)
commit 09fa57f987445e8654de6a0d0cf7c45f7625600c
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 17 16:16:40 2016 +0900
regenerate bioruby.gemspec with rake regemspec
bioruby.gemspec | 10 +---------
1 file changed, 1 insertion(+), 9 deletions(-)
commit 87812d119820bf66767c7767cfec7554d7a00f3b
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 17 15:45:46 2016 +0900
README.rdoc: about bioruby-phyloxml and bio-biosql
README.rdoc | 10 ++++++++++
1 file changed, 10 insertions(+)
commit 2294f255f5f05f9f629a1e88c0e1f59bb74b32bc
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 17 15:42:46 2016 +0900
KNOWN_ISSUES.rdoc: remove descriptions about Bio::SQL
KNOWN_ISSUES.rdoc | 5 -----
1 file changed, 5 deletions(-)
commit 35a6f761dc5fa493b8311747dde7f2a54d8aee75
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 17 15:40:57 2016 +0900
README.rdoc: remove descriptions about Bio::SQL
README.rdoc | 13 +------------
1 file changed, 1 insertion(+), 12 deletions(-)
commit 46a5bf7acdc803b7e75225c41b23396c4619f25d
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 17 14:59:41 2016 +0900
remove autoload of Bio::SQL
lib/bio.rb | 1 -
1 file changed, 1 deletion(-)
commit 57bf535da34715beafccb902404cf1bb35b18af4
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Jun 17 14:48:46 2016 +0900
Removed Bio::SQL that have been moved to separate repository
* Bio::SQL is moved to https://github.com/bioruby/bioruby-biosql
and removed from this repository.
* List of deleted files:
* deleted: lib/bio/db/biosql/biosql_to_biosequence.rb
* deleted: lib/bio/db/biosql/sequence.rb
* deleted: lib/bio/io/biosql/ar-biosql.rb
* deleted: lib/bio/io/biosql/biosql.rb
* deleted: lib/bio/io/biosql/config/database.yml
* deleted: lib/bio/io/sql.rb
* deleted: test/unit/bio/db/biosql/tc_biosql.rb
* deleted: test/unit/bio/db/biosql/ts_suite_biosql.rb
lib/bio/db/biosql/biosql_to_biosequence.rb | 78 -----
lib/bio/db/biosql/sequence.rb | 444 -----------------------------
lib/bio/io/biosql/ar-biosql.rb | 257 -----------------
lib/bio/io/biosql/biosql.rb | 39 ---
lib/bio/io/biosql/config/database.yml | 21 --
lib/bio/io/sql.rb | 79 -----
test/unit/bio/db/biosql/tc_biosql.rb | 114 --------
test/unit/bio/db/biosql/ts_suite_biosql.rb | 8 -
8 files changed, 1040 deletions(-)
delete mode 100644 lib/bio/db/biosql/biosql_to_biosequence.rb
delete mode 100644 lib/bio/db/biosql/sequence.rb
delete mode 100644 lib/bio/io/biosql/ar-biosql.rb
delete mode 100644 lib/bio/io/biosql/biosql.rb
delete mode 100644 lib/bio/io/biosql/config/database.yml
delete mode 100644 lib/bio/io/sql.rb
delete mode 100644 test/unit/bio/db/biosql/tc_biosql.rb
delete mode 100644 test/unit/bio/db/biosql/ts_suite_biosql.rb
commit 476dcdbe2b21cd5adb641952ee3da92c2d593121
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Jun 8 12:38:22 2016 +0900
appveyor.yml: eliminate old Ruby versions and add Ruby 2.3
appveyor.yml | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
commit c26e2b77b75b5505a274822f53c6c5a8f842f6c0
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Jun 8 01:50:19 2016 +0900
.travis.yml: fix to use rbx-3.29
.travis.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit b524abedac9c85d4f8259191b973bc38a9fc557c
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Jun 8 01:45:48 2016 +0900
gemfiles/Gemfile.travis-jruby1.8: use old gem versions supporting Ruby 1.8
gemfiles/Gemfile.travis-jruby1.8 | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
commit c5df9268b77f1d4dc2b29e7cfb7baf3c528c1558
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Jun 8 01:42:40 2016 +0900
.travis.yml: use rbx-3.29 instead of rbx-3
.travis.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit b51b54894ca2d76d9c13680fd72b87951a10a1df
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Jun 8 01:25:18 2016 +0900
Workaround to avoid bug in old versions of Bundler
* gemfiles/prepare-gemspec.rb: execute "gem update bundler" to avoid
"NoMethodError: undefined method `spec' for nil:NilClass"
during "bundle install". This error may be due to a bug of Bundler
and the bug seems to be fixed in the latest version of Budler.
gemfiles/prepare-gemspec.rb | 4 ++++
1 file changed, 4 insertions(+)
commit a82424b4864e243ebf1f8cc7f181044798b34b5a
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Jun 8 01:20:15 2016 +0900
.travis.yml: add Ruby 2.3.1; use Ruby 2.2.5 instead of 2.2
.travis.yml | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
commit ae927514a5c2853d3839750af86bfcc1fc53e4f1
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Jun 8 00:54:22 2016 +0900
.travis.yml: add "sudo: false" for faster testing
.travis.yml | 1 +
1 file changed, 1 insertion(+)