bio 1.5.1 → 2.0.2
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +5 -5
- data/.travis.yml +35 -36
- data/ChangeLog +911 -2554
- data/{gemfiles/Gemfile.travis-ruby2.2 → Gemfile} +0 -3
- data/KNOWN_ISSUES.rdoc +10 -13
- data/LEGAL +0 -10
- data/README.rdoc +40 -96
- data/README_DEV.rdoc +5 -5
- data/RELEASE_NOTES.rdoc +118 -234
- data/Rakefile +13 -43
- data/appveyor.yml +29 -0
- data/bioruby.gemspec +18 -81
- data/bioruby.gemspec.erb +8 -28
- data/doc/ChangeLog-1.5.0 +2919 -0
- data/doc/RELEASE_NOTES-1.5.0.rdoc +285 -0
- data/doc/Tutorial.rd +6 -108
- data/doc/Tutorial.rd.html +19 -98
- data/gemfiles/Gemfile.travis-jruby1.8 +3 -5
- data/gemfiles/Gemfile.travis-jruby1.9 +0 -3
- data/gemfiles/Gemfile.travis-rbx +0 -3
- data/gemfiles/Gemfile.travis-ruby1.8 +3 -5
- data/gemfiles/Gemfile.travis-ruby1.9 +0 -3
- data/gemfiles/Gemfile.windows +6 -0
- data/gemfiles/prepare-gemspec.rb +4 -0
- data/lib/bio.rb +0 -10
- data/lib/bio/appl/blast/genomenet.rb +4 -4
- data/lib/bio/appl/blast/report.rb +40 -8
- data/lib/bio/appl/fasta/format10.rb +2 -1
- data/lib/bio/command.rb +10 -0
- data/lib/bio/data/codontable.rb +99 -3
- data/lib/bio/db/aaindex.rb +74 -5
- data/lib/bio/db/gff.rb +3 -1
- data/lib/bio/db/kegg/common.rb +14 -0
- data/lib/bio/db/kegg/genes.rb +26 -0
- data/lib/bio/db/kegg/pathway.rb +5 -11
- data/lib/bio/db/soft.rb +2 -2
- data/lib/bio/io/flatfile/autodetection.rb +5 -0
- data/lib/bio/io/togows.rb +5 -5
- data/lib/bio/map.rb +4 -4
- data/lib/bio/sequence/format.rb +1 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +1 -1
- data/lib/bio/util/sirna.rb +2 -0
- data/lib/bio/version.rb +6 -8
- data/sample/color_scheme_aa.rb +82 -0
- data/sample/color_scheme_na.rb +5 -6
- data/sample/fastq2html.cwl +23 -0
- data/sample/fastq2html.rb +94 -0
- data/sample/fastq2html.testdata.yaml +5 -0
- data/sample/na2aa.cwl +23 -0
- data/sample/na2aa.rb +11 -25
- data/sample/na2aa.testdata.yaml +7 -0
- data/sample/rev_comp.cwl +23 -0
- data/sample/rev_comp.rb +20 -0
- data/sample/rev_comp.testdata.yaml +7 -0
- data/sample/test_restriction_enzyme_long.rb +1 -1
- data/test/network/bio/db/kegg/test_genes_hsa7422.rb +91 -0
- data/test/unit/bio/appl/blast/test_report.rb +4 -4
- data/test/unit/bio/data/test_codontable.rb +3 -0
- data/test/unit/bio/db/test_gff.rb +5 -0
- data/test/unit/bio/test_alignment.rb +2 -2
- metadata +20 -77
- data/bin/bioruby +0 -47
- data/bin/br_biofetch.rb +0 -71
- data/bin/br_bioflat.rb +0 -293
- data/bin/br_biogetseq.rb +0 -45
- data/bin/br_pmfetch.rb +0 -422
- data/lib/bio/appl/blast/xmlparser.rb +0 -236
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +0 -78
- data/lib/bio/db/biosql/sequence.rb +0 -444
- data/lib/bio/db/phyloxml/phyloxml.xsd +0 -582
- data/lib/bio/db/phyloxml/phyloxml_elements.rb +0 -1197
- data/lib/bio/db/phyloxml/phyloxml_parser.rb +0 -1001
- data/lib/bio/db/phyloxml/phyloxml_writer.rb +0 -227
- data/lib/bio/io/biosql/ar-biosql.rb +0 -257
- data/lib/bio/io/biosql/biosql.rb +0 -39
- data/lib/bio/io/biosql/config/database.yml +0 -21
- data/lib/bio/io/sql.rb +0 -79
- data/lib/bio/shell.rb +0 -44
- data/lib/bio/shell/core.rb +0 -578
- data/lib/bio/shell/demo.rb +0 -146
- data/lib/bio/shell/interface.rb +0 -217
- data/lib/bio/shell/irb.rb +0 -94
- data/lib/bio/shell/object.rb +0 -71
- data/lib/bio/shell/plugin/blast.rb +0 -42
- data/lib/bio/shell/plugin/codon.rb +0 -218
- data/lib/bio/shell/plugin/das.rb +0 -58
- data/lib/bio/shell/plugin/emboss.rb +0 -23
- data/lib/bio/shell/plugin/entry.rb +0 -137
- data/lib/bio/shell/plugin/flatfile.rb +0 -101
- data/lib/bio/shell/plugin/midi.rb +0 -430
- data/lib/bio/shell/plugin/ncbirest.rb +0 -68
- data/lib/bio/shell/plugin/obda.rb +0 -45
- data/lib/bio/shell/plugin/psort.rb +0 -56
- data/lib/bio/shell/plugin/seq.rb +0 -248
- data/lib/bio/shell/plugin/togows.rb +0 -40
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +0 -29
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +0 -4
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +0 -27
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +0 -11
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +0 -4
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +0 -7
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +0 -368
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +0 -47
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +0 -144
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +0 -47
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +0 -8
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +0 -10
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +0 -26
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +0 -25
- data/lib/bio/shell/setup.rb +0 -108
- data/lib/bio/shell/web.rb +0 -102
- data/sample/test_phyloxml_big.rb +0 -205
- data/setup.rb +0 -1600
- data/test/data/phyloxml/apaf.xml +0 -666
- data/test/data/phyloxml/bcl_2.xml +0 -2097
- data/test/data/phyloxml/made_up.xml +0 -144
- data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +0 -65
- data/test/data/phyloxml/phyloxml_examples.xml +0 -415
- data/test/unit/bio/db/biosql/tc_biosql.rb +0 -114
- data/test/unit/bio/db/biosql/ts_suite_biosql.rb +0 -8
- data/test/unit/bio/db/test_phyloxml.rb +0 -821
- data/test/unit/bio/db/test_phyloxml_writer.rb +0 -334
- data/test/unit/bio/shell/plugin/test_seq.rb +0 -187
- data/test/unit/bio/test_shell.rb +0 -20
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
|
-
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
2
|
+
SHA256:
|
3
|
+
metadata.gz: 9c68318f6e170c45020baac59d2be85490d901837ffe5ec136b86ac80901618f
|
4
|
+
data.tar.gz: 5e2813540c9789252d3be786076fe56e6b64dc07655c0bee0873847b643c3dfa
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 03b065e96fcd4afcf1e6c95207ca2999d8855a16e25c11a3d2aa1478ff9ae3e0686887e501f53ff7b3fa4cbf10cd8200a0ac667282b191d7ade47e6122dfd678
|
7
|
+
data.tar.gz: 0c152f67d43b8ad359f2beef4dc84f134ab26f08490fb151a76fa5149380174cb65058831095c21618836eb01f1b785b88ed5cbf3cfb90687a6649f002aa51be
|
data/.travis.yml
CHANGED
@@ -1,60 +1,58 @@
|
|
1
1
|
language: ruby
|
2
2
|
rvm:
|
3
|
-
- 2.
|
4
|
-
- 2.
|
5
|
-
-
|
3
|
+
- 2.6
|
4
|
+
- 2.5
|
5
|
+
- 2.4
|
6
|
+
- 2.3.8
|
7
|
+
- 2.2.10
|
6
8
|
env:
|
7
9
|
- TESTOPTS=-v
|
8
10
|
gemfile:
|
9
|
-
-
|
11
|
+
- Gemfile
|
10
12
|
before_install:
|
11
|
-
- gem update --system 2.1.11
|
12
|
-
- gem --version
|
13
13
|
- mkdir /tmp/bioruby
|
14
14
|
- ruby gemfiles/modify-Gemfile.rb
|
15
15
|
- ruby gemfiles/prepare-gemspec.rb
|
16
16
|
matrix:
|
17
17
|
include:
|
18
|
-
- rvm:
|
19
|
-
gemfile: gemfiles/Gemfile.travis-ruby1.
|
18
|
+
- rvm: 2.0.0
|
19
|
+
gemfile: gemfiles/Gemfile.travis-ruby1.9
|
20
|
+
env: TESTOPTS=-v
|
21
|
+
- rvm: 2.1.10
|
22
|
+
gemfile: gemfiles/Gemfile.travis-ruby1.9
|
20
23
|
env: TESTOPTS=-v
|
21
|
-
- rvm:
|
24
|
+
- rvm: truffleruby
|
25
|
+
gemfile: gemfiles/Gemfile.travis-jruby1.9
|
26
|
+
env: TESTOPTS=-v
|
27
|
+
- rvm: rbx-3.29
|
22
28
|
gemfile: gemfiles/Gemfile.travis-rbx
|
23
29
|
env: TESTOPTS=-v
|
24
|
-
- rvm: jruby
|
25
|
-
gemfile: gemfiles/Gemfile.travis-jruby1.8
|
26
|
-
env: TMPDIR=/tmp/bioruby TESTOPTS=-v
|
27
|
-
- rvm: jruby-19mode
|
30
|
+
- rvm: jruby
|
28
31
|
gemfile: gemfiles/Gemfile.travis-jruby1.9
|
29
32
|
env: TMPDIR=/tmp/bioruby TESTOPTS=-v
|
30
|
-
- rvm: 2.
|
31
|
-
gemfile:
|
32
|
-
- rvm: 2.1.6
|
33
|
-
gemfile: gemfiles/Gemfile.travis-ruby1.9
|
34
|
-
env: BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test TESTOPTS=-v
|
35
|
-
- rvm: 2.1.6
|
36
|
-
gemfile: gemfiles/Gemfile.travis-ruby1.9
|
33
|
+
- rvm: 2.5
|
34
|
+
gemfile: Gemfile
|
37
35
|
env: BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
|
38
|
-
- rvm: jruby
|
39
|
-
gemfile: gemfiles/Gemfile.travis-jruby1.9
|
40
|
-
env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test TESTOPTS=-v
|
41
|
-
- rvm: jruby-19mode
|
36
|
+
- rvm: jruby
|
42
37
|
gemfile: gemfiles/Gemfile.travis-jruby1.9
|
43
38
|
env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
|
44
39
|
allow_failures:
|
45
|
-
- rvm:
|
40
|
+
- rvm: 1.8.7
|
41
|
+
gemfile: gemfiles/Gemfile.travis-ruby1.8
|
42
|
+
env: TESTOPTS=-v
|
43
|
+
- rvm: 1.9.3
|
44
|
+
gemfile: gemfiles/Gemfile.travis-ruby1.9
|
45
|
+
env: TESTOPTS=-v
|
46
|
+
- rvm: truffleruby
|
47
|
+
gemfile: gemfiles/Gemfile.travis-jruby1.9
|
48
|
+
env: TESTOPTS=-v
|
49
|
+
- rvm: rbx-3.29
|
46
50
|
gemfile: gemfiles/Gemfile.travis-rbx
|
47
51
|
env: TESTOPTS=-v
|
48
|
-
- rvm: jruby
|
49
|
-
gemfile: gemfiles/Gemfile.travis-jruby1.8
|
50
|
-
env: TMPDIR=/tmp/bioruby TESTOPTS=-v
|
51
|
-
- rvm: jruby-19mode
|
52
|
+
- rvm: jruby
|
52
53
|
gemfile: gemfiles/Gemfile.travis-jruby1.9
|
53
54
|
env: TMPDIR=/tmp/bioruby TESTOPTS=-v
|
54
|
-
- rvm: jruby
|
55
|
-
gemfile: gemfiles/Gemfile.travis-jruby1.9
|
56
|
-
env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=tar-integration-test TESTOPTS=-v
|
57
|
-
- rvm: jruby-19mode
|
55
|
+
- rvm: jruby
|
58
56
|
gemfile: gemfiles/Gemfile.travis-jruby1.9
|
59
57
|
env: TMPDIR=/tmp/bioruby BIORUBY_RAKE_DEFAULT_TASK=gem-test TESTOPTS=-v
|
60
58
|
|
@@ -65,8 +63,9 @@ matrix:
|
|
65
63
|
# - sudo apt-get update
|
66
64
|
# - sudo apt-get install libxml2-dev libexpat1-dev
|
67
65
|
|
68
|
-
#
|
66
|
+
# block build for the branches
|
69
67
|
branches:
|
70
|
-
|
71
|
-
-
|
68
|
+
except:
|
69
|
+
- biohackathon2008
|
70
|
+
- bioruby-1.4.3
|
72
71
|
|
data/ChangeLog
CHANGED
@@ -1,2999 +1,1356 @@
|
|
1
|
-
commit
|
1
|
+
commit fd420b713ca364e677ef3551919ec907791df86d
|
2
2
|
Author: Naohisa Goto <ng@bioruby.org>
|
3
|
-
Date:
|
3
|
+
Date: Thu Dec 31 23:51:08 2020 +0900
|
4
4
|
|
5
|
-
|
5
|
+
RELEASE_NOTES.rdoc: change some description
|
6
6
|
|
7
|
-
|
7
|
+
RELEASE_NOTES.rdoc | 2 +-
|
8
8
|
1 file changed, 1 insertion(+), 1 deletion(-)
|
9
9
|
|
10
|
-
commit
|
10
|
+
commit 0ed9b37f38fa1b00dcc1d422914e4cbdbbc5f6ab
|
11
11
|
Author: Naohisa Goto <ng@bioruby.org>
|
12
|
-
Date:
|
12
|
+
Date: Thu Dec 31 23:46:46 2020 +0900
|
13
13
|
|
14
|
-
|
14
|
+
regenerate bioruby.gemspec with rake regemspec
|
15
15
|
|
16
|
-
|
16
|
+
bioruby.gemspec | 2 +-
|
17
17
|
1 file changed, 1 insertion(+), 1 deletion(-)
|
18
18
|
|
19
|
-
commit
|
20
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
21
|
-
Date: Wed Sep 7 21:49:20 2016 +0900
|
22
|
-
|
23
|
-
Added release notes for 1.5.1 release
|
24
|
-
|
25
|
-
RELEASE_NOTES.rdoc | 26 ++++++++++++++++++++++++++
|
26
|
-
1 file changed, 26 insertions(+)
|
27
|
-
|
28
|
-
commit 47ada241ad6f3632dbbd77542befb82500b7195e
|
29
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
30
|
-
Date: Sat Aug 13 08:22:22 2016 +0900
|
31
|
-
|
32
|
-
Update URLs and use https for NCBI REST web services
|
33
|
-
|
34
|
-
lib/bio/io/ncbirest.rb | 50 ++++++++++++++++++++++++++------------------------
|
35
|
-
1 file changed, 26 insertions(+), 24 deletions(-)
|
36
|
-
|
37
|
-
commit 018c2aff1c7813e7b07362ecc8a25db334c0ae95
|
19
|
+
commit fa84b8fac653c26b9f8db429321ef49202554a69
|
38
20
|
Author: Naohisa Goto <ng@bioruby.org>
|
39
|
-
Date:
|
21
|
+
Date: Thu Dec 31 23:45:38 2020 +0900
|
40
22
|
|
41
|
-
|
42
|
-
|
43
|
-
* lib/bio/command.rb: New method Bio::Command#start_http_uri(uri)
|
44
|
-
that supports HTTPS. Note that this method is intended to be
|
45
|
-
called only from BioRuby internals.
|
46
|
-
* lib/bio/command.rb: Bio::Command#post and #post_form are changed
|
47
|
-
to use the start_http_uri().
|
48
|
-
* test/network/bio/test_command.rb: tests for start_http_uri().
|
23
|
+
prepare for BioRuby 2.0.2 release
|
49
24
|
|
50
|
-
lib/bio/
|
51
|
-
|
52
|
-
2 files changed, 57 insertions(+), 2 deletions(-)
|
25
|
+
lib/bio/version.rb | 2 +-
|
26
|
+
1 file changed, 1 insertion(+), 1 deletion(-)
|
53
27
|
|
54
|
-
commit
|
28
|
+
commit 32c5efccbad4e0d3440726383f863520ee242cc5
|
55
29
|
Author: Naohisa Goto <ng@bioruby.org>
|
56
|
-
Date: Thu
|
30
|
+
Date: Thu Dec 31 23:39:18 2020 +0900
|
57
31
|
|
58
|
-
|
32
|
+
update release notes for upcoming BioRuby 2.0.2
|
59
33
|
|
60
|
-
|
61
|
-
1 file changed,
|
34
|
+
RELEASE_NOTES.rdoc | 19 +++++++++++++++++++
|
35
|
+
1 file changed, 19 insertions(+)
|
62
36
|
|
63
|
-
commit
|
37
|
+
commit c2f6e62ab64bc532f442bccc0d76ced5380664ec
|
64
38
|
Author: Naohisa Goto <ng@bioruby.org>
|
65
|
-
Date: Thu
|
39
|
+
Date: Thu Dec 31 23:38:43 2020 +0900
|
66
40
|
|
67
|
-
|
41
|
+
add a known issue about Ruby 3.0
|
68
42
|
|
69
|
-
|
70
|
-
1 file changed,
|
43
|
+
KNOWN_ISSUES.rdoc | 10 +++++++++-
|
44
|
+
1 file changed, 9 insertions(+), 1 deletion(-)
|
71
45
|
|
72
|
-
commit
|
46
|
+
commit a733c0816da7c97ca0c23016b473b004fb755f54
|
73
47
|
Author: Naohisa Goto <ng@bioruby.org>
|
74
|
-
Date:
|
48
|
+
Date: Thu Dec 31 23:04:55 2020 +0900
|
75
49
|
|
76
|
-
|
50
|
+
remove deprecation warning of Gem::Specification#has_rdoc=
|
51
|
+
|
52
|
+
Gem::Specification#has_rdoc= have been deprecated since RubyGems 1.3.3
|
53
|
+
in 2009. (https://blog.rubygems.org/2009/05/04/1.3.3-released.html )
|
54
|
+
RDoc is always generated regardless of the value, and the line is
|
55
|
+
safely removed.
|
56
|
+
|
57
|
+
This fixes https://github.com/bioruby/bioruby/issues/138 .
|
58
|
+
Thanks to @jaysonvirissimo for reporting the issue.
|
77
59
|
|
78
|
-
|
79
|
-
|
60
|
+
bioruby.gemspec | 1 -
|
61
|
+
bioruby.gemspec.erb | 1 -
|
62
|
+
2 files changed, 2 deletions(-)
|
80
63
|
|
81
|
-
commit
|
64
|
+
commit bed6746ce62059795996eeb6e5ac65655bab12b5
|
82
65
|
Author: Naohisa Goto <ng@bioruby.org>
|
83
|
-
Date:
|
66
|
+
Date: Thu Dec 31 22:51:56 2020 +0900
|
84
67
|
|
85
|
-
|
68
|
+
require ruby's date library to avoid NameError for Date
|
69
|
+
|
70
|
+
In Bio::Sequence#output(:embl), NameError (uninitialized constant
|
71
|
+
Bio::Sequence::Format::INSDFeatureHelper::Date) is observed.
|
72
|
+
The error message is misleading because Date is provided by Ruby's
|
73
|
+
standard date library.
|
74
|
+
|
75
|
+
This fixes https://github.com/bioruby/bioruby/issues/135 .
|
76
|
+
Thanks to Dr. Mark Wilkinson for reporting the issue.
|
86
77
|
|
87
|
-
|
88
|
-
1 file changed,
|
78
|
+
lib/bio/sequence/format.rb | 1 +
|
79
|
+
1 file changed, 1 insertion(+)
|
89
80
|
|
90
|
-
commit
|
81
|
+
commit 5f3aa79fdaf6dd5551d51663ca2e9b6f5e56d855
|
91
82
|
Author: Naohisa Goto <ng@bioruby.org>
|
92
|
-
Date:
|
83
|
+
Date: Fri Nov 6 17:45:12 2020 +0900
|
93
84
|
|
94
|
-
|
85
|
+
fix mistaken URLs
|
95
86
|
|
96
|
-
.
|
97
|
-
1 file changed,
|
87
|
+
README.rdoc | 6 +++---
|
88
|
+
1 file changed, 3 insertions(+), 3 deletions(-)
|
98
89
|
|
99
|
-
commit
|
90
|
+
commit d5e1670ee4863cc60d3aa08432a7ee3b1e445439
|
100
91
|
Author: Naohisa Goto <ng@bioruby.org>
|
101
|
-
Date:
|
92
|
+
Date: Fri Sep 6 15:48:45 2019 +0900
|
102
93
|
|
103
|
-
|
94
|
+
BioRuby 2.0.1 is released
|
104
95
|
|
105
|
-
|
106
|
-
|
107
|
-
2 files changed, 22 insertions(+)
|
96
|
+
ChangeLog | 185 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|
97
|
+
1 file changed, 185 insertions(+)
|
108
98
|
|
109
|
-
commit
|
99
|
+
commit 21bf51a1ec8c18c9cdf8528ffc3c59c503cef042
|
110
100
|
Author: Naohisa Goto <ng@bioruby.org>
|
111
|
-
Date:
|
101
|
+
Date: Fri Sep 6 15:45:47 2019 +0900
|
112
102
|
|
113
|
-
|
103
|
+
RELEASE_NOTES.rdoc: describe notable changes since 2.0.0
|
114
104
|
|
115
|
-
|
116
|
-
1 file changed,
|
105
|
+
RELEASE_NOTES.rdoc | 40 ++++++++++++++++++++++++++++++++++++++++
|
106
|
+
1 file changed, 40 insertions(+)
|
117
107
|
|
118
|
-
commit
|
108
|
+
commit 9092a629e0e28b416ee7288d349fb9d73dd2b961
|
119
109
|
Author: Naohisa Goto <ng@bioruby.org>
|
120
|
-
Date:
|
110
|
+
Date: Fri Sep 6 15:06:11 2019 +0900
|
121
111
|
|
122
112
|
regenerate bioruby.gemspec with rake regemspec
|
123
113
|
|
124
|
-
bioruby.gemspec |
|
125
|
-
1 file changed,
|
126
|
-
|
127
|
-
commit 608850beb33f3f7333f05307202b766adb350eb9
|
128
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
129
|
-
Date: Tue Jun 30 23:54:59 2015 +0900
|
130
|
-
|
131
|
-
description about updating of Ruby's License
|
114
|
+
bioruby.gemspec | 11 ++++++++++-
|
115
|
+
1 file changed, 10 insertions(+), 1 deletion(-)
|
132
116
|
|
133
|
-
|
134
|
-
1 file changed, 9 insertions(+)
|
135
|
-
|
136
|
-
commit f54bcfc20d20935db4e342e5988c0b7f59c131b3
|
117
|
+
commit 59e24b6e55d2c9a8887e8e01a91999d33a008042
|
137
118
|
Author: Naohisa Goto <ng@bioruby.org>
|
138
|
-
Date:
|
119
|
+
Date: Fri Sep 6 15:04:33 2019 +0900
|
139
120
|
|
140
|
-
|
121
|
+
prepare for BioRuby 2.0.1 release
|
141
122
|
|
142
|
-
|
143
|
-
1 file changed,
|
144
|
-
create mode 100644 BSDL
|
123
|
+
lib/bio/version.rb | 2 +-
|
124
|
+
1 file changed, 1 insertion(+), 1 deletion(-)
|
145
125
|
|
146
|
-
commit
|
126
|
+
commit 9635a38a158db434fd2b6aff7a2ee75622ddecef
|
147
127
|
Author: Naohisa Goto <ng@bioruby.org>
|
148
|
-
Date:
|
128
|
+
Date: Fri Sep 6 14:51:23 2019 +0900
|
149
129
|
|
150
|
-
|
130
|
+
sample/fastq2html.rb: A html visualization of FASTQ sequences
|
131
|
+
|
132
|
+
* sample/fastq2html: A html visualization of FASTQ sequences.
|
133
|
+
Each sequence is colored with the quality score.
|
134
|
+
* sample/fastq2html.cwl: CWL workflow for the above sample script
|
135
|
+
* sample/fastq2html.testdata.yaml: Test data for the above workflow
|
151
136
|
|
152
|
-
|
153
|
-
|
154
|
-
|
137
|
+
sample/fastq2html.cwl | 23 ++++++++++
|
138
|
+
sample/fastq2html.rb | 94 +++++++++++++++++++++++++++++++++++++++++
|
139
|
+
sample/fastq2html.testdata.yaml | 5 +++
|
140
|
+
3 files changed, 122 insertions(+)
|
141
|
+
create mode 100644 sample/fastq2html.cwl
|
142
|
+
create mode 100644 sample/fastq2html.rb
|
143
|
+
create mode 100644 sample/fastq2html.testdata.yaml
|
155
144
|
|
156
|
-
commit
|
145
|
+
commit 6bbcf8b66310c225d686f2c59359680a0bc0b4b6
|
157
146
|
Author: Naohisa Goto <ng@bioruby.org>
|
158
|
-
Date:
|
147
|
+
Date: Fri Sep 6 14:42:19 2019 +0900
|
159
148
|
|
160
|
-
|
149
|
+
sample/rev_comp.rb: Generates reverse-complement sequences
|
150
|
+
|
151
|
+
* sample/rev_comp.rb: Generates reverse-complement sequences of
|
152
|
+
the given nucleotide sequences.
|
153
|
+
* sample/rev_comp.cwl: CWL cowkflow for the sample script
|
154
|
+
* sample/rev_comp.testdata.yaml: Test data for the above CWL workflow
|
161
155
|
|
162
|
-
|
163
|
-
|
156
|
+
sample/rev_comp.cwl | 23 +++++++++++++++++++++++
|
157
|
+
sample/rev_comp.rb | 20 ++++++++++++++++++++
|
158
|
+
sample/rev_comp.testdata.yaml | 7 +++++++
|
159
|
+
3 files changed, 50 insertions(+)
|
160
|
+
create mode 100644 sample/rev_comp.cwl
|
161
|
+
create mode 100644 sample/rev_comp.rb
|
162
|
+
create mode 100644 sample/rev_comp.testdata.yaml
|
164
163
|
|
165
|
-
commit
|
164
|
+
commit ff0e6c3c6b6f1b56d81b5a4b579a6d0984bfc607
|
166
165
|
Author: Naohisa Goto <ng@bioruby.org>
|
167
|
-
Date:
|
166
|
+
Date: Fri Sep 6 14:40:45 2019 +0900
|
168
167
|
|
169
|
-
|
168
|
+
sample/color_scheme_(na|aa).rb: use String#each_char instead of each_byte
|
170
169
|
|
171
|
-
|
172
|
-
|
170
|
+
sample/color_scheme_aa.rb | 6 +++---
|
171
|
+
sample/color_scheme_na.rb | 6 +++---
|
172
|
+
2 files changed, 6 insertions(+), 6 deletions(-)
|
173
173
|
|
174
|
-
commit
|
174
|
+
commit 6f7c1be09aa3d6cdb76fd029fc0f84efda31c907
|
175
175
|
Author: Naohisa Goto <ng@bioruby.org>
|
176
|
-
Date:
|
176
|
+
Date: Thu Sep 5 17:32:07 2019 +0900
|
177
177
|
|
178
|
-
|
178
|
+
sample/color_scheme_aa.rb: new sample based on color_scheme_na.rb
|
179
179
|
|
180
|
-
|
181
|
-
|
182
|
-
|
180
|
+
sample/color_scheme_aa.rb | 82 +++++++++++++++++++++++++++++++++++++++++++++++
|
181
|
+
1 file changed, 82 insertions(+)
|
182
|
+
create mode 100644 sample/color_scheme_aa.rb
|
183
183
|
|
184
|
-
commit
|
184
|
+
commit 51864c3857178f58133b759f7608b8d6d8991c44
|
185
185
|
Author: Naohisa Goto <ng@bioruby.org>
|
186
|
-
Date:
|
186
|
+
Date: Thu Sep 5 17:13:20 2019 +0900
|
187
187
|
|
188
|
-
|
188
|
+
sample/color_scheme_na.rb: use const_get instead of eval
|
189
189
|
|
190
|
-
|
191
|
-
1 file changed,
|
190
|
+
sample/color_scheme_na.rb | 2 +-
|
191
|
+
1 file changed, 1 insertion(+), 1 deletion(-)
|
192
192
|
|
193
|
-
commit
|
193
|
+
commit ba0b554971a9a387a54fc04c5002853d91357347
|
194
194
|
Author: Naohisa Goto <ng@bioruby.org>
|
195
|
-
Date:
|
195
|
+
Date: Thu Sep 5 17:02:20 2019 +0900
|
196
196
|
|
197
|
-
|
197
|
+
sample/na2aa.cwl: inputBinding position -1 for the script
|
198
198
|
|
199
|
-
*
|
200
|
-
|
201
|
-
Thanks to Jose Irizarry who reports and sends suggested fix.
|
202
|
-
(https://github.com/bioruby/bioruby/pull/83 )
|
199
|
+
* sample/na2aa.cwl: inputBinding position -1 is used for the script
|
200
|
+
to emphasize that the argument is the first one.
|
203
201
|
|
204
|
-
|
202
|
+
sample/na2aa.cwl | 2 +-
|
205
203
|
1 file changed, 1 insertion(+), 1 deletion(-)
|
206
204
|
|
207
|
-
commit
|
208
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
209
|
-
Date: Tue Jun 30 18:45:51 2015 +0900
|
210
|
-
|
211
|
-
regenerate bioruby.gemspec with rake regemspec
|
212
|
-
|
213
|
-
bioruby.gemspec | 1 +
|
214
|
-
1 file changed, 1 insertion(+)
|
215
|
-
|
216
|
-
commit a151e51a44b3dd93e5d075d71954f639eaec339e
|
205
|
+
commit 26a27ec261e2251f3ff3a85007147d33682778d0
|
217
206
|
Author: Naohisa Goto <ng@bioruby.org>
|
218
|
-
Date:
|
207
|
+
Date: Thu Sep 5 16:56:08 2019 +0900
|
219
208
|
|
220
|
-
|
209
|
+
sample/color_scheme_na.rb: Supports more file formats
|
210
|
+
|
211
|
+
* sample/color_scheme_na.rb: Supports more file formats other than
|
212
|
+
fasta format, by using Bio::Flatfile.
|
221
213
|
|
222
|
-
|
223
|
-
1 file changed,
|
214
|
+
sample/color_scheme_na.rb | 3 +--
|
215
|
+
1 file changed, 1 insertion(+), 2 deletions(-)
|
224
216
|
|
225
|
-
commit
|
217
|
+
commit 5c053a606382bb578a2b6884ee639805154433e5
|
226
218
|
Author: Naohisa Goto <ng@bioruby.org>
|
227
|
-
Date:
|
219
|
+
Date: Thu Sep 5 12:32:00 2019 +0900
|
228
220
|
|
229
|
-
|
221
|
+
sample/na2aa.cwl: use inputBinding
|
230
222
|
|
231
|
-
|
232
|
-
1 file changed,
|
223
|
+
sample/na2aa.cwl | 5 ++++-
|
224
|
+
1 file changed, 4 insertions(+), 1 deletion(-)
|
233
225
|
|
234
|
-
commit
|
226
|
+
commit 6a3c3e02f08549d47dda00dca92d55bbadfc468f
|
235
227
|
Author: Naohisa Goto <ng@bioruby.org>
|
236
|
-
Date:
|
228
|
+
Date: Wed Sep 4 22:59:21 2019 +0900
|
237
229
|
|
238
|
-
|
230
|
+
Sample CWL workflow to run sample/na2aa.rb
|
239
231
|
|
240
|
-
*
|
241
|
-
|
242
|
-
provided by bundled gem since Ruby 2.2.
|
232
|
+
* na2aa.cwl: A sample CWL workflow to run na2aa.rb in sample/ dir
|
233
|
+
* na2aa.testdata.yaml: Test data for the workflow
|
243
234
|
|
244
|
-
.
|
245
|
-
|
246
|
-
2 files changed,
|
247
|
-
create mode 100644
|
235
|
+
sample/na2aa.cwl | 20 ++++++++++++++++++++
|
236
|
+
sample/na2aa.testdata.yaml | 7 +++++++
|
237
|
+
2 files changed, 27 insertions(+)
|
238
|
+
create mode 100644 sample/na2aa.cwl
|
239
|
+
create mode 100644 sample/na2aa.testdata.yaml
|
248
240
|
|
249
|
-
commit
|
241
|
+
commit 960b885036f549863e3cfe9c693c90f9bef27d3d
|
250
242
|
Author: Naohisa Goto <ng@bioruby.org>
|
251
|
-
Date:
|
243
|
+
Date: Wed Sep 4 21:00:50 2019 +0900
|
252
244
|
|
253
|
-
|
254
|
-
|
255
|
-
* Bump up version to 1.5.0-dev (1.5.0.20150630)
|
256
|
-
* Simplify the versioning rules.
|
257
|
-
* We will adopt the Semantic Versioning since BioRuby 1.5.1.
|
245
|
+
LEGAL: na2aa.rb is now Ruby's License
|
258
246
|
|
259
|
-
|
260
|
-
|
261
|
-
lib/bio/version.rb | 17 ++++++++---------
|
262
|
-
3 files changed, 13 insertions(+), 27 deletions(-)
|
247
|
+
LEGAL | 1 -
|
248
|
+
1 file changed, 1 deletion(-)
|
263
249
|
|
264
|
-
commit
|
250
|
+
commit 7af9e81988939007eb36dab6b102a7422e8196d8
|
265
251
|
Author: Naohisa Goto <ng@bioruby.org>
|
266
|
-
Date:
|
252
|
+
Date: Wed Sep 4 14:34:05 2019 +0900
|
267
253
|
|
268
|
-
|
254
|
+
sample/na2aa.rb: Completely rewritten
|
269
255
|
|
270
|
-
*
|
271
|
-
|
256
|
+
* sample/na2aa.rb: Completely rewritten. License is changed because
|
257
|
+
old code is completely wiped out. Note that the old code always
|
258
|
+
raises error due to a bug in the code.
|
259
|
+
* The old code was trying to replace 'X' (any) to '-' (gap) but
|
260
|
+
the new code does not modify translated sequences anymore.
|
272
261
|
|
273
|
-
|
274
|
-
1 file changed,
|
262
|
+
sample/na2aa.rb | 36 +++++++++++-------------------------
|
263
|
+
1 file changed, 11 insertions(+), 25 deletions(-)
|
275
264
|
|
276
|
-
commit
|
265
|
+
commit cf8cac5e32db42b6683c1a837adc9e1c04994062
|
277
266
|
Author: Naohisa Goto <ng@bioruby.org>
|
278
|
-
Date:
|
267
|
+
Date: Mon Sep 2 17:11:08 2019 +0900
|
279
268
|
|
280
|
-
|
269
|
+
Bug fix: Bio::GFF::GFF2::Record.parse did not return correct object
|
281
270
|
|
282
|
-
lib/bio/
|
283
|
-
|
271
|
+
lib/bio/db/gff.rb | 4 +++-
|
272
|
+
test/unit/bio/db/test_gff.rb | 5 +++++
|
273
|
+
2 files changed, 8 insertions(+), 1 deletion(-)
|
284
274
|
|
285
|
-
commit
|
275
|
+
commit 80b387e7e2bb8570d9204e389b6c5d90c6ea31de
|
286
276
|
Author: Naohisa Goto <ng@bioruby.org>
|
287
|
-
Date:
|
277
|
+
Date: Fri Jun 14 14:33:19 2019 +0900
|
288
278
|
|
289
|
-
|
279
|
+
BioRuby 2.0.0 is released
|
290
280
|
|
291
|
-
|
292
|
-
1 file changed,
|
281
|
+
ChangeLog | 1051 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
|
282
|
+
1 file changed, 1043 insertions(+), 8 deletions(-)
|
293
283
|
|
294
|
-
commit
|
284
|
+
commit 2e4046517fd8ee1c105ef53131e69f787d790099
|
295
285
|
Author: Naohisa Goto <ng@bioruby.org>
|
296
|
-
Date:
|
286
|
+
Date: Fri Jun 14 14:23:19 2019 +0900
|
297
287
|
|
298
|
-
|
288
|
+
Add "Recommended Plugins" section and description is moved to it
|
299
289
|
|
300
|
-
|
301
|
-
|
302
|
-
gemfiles/Gemfile.travis-ruby1.9 | 3 ---
|
303
|
-
3 files changed, 9 deletions(-)
|
290
|
+
README.rdoc | 22 +++++++++++++++-------
|
291
|
+
1 file changed, 15 insertions(+), 7 deletions(-)
|
304
292
|
|
305
|
-
commit
|
293
|
+
commit 7a533e4f57edcebb5dfe15fdddc9fbc986d2b7ec
|
306
294
|
Author: Naohisa Goto <ng@bioruby.org>
|
307
|
-
Date:
|
295
|
+
Date: Fri Jun 14 14:17:08 2019 +0900
|
308
296
|
|
309
|
-
|
297
|
+
fix directory name
|
310
298
|
|
311
|
-
.
|
312
|
-
1 file changed,
|
299
|
+
README.rdoc | 2 +-
|
300
|
+
1 file changed, 1 insertion(+), 1 deletion(-)
|
313
301
|
|
314
|
-
commit
|
302
|
+
commit 805266c9c900903156efd0baa8c1e6ee524a8147
|
315
303
|
Author: Naohisa Goto <ng@bioruby.org>
|
316
|
-
Date:
|
304
|
+
Date: Fri Jun 14 14:14:52 2019 +0900
|
317
305
|
|
318
|
-
|
306
|
+
add description about recommended plugins
|
319
307
|
|
320
|
-
|
321
|
-
1 file changed,
|
308
|
+
README.rdoc | 11 +++++++++++
|
309
|
+
1 file changed, 11 insertions(+)
|
322
310
|
|
323
|
-
commit
|
311
|
+
commit 02b7d8b9bc5dcd56f501a15e5e820f450153aa1c
|
324
312
|
Author: Naohisa Goto <ng@bioruby.org>
|
325
|
-
Date:
|
313
|
+
Date: Fri Jun 14 13:33:30 2019 +0900
|
326
314
|
|
327
|
-
|
315
|
+
prepare to release BioRuby 2.0.0
|
328
316
|
|
329
|
-
|
330
|
-
1 file changed,
|
317
|
+
lib/bio/version.rb | 4 ++--
|
318
|
+
1 file changed, 2 insertions(+), 2 deletions(-)
|
331
319
|
|
332
|
-
commit
|
320
|
+
commit f1fed8dacb425d19c12abec5d4faeb733827f80f
|
333
321
|
Author: Naohisa Goto <ng@bioruby.org>
|
334
|
-
Date:
|
322
|
+
Date: Fri Jun 14 13:31:08 2019 +0900
|
335
323
|
|
336
|
-
|
324
|
+
regenerate bioruby.gemspec with rake regemspec
|
337
325
|
|
338
|
-
|
339
|
-
1 file changed,
|
326
|
+
bioruby.gemspec | 6 +++---
|
327
|
+
1 file changed, 3 insertions(+), 3 deletions(-)
|
340
328
|
|
341
|
-
commit
|
329
|
+
commit 3952ec9d5ce1e3ceea9734f667d36595808c4989
|
342
330
|
Author: Naohisa Goto <ng@bioruby.org>
|
343
|
-
Date:
|
331
|
+
Date: Fri Jun 14 13:28:19 2019 +0900
|
344
332
|
|
345
|
-
|
346
|
-
|
347
|
-
* deleted lib/bio/shell/plugin/soap.rb because Bio::SOAPWSDL and
|
348
|
-
all SOAP client classes in BioRuby are removed.
|
333
|
+
Remove xmlparser dependency from Gemfile and gemfiles/Gemfile.*
|
349
334
|
|
350
|
-
|
351
|
-
|
352
|
-
|
335
|
+
Gemfile | 2 --
|
336
|
+
gemfiles/Gemfile.travis-rbx | 2 --
|
337
|
+
gemfiles/Gemfile.travis-ruby1.8 | 2 --
|
338
|
+
gemfiles/Gemfile.travis-ruby1.9 | 2 --
|
339
|
+
gemfiles/Gemfile.windows | 2 --
|
340
|
+
5 files changed, 10 deletions(-)
|
353
341
|
|
354
|
-
commit
|
342
|
+
commit d4a8ee7ae3d3b13a8be4c57c1f8db5b29f2c4a13
|
355
343
|
Author: Naohisa Goto <ng@bioruby.org>
|
356
|
-
Date:
|
344
|
+
Date: Fri Jun 14 12:34:45 2019 +0900
|
357
345
|
|
358
|
-
|
346
|
+
RELEASE_NOTES.rdoc: update aboue new features and improvements
|
359
347
|
|
360
|
-
|
361
|
-
1 file changed,
|
348
|
+
RELEASE_NOTES.rdoc | 15 +++++++++++++--
|
349
|
+
1 file changed, 13 insertions(+), 2 deletions(-)
|
362
350
|
|
363
|
-
commit
|
351
|
+
commit 2d4170a2a0262f5d75cef5a54b5d6f3da298f145
|
364
352
|
Author: Naohisa Goto <ng@bioruby.org>
|
365
|
-
Date:
|
353
|
+
Date: Fri Jun 14 12:24:12 2019 +0900
|
366
354
|
|
367
|
-
|
355
|
+
Tests added in the previous commit is moved and modified
|
368
356
|
|
369
|
-
*
|
370
|
-
|
357
|
+
* test/network/bio/db/kegg/test_genes_hsa7422.rb: tests added in the
|
358
|
+
previous commit is moved to the file and modified to get data
|
359
|
+
from the internet for avoiding KEGG data license issue.
|
360
|
+
Note that some of the tests might be fail in the near future due to
|
361
|
+
the database entry updates.
|
371
362
|
|
372
|
-
|
373
|
-
|
374
|
-
|
363
|
+
test/network/bio/db/kegg/test_genes_hsa7422.rb | 91 ++++++++++++++++++++++++++
|
364
|
+
test/unit/bio/db/kegg/test_genes.rb | 51 ---------------
|
365
|
+
2 files changed, 91 insertions(+), 51 deletions(-)
|
366
|
+
create mode 100644 test/network/bio/db/kegg/test_genes_hsa7422.rb
|
375
367
|
|
376
|
-
commit
|
377
|
-
Author:
|
378
|
-
Date:
|
368
|
+
commit 67f8105acf22e88a7624305743ad13802ffed124
|
369
|
+
Author: kojix2 <2xijok@gmail.com>
|
370
|
+
Date: Mon Oct 22 00:46:31 2018 +0900
|
379
371
|
|
380
|
-
|
372
|
+
add DiseasesAsHash to KEGG/Common
|
381
373
|
|
382
|
-
lib/bio.rb
|
383
|
-
|
374
|
+
lib/bio/db/kegg/common.rb | 14 ++++++++++
|
375
|
+
lib/bio/db/kegg/genes.rb | 26 +++++++++++++++++++
|
376
|
+
lib/bio/db/kegg/pathway.rb | 16 ++++--------
|
377
|
+
test/unit/bio/db/kegg/test_genes.rb | 51 +++++++++++++++++++++++++++++++++++++
|
378
|
+
4 files changed, 96 insertions(+), 11 deletions(-)
|
384
379
|
|
385
|
-
commit
|
380
|
+
commit 9dbb655e1c3ec7460b77f1d0ea475531ac3a9361
|
386
381
|
Author: Naohisa Goto <ng@bioruby.org>
|
387
|
-
Date:
|
382
|
+
Date: Fri Jun 14 11:37:11 2019 +0900
|
388
383
|
|
389
|
-
|
390
|
-
|
391
|
-
* Bio::SOAPWSDL is removed because SOAP4R (SOAP/WSDL library in Ruby)
|
392
|
-
is no longer bundled with Ruby since Ruby 1.9. For Ruby 1.9 or later,
|
393
|
-
some gems of SOAP4R are available, but we think they are not
|
394
|
-
well-maintained. Moreover, many SOAP servers have been retired
|
395
|
-
(see previous commits). So, we give up maintaining Bio::SOAPWSDL.
|
384
|
+
update documents for upcoming new release
|
396
385
|
|
397
|
-
|
398
|
-
|
399
|
-
|
400
|
-
|
401
|
-
|
402
|
-
|
403
|
-
delete mode 100644 test/unit/bio/io/test_soapwsdl.rb
|
386
|
+
KNOWN_ISSUES.rdoc | 14 +++-----
|
387
|
+
LEGAL | 9 ------
|
388
|
+
README.rdoc | 92 +++++++----------------------------------------------
|
389
|
+
README_DEV.rdoc | 10 +++---
|
390
|
+
RELEASE_NOTES.rdoc | 93 +++++++++++++++++++++++++++++++++++++++++++-----------
|
391
|
+
5 files changed, 96 insertions(+), 122 deletions(-)
|
404
392
|
|
405
|
-
commit
|
393
|
+
commit 6f388019a035a41a8867c6a03ef7e2707d1edce4
|
406
394
|
Author: Naohisa Goto <ng@bioruby.org>
|
407
|
-
Date:
|
395
|
+
Date: Fri Jun 14 11:32:40 2019 +0900
|
408
396
|
|
409
|
-
|
397
|
+
.travis.yml: move 1.8.7 and 1.9.3 to allow_failures; update ruby versions
|
410
398
|
|
411
|
-
|
412
|
-
1 file changed,
|
399
|
+
.travis.yml | 23 ++++++++++++-----------
|
400
|
+
1 file changed, 12 insertions(+), 11 deletions(-)
|
413
401
|
|
414
|
-
commit
|
402
|
+
commit f2cbe9db9b78df653d774a7676e00f6f1a212b23
|
415
403
|
Author: Naohisa Goto <ng@bioruby.org>
|
416
|
-
Date:
|
404
|
+
Date: Fri Jun 14 11:18:27 2019 +0900
|
417
405
|
|
418
|
-
|
406
|
+
.travis.yml: Remove jobs using "tar-integration-test"
|
419
407
|
|
420
|
-
|
421
|
-
1 file changed,
|
408
|
+
.travis.yml | 9 ---------
|
409
|
+
1 file changed, 9 deletions(-)
|
422
410
|
|
423
|
-
commit
|
411
|
+
commit 68f28e81e3fa566843b548f1899549adcad5225a
|
424
412
|
Author: Naohisa Goto <ng@bioruby.org>
|
425
|
-
Date:
|
413
|
+
Date: Fri Jun 14 11:10:18 2019 +0900
|
426
414
|
|
427
|
-
remove
|
415
|
+
remove "rake tar-install" and "rake tar-integration-test" tasks
|
416
|
+
|
417
|
+
* Rakefile: Remove "tar-install" and "tar-integration-test" tasks
|
418
|
+
because they use setup.rb that is removed from the repository.
|
428
419
|
|
429
|
-
|
430
|
-
1 file changed,
|
431
|
-
delete mode 100644 lib/bio/io/higet.rb
|
420
|
+
Rakefile | 34 ----------------------------------
|
421
|
+
1 file changed, 34 deletions(-)
|
432
422
|
|
433
|
-
commit
|
423
|
+
commit 0cbdb4586f2231a68579105dbc7f0fb413b38a96
|
434
424
|
Author: Naohisa Goto <ng@bioruby.org>
|
435
|
-
Date:
|
425
|
+
Date: Fri Jun 14 10:48:15 2019 +0900
|
436
426
|
|
437
|
-
|
427
|
+
next bioruby version will be 2.0.0
|
438
428
|
|
439
|
-
|
440
|
-
1 file changed,
|
429
|
+
lib/bio/version.rb | 2 +-
|
430
|
+
1 file changed, 1 insertion(+), 1 deletion(-)
|
441
431
|
|
442
|
-
commit
|
432
|
+
commit 300d10b9791b7f0c0eff1d0544cae63fecc3b31a
|
443
433
|
Author: Naohisa Goto <ng@bioruby.org>
|
444
|
-
Date:
|
434
|
+
Date: Fri Jun 14 10:41:12 2019 +0900
|
445
435
|
|
446
|
-
|
436
|
+
Remove setup.rb. Use RubyGems to install BioRuby.
|
447
437
|
|
448
|
-
|
449
|
-
1 file changed,
|
438
|
+
setup.rb | 1600 --------------------------------------------------------------
|
439
|
+
1 file changed, 1600 deletions(-)
|
440
|
+
delete mode 100644 setup.rb
|
450
441
|
|
451
|
-
commit
|
442
|
+
commit a74683d9acfc16d0d715b020839839afc8b43350
|
452
443
|
Author: Naohisa Goto <ng@bioruby.org>
|
453
|
-
Date:
|
444
|
+
Date: Fri Jun 14 02:28:31 2019 +0900
|
454
445
|
|
455
|
-
|
456
|
-
|
457
|
-
* extconf.rb is deleted because no native extensions are included in
|
458
|
-
BioRuby and to avoid potential confusions. Nowadays, extconf.rb is
|
459
|
-
usually used only for building native extensions. Use gem or
|
460
|
-
setup.rb to install BioRuby.
|
446
|
+
try to require "bio-blast-xmlparser" provided by separete gem
|
461
447
|
|
462
|
-
|
463
|
-
1 file changed,
|
464
|
-
delete mode 100644 extconf.rb
|
448
|
+
lib/bio/appl/blast/report.rb | 8 ++++++++
|
449
|
+
1 file changed, 8 insertions(+)
|
465
450
|
|
466
|
-
commit
|
451
|
+
commit de1c1e33aed392d4e2265a028b8acb50501f56bd
|
467
452
|
Author: Naohisa Goto <ng@bioruby.org>
|
468
|
-
Date:
|
453
|
+
Date: Sat Sep 16 04:49:21 2017 +0900
|
469
454
|
|
470
|
-
|
455
|
+
check existance of a private method instead of XMLParser constant
|
471
456
|
|
472
|
-
test/unit/bio/
|
473
|
-
1 file changed,
|
457
|
+
test/unit/bio/appl/blast/test_report.rb | 8 ++++----
|
458
|
+
1 file changed, 4 insertions(+), 4 deletions(-)
|
474
459
|
|
475
|
-
commit
|
460
|
+
commit 3f54d19c44411e845b32c522fc0deca4288dcf07
|
476
461
|
Author: Naohisa Goto <ng@bioruby.org>
|
477
|
-
Date:
|
462
|
+
Date: Sat Sep 16 04:39:19 2017 +0900
|
478
463
|
|
479
|
-
|
464
|
+
xml_set_parameter is moved from xmlparser.rb etc.
|
480
465
|
|
481
|
-
*
|
482
|
-
|
483
|
-
|
466
|
+
* The method xml_set_parameter is moved from
|
467
|
+
lib/bio/appl/blast/xmlparser.rb because it is used by
|
468
|
+
the REXML parser.
|
469
|
+
* The method Bio::Blast::Report.xmlparser is move to
|
470
|
+
lib/bio/appl/blast/xmlparser.rb in the separate repo.
|
471
|
+
* Use "defined? xmlparser_parse" for checking existance of
|
472
|
+
the blast xmlparser component.
|
473
|
+
* Removed line to require bio/appl/blast/xmlparser.
|
484
474
|
|
485
|
-
|
486
|
-
|
487
|
-
2 files changed, 2 insertions(+)
|
475
|
+
lib/bio/appl/blast/report.rb | 40 ++++++++++++++++++++++++++++++++--------
|
476
|
+
1 file changed, 32 insertions(+), 8 deletions(-)
|
488
477
|
|
489
|
-
commit
|
478
|
+
commit b19cd507c432739c5aaac700e222e6e4ecc63ddc
|
490
479
|
Author: Naohisa Goto <ng@bioruby.org>
|
491
|
-
Date:
|
480
|
+
Date: Sat Sep 16 03:32:54 2017 +0900
|
492
481
|
|
493
|
-
|
482
|
+
lib/bio/appl/blast/xmlparser.rb is removed and moved to separate gem
|
483
|
+
|
484
|
+
* lib/bio/appl/blast/xmlparser.rb is removed and moved to separate gem
|
485
|
+
to eliminate dependency to xmlparser that includes native extension.
|
494
486
|
|
495
|
-
|
496
|
-
|
497
|
-
|
487
|
+
lib/bio/appl/blast/xmlparser.rb | 236 ----------------------------------------
|
488
|
+
1 file changed, 236 deletions(-)
|
489
|
+
delete mode 100644 lib/bio/appl/blast/xmlparser.rb
|
498
490
|
|
499
|
-
commit
|
491
|
+
commit 525d3450ad3440bfbbe3a1540fe60d83c3845ec7
|
500
492
|
Author: Naohisa Goto <ng@bioruby.org>
|
501
|
-
Date: Sat
|
493
|
+
Date: Sat Dec 15 11:33:08 2018 +0900
|
502
494
|
|
503
|
-
|
495
|
+
.travis.yml: remove jruby-18mode and jruby-19mode; add jruby and truffleruby
|
504
496
|
|
505
|
-
|
506
|
-
1 file changed,
|
497
|
+
.travis.yml | 24 ++++++++++++------------
|
498
|
+
1 file changed, 12 insertions(+), 12 deletions(-)
|
507
499
|
|
508
|
-
commit
|
500
|
+
commit 5bc0042b7fc39c62222534e0e4129d3f9794fd8c
|
509
501
|
Author: Naohisa Goto <ng@bioruby.org>
|
510
|
-
Date:
|
502
|
+
Date: Fri Dec 14 22:46:08 2018 +0900
|
511
503
|
|
512
|
-
|
504
|
+
appveyor.yml: regenerate bioruby.gemspec before creating gem
|
513
505
|
|
514
|
-
|
515
|
-
1 file changed,
|
506
|
+
appveyor.yml | 1 +
|
507
|
+
1 file changed, 1 insertion(+)
|
516
508
|
|
517
|
-
commit
|
509
|
+
commit 5582dc1db60ffc812211d9803d5adce9c0dd70d3
|
518
510
|
Author: Naohisa Goto <ng@bioruby.org>
|
519
|
-
Date:
|
511
|
+
Date: Fri Dec 14 22:39:35 2018 +0900
|
520
512
|
|
521
|
-
|
513
|
+
appveyor.yml: modify gemfile/Gemfile.windows after bundle install
|
522
514
|
|
523
|
-
|
524
|
-
1 file changed, 1
|
515
|
+
appveyor.yml | 1 +
|
516
|
+
1 file changed, 1 insertion(+)
|
525
517
|
|
526
|
-
commit
|
518
|
+
commit 09031bcae0a42fe93d07b46eb489ffbabc8c1319
|
527
519
|
Author: Naohisa Goto <ng@bioruby.org>
|
528
|
-
Date:
|
520
|
+
Date: Fri Dec 14 22:30:09 2018 +0900
|
529
521
|
|
530
|
-
|
522
|
+
appveyor.yml: give up using vendor/bundle; set BUNDLE_GEMFILE
|
531
523
|
|
532
|
-
|
533
|
-
1 file changed,
|
524
|
+
appveyor.yml | 6 ++----
|
525
|
+
1 file changed, 2 insertions(+), 4 deletions(-)
|
534
526
|
|
535
|
-
commit
|
527
|
+
commit 44fb6c67aef1b0311d32ac806fc9a62f09d401d5
|
536
528
|
Author: Naohisa Goto <ng@bioruby.org>
|
537
|
-
Date:
|
529
|
+
Date: Fri Dec 14 21:59:44 2018 +0900
|
538
530
|
|
539
|
-
|
531
|
+
appveyor.yml: Specify gemfiles/Gemfile.windows
|
532
|
+
|
533
|
+
* appveyor.yml: Specify gemfiles/Gemfile.windows in which xmlparser gem
|
534
|
+
is excluded because of build failure of the xmlparser gem on Windows.
|
535
|
+
* gemfiles/Gemfile.windows: Gemfile for Appveyor, running on Microsoft
|
536
|
+
Windows.
|
540
537
|
|
541
|
-
|
542
|
-
|
538
|
+
appveyor.yml | 2 +-
|
539
|
+
gemfiles/Gemfile.windows | 8 ++++++++
|
540
|
+
2 files changed, 9 insertions(+), 1 deletion(-)
|
541
|
+
create mode 100644 gemfiles/Gemfile.windows
|
543
542
|
|
544
|
-
commit
|
543
|
+
commit fe55e52b42660dda1d21749bf714e989e7db754e
|
545
544
|
Author: Naohisa Goto <ng@bioruby.org>
|
546
|
-
Date:
|
545
|
+
Date: Fri Dec 14 21:48:06 2018 +0900
|
547
546
|
|
548
|
-
|
547
|
+
appveyor.yml: update ruby versions and test procedure
|
549
548
|
|
550
|
-
|
551
|
-
1 file changed,
|
549
|
+
appveyor.yml | 22 +++++++++++++++-------
|
550
|
+
1 file changed, 15 insertions(+), 7 deletions(-)
|
552
551
|
|
553
|
-
commit
|
552
|
+
commit 739f5c9a512074a7de25d87e8104ed15bdb28b5d
|
554
553
|
Author: Naohisa Goto <ng@bioruby.org>
|
555
|
-
Date:
|
554
|
+
Date: Fri Dec 14 11:57:43 2018 +0900
|
556
555
|
|
557
|
-
|
556
|
+
.travis.yml: change default Gemfile
|
557
|
+
|
558
|
+
* Change default Gemfile to Gemfile
|
559
|
+
* Move old Ruby versions to "include" matrix.
|
560
|
+
* Change ruby version for gem-integration-test and tar-integration-test
|
558
561
|
|
559
|
-
|
560
|
-
1 file changed,
|
562
|
+
.travis.yml | 22 ++++++++++++----------
|
563
|
+
1 file changed, 12 insertions(+), 10 deletions(-)
|
561
564
|
|
562
|
-
commit
|
565
|
+
commit 2f54a9cbf8fb6d8580d488b20007d5ce4562e5e9
|
563
566
|
Author: Naohisa Goto <ng@bioruby.org>
|
564
|
-
Date:
|
567
|
+
Date: Fri Dec 14 11:42:58 2018 +0900
|
565
568
|
|
566
|
-
|
569
|
+
.travis.yml: No more limit to master branch. Instead, add blocklist.
|
567
570
|
|
568
|
-
|
569
|
-
1 file changed, 4 insertions(+),
|
571
|
+
.travis.yml | 7 ++++---
|
572
|
+
1 file changed, 4 insertions(+), 3 deletions(-)
|
570
573
|
|
571
|
-
commit
|
572
|
-
Author:
|
573
|
-
Date:
|
574
|
+
commit 9ac3e44318c67fd4415a2118dd5631902e784e12
|
575
|
+
Author: Kozo Nishida <knishida@riken.jp>
|
576
|
+
Date: Thu Dec 13 22:47:54 2018 +0900
|
574
577
|
|
575
|
-
|
578
|
+
ci(travis): Add rvm versions
|
576
579
|
|
577
|
-
|
578
|
-
1 file changed, 1 deletion(-)
|
580
|
+
.travis.yml | 5 ++++-
|
581
|
+
1 file changed, 4 insertions(+), 1 deletion(-)
|
579
582
|
|
580
|
-
commit
|
583
|
+
commit 258dd67c9d65f1247e56d5c5228cc6f9c019d133
|
581
584
|
Author: Naohisa Goto <ng@bioruby.org>
|
582
|
-
Date:
|
585
|
+
Date: Mon Dec 10 21:56:16 2018 +0900
|
583
586
|
|
584
|
-
|
587
|
+
regenerate bioruby.gemspec with rake regemspec
|
585
588
|
|
586
|
-
|
587
|
-
1 file changed,
|
589
|
+
bioruby.gemspec | 2 +-
|
590
|
+
1 file changed, 1 insertion(+), 1 deletion(-)
|
588
591
|
|
589
|
-
commit
|
592
|
+
commit 3920483d6b5a3759e6c610d7ee9fb1a63dcc9ce4
|
590
593
|
Author: Naohisa Goto <ng@bioruby.org>
|
591
|
-
Date:
|
594
|
+
Date: Mon Dec 10 21:55:19 2018 +0900
|
592
595
|
|
593
|
-
|
596
|
+
Simplify version number processing
|
594
597
|
|
595
|
-
|
596
|
-
|
598
|
+
bioruby.gemspec.erb | 14 +++++++-------
|
599
|
+
lib/bio/version.rb | 12 +++++-------
|
600
|
+
2 files changed, 12 insertions(+), 14 deletions(-)
|
597
601
|
|
598
|
-
commit
|
602
|
+
commit 80949a10ea5e4f88d21d893905b720925f5a9e7b
|
599
603
|
Author: Naohisa Goto <ng@bioruby.org>
|
600
|
-
Date:
|
604
|
+
Date: Mon Dec 10 18:54:00 2018 +0900
|
601
605
|
|
602
|
-
|
606
|
+
next bioruby version will be 1.6.0
|
603
607
|
|
604
|
-
lib/bio/
|
608
|
+
lib/bio/version.rb | 2 +-
|
605
609
|
1 file changed, 1 insertion(+), 1 deletion(-)
|
606
610
|
|
607
|
-
commit
|
608
|
-
|
609
|
-
|
610
|
-
|
611
|
-
delete obsolete $Id:$ line
|
612
|
-
|
613
|
-
test/unit/bio/test_db.rb | 1 -
|
614
|
-
1 file changed, 1 deletion(-)
|
615
|
-
|
616
|
-
commit 20381ad45c674c0844a92891cb8ae71edaa6e333
|
617
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
618
|
-
Date: Sat Mar 28 01:08:04 2015 +0900
|
611
|
+
commit 2b542865a4d4af2684ace41f79e273ebceb51807
|
612
|
+
Merge: 02a96424 d71e07a0
|
613
|
+
Author: Toshiaki Katayama <k@bioruby.org>
|
614
|
+
Date: Fri Oct 19 06:45:49 2018 +0900
|
619
615
|
|
620
|
-
|
616
|
+
Merge pull request #125 from kojix2/master
|
621
617
|
|
622
|
-
|
623
|
-
@tagsize not initialized" when executing Bio::TestDB#test_fetch,
|
624
|
-
@tagsize is set in setup.
|
625
|
-
|
626
|
-
test/unit/bio/test_db.rb | 5 ++++-
|
627
|
-
1 file changed, 4 insertions(+), 1 deletion(-)
|
628
|
-
|
629
|
-
commit d194edfc68bc10fde11f2cf014a59113ddc63b24
|
630
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
631
|
-
Date: Sat Mar 28 00:59:21 2015 +0900
|
632
|
-
|
633
|
-
delete obsolete $Id:$ line
|
634
|
-
|
635
|
-
lib/bio/data/codontable.rb | 1 -
|
636
|
-
1 file changed, 1 deletion(-)
|
618
|
+
update TogoWS documentation. genbank -> ncbi-nucleotide
|
637
619
|
|
638
|
-
commit
|
639
|
-
Author:
|
640
|
-
Date:
|
620
|
+
commit d71e07a0cb1cc441241be91273bd44e3717b8773
|
621
|
+
Author: kojix2 <2xijok@gmail.com>
|
622
|
+
Date: Thu Oct 18 19:10:29 2018 +0900
|
641
623
|
|
642
|
-
|
624
|
+
update TogoWS documentation. genbank -> ncbi-nucleotide
|
643
625
|
|
644
|
-
lib/bio/
|
645
|
-
|
626
|
+
lib/bio/io/togows.rb | 10 +++++-----
|
627
|
+
sample/test_restriction_enzyme_long.rb | 2 +-
|
628
|
+
2 files changed, 6 insertions(+), 6 deletions(-)
|
646
629
|
|
647
|
-
commit
|
630
|
+
commit 02a964241b79e2307d0a00473427ea6bc2ea6932
|
648
631
|
Author: Naohisa Goto <ng@bioruby.org>
|
649
|
-
Date:
|
632
|
+
Date: Thu Sep 20 07:06:08 2018 +0900
|
650
633
|
|
651
|
-
|
634
|
+
Improvement documentation
|
635
|
+
|
636
|
+
* Improve documentation.
|
637
|
+
* Close https://github.com/bioruby/bioruby/pull/120 .
|
652
638
|
|
653
|
-
lib/bio/
|
654
|
-
1 file changed,
|
639
|
+
lib/bio/db/aaindex.rb | 79 +++++++++++++++++++++++++++++++++++++++++++++++----
|
640
|
+
1 file changed, 74 insertions(+), 5 deletions(-)
|
655
641
|
|
656
|
-
commit
|
642
|
+
commit 6bfef40ae87099565371abf94cf2cc8bfac76b12
|
657
643
|
Author: Naohisa Goto <ng@bioruby.org>
|
658
|
-
Date:
|
644
|
+
Date: Thu Sep 20 05:01:12 2018 +0900
|
659
645
|
|
660
|
-
|
646
|
+
Bug fix: Bio::Command.new_https should support proxy
|
661
647
|
|
662
|
-
lib/bio/
|
663
|
-
1 file changed,
|
648
|
+
lib/bio/command.rb | 18 +++++++-----------
|
649
|
+
1 file changed, 7 insertions(+), 11 deletions(-)
|
664
650
|
|
665
|
-
commit
|
651
|
+
commit 4e3251d2172f58239f103e7edf8f4c351140f378
|
666
652
|
Author: Naohisa Goto <ng@bioruby.org>
|
667
|
-
Date:
|
653
|
+
Date: Thu Sep 20 04:58:56 2018 +0900
|
668
654
|
|
669
|
-
|
655
|
+
https support for Bio::Blast::Remote::GenomeNet::Information
|
670
656
|
|
671
|
-
lib/bio/
|
672
|
-
1 file changed,
|
657
|
+
lib/bio/appl/blast/genomenet.rb | 6 +++---
|
658
|
+
1 file changed, 3 insertions(+), 3 deletions(-)
|
673
659
|
|
674
|
-
commit
|
675
|
-
Author:
|
676
|
-
Date: Sat
|
660
|
+
commit 6dd1f9fb8c2b4ba95086eab7bffc01583feccf3a
|
661
|
+
Author: ramadis <rramiro.o@hotmail.com>
|
662
|
+
Date: Sat Jul 7 15:12:33 2018 -0300
|
677
663
|
|
678
|
-
|
664
|
+
Add https requests in command. Fix genomenet query by allowing https requests.
|
679
665
|
|
680
|
-
lib/bio/
|
681
|
-
|
666
|
+
lib/bio/appl/blast/genomenet.rb | 2 +-
|
667
|
+
lib/bio/command.rb | 14 ++++++++++++++
|
668
|
+
2 files changed, 15 insertions(+), 1 deletion(-)
|
682
669
|
|
683
|
-
commit
|
684
|
-
Author:
|
685
|
-
Date:
|
670
|
+
commit 4b6f87c9fd2dc62418ddfc4b57bcc4b73287a603
|
671
|
+
Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>
|
672
|
+
Date: Sat Mar 31 13:08:07 2018 +0900
|
686
673
|
|
687
|
-
|
674
|
+
directly refer to the given hash
|
688
675
|
|
689
|
-
lib/bio/
|
676
|
+
lib/bio/data/codontable.rb | 2 +-
|
690
677
|
1 file changed, 1 insertion(+), 1 deletion(-)
|
691
678
|
|
692
|
-
commit
|
693
|
-
Author:
|
694
|
-
Date:
|
679
|
+
commit 25636ffa08c6ea9a9e4d1b451a456bc1f482ad40
|
680
|
+
Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>
|
681
|
+
Date: Sat Jun 2 15:10:12 2018 +0900
|
695
682
|
|
696
|
-
|
683
|
+
precalculated ambiguity codontable
|
697
684
|
|
698
|
-
lib/bio/
|
699
|
-
1 file changed,
|
685
|
+
lib/bio/data/codontable.rb | 55 +++++++++++++++++++++++++++++++++++++++++++---
|
686
|
+
1 file changed, 52 insertions(+), 3 deletions(-)
|
700
687
|
|
701
|
-
commit
|
702
|
-
Author:
|
703
|
-
Date:
|
688
|
+
commit b2d924045202ec3aa4e1b79341fd939a881d4c2e
|
689
|
+
Author: Tomoaki NISHIYAMA <tomoakin@kenroku.kanazawa-u.ac.jp>
|
690
|
+
Date: Sat Mar 31 11:55:57 2018 +0900
|
704
691
|
|
705
|
-
|
706
|
-
|
707
|
-
* suppress warning: instance variable @sc_match not initialized
|
708
|
-
* suppress warning: instance variable @sc_mismatch not initialized
|
709
|
-
* suppress warning: instance variable @gaps not initialized
|
710
|
-
* suppress warning: instance variable @hit_frame not initialized
|
711
|
-
* suppress warning: instance variable @query_frame not initialized
|
692
|
+
construct ambiguity nucleotide to amino acid table
|
712
693
|
|
713
|
-
lib/bio/
|
714
|
-
|
694
|
+
lib/bio/data/codontable.rb | 49 ++++++++++++++++++++++++++++++++++-
|
695
|
+
test/unit/bio/data/test_codontable.rb | 3 +++
|
696
|
+
2 files changed, 51 insertions(+), 1 deletion(-)
|
715
697
|
|
716
|
-
commit
|
717
|
-
Author:
|
718
|
-
Date:
|
698
|
+
commit a7378b6b269ea1c0391e259dd8e4868f03b064ea
|
699
|
+
Author: markwilkinson <markw@illuminae.com>
|
700
|
+
Date: Tue Dec 12 14:13:51 2017 +0100
|
719
701
|
|
720
|
-
|
702
|
+
fixing Fasta Report parser for fasta36 -m10
|
721
703
|
|
722
|
-
lib/bio/appl/
|
723
|
-
1 file changed,
|
704
|
+
lib/bio/appl/fasta/format10.rb | 3 ++-
|
705
|
+
1 file changed, 2 insertions(+), 1 deletion(-)
|
724
706
|
|
725
|
-
commit
|
707
|
+
commit c89c40c29c3c92f8e548c79d2d04698123559007
|
726
708
|
Author: Naohisa Goto <ng@bioruby.org>
|
727
|
-
Date:
|
709
|
+
Date: Fri Sep 15 16:33:19 2017 +0900
|
728
710
|
|
729
|
-
|
711
|
+
Remove settings about executables
|
712
|
+
|
713
|
+
* Definitions and settings about executables are removed because
|
714
|
+
all files in bin/ have been moved to separate gem packages
|
715
|
+
(bio-shell and bio-executables).
|
730
716
|
|
731
|
-
|
732
|
-
|
717
|
+
bioruby.gemspec | 13 -------------
|
718
|
+
bioruby.gemspec.erb | 21 +--------------------
|
719
|
+
2 files changed, 1 insertion(+), 33 deletions(-)
|
733
720
|
|
734
|
-
commit
|
721
|
+
commit b5a8d385da8f2c1b6e1caf77295e590f55595944
|
735
722
|
Author: Naohisa Goto <ng@bioruby.org>
|
736
|
-
Date:
|
723
|
+
Date: Fri Sep 15 16:20:03 2017 +0900
|
737
724
|
|
738
|
-
|
725
|
+
bin/br_*.rb is moved to bio-executables gem
|
739
726
|
|
740
|
-
*
|
741
|
-
|
742
|
-
|
743
|
-
|
727
|
+
* The following executable files are moved to "bio-executables" gem.
|
728
|
+
* bin/br_biofetch.rb
|
729
|
+
* bin/br_bioflat.rb
|
730
|
+
* bin/br_biogetseq.rb
|
731
|
+
* bin/br_pmfetch.rb
|
744
732
|
|
745
|
-
|
746
|
-
|
747
|
-
|
733
|
+
bin/br_biofetch.rb | 71 ---------
|
734
|
+
bin/br_bioflat.rb | 293 ------------------------------------
|
735
|
+
bin/br_biogetseq.rb | 45 ------
|
736
|
+
bin/br_pmfetch.rb | 422 ----------------------------------------------------
|
737
|
+
4 files changed, 831 deletions(-)
|
738
|
+
delete mode 100755 bin/br_biofetch.rb
|
739
|
+
delete mode 100755 bin/br_bioflat.rb
|
740
|
+
delete mode 100755 bin/br_biogetseq.rb
|
741
|
+
delete mode 100755 bin/br_pmfetch.rb
|
748
742
|
|
749
|
-
commit
|
743
|
+
commit eb61d89a366437570a0590a629cb75718866b236
|
750
744
|
Author: Naohisa Goto <ng@bioruby.org>
|
751
|
-
Date:
|
745
|
+
Date: Fri Sep 15 09:31:14 2017 +0900
|
752
746
|
|
753
|
-
|
747
|
+
regenerate bioruby.gemspec with rake regemspec
|
754
748
|
|
755
|
-
|
756
|
-
1 file changed, 1
|
749
|
+
bioruby.gemspec | 44 +-------------------------------------------
|
750
|
+
1 file changed, 1 insertion(+), 43 deletions(-)
|
751
|
+
|
752
|
+
commit 6d40721d039fdb6b77af656f32ccabeabc427409
|
753
|
+
Author: Naohisa Goto <ng@bioruby.org>
|
754
|
+
Date: Fri Sep 15 09:29:33 2017 +0900
|
755
|
+
|
756
|
+
Remove BioRuby Shell files that are released as independent gem package
|
757
|
+
|
758
|
+
bin/bioruby | 47 --
|
759
|
+
lib/bio/shell.rb | 44 --
|
760
|
+
lib/bio/shell/core.rb | 578 ---------------------
|
761
|
+
lib/bio/shell/demo.rb | 146 ------
|
762
|
+
lib/bio/shell/interface.rb | 217 --------
|
763
|
+
lib/bio/shell/irb.rb | 94 ----
|
764
|
+
lib/bio/shell/object.rb | 71 ---
|
765
|
+
lib/bio/shell/plugin/blast.rb | 42 --
|
766
|
+
lib/bio/shell/plugin/codon.rb | 218 --------
|
767
|
+
lib/bio/shell/plugin/das.rb | 58 ---
|
768
|
+
lib/bio/shell/plugin/emboss.rb | 23 -
|
769
|
+
lib/bio/shell/plugin/entry.rb | 137 -----
|
770
|
+
lib/bio/shell/plugin/flatfile.rb | 101 ----
|
771
|
+
lib/bio/shell/plugin/midi.rb | 430 ---------------
|
772
|
+
lib/bio/shell/plugin/ncbirest.rb | 68 ---
|
773
|
+
lib/bio/shell/plugin/obda.rb | 45 --
|
774
|
+
lib/bio/shell/plugin/psort.rb | 56 --
|
775
|
+
lib/bio/shell/plugin/seq.rb | 248 ---------
|
776
|
+
lib/bio/shell/plugin/togows.rb | 40 --
|
777
|
+
.../generators/bioruby/bioruby_generator.rb | 29 --
|
778
|
+
.../generators/bioruby/templates/_classes.rhtml | 4 -
|
779
|
+
.../generators/bioruby/templates/_log.rhtml | 27 -
|
780
|
+
.../generators/bioruby/templates/_methods.rhtml | 11 -
|
781
|
+
.../generators/bioruby/templates/_modules.rhtml | 4 -
|
782
|
+
.../generators/bioruby/templates/_variables.rhtml | 7 -
|
783
|
+
.../generators/bioruby/templates/bioruby-bg.gif | Bin 1431 -> 0 bytes
|
784
|
+
.../generators/bioruby/templates/bioruby-gem.png | Bin 6951 -> 0 bytes
|
785
|
+
.../generators/bioruby/templates/bioruby-link.gif | Bin 2758 -> 0 bytes
|
786
|
+
.../generators/bioruby/templates/bioruby.css | 368 -------------
|
787
|
+
.../generators/bioruby/templates/bioruby.rhtml | 47 --
|
788
|
+
.../bioruby/templates/bioruby_controller.rb | 144 -----
|
789
|
+
.../generators/bioruby/templates/bioruby_helper.rb | 47 --
|
790
|
+
.../generators/bioruby/templates/commands.rhtml | 8 -
|
791
|
+
.../generators/bioruby/templates/history.rhtml | 10 -
|
792
|
+
.../generators/bioruby/templates/index.rhtml | 26 -
|
793
|
+
.../generators/bioruby/templates/spinner.gif | Bin 1542 -> 0 bytes
|
794
|
+
lib/bio/shell/script.rb | 25 -
|
795
|
+
lib/bio/shell/setup.rb | 108 ----
|
796
|
+
lib/bio/shell/web.rb | 102 ----
|
797
|
+
test/unit/bio/shell/plugin/test_seq.rb | 187 -------
|
798
|
+
test/unit/bio/test_shell.rb | 20 -
|
799
|
+
41 files changed, 3837 deletions(-)
|
800
|
+
delete mode 100755 bin/bioruby
|
801
|
+
delete mode 100644 lib/bio/shell.rb
|
802
|
+
delete mode 100644 lib/bio/shell/core.rb
|
803
|
+
delete mode 100644 lib/bio/shell/demo.rb
|
804
|
+
delete mode 100644 lib/bio/shell/interface.rb
|
805
|
+
delete mode 100644 lib/bio/shell/irb.rb
|
806
|
+
delete mode 100644 lib/bio/shell/object.rb
|
807
|
+
delete mode 100644 lib/bio/shell/plugin/blast.rb
|
808
|
+
delete mode 100644 lib/bio/shell/plugin/codon.rb
|
809
|
+
delete mode 100644 lib/bio/shell/plugin/das.rb
|
810
|
+
delete mode 100644 lib/bio/shell/plugin/emboss.rb
|
811
|
+
delete mode 100644 lib/bio/shell/plugin/entry.rb
|
812
|
+
delete mode 100644 lib/bio/shell/plugin/flatfile.rb
|
813
|
+
delete mode 100644 lib/bio/shell/plugin/midi.rb
|
814
|
+
delete mode 100644 lib/bio/shell/plugin/ncbirest.rb
|
815
|
+
delete mode 100644 lib/bio/shell/plugin/obda.rb
|
816
|
+
delete mode 100644 lib/bio/shell/plugin/psort.rb
|
817
|
+
delete mode 100644 lib/bio/shell/plugin/seq.rb
|
818
|
+
delete mode 100644 lib/bio/shell/plugin/togows.rb
|
819
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb
|
820
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml
|
821
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml
|
822
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml
|
823
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml
|
824
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml
|
825
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif
|
826
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png
|
827
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif
|
828
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css
|
829
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml
|
830
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb
|
831
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb
|
832
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml
|
833
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml
|
834
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml
|
835
|
+
delete mode 100644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif
|
836
|
+
delete mode 100644 lib/bio/shell/script.rb
|
837
|
+
delete mode 100644 lib/bio/shell/setup.rb
|
838
|
+
delete mode 100644 lib/bio/shell/web.rb
|
839
|
+
delete mode 100644 test/unit/bio/shell/plugin/test_seq.rb
|
840
|
+
delete mode 100644 test/unit/bio/test_shell.rb
|
841
|
+
|
842
|
+
commit ab9feb6f1f495a2b3ca350005c6162c51178aecb
|
843
|
+
Author: Naohisa Goto <ng@bioruby.org>
|
844
|
+
Date: Wed Sep 13 22:13:59 2017 +0900
|
845
|
+
|
846
|
+
Suppress warning "assigned but unused variable"
|
847
|
+
|
848
|
+
lib/bio/io/flatfile/autodetection.rb | 5 +++++
|
849
|
+
1 file changed, 5 insertions(+)
|
850
|
+
|
851
|
+
commit cf486e327c253482f54e59b2e18f73db27641135
|
852
|
+
Author: Naohisa Goto <ng@bioruby.org>
|
853
|
+
Date: Wed Sep 13 22:10:53 2017 +0900
|
854
|
+
|
855
|
+
Suppress warning: "instance variable @top_strand not initialized"
|
856
|
+
|
857
|
+
* Suppress warning: "instance variable @top_strand not initialized".
|
858
|
+
To do so, force to raise NoMethodError when @top_strand is not
|
859
|
+
initialized or is nil. This should be changed to appropriate
|
860
|
+
exception in the future.
|
861
|
+
|
862
|
+
lib/bio/util/sirna.rb | 2 ++
|
863
|
+
1 file changed, 2 insertions(+)
|
757
864
|
|
758
|
-
commit
|
865
|
+
commit 88477698f0e1b5a74f9682f26e97c5f90f6912b4
|
759
866
|
Author: Naohisa Goto <ng@bioruby.org>
|
760
|
-
Date: Wed
|
867
|
+
Date: Wed Sep 13 21:31:38 2017 +0900
|
761
868
|
|
762
|
-
|
869
|
+
Suppress warning in Ruby 2.4: "constant ::Fixnum is deprecated"
|
763
870
|
|
764
|
-
|
765
|
-
|
871
|
+
lib/bio/db/soft.rb | 4 ++--
|
872
|
+
.../util/restriction_enzyme/range/sequence_range/calculated_cuts.rb | 2 +-
|
873
|
+
test/unit/bio/test_alignment.rb | 4 ++--
|
874
|
+
3 files changed, 5 insertions(+), 5 deletions(-)
|
766
875
|
|
767
|
-
commit
|
876
|
+
commit f8cff14179cfeea0d685f4df756db71ceb6d5fab
|
768
877
|
Author: Naohisa Goto <ng@bioruby.org>
|
769
|
-
Date: Wed
|
878
|
+
Date: Wed Sep 13 21:19:12 2017 +0900
|
770
879
|
|
771
|
-
|
880
|
+
Suppress warning "parentheses after method name is interpreted as an argument list, not a decomposed argument" in Ruby 2.4
|
772
881
|
|
773
|
-
|
774
|
-
1 file changed,
|
882
|
+
lib/bio/map.rb | 8 ++++----
|
883
|
+
1 file changed, 4 insertions(+), 4 deletions(-)
|
775
884
|
|
776
|
-
commit
|
777
|
-
Author:
|
778
|
-
Date:
|
885
|
+
commit ddb25c2bf3872c6306a91e407d95caa2e136cee9
|
886
|
+
Author: Jun Aruga <jaruga@redhat.com>
|
887
|
+
Date: Fri Nov 18 11:14:38 2016 +0100
|
779
888
|
|
780
|
-
|
889
|
+
Gemfile for local development.
|
781
890
|
|
782
|
-
|
783
|
-
|
891
|
+
.travis.yml | 8 ++++----
|
892
|
+
gemfiles/Gemfile.travis-ruby2.2 => Gemfile | 0
|
893
|
+
bioruby.gemspec | 2 +-
|
894
|
+
3 files changed, 5 insertions(+), 5 deletions(-)
|
895
|
+
rename gemfiles/Gemfile.travis-ruby2.2 => Gemfile (100%)
|
784
896
|
|
785
|
-
commit
|
786
|
-
Author:
|
787
|
-
Date:
|
897
|
+
commit 16faf6473b74eb172716b713ab757cb2ab2bcacc
|
898
|
+
Author: Jun Aruga <jaruga@redhat.com>
|
899
|
+
Date: Thu Nov 17 17:50:40 2016 +0100
|
788
900
|
|
789
|
-
|
901
|
+
Fixes ruby1.8 Travis failure that is because rdoc 4.3.0 requires Ruby >= 1.9.3.
|
790
902
|
|
791
|
-
|
792
|
-
|
903
|
+
gemfiles/Gemfile.travis-jruby1.8 | 3 ++-
|
904
|
+
gemfiles/Gemfile.travis-ruby1.8 | 3 ++-
|
905
|
+
2 files changed, 4 insertions(+), 2 deletions(-)
|
793
906
|
|
794
|
-
commit
|
907
|
+
commit 146fd66b3a14972bcfd0e9bf8ec007d38c55ac39
|
795
908
|
Author: Naohisa Goto <ng@bioruby.org>
|
796
|
-
Date:
|
909
|
+
Date: Sat Aug 13 08:22:22 2016 +0900
|
797
910
|
|
798
|
-
|
799
|
-
|
800
|
-
* lib/bio/io/togows.rb: Bug fix: Bio::TogoWS::REST#search with offset
|
801
|
-
and limit did not work due to TogoWS server change about URI escape.
|
802
|
-
For example,
|
803
|
-
http://togows.org/search/nuccore/Milnesium+tardigradum/2%2C3 fails,
|
804
|
-
http://togows.org/search/nuccore/Milnesium+tardigradum/2,3 works fine.
|
911
|
+
Update URLs and use https for NCBI REST web services
|
805
912
|
|
806
|
-
lib/bio/io/
|
807
|
-
1 file changed,
|
913
|
+
lib/bio/io/ncbirest.rb | 50 ++++++++++++++++++++++++++------------------------
|
914
|
+
1 file changed, 26 insertions(+), 24 deletions(-)
|
808
915
|
|
809
|
-
commit
|
916
|
+
commit 7abd46f058a17ac34b263714449756383622012d
|
810
917
|
Author: Naohisa Goto <ng@bioruby.org>
|
811
|
-
Date:
|
918
|
+
Date: Sat Aug 13 08:12:08 2016 +0900
|
812
919
|
|
813
|
-
|
920
|
+
New method Bio::Command#start_http_uri(uri) with tests
|
814
921
|
|
815
|
-
* lib/bio/
|
816
|
-
|
817
|
-
|
818
|
-
lib/bio/
|
819
|
-
|
820
|
-
|
821
|
-
commit 1a9b1063af4c0b32cd287d4a2c2466343aeddb98
|
822
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
823
|
-
Date: Wed Mar 25 01:30:34 2015 +0900
|
824
|
-
|
825
|
-
improve tests for bio/command.rb for methods using http protocol
|
826
|
-
|
827
|
-
test/network/bio/test_command.rb | 67 ++++++++++++++++++++++++++++++++++++++--
|
828
|
-
1 file changed, 65 insertions(+), 2 deletions(-)
|
829
|
-
|
830
|
-
commit c63920e4d8569e3eaef201d4d60fcddfa15f1f34
|
831
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
832
|
-
Date: Wed Mar 25 01:30:06 2015 +0900
|
833
|
-
|
834
|
-
delete obsolete $Id:$ line
|
922
|
+
* lib/bio/command.rb: New method Bio::Command#start_http_uri(uri)
|
923
|
+
that supports HTTPS. Note that this method is intended to be
|
924
|
+
called only from BioRuby internals.
|
925
|
+
* lib/bio/command.rb: Bio::Command#post and #post_form are changed
|
926
|
+
to use the start_http_uri().
|
927
|
+
* test/network/bio/test_command.rb: tests for start_http_uri().
|
835
928
|
|
836
|
-
lib/bio/command.rb
|
837
|
-
|
929
|
+
lib/bio/command.rb | 42 ++++++++++++++++++++++++++++++++++++++--
|
930
|
+
test/network/bio/test_command.rb | 17 ++++++++++++++++
|
931
|
+
2 files changed, 57 insertions(+), 2 deletions(-)
|
838
932
|
|
839
|
-
commit
|
933
|
+
commit 11c680f6d64a60bdc0f4248951bf2d2ebafbc433
|
840
934
|
Author: Naohisa Goto <ng@bioruby.org>
|
841
|
-
Date:
|
935
|
+
Date: Fri Jun 17 20:40:41 2016 +0900
|
842
936
|
|
843
|
-
|
937
|
+
gemfiles/Gemfile.*: remove dependency on libxml-ruby
|
938
|
+
|
939
|
+
* gemfiles/Gemfile.*: remove dependency on libxml-ruby.
|
940
|
+
Bio::PhyloXML required libxml-ruby but was already removed.
|
844
941
|
|
845
|
-
|
846
|
-
|
942
|
+
gemfiles/Gemfile.travis-jruby1.8 | 3 ---
|
943
|
+
gemfiles/Gemfile.travis-jruby1.9 | 3 ---
|
944
|
+
gemfiles/Gemfile.travis-rbx | 1 -
|
945
|
+
gemfiles/Gemfile.travis-ruby1.8 | 1 -
|
946
|
+
gemfiles/Gemfile.travis-ruby1.9 | 1 -
|
947
|
+
gemfiles/Gemfile.travis-ruby2.2 | 1 -
|
948
|
+
6 files changed, 10 deletions(-)
|
847
949
|
|
848
|
-
commit
|
950
|
+
commit 09fa57f987445e8654de6a0d0cf7c45f7625600c
|
849
951
|
Author: Naohisa Goto <ng@bioruby.org>
|
850
|
-
Date:
|
952
|
+
Date: Fri Jun 17 16:16:40 2016 +0900
|
851
953
|
|
852
|
-
|
954
|
+
regenerate bioruby.gemspec with rake regemspec
|
853
955
|
|
854
|
-
|
855
|
-
1 file changed,
|
956
|
+
bioruby.gemspec | 10 +---------
|
957
|
+
1 file changed, 1 insertion(+), 9 deletions(-)
|
856
958
|
|
857
|
-
commit
|
959
|
+
commit 87812d119820bf66767c7767cfec7554d7a00f3b
|
858
960
|
Author: Naohisa Goto <ng@bioruby.org>
|
859
|
-
Date:
|
961
|
+
Date: Fri Jun 17 15:45:46 2016 +0900
|
860
962
|
|
861
|
-
|
963
|
+
README.rdoc: about bioruby-phyloxml and bio-biosql
|
862
964
|
|
863
|
-
|
864
|
-
1 file changed,
|
965
|
+
README.rdoc | 10 ++++++++++
|
966
|
+
1 file changed, 10 insertions(+)
|
865
967
|
|
866
|
-
commit
|
968
|
+
commit 2294f255f5f05f9f629a1e88c0e1f59bb74b32bc
|
867
969
|
Author: Naohisa Goto <ng@bioruby.org>
|
868
|
-
Date:
|
970
|
+
Date: Fri Jun 17 15:42:46 2016 +0900
|
869
971
|
|
870
|
-
|
972
|
+
KNOWN_ISSUES.rdoc: remove descriptions about Bio::SQL
|
871
973
|
|
872
|
-
|
873
|
-
1 file changed,
|
974
|
+
KNOWN_ISSUES.rdoc | 5 -----
|
975
|
+
1 file changed, 5 deletions(-)
|
874
976
|
|
875
|
-
commit
|
977
|
+
commit 35a6f761dc5fa493b8311747dde7f2a54d8aee75
|
876
978
|
Author: Naohisa Goto <ng@bioruby.org>
|
877
|
-
Date:
|
979
|
+
Date: Fri Jun 17 15:40:57 2016 +0900
|
878
980
|
|
879
|
-
|
981
|
+
README.rdoc: remove descriptions about Bio::SQL
|
880
982
|
|
881
|
-
|
882
|
-
1 file changed,
|
983
|
+
README.rdoc | 13 +------------
|
984
|
+
1 file changed, 1 insertion(+), 12 deletions(-)
|
883
985
|
|
884
|
-
commit
|
986
|
+
commit 46a5bf7acdc803b7e75225c41b23396c4619f25d
|
885
987
|
Author: Naohisa Goto <ng@bioruby.org>
|
886
|
-
Date:
|
988
|
+
Date: Fri Jun 17 14:59:41 2016 +0900
|
887
989
|
|
888
|
-
|
990
|
+
remove autoload of Bio::SQL
|
889
991
|
|
890
|
-
lib/bio
|
992
|
+
lib/bio.rb | 1 -
|
891
993
|
1 file changed, 1 deletion(-)
|
892
994
|
|
893
|
-
commit
|
995
|
+
commit 57bf535da34715beafccb902404cf1bb35b18af4
|
894
996
|
Author: Naohisa Goto <ng@bioruby.org>
|
895
|
-
Date:
|
997
|
+
Date: Fri Jun 17 14:48:46 2016 +0900
|
896
998
|
|
897
|
-
|
999
|
+
Removed Bio::SQL that have been moved to separate repository
|
1000
|
+
|
1001
|
+
* Bio::SQL is moved to https://github.com/bioruby/bioruby-biosql
|
1002
|
+
and removed from this repository.
|
1003
|
+
|
1004
|
+
* List of deleted files:
|
1005
|
+
* deleted: lib/bio/db/biosql/biosql_to_biosequence.rb
|
1006
|
+
* deleted: lib/bio/db/biosql/sequence.rb
|
1007
|
+
* deleted: lib/bio/io/biosql/ar-biosql.rb
|
1008
|
+
* deleted: lib/bio/io/biosql/biosql.rb
|
1009
|
+
* deleted: lib/bio/io/biosql/config/database.yml
|
1010
|
+
* deleted: lib/bio/io/sql.rb
|
1011
|
+
* deleted: test/unit/bio/db/biosql/tc_biosql.rb
|
1012
|
+
* deleted: test/unit/bio/db/biosql/ts_suite_biosql.rb
|
898
1013
|
|
899
|
-
lib/bio/
|
900
|
-
|
1014
|
+
lib/bio/db/biosql/biosql_to_biosequence.rb | 78 -----
|
1015
|
+
lib/bio/db/biosql/sequence.rb | 444 -----------------------------
|
1016
|
+
lib/bio/io/biosql/ar-biosql.rb | 257 -----------------
|
1017
|
+
lib/bio/io/biosql/biosql.rb | 39 ---
|
1018
|
+
lib/bio/io/biosql/config/database.yml | 21 --
|
1019
|
+
lib/bio/io/sql.rb | 79 -----
|
1020
|
+
test/unit/bio/db/biosql/tc_biosql.rb | 114 --------
|
1021
|
+
test/unit/bio/db/biosql/ts_suite_biosql.rb | 8 -
|
1022
|
+
8 files changed, 1040 deletions(-)
|
1023
|
+
delete mode 100644 lib/bio/db/biosql/biosql_to_biosequence.rb
|
1024
|
+
delete mode 100644 lib/bio/db/biosql/sequence.rb
|
1025
|
+
delete mode 100644 lib/bio/io/biosql/ar-biosql.rb
|
1026
|
+
delete mode 100644 lib/bio/io/biosql/biosql.rb
|
1027
|
+
delete mode 100644 lib/bio/io/biosql/config/database.yml
|
1028
|
+
delete mode 100644 lib/bio/io/sql.rb
|
1029
|
+
delete mode 100644 test/unit/bio/db/biosql/tc_biosql.rb
|
1030
|
+
delete mode 100644 test/unit/bio/db/biosql/ts_suite_biosql.rb
|
901
1031
|
|
902
|
-
commit
|
1032
|
+
commit 476dcdbe2b21cd5adb641952ee3da92c2d593121
|
903
1033
|
Author: Naohisa Goto <ng@bioruby.org>
|
904
|
-
Date:
|
1034
|
+
Date: Wed Jun 8 12:38:22 2016 +0900
|
905
1035
|
|
906
|
-
|
1036
|
+
appveyor.yml: eliminate old Ruby versions and add Ruby 2.3
|
907
1037
|
|
908
|
-
|
909
|
-
1 file changed,
|
1038
|
+
appveyor.yml | 5 ++---
|
1039
|
+
1 file changed, 2 insertions(+), 3 deletions(-)
|
910
1040
|
|
911
|
-
commit
|
1041
|
+
commit c26e2b77b75b5505a274822f53c6c5a8f842f6c0
|
912
1042
|
Author: Naohisa Goto <ng@bioruby.org>
|
913
|
-
Date:
|
1043
|
+
Date: Wed Jun 8 01:50:19 2016 +0900
|
914
1044
|
|
915
|
-
|
1045
|
+
.travis.yml: fix to use rbx-3.29
|
916
1046
|
|
917
|
-
|
1047
|
+
.travis.yml | 2 +-
|
918
1048
|
1 file changed, 1 insertion(+), 1 deletion(-)
|
919
1049
|
|
920
|
-
commit
|
1050
|
+
commit b524abedac9c85d4f8259191b973bc38a9fc557c
|
921
1051
|
Author: Naohisa Goto <ng@bioruby.org>
|
922
|
-
Date:
|
1052
|
+
Date: Wed Jun 8 01:45:48 2016 +0900
|
923
1053
|
|
924
|
-
|
1054
|
+
gemfiles/Gemfile.travis-jruby1.8: use old gem versions supporting Ruby 1.8
|
925
1055
|
|
926
|
-
|
927
|
-
1 file changed,
|
1056
|
+
gemfiles/Gemfile.travis-jruby1.8 | 6 +++---
|
1057
|
+
1 file changed, 3 insertions(+), 3 deletions(-)
|
928
1058
|
|
929
|
-
commit
|
1059
|
+
commit c5df9268b77f1d4dc2b29e7cfb7baf3c528c1558
|
930
1060
|
Author: Naohisa Goto <ng@bioruby.org>
|
931
|
-
Date:
|
1061
|
+
Date: Wed Jun 8 01:42:40 2016 +0900
|
932
1062
|
|
933
|
-
|
1063
|
+
.travis.yml: use rbx-3.29 instead of rbx-3
|
934
1064
|
|
935
|
-
|
1065
|
+
.travis.yml | 2 +-
|
936
1066
|
1 file changed, 1 insertion(+), 1 deletion(-)
|
937
1067
|
|
938
|
-
commit
|
1068
|
+
commit b51b54894ca2d76d9c13680fd72b87951a10a1df
|
939
1069
|
Author: Naohisa Goto <ng@bioruby.org>
|
940
|
-
Date:
|
1070
|
+
Date: Wed Jun 8 01:25:18 2016 +0900
|
941
1071
|
|
942
|
-
|
1072
|
+
Workaround to avoid bug in old versions of Bundler
|
1073
|
+
|
1074
|
+
* gemfiles/prepare-gemspec.rb: execute "gem update bundler" to avoid
|
1075
|
+
"NoMethodError: undefined method `spec' for nil:NilClass"
|
1076
|
+
during "bundle install". This error may be due to a bug of Bundler
|
1077
|
+
and the bug seems to be fixed in the latest version of Budler.
|
943
1078
|
|
944
|
-
|
945
|
-
1 file changed,
|
1079
|
+
gemfiles/prepare-gemspec.rb | 4 ++++
|
1080
|
+
1 file changed, 4 insertions(+)
|
946
1081
|
|
947
|
-
commit
|
1082
|
+
commit a82424b4864e243ebf1f8cc7f181044798b34b5a
|
948
1083
|
Author: Naohisa Goto <ng@bioruby.org>
|
949
|
-
Date:
|
1084
|
+
Date: Wed Jun 8 01:20:15 2016 +0900
|
950
1085
|
|
951
|
-
|
1086
|
+
.travis.yml: add Ruby 2.3.1; use Ruby 2.2.5 instead of 2.2
|
952
1087
|
|
953
|
-
|
954
|
-
1 file changed,
|
1088
|
+
.travis.yml | 8 +++++---
|
1089
|
+
1 file changed, 5 insertions(+), 3 deletions(-)
|
955
1090
|
|
956
|
-
commit
|
1091
|
+
commit ae927514a5c2853d3839750af86bfcc1fc53e4f1
|
957
1092
|
Author: Naohisa Goto <ng@bioruby.org>
|
958
|
-
Date:
|
1093
|
+
Date: Wed Jun 8 00:54:22 2016 +0900
|
959
1094
|
|
960
|
-
|
1095
|
+
.travis.yml: add "sudo: false" for faster testing
|
961
1096
|
|
962
|
-
|
963
|
-
1 file changed, 1
|
1097
|
+
.travis.yml | 1 +
|
1098
|
+
1 file changed, 1 insertion(+)
|
964
1099
|
|
965
|
-
commit
|
1100
|
+
commit 832c4dd94a5602a9deadf599ce1778fac870ac81
|
966
1101
|
Author: Naohisa Goto <ng@bioruby.org>
|
967
|
-
Date:
|
1102
|
+
Date: Wed Jun 8 00:46:26 2016 +0900
|
968
1103
|
|
969
|
-
|
1104
|
+
gemfiles/Gemfile.travis-ruby1.8: use old gem versions supporting Ruby 1.8
|
970
1105
|
|
971
|
-
|
972
|
-
1 file changed,
|
1106
|
+
gemfiles/Gemfile.travis-ruby1.8 | 8 ++++----
|
1107
|
+
1 file changed, 4 insertions(+), 4 deletions(-)
|
973
1108
|
|
974
|
-
commit
|
1109
|
+
commit 6cf0ab84cd67aab0f6f4012438c1852a19f3ac7a
|
975
1110
|
Author: Naohisa Goto <ng@bioruby.org>
|
976
|
-
Date:
|
1111
|
+
Date: Wed Jun 8 00:04:36 2016 +0900
|
977
1112
|
|
978
|
-
|
1113
|
+
regenerate bioruby.gemspec with rake regemspec
|
979
1114
|
|
980
|
-
|
981
|
-
1 file changed, 1 deletion(-)
|
1115
|
+
bioruby.gemspec | 3 ++-
|
1116
|
+
1 file changed, 2 insertions(+), 1 deletion(-)
|
982
1117
|
|
983
|
-
commit
|
1118
|
+
commit 8e986984892d661b4f09a06158a634554d931718
|
984
1119
|
Author: Naohisa Goto <ng@bioruby.org>
|
985
|
-
Date:
|
1120
|
+
Date: Tue Jun 7 23:59:35 2016 +0900
|
986
1121
|
|
987
|
-
|
1122
|
+
.travis.yml: Update ruby versions and remove temporary workaround
|
1123
|
+
|
1124
|
+
* Update Ruby versions to 2.2, 2.1.10, and rbx-3.
|
1125
|
+
* Remove temporary workaround about RubyGems introduced in
|
1126
|
+
e92e09edf5904f51d3e73e61d13fce4159a543c5.
|
988
1127
|
|
989
|
-
|
990
|
-
1 file changed,
|
1128
|
+
.travis.yml | 18 ++++++++----------
|
1129
|
+
1 file changed, 8 insertions(+), 10 deletions(-)
|
991
1130
|
|
992
|
-
commit
|
1131
|
+
commit 90e678d6d74d86c45631128c0f16181679f0d599
|
993
1132
|
Author: Naohisa Goto <ng@bioruby.org>
|
994
|
-
Date:
|
1133
|
+
Date: Tue Jun 7 23:37:45 2016 +0900
|
995
1134
|
|
996
|
-
|
1135
|
+
Test bug: fix gem version mismatch error on Travis-CI
|
1136
|
+
|
1137
|
+
* Rakefile: prefer to use spec read from existing bioruby.gemspec file
|
1138
|
+
instead of that of generated from bioruby.gemspec.erb.
|
1139
|
+
This fixes "can't activate bio (= 1.5.1.2016XXXX), already activated
|
1140
|
+
bio-1.5.1.2015NNNN" occurred on Travis-CI during gem integration tests.
|
997
1141
|
|
998
|
-
|
999
|
-
1 file changed,
|
1142
|
+
Rakefile | 20 ++++++++++++--------
|
1143
|
+
1 file changed, 12 insertions(+), 8 deletions(-)
|
1000
1144
|
|
1001
|
-
commit
|
1002
|
-
Author:
|
1003
|
-
Date:
|
1145
|
+
commit bdb33fe752b7dddcb35f57d826f85dbdd512c3c1
|
1146
|
+
Author: Kozo Nishida <knishida@riken.jp>
|
1147
|
+
Date: Wed Nov 4 12:08:24 2015 +0900
|
1004
1148
|
|
1005
|
-
|
1149
|
+
add appveyor.yml
|
1006
1150
|
|
1007
|
-
|
1008
|
-
1 file changed,
|
1151
|
+
appveyor.yml | 22 ++++++++++++++++++++++
|
1152
|
+
1 file changed, 22 insertions(+)
|
1153
|
+
create mode 100644 appveyor.yml
|
1009
1154
|
|
1010
|
-
commit
|
1155
|
+
commit 8b0fa73c57232a6a86d2d6fd0711f51bc50aa333
|
1011
1156
|
Author: Naohisa Goto <ng@bioruby.org>
|
1012
|
-
Date:
|
1157
|
+
Date: Thu Sep 17 23:34:34 2015 +0900
|
1013
1158
|
|
1014
|
-
|
1159
|
+
regenerate bioruby.gemspec with rake regemspec
|
1015
1160
|
|
1016
|
-
|
1017
|
-
1 file changed,
|
1161
|
+
bioruby.gemspec | 14 +-------------
|
1162
|
+
1 file changed, 1 insertion(+), 13 deletions(-)
|
1018
1163
|
|
1019
|
-
commit
|
1164
|
+
commit 813fc808e9a235e03ed2d5bad2d15f74946bd65a
|
1020
1165
|
Author: Naohisa Goto <ng@bioruby.org>
|
1021
|
-
Date:
|
1166
|
+
Date: Thu Sep 17 23:30:46 2015 +0900
|
1022
1167
|
|
1023
|
-
|
1168
|
+
Tutorial.rd.html is regenerated by rake retutorial2html
|
1024
1169
|
|
1025
|
-
|
1026
|
-
1 file changed,
|
1170
|
+
doc/Tutorial.rd.html | 117 +++++++++------------------------------------------
|
1171
|
+
1 file changed, 19 insertions(+), 98 deletions(-)
|
1027
1172
|
|
1028
|
-
commit
|
1173
|
+
commit 756f14122a45973289172a88241490a1bcc0054a
|
1029
1174
|
Author: Naohisa Goto <ng@bioruby.org>
|
1030
|
-
Date:
|
1175
|
+
Date: Thu Sep 17 23:25:07 2015 +0900
|
1031
1176
|
|
1032
|
-
|
1177
|
+
Delete Bio::PhyloXML tutorial
|
1178
|
+
|
1179
|
+
* Tutorial for Bio::PhyloXML is deleted from BioRuby core.
|
1180
|
+
It is now moved to bio-phyloxml gem. New tutorial for
|
1181
|
+
Bio::PhyloXML is available at:
|
1182
|
+
https://github.com/bioruby/bioruby-phyloxml/blob/master/doc/Tutorial.rd
|
1033
1183
|
|
1034
|
-
|
1035
|
-
1 file changed,
|
1184
|
+
doc/Tutorial.rd | 114 +++-----------------------------------------------------
|
1185
|
+
1 file changed, 6 insertions(+), 108 deletions(-)
|
1036
1186
|
|
1037
|
-
commit
|
1187
|
+
commit bb42efdd2eec380c99cbd3e505577a550dda8ce7
|
1038
1188
|
Author: Naohisa Goto <ng@bioruby.org>
|
1039
|
-
Date:
|
1189
|
+
Date: Thu Sep 17 23:20:50 2015 +0900
|
1040
1190
|
|
1041
|
-
|
1191
|
+
Delete description of Bio::PhyloXML and its dependency libxml-ruby.
|
1042
1192
|
|
1043
|
-
|
1044
|
-
1 file changed,
|
1193
|
+
README.rdoc | 6 ------
|
1194
|
+
1 file changed, 6 deletions(-)
|
1045
1195
|
|
1046
|
-
commit
|
1196
|
+
commit 4202ae936baf0f4c8a722af240a6613f4e8a8cee
|
1047
1197
|
Author: Naohisa Goto <ng@bioruby.org>
|
1048
|
-
Date:
|
1198
|
+
Date: Thu Sep 17 22:48:23 2015 +0900
|
1049
1199
|
|
1050
|
-
|
1200
|
+
Remove PhyloXML (split out bio-phyloxml gem)
|
1201
|
+
|
1202
|
+
* Bio::PhyloXML is removed from BioRuby core.
|
1203
|
+
It will soon be released as separate bio-phyloxml gem.
|
1204
|
+
The development repository of the new Bio::PhyloXML is
|
1205
|
+
https://github.com/bioruby/bioruby-phyloxml
|
1051
1206
|
|
1052
|
-
|
1053
|
-
|
1207
|
+
lib/bio/db/phyloxml/phyloxml.xsd | 582 ------
|
1208
|
+
lib/bio/db/phyloxml/phyloxml_elements.rb | 1194 -----------
|
1209
|
+
lib/bio/db/phyloxml/phyloxml_parser.rb | 1001 ----------
|
1210
|
+
lib/bio/db/phyloxml/phyloxml_writer.rb | 227 ---
|
1211
|
+
sample/test_phyloxml_big.rb | 205 --
|
1212
|
+
test/data/phyloxml/apaf.xml | 666 -------
|
1213
|
+
test/data/phyloxml/bcl_2.xml | 2097 --------------------
|
1214
|
+
test/data/phyloxml/made_up.xml | 144 --
|
1215
|
+
.../data/phyloxml/ncbi_taxonomy_mollusca_short.xml | 65 -
|
1216
|
+
test/data/phyloxml/phyloxml_examples.xml | 415 ----
|
1217
|
+
test/unit/bio/db/test_phyloxml.rb | 821 --------
|
1218
|
+
test/unit/bio/db/test_phyloxml_writer.rb | 334 ----
|
1219
|
+
12 files changed, 7751 deletions(-)
|
1220
|
+
delete mode 100644 lib/bio/db/phyloxml/phyloxml.xsd
|
1221
|
+
delete mode 100644 lib/bio/db/phyloxml/phyloxml_elements.rb
|
1222
|
+
delete mode 100644 lib/bio/db/phyloxml/phyloxml_parser.rb
|
1223
|
+
delete mode 100644 lib/bio/db/phyloxml/phyloxml_writer.rb
|
1224
|
+
delete mode 100644 sample/test_phyloxml_big.rb
|
1225
|
+
delete mode 100644 test/data/phyloxml/apaf.xml
|
1226
|
+
delete mode 100644 test/data/phyloxml/bcl_2.xml
|
1227
|
+
delete mode 100644 test/data/phyloxml/made_up.xml
|
1228
|
+
delete mode 100644 test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml
|
1229
|
+
delete mode 100644 test/data/phyloxml/phyloxml_examples.xml
|
1230
|
+
delete mode 100644 test/unit/bio/db/test_phyloxml.rb
|
1231
|
+
delete mode 100644 test/unit/bio/db/test_phyloxml_writer.rb
|
1054
1232
|
|
1055
|
-
commit
|
1233
|
+
commit e3a85ad9eb6d258e79fdfbe600711a5296a20e8c
|
1056
1234
|
Author: Naohisa Goto <ng@bioruby.org>
|
1057
|
-
Date:
|
1235
|
+
Date: Thu Sep 17 22:45:32 2015 +0900
|
1058
1236
|
|
1059
|
-
|
1237
|
+
Delete autoload of Bio::PhyloXML
|
1238
|
+
|
1239
|
+
* Delete autoload of Bio::PhyloXML, for preparation of spliting
|
1240
|
+
out Bio::PhyloXML.
|
1060
1241
|
|
1061
|
-
|
1062
|
-
1 file changed,
|
1242
|
+
lib/bio.rb | 7 -------
|
1243
|
+
1 file changed, 7 deletions(-)
|
1063
1244
|
|
1064
|
-
commit
|
1245
|
+
commit 422ffe6fedecf41d83327c01f7a55ebce4afd70d
|
1065
1246
|
Author: Naohisa Goto <ng@bioruby.org>
|
1066
|
-
Date:
|
1247
|
+
Date: Tue Sep 15 22:33:14 2015 +0900
|
1067
1248
|
|
1068
|
-
|
1249
|
+
Incompatible change about deprecated Bio::Taxonomy is described.
|
1069
1250
|
|
1070
|
-
|
1071
|
-
1 file changed,
|
1251
|
+
RELEASE_NOTES.rdoc | 21 +++++++++++++++++++++
|
1252
|
+
1 file changed, 21 insertions(+)
|
1072
1253
|
|
1073
|
-
commit
|
1254
|
+
commit 3ea10d73340d8ad571ab6ca386cffca18ec725d1
|
1074
1255
|
Author: Naohisa Goto <ng@bioruby.org>
|
1075
|
-
Date:
|
1256
|
+
Date: Tue Sep 15 21:06:29 2015 +0900
|
1076
1257
|
|
1077
|
-
|
1258
|
+
Bio::Taxonomy is removed and merged to Bio::PhyloXML::Taxonomy
|
1259
|
+
|
1260
|
+
* Bio::Taxonomy in lib/bio/db/phyloxml/phyloxml_elements.rb was
|
1261
|
+
written for PhyloXML, but it was intended to become general
|
1262
|
+
taxonomy data class in BioRuby. However, no efforts have been
|
1263
|
+
made to improve the Bio::Taxonomy class, and it still remains
|
1264
|
+
to be a PhyloXML specific class. As the first step to split out
|
1265
|
+
Bio::PhyloXML to a new Gem (Biogem) package, we now decide to
|
1266
|
+
remove Bio::Taxonomy and merge it to Bio::PhyloXML::Taxonomy.
|
1267
|
+
|
1268
|
+
* Codes using Bio::Taxonomy should be modified. Changing
|
1269
|
+
Bio::Taxonomy to Bio::PhyloXML::Taxonomy, or adding the
|
1270
|
+
following monkey patch is needed.
|
1271
|
+
|
1272
|
+
module Bio
|
1273
|
+
unless defined? Taxonomy
|
1274
|
+
Taxonomy = Bio::PhyloXML::Taxonomy
|
1275
|
+
end
|
1276
|
+
end
|
1078
1277
|
|
1079
|
-
lib/bio
|
1080
|
-
|
1278
|
+
lib/bio.rb | 2 --
|
1279
|
+
lib/bio/db/phyloxml/phyloxml_elements.rb | 21 +++++++++------------
|
1280
|
+
2 files changed, 9 insertions(+), 14 deletions(-)
|
1081
1281
|
|
1082
|
-
commit
|
1282
|
+
commit f89f49223f7d6ed74a8fc50aa2355fb5912c885f
|
1083
1283
|
Author: Naohisa Goto <ng@bioruby.org>
|
1084
|
-
Date:
|
1284
|
+
Date: Mon Sep 14 15:15:56 2015 +0900
|
1085
1285
|
|
1086
|
-
|
1286
|
+
regenerate bioruby.gemspec with rake regemspec
|
1087
1287
|
|
1088
|
-
|
1089
|
-
1 file changed,
|
1288
|
+
bioruby.gemspec | 7 +++++--
|
1289
|
+
1 file changed, 5 insertions(+), 2 deletions(-)
|
1090
1290
|
|
1091
|
-
commit
|
1291
|
+
commit 809e190d710caceee1c213da1aa067dee87e6ebd
|
1092
1292
|
Author: Naohisa Goto <ng@bioruby.org>
|
1093
|
-
Date:
|
1293
|
+
Date: Mon Sep 14 15:14:05 2015 +0900
|
1094
1294
|
|
1095
|
-
|
1295
|
+
New RELEASE_NOTES.rdoc for the next release version
|
1096
1296
|
|
1097
|
-
|
1098
|
-
1 file changed,
|
1297
|
+
RELEASE_NOTES.rdoc | 47 +++++++++++++++++++++++++++++++++++++++++++++++
|
1298
|
+
1 file changed, 47 insertions(+)
|
1299
|
+
create mode 100644 RELEASE_NOTES.rdoc
|
1099
1300
|
|
1100
|
-
commit
|
1301
|
+
commit a44257e933165509f3d2b164ea547ed8fba18ea5
|
1101
1302
|
Author: Naohisa Goto <ng@bioruby.org>
|
1102
|
-
Date:
|
1303
|
+
Date: Mon Sep 14 15:10:42 2015 +0900
|
1103
1304
|
|
1104
|
-
|
1305
|
+
move RELEASE_NOTES.rdoc to doc/RELEASE_NOTES-1.5.0.rdoc
|
1105
1306
|
|
1106
|
-
|
1107
|
-
1 file changed,
|
1307
|
+
RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.5.0.rdoc | 0
|
1308
|
+
1 file changed, 0 insertions(+), 0 deletions(-)
|
1309
|
+
rename RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.5.0.rdoc (100%)
|
1108
1310
|
|
1109
|
-
commit
|
1311
|
+
commit 4d53755b0181255e2ee69193a5a3b064ef4f4b77
|
1110
1312
|
Author: Naohisa Goto <ng@bioruby.org>
|
1111
|
-
Date:
|
1313
|
+
Date: Thu Jul 2 22:19:03 2015 +0900
|
1112
1314
|
|
1113
|
-
|
1315
|
+
ChangeLog since 1.5.0 release
|
1114
1316
|
|
1115
|
-
|
1116
|
-
1 file changed,
|
1317
|
+
ChangeLog | 38 ++++++++++++++++++++++++++++++++++++++
|
1318
|
+
1 file changed, 38 insertions(+)
|
1319
|
+
create mode 100644 ChangeLog
|
1117
1320
|
|
1118
|
-
commit
|
1321
|
+
commit e066e3c8bcf0c6b7eadd3573576d4550aca77cc5
|
1119
1322
|
Author: Naohisa Goto <ng@bioruby.org>
|
1120
|
-
Date:
|
1323
|
+
Date: Thu Jul 2 22:17:06 2015 +0900
|
1121
1324
|
|
1122
|
-
|
1325
|
+
ChangeLog is moved to doc/ChangeLog-1.5.0
|
1123
1326
|
|
1124
|
-
|
1125
|
-
1 file changed,
|
1327
|
+
ChangeLog => doc/ChangeLog-1.5.0 | 0
|
1328
|
+
1 file changed, 0 insertions(+), 0 deletions(-)
|
1329
|
+
rename ChangeLog => doc/ChangeLog-1.5.0 (100%)
|
1126
1330
|
|
1127
|
-
commit
|
1331
|
+
commit dd53e885c1baa765bc094897d53309af7b15497b
|
1128
1332
|
Author: Naohisa Goto <ng@bioruby.org>
|
1129
|
-
Date:
|
1333
|
+
Date: Thu Jul 2 22:09:26 2015 +0900
|
1130
1334
|
|
1131
|
-
|
1335
|
+
change version for generating ChangeLog to 1.5.0
|
1132
1336
|
|
1133
|
-
|
1134
|
-
1 file changed, 1 deletion(-)
|
1337
|
+
Rakefile | 2 +-
|
1338
|
+
1 file changed, 1 insertion(+), 1 deletion(-)
|
1135
1339
|
|
1136
|
-
commit
|
1340
|
+
commit 7a5d897ebc45d9ec5357918a42eb2980decf01e4
|
1137
1341
|
Author: Naohisa Goto <ng@bioruby.org>
|
1138
|
-
Date:
|
1342
|
+
Date: Thu Jul 2 21:52:17 2015 +0900
|
1139
1343
|
|
1140
|
-
|
1344
|
+
version changed to 1.5.1-dev (pre-release version of 1.5.1)
|
1141
1345
|
|
1142
|
-
lib/bio/
|
1346
|
+
lib/bio/version.rb | 4 ++--
|
1143
1347
|
1 file changed, 2 insertions(+), 2 deletions(-)
|
1144
1348
|
|
1145
|
-
commit
|
1349
|
+
commit 8fc4d6c64f6958a352c36b171b00d1f1ff2a2354
|
1146
1350
|
Author: Naohisa Goto <ng@bioruby.org>
|
1147
|
-
Date:
|
1351
|
+
Date: Thu Jul 2 21:47:28 2015 +0900
|
1148
1352
|
|
1149
|
-
|
1353
|
+
fix English syntax and unexpected word insertion
|
1150
1354
|
|
1151
|
-
|
1152
|
-
1 file changed, 1 deletion(-)
|
1153
|
-
|
1154
|
-
commit 46a4edc8729ff836ae28d11f1503c9923275b9f6
|
1155
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1156
|
-
Date: Sat Mar 21 10:00:04 2015 +0900
|
1157
|
-
|
1158
|
-
Ruby 1.9 support: suppress warning "shadowing outer local variable - flag"
|
1159
|
-
|
1160
|
-
lib/bio/db/phyloxml/phyloxml_parser.rb | 2 +-
|
1161
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
1162
|
-
|
1163
|
-
commit db3552c683edf79adbfa5ed897f5ef91e8417585
|
1164
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1165
|
-
Date: Fri Mar 20 16:33:45 2015 +0900
|
1166
|
-
|
1167
|
-
Bug fix: Bio::PhyloXML::Parser.open_uri did not return block return value
|
1168
|
-
|
1169
|
-
* Bug fix: Bio::PhyloXML::Parser.open_uri did not return block
|
1170
|
-
return value when giving block.
|
1171
|
-
* Suppress warning "assigned but unused variable - ret"
|
1172
|
-
|
1173
|
-
lib/bio/db/phyloxml/phyloxml_parser.rb | 1 +
|
1174
|
-
1 file changed, 1 insertion(+)
|
1175
|
-
|
1176
|
-
commit 84c2c4e94352cc9cef982d3b505b4f439617e01e
|
1177
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1178
|
-
Date: Fri Mar 20 16:21:49 2015 +0900
|
1179
|
-
|
1180
|
-
delete obsolete $Id:$ line
|
1181
|
-
|
1182
|
-
lib/bio/appl/genscan/report.rb | 1 -
|
1183
|
-
1 file changed, 1 deletion(-)
|
1184
|
-
|
1185
|
-
commit 05c55d0aaf1dc130ac04155622ccebb3394fc3c0
|
1186
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1187
|
-
Date: Fri Mar 20 16:21:06 2015 +0900
|
1188
|
-
|
1189
|
-
Ruby 1.9 support: suppress warning "shadowing outer local variable - i"
|
1190
|
-
|
1191
|
-
lib/bio/appl/genscan/report.rb | 2 +-
|
1192
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
1193
|
-
|
1194
|
-
commit 5edcc1c97ca7c292fa6551509570daf68ac36837
|
1195
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1196
|
-
Date: Fri Mar 20 16:13:57 2015 +0900
|
1197
|
-
|
1198
|
-
Ruby 1.9 support: suppress warning "shadowing outer local variable - y"
|
1199
|
-
|
1200
|
-
lib/bio/appl/blast/format0.rb | 2 +-
|
1201
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
1202
|
-
|
1203
|
-
commit 813d53a06258244a47784697e8fc95f1f15db8da
|
1204
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1205
|
-
Date: Fri Mar 20 16:03:19 2015 +0900
|
1206
|
-
|
1207
|
-
delete obsolete $Id:$ line
|
1208
|
-
|
1209
|
-
lib/bio/io/das.rb | 1 -
|
1210
|
-
1 file changed, 1 deletion(-)
|
1211
|
-
|
1212
|
-
commit b6ae4a423dd763969c8e18ca6a578fd0600d6159
|
1213
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1214
|
-
Date: Fri Mar 20 16:02:20 2015 +0900
|
1215
|
-
|
1216
|
-
Ruby 1.9 support: suppress "warning: shadowing outer local variable - e"
|
1217
|
-
|
1218
|
-
lib/bio/io/das.rb | 80 +++++++++++++++++++++++++++----------------------------
|
1219
|
-
1 file changed, 40 insertions(+), 40 deletions(-)
|
1220
|
-
|
1221
|
-
commit 7fa75a644167dd8c189f681e29c1cf5f1bf2fe0b
|
1222
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1223
|
-
Date: Fri Mar 20 15:36:00 2015 +0900
|
1224
|
-
|
1225
|
-
delete obsolete $Id:$ line
|
1226
|
-
|
1227
|
-
lib/bio/shell/plugin/seq.rb | 1 -
|
1228
|
-
1 file changed, 1 deletion(-)
|
1229
|
-
|
1230
|
-
commit 051aba1519d71f1205363c4421feb6c06881ab0c
|
1231
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1232
|
-
Date: Fri Mar 20 15:29:02 2015 +0900
|
1233
|
-
|
1234
|
-
Bug fix: Ruby 1.9 support: did not yield the last part of the string
|
1235
|
-
|
1236
|
-
* lib/bio/shell/plugin/seq.rb: Bug fix: Ruby 1.9 support:
|
1237
|
-
String#step and #skip (extended by bioruby-shell) did not yield
|
1238
|
-
the last part of the string due to a change from Ruby 1.8 to 1.9.
|
1239
|
-
* Suppress warning message "shadowing outer local variable - i"
|
1240
|
-
|
1241
|
-
lib/bio/shell/plugin/seq.rb | 12 +++++++-----
|
1242
|
-
1 file changed, 7 insertions(+), 5 deletions(-)
|
1243
|
-
|
1244
|
-
commit a9f2bff92de58c2ab4cefc67e721d3ad69e9de98
|
1245
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1246
|
-
Date: Fri Mar 20 15:09:16 2015 +0900
|
1247
|
-
|
1248
|
-
Ruby 2.2 support: suppress a "shadowing outer local variable" warning
|
1249
|
-
|
1250
|
-
lib/bio/alignment.rb | 6 +++---
|
1251
|
-
1 file changed, 3 insertions(+), 3 deletions(-)
|
1252
|
-
|
1253
|
-
commit d0bcc8766d91eb7cacea2a6d5b32b3e0b3c5ce56
|
1254
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1255
|
-
Date: Fri Mar 20 14:31:04 2015 +0900
|
1256
|
-
|
1257
|
-
delete obsolete $Id:$ line
|
1258
|
-
|
1259
|
-
test/unit/bio/test_alignment.rb | 1 -
|
1260
|
-
1 file changed, 1 deletion(-)
|
1261
|
-
|
1262
|
-
commit 0c8fa8fd558088822a98e11b6fa4bec9b37ebec7
|
1263
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1264
|
-
Date: Fri Mar 20 14:26:38 2015 +0900
|
1265
|
-
|
1266
|
-
Ruby 2.2 support: comment out duplicated line to suppress warning
|
1267
|
-
|
1268
|
-
* Ruby 2.2 support: test/unit/bio/test_alignment.rb:
|
1269
|
-
Suppress warning: duplicated key at line 182 ignored: "t"
|
1270
|
-
|
1271
|
-
test/unit/bio/test_alignment.rb | 2 +-
|
1272
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
1273
|
-
|
1274
|
-
commit ab17c40e1ce492dc924205e8e2f90d31adae4464
|
1275
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1276
|
-
Date: Fri Mar 20 14:18:08 2015 +0900
|
1277
|
-
|
1278
|
-
Ruby 2.2 support: some tests did not run with test-unit gem
|
1279
|
-
|
1280
|
-
* Ruby 2.2 support: test/unit/bio/db/test_fastq.rb
|
1281
|
-
Support for test-unit gem bundled in Ruby 2.2.
|
1282
|
-
See commit log b9488a64abb780c5e9b6cd28e8264bad399fa749 for details.
|
1283
|
-
|
1284
|
-
test/unit/bio/db/test_fastq.rb | 18 ++++++++++++++----
|
1285
|
-
1 file changed, 14 insertions(+), 4 deletions(-)
|
1286
|
-
|
1287
|
-
commit ea668d73c18e3df33625cba4352ad5f6966e0eb4
|
1288
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1289
|
-
Date: Fri Mar 20 14:03:43 2015 +0900
|
1290
|
-
|
1291
|
-
delete obsolete $Id:$ line
|
1292
|
-
|
1293
|
-
test/unit/bio/appl/sim4/test_report.rb | 1 -
|
1294
|
-
1 file changed, 1 deletion(-)
|
1295
|
-
|
1296
|
-
commit 1abb8d362a0f2443b48923bcccba3d7d0caa1f1d
|
1297
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1298
|
-
Date: Fri Mar 20 13:57:33 2015 +0900
|
1299
|
-
|
1300
|
-
Ruby 2.2 support: some tests did not run with test-unit gem
|
1301
|
-
|
1302
|
-
* Ruby 2.2 support: test/unit/bio/appl/sim4/test_report.rb
|
1303
|
-
Support for test-unit gem bundled in Ruby 2.2.
|
1304
|
-
See commit log b9488a64abb780c5e9b6cd28e8264bad399fa749 for details.
|
1305
|
-
|
1306
|
-
test/unit/bio/appl/sim4/test_report.rb | 62 +++++++++++++++++++++++++---------
|
1307
|
-
1 file changed, 46 insertions(+), 16 deletions(-)
|
1308
|
-
|
1309
|
-
commit b9488a64abb780c5e9b6cd28e8264bad399fa749
|
1310
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1311
|
-
Date: Fri Mar 20 13:13:28 2015 +0900
|
1312
|
-
|
1313
|
-
Ruby 2.2 support: some tests did not run with test-unit gem
|
1314
|
-
|
1315
|
-
* Ruby 2.2 support: test/unit/bio/appl/blast/test_report.rb:
|
1316
|
-
With test-unit gem bundled in Ruby 2.2, test methods inherited
|
1317
|
-
from a parent class and executed in the parent class do not
|
1318
|
-
run in the child class. To avoid the behavior, test methods
|
1319
|
-
are moved to modules and test classes are changed to include
|
1320
|
-
the modules.
|
1321
|
-
|
1322
|
-
test/unit/bio/appl/blast/test_report.rb | 156 ++++++++++++++++++++++----------
|
1323
|
-
1 file changed, 110 insertions(+), 46 deletions(-)
|
1324
|
-
|
1325
|
-
commit febe8bbf614e530f597d7306d33df5f5f4ee6699
|
1326
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1327
|
-
Date: Thu Mar 19 00:55:09 2015 +0900
|
1328
|
-
|
1329
|
-
try to use bio-old-biofetch-emulator gem
|
1330
|
-
|
1331
|
-
* bin/br_biofetch.rb: try to use bio-old-biofetch-emulator gem.
|
1332
|
-
Without bio-old-biofetch-emulator, the program exits with error
|
1333
|
-
message when default BioRuby BioFetch server is specified.
|
1334
|
-
|
1335
|
-
bin/br_biofetch.rb | 19 +++++++++++++++++++
|
1336
|
-
1 file changed, 19 insertions(+)
|
1337
|
-
|
1338
|
-
commit 08450e0a35cbf5596dd30238d23aa7a7296c8f67
|
1339
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1340
|
-
Date: Thu Mar 19 00:36:10 2015 +0900
|
1341
|
-
|
1342
|
-
do not repeat default_url and another_url
|
1343
|
-
|
1344
|
-
bin/br_biofetch.rb | 14 ++++++++++----
|
1345
|
-
1 file changed, 10 insertions(+), 4 deletions(-)
|
1346
|
-
|
1347
|
-
commit 8e39d3411405b09cc6ea55ba31e5206536ebf59d
|
1348
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1349
|
-
Date: Wed Mar 18 23:57:59 2015 +0900
|
1350
|
-
|
1351
|
-
Revert e29fc5fadbe0dae6528cf49637496dc2df3ec0dc
|
1352
|
-
|
1353
|
-
* bin/br_biofetch.rb: revert e29fc5fadbe0dae6528cf49637496dc2df3ec0dc
|
1354
|
-
because the old deprecated bioruby biofetch server can be emulated
|
1355
|
-
by bio-old-biofetch-emulator gem package.
|
1356
|
-
|
1357
|
-
bin/br_biofetch.rb | 15 ++++++++-------
|
1358
|
-
1 file changed, 8 insertions(+), 7 deletions(-)
|
1359
|
-
|
1360
|
-
commit 849c38931a64b7ff2ba7ec46a495e65a99a869fb
|
1361
|
-
Author: Ben J. Woodcroft <donttrustben near gmail.com>
|
1362
|
-
Date: Wed Aug 8 09:44:09 2012 +1000
|
1363
|
-
|
1364
|
-
add FastaFormat#first_name method
|
1365
|
-
|
1366
|
-
lib/bio/db/fasta.rb | 17 +++++++++++++++++
|
1367
|
-
test/unit/bio/db/test_fasta.rb | 42 +++++++++++++++++++++++++++++++++++++++++-
|
1368
|
-
2 files changed, 58 insertions(+), 1 deletion(-)
|
1369
|
-
|
1370
|
-
commit 888a70508c0392cae89021feba5c4a6a62228a11
|
1371
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1372
|
-
Date: Fri Nov 14 15:08:35 2014 +0900
|
1373
|
-
|
1374
|
-
fix typo
|
1375
|
-
|
1376
|
-
* fix typo. Thanks to Iain Barnett who reported the bug in
|
1377
|
-
https://github.com/bioruby/bioruby/pull/93
|
1378
|
-
(c4843d65447f6a434da523c9c313f34d025f36f8)
|
1379
|
-
|
1380
|
-
lib/bio/sequence/compat.rb | 2 +-
|
1381
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
1382
|
-
|
1383
|
-
commit afc6df190109649e8eb11b2af1184ddfcf5327d3
|
1384
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1385
|
-
Date: Fri Nov 14 14:29:42 2014 +0900
|
1386
|
-
|
1387
|
-
add documentation when gc_percent is not enough
|
1388
|
-
|
1389
|
-
lib/bio/sequence/na.rb | 8 ++++++++
|
1390
|
-
1 file changed, 8 insertions(+)
|
1391
|
-
|
1392
|
-
commit bb63f67f2dfe6dba5c70ada033ca0cc1ecaa7783
|
1393
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1394
|
-
Date: Thu Nov 13 21:43:00 2014 +0900
|
1395
|
-
|
1396
|
-
Add tests for Bio::PubMed#search, query, pmfetch
|
1397
|
-
|
1398
|
-
* Add tests for Bio::PubMed#search, query, pmfetch, although
|
1399
|
-
they will be deprecated in the future.
|
1400
|
-
* This commit and commit bfe4292c51bba5c4032027c36c35e98f28a9605a
|
1401
|
-
are inspired by https://github.com/bioruby/bioruby/pull/76
|
1402
|
-
(though the pull request have not been merged), and the commits
|
1403
|
-
fix the issue https://github.com/bioruby/bioruby/issues/75.
|
1404
|
-
Thanks to Paul Leader who reported the issue and the pull request.
|
1405
|
-
|
1406
|
-
test/network/bio/io/test_pubmed.rb | 49 ++++++++++++++++++++++++++++++++++++++
|
1407
|
-
1 file changed, 49 insertions(+)
|
1408
|
-
|
1409
|
-
commit 74edba100da83c27f2edb7a9edc9ec98265a7cff
|
1410
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1411
|
-
Date: Thu Nov 13 12:05:12 2014 +0900
|
1412
|
-
|
1413
|
-
Change default tool and email values
|
1414
|
-
|
1415
|
-
* Default "tool" and "email" values are changed to "bioruby" and
|
1416
|
-
"staff@bioruby.org" respectively. Now, the author of a script
|
1417
|
-
do not need to set his/her email address unless the script makes
|
1418
|
-
excess traffic to NCBI.
|
1419
|
-
* Update RDoc documentation
|
1420
|
-
|
1421
|
-
lib/bio/io/ncbirest.rb | 48 +++++++++++++++++++++++++++++++++++++++++++-----
|
1422
|
-
1 file changed, 43 insertions(+), 5 deletions(-)
|
1423
|
-
|
1424
|
-
commit bfe4292c51bba5c4032027c36c35e98f28a9605a
|
1425
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1426
|
-
Date: Thu Nov 13 11:54:53 2014 +0900
|
1427
|
-
|
1428
|
-
Bug fix: use NCBI E-Utilities instead of old deprecated API
|
1429
|
-
|
1430
|
-
* Bio::PubMed#search, query, pmfetch: remove old code using deprecated
|
1431
|
-
and/or unofficial web API, and change use esearch or efetch methods
|
1432
|
-
which use NCBI E-utilities. These methods will be deprecated in the
|
1433
|
-
future. To indicate this, show warning message if $VERBOSE is true.
|
1434
|
-
* Update RDoc documentation
|
1435
|
-
|
1436
|
-
lib/bio/io/pubmed.rb | 157 +++++++++++++++++++++++++--------------------------
|
1437
|
-
1 file changed, 76 insertions(+), 81 deletions(-)
|
1438
|
-
|
1439
|
-
commit d78173a6eb6d8177e733decc0b8137fac067aa82
|
1440
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1441
|
-
Date: Tue Nov 11 17:41:32 2014 +0900
|
1442
|
-
|
1443
|
-
remove unused $Id:$ line
|
1444
|
-
|
1445
|
-
bin/br_biofetch.rb | 1 -
|
1446
|
-
1 file changed, 1 deletion(-)
|
1447
|
-
|
1448
|
-
commit e29fc5fadbe0dae6528cf49637496dc2df3ec0dc
|
1449
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1450
|
-
Date: Tue Nov 11 17:31:38 2014 +0900
|
1451
|
-
|
1452
|
-
Change default server to EBI Dbfetch server; remove BioRuby BioFetch server
|
1453
|
-
|
1454
|
-
* Change default server to EBI Dbfetch server.
|
1455
|
-
* The BioRuby BioFetch server is removed. When "-r" option (force to use
|
1456
|
-
BioRuby server) is specified, warning message is shown, and the program
|
1457
|
-
exits with code 1 (abnormal exit).
|
1458
|
-
* Usage message is also changed.
|
1459
|
-
|
1460
|
-
bin/br_biofetch.rb | 15 +++++++--------
|
1461
|
-
1 file changed, 7 insertions(+), 8 deletions(-)
|
1462
|
-
|
1463
|
-
commit 94ecac33e87e444d9fe991340c2d8f3709bc6d90
|
1464
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1465
|
-
Date: Tue Nov 11 17:19:30 2014 +0900
|
1466
|
-
|
1467
|
-
fix documentation reflecting recent changes of Bio::Fetch
|
1468
|
-
|
1469
|
-
lib/bio/io/fetch.rb | 33 ++++++++++++++++++++-------------
|
1470
|
-
1 file changed, 20 insertions(+), 13 deletions(-)
|
1471
|
-
|
1472
|
-
commit 06a9db014614818ef35108928415ef18e8c8ae2c
|
1473
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1474
|
-
Date: Tue Nov 11 16:41:26 2014 +0900
|
1475
|
-
|
1476
|
-
documentation about incompatible changes of Bio::Fetch
|
1477
|
-
|
1478
|
-
RELEASE_NOTES.rdoc | 22 ++++++++++++++++++++++
|
1479
|
-
1 file changed, 22 insertions(+)
|
1480
|
-
|
1481
|
-
commit 6d94e949b6d325f27b45b816a8305f828d049ec6
|
1482
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1483
|
-
Date: Tue Nov 11 16:35:50 2014 +0900
|
1484
|
-
|
1485
|
-
Issue about Bio::Fetch and BioRuby BioFetch server is resolved
|
1486
|
-
|
1487
|
-
* Issue about Bio::Fetch is resolved by recent commits.
|
1488
|
-
|
1489
|
-
* The BioRuby BioFetch server is deprecated. There is no hope to restart
|
1490
|
-
the service again. EBI Dbfetch server is an alternative.
|
1491
|
-
|
1492
|
-
KNOWN_ISSUES.rdoc | 9 ---------
|
1493
|
-
1 file changed, 9 deletions(-)
|
1494
|
-
|
1495
|
-
commit 699cd3ff136310a551d30e0ddd7fbe66e483b5be
|
1496
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1497
|
-
Date: Tue Nov 11 15:27:11 2014 +0900
|
1498
|
-
|
1499
|
-
update RDoc documents for Bio::Fetch
|
1500
|
-
|
1501
|
-
lib/bio/io/fetch.rb | 61 +++++++++++++++++++++++++++++++++++------------------
|
1502
|
-
1 file changed, 40 insertions(+), 21 deletions(-)
|
1503
|
-
|
1504
|
-
commit c7837f8e5ee2cc1c3085da74567a2b25280bbb8f
|
1505
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1506
|
-
Date: Tue Nov 11 14:48:48 2014 +0900
|
1507
|
-
|
1508
|
-
Incompatibile change: remove Bio::Fetch.query; add Bio::Fetch::EBI.query
|
1509
|
-
|
1510
|
-
* Incompatible change: remove a class method Bio::Fetch.query because
|
1511
|
-
default server URL in Bio::Fetch is deprecated.
|
1512
|
-
|
1513
|
-
* New class method: Bio::Fetch::EBI.query. This can be used as an
|
1514
|
-
alternative method of deprecated Bio::Fetch.query method.
|
1515
|
-
|
1516
|
-
lib/bio/io/fetch.rb | 35 ++++++++++++++++++-----------------
|
1517
|
-
1 file changed, 18 insertions(+), 17 deletions(-)
|
1518
|
-
|
1519
|
-
commit f9048684acaff0fcd00b458a946d5f692706325b
|
1520
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1521
|
-
Date: Tue Nov 11 14:24:22 2014 +0900
|
1522
|
-
|
1523
|
-
Incompatible change: Default server in Bio::Fetch.new is deperecated
|
1524
|
-
|
1525
|
-
* Incompatible change: Default server URL in Bio::Fetch.new is deprecated.
|
1526
|
-
Users must explicitly specify the URL. Alternatively, users must change
|
1527
|
-
their code to use Bio::Fetch::EBI.
|
1528
|
-
|
1529
|
-
* New class Bio::Fetch::EBI, EBI Dbfetch client. This acts the same as
|
1530
|
-
Bio::Fetch.new(Bio::Fetch::EBI::URL) with default database name
|
1531
|
-
"ena_sequence".
|
1532
|
-
|
1533
|
-
lib/bio/io/fetch.rb | 36 +++++++++++++++++++++++++++++++++---
|
1534
|
-
1 file changed, 33 insertions(+), 3 deletions(-)
|
1535
|
-
|
1536
|
-
commit e8919f4f57fc545ca194bebb08c11159b36071cb
|
1537
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1538
|
-
Date: Tue Nov 11 13:43:28 2014 +0900
|
1539
|
-
|
1540
|
-
removed unused variables
|
1541
|
-
|
1542
|
-
lib/bio/io/fetch.rb | 1 -
|
1543
|
-
1 file changed, 1 deletion(-)
|
1544
|
-
|
1545
|
-
commit faec95656b846a7a17cd6a1dbc633dda63cb5b6e
|
1546
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1547
|
-
Date: Tue Nov 11 11:44:00 2014 +0900
|
1548
|
-
|
1549
|
-
Updated URL of EMBL-EBI Dbfetch
|
1550
|
-
|
1551
|
-
lib/bio/io/fetch.rb | 2 +-
|
1552
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
1553
|
-
|
1554
|
-
commit 85be893655f68aafbf7e13badd20bf7f26cd7328
|
1555
|
-
Author: Jose Irizarry <protechpr@gmail.com>
|
1556
|
-
Date: Mon Dec 24 12:30:55 2012 -0400
|
1557
|
-
|
1558
|
-
Update lib/bio/io/fetch.rb
|
1559
|
-
|
1560
|
-
Use EBI's dbfetch endpoint as default since BioRuby's endpoint has been disabled for a while now.
|
1561
|
-
|
1562
|
-
lib/bio/io/fetch.rb | 2 +-
|
1563
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
1564
|
-
|
1565
|
-
commit 163cc06547beed653e19b8c6e71e829d85f2f99c
|
1566
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1567
|
-
Date: Tue Oct 21 16:42:30 2014 +0900
|
1568
|
-
|
1569
|
-
Doc bug fix: wrong sample code
|
1570
|
-
|
1571
|
-
lib/bio/appl/paml/codeml.rb | 4 ++--
|
1572
|
-
1 file changed, 2 insertions(+), 2 deletions(-)
|
1573
|
-
|
1574
|
-
commit 97143139d2d4a66366576a8e62518e93fa5afccf
|
1575
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1576
|
-
Date: Tue Oct 21 15:47:52 2014 +0900
|
1577
|
-
|
1578
|
-
Prevent to repeat calculations of total bases
|
1579
|
-
|
1580
|
-
* Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Prevent to
|
1581
|
-
repeat calculations of total bases.
|
1582
|
-
|
1583
|
-
lib/bio/sequence/na.rb | 20 ++++++++++++--------
|
1584
|
-
1 file changed, 12 insertions(+), 8 deletions(-)
|
1585
|
-
|
1586
|
-
commit b5dbd882e000842fef65e10290b379bfafdddf06
|
1587
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1588
|
-
Date: Tue Oct 21 15:41:13 2014 +0900
|
1589
|
-
|
1590
|
-
Documentation bug fix: Return value is Rational or Float.
|
1591
|
-
|
1592
|
-
* Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Return value
|
1593
|
-
is Rational or Float in recent versions of Ruby. Documentation added for
|
1594
|
-
the treatment of "u" and to return 0.0 if there are no bases.
|
1595
|
-
Reported by ctSkennerton (https://github.com/bioruby/bioruby/issues/73 ).
|
1596
|
-
|
1597
|
-
lib/bio/sequence/na.rb | 47 +++++++++++++++++++++++++++++++++++++++++++----
|
1598
|
-
1 file changed, 43 insertions(+), 4 deletions(-)
|
1599
|
-
|
1600
|
-
commit 3ba98d52ce57488e604dd7ac388a874e5b40ae9d
|
1601
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1602
|
-
Date: Tue Aug 12 00:58:38 2014 +0900
|
1603
|
-
|
1604
|
-
regenerate bioruby.gemspec with rake regemspec
|
1605
|
-
|
1606
|
-
bioruby.gemspec | 14 ++++++--------
|
1607
|
-
1 file changed, 6 insertions(+), 8 deletions(-)
|
1608
|
-
|
1609
|
-
commit a9724d339582952b40c928beccf91376d4e63315
|
1610
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1611
|
-
Date: Tue Aug 5 19:20:42 2014 +0900
|
1612
|
-
|
1613
|
-
Update URIs
|
1614
|
-
|
1615
|
-
* Update URIs.
|
1616
|
-
* Remove links to RubyForge and RAA which have already been closed.
|
1617
|
-
* Add some words for Ruby 1.9 or later.
|
1618
|
-
|
1619
|
-
README.rdoc | 24 +++++++++++-------------
|
1620
|
-
1 file changed, 11 insertions(+), 13 deletions(-)
|
1621
|
-
|
1622
|
-
commit 5f3569faaf89ebcd2b2cf9cbe6b3c1f0544b2679
|
1623
|
-
Author: Iain Barnett <iainspeed@gmail.com>
|
1624
|
-
Date: Wed Mar 5 02:11:07 2014 +0000
|
1625
|
-
|
1626
|
-
Refactor Bio::AminoAcid#weight: Early return clearer and idiomatic.
|
1627
|
-
|
1628
|
-
lib/bio/data/aa.rb | 26 ++++++++++++--------------
|
1629
|
-
1 file changed, 12 insertions(+), 14 deletions(-)
|
1630
|
-
|
1631
|
-
commit c229a20887fcb6df9a7ba49ad5a23e175056fa8d
|
1632
|
-
Author: Iain Barnett <iainspeed@gmail.com>
|
1633
|
-
Date: Wed Mar 5 02:02:45 2014 +0000
|
1634
|
-
|
1635
|
-
Fixed the stack level too deep errors by using Hash#invert.
|
1636
|
-
|
1637
|
-
lib/bio/data/aa.rb | 18 +-----------------
|
1638
|
-
1 file changed, 1 insertion(+), 17 deletions(-)
|
1639
|
-
|
1640
|
-
commit 08dd928df30f5b39c255f9f70dbed8410d395cdf
|
1641
|
-
Author: Iain Barnett <iainspeed@gmail.com>
|
1642
|
-
Date: Tue Mar 4 01:22:51 2014 +0000
|
1643
|
-
|
1644
|
-
Refactored to shorten, remove rescues, and clarify.
|
1645
|
-
|
1646
|
-
lib/bio/alignment.rb | 19 +++++++------------
|
1647
|
-
1 file changed, 7 insertions(+), 12 deletions(-)
|
1648
|
-
|
1649
|
-
commit 112aa284cb1ebecc1d5de186edf2b385649a7268
|
1650
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1651
|
-
Date: Wed Mar 19 14:48:32 2014 +0900
|
1652
|
-
|
1653
|
-
Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008)
|
1654
|
-
|
1655
|
-
* Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008).
|
1656
|
-
Thanks to a researcher who reports the patch via email.
|
1657
|
-
|
1658
|
-
lib/bio/db/pdb/pdb.rb | 4 ++--
|
1659
|
-
1 file changed, 2 insertions(+), 2 deletions(-)
|
1660
|
-
|
1661
|
-
commit ecd5e0c86b04aa918b71c859568425fa39ebbde5
|
1662
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1663
|
-
Date: Sat Jan 18 04:22:51 2014 +0900
|
1664
|
-
|
1665
|
-
suppress "source :rubygems is deprecated" warning
|
1666
|
-
|
1667
|
-
gemfiles/Gemfile.travis-jruby1.8 | 2 +-
|
1668
|
-
gemfiles/Gemfile.travis-jruby1.9 | 2 +-
|
1669
|
-
gemfiles/Gemfile.travis-ruby1.8 | 2 +-
|
1670
|
-
gemfiles/Gemfile.travis-ruby1.9 | 2 +-
|
1671
|
-
4 files changed, 4 insertions(+), 4 deletions(-)
|
1672
|
-
|
1673
|
-
commit 4bda345fe3de9cf1b64c26f3dca1cb3727c946d0
|
1674
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1675
|
-
Date: Sat Jan 18 04:22:03 2014 +0900
|
1676
|
-
|
1677
|
-
gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci
|
1678
|
-
|
1679
|
-
* gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci
|
1680
|
-
* .travis.yml is modified to use gemfile/Gemfile.travis-rbx for rbx.
|
1681
|
-
|
1682
|
-
.travis.yml | 4 ++--
|
1683
|
-
gemfiles/Gemfile.travis-rbx | 16 ++++++++++++++++
|
1684
|
-
2 files changed, 18 insertions(+), 2 deletions(-)
|
1685
|
-
create mode 100644 gemfiles/Gemfile.travis-rbx
|
1686
|
-
|
1687
|
-
commit dcff544d6d0a967eb853b97ba9faa30eaa6fd9dc
|
1688
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1689
|
-
Date: Sat Jan 18 04:13:50 2014 +0900
|
1690
|
-
|
1691
|
-
.travis.yml: fix mistakes
|
1692
|
-
|
1693
|
-
.travis.yml | 8 +-------
|
1694
|
-
1 file changed, 1 insertion(+), 7 deletions(-)
|
1695
|
-
|
1696
|
-
commit f0f67f295f05a5e1e30c479621c25498e2c8f6f2
|
1697
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1698
|
-
Date: Sat Jan 18 03:56:54 2014 +0900
|
1699
|
-
|
1700
|
-
Ruby 2.1 workaround: Array#uniq does not always choose the first item
|
1701
|
-
|
1702
|
-
* Ruby 2.1 workaround: Array#uniq does not always choose the first item.
|
1703
|
-
Thanks to Andrew Grimm who reported the issue.
|
1704
|
-
(https://github.com/bioruby/bioruby/issues/92 )
|
1705
|
-
Note that the behavior change is also regarded as a bug in Ruby and
|
1706
|
-
is fixed. (https://bugs.ruby-lang.org/issues/9340 )
|
1707
|
-
|
1708
|
-
test/unit/bio/test_pathway.rb | 35 +++++++++++++++++++++++++----------
|
1709
|
-
1 file changed, 25 insertions(+), 10 deletions(-)
|
1710
|
-
|
1711
|
-
commit e92e09edf5904f51d3e73e61d13fce4159a543c5
|
1712
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1713
|
-
Date: Sat Jan 18 03:32:05 2014 +0900
|
1714
|
-
|
1715
|
-
.travis.yml: workaround to avoid error in Ruby 1.8.7 and jruby-18mode
|
1716
|
-
|
1717
|
-
* workaround to avoid error in Ruby 1.8.7 and jruby-18mode
|
1718
|
-
(reference: https://github.com/rubygems/rubygems/pull/763 )
|
1719
|
-
|
1720
|
-
.travis.yml | 2 ++
|
1721
|
-
1 file changed, 2 insertions(+)
|
1722
|
-
|
1723
|
-
commit 655a675096962710896fb458afcac9b5deb1fa5f
|
1724
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1725
|
-
Date: Sat Jan 18 03:22:44 2014 +0900
|
1726
|
-
|
1727
|
-
.travis.yml: rbx version is changed to 2.2.3
|
1728
|
-
|
1729
|
-
* rbx version is changed to 2.2.3
|
1730
|
-
* add dependent gems for rbx platforms, described in
|
1731
|
-
http://docs.travis-ci.com/user/languages/ruby/
|
1732
|
-
|
1733
|
-
.travis.yml | 7 ++++++-
|
1734
|
-
1 file changed, 6 insertions(+), 1 deletion(-)
|
1735
|
-
|
1736
|
-
commit d2f5b882d5e2acf35d0c783a56aa47533b9f2bd5
|
1737
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1738
|
-
Date: Sat Jan 11 03:46:45 2014 +0900
|
1739
|
-
|
1740
|
-
.travis.yml: change ruby versions for tar and gem integration tests
|
1741
|
-
|
1742
|
-
* In tar and gem integration tests, Ruby versions are changed to
|
1743
|
-
MRI 2.0.0 and jruby-19mode.
|
1744
|
-
* Add jruby-18mode
|
1745
|
-
* Add rbx-2.1.1
|
1746
|
-
|
1747
|
-
.travis.yml | 32 ++++++++++++++++++++++----------
|
1748
|
-
1 file changed, 22 insertions(+), 10 deletions(-)
|
1749
|
-
|
1750
|
-
commit 71991af394b937d35e2bbbc84a21e65ffba7714d
|
1751
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1752
|
-
Date: Thu Jan 9 00:57:25 2014 +0900
|
1753
|
-
|
1754
|
-
.travis.yml: Add 2.1.0 and 2.0.0, remove rbx-XXmode
|
1755
|
-
|
1756
|
-
* Add 2.1.0 and 2.0.0
|
1757
|
-
* Remove rbx-18mode and rbx-19mode
|
1758
|
-
* 1.9.2 is moved from "include" to "rvm".
|
1759
|
-
* 1.8.7 is moved from "rvm" to "include", and remove
|
1760
|
-
"gemfiles/Gemfile.travis-ruby1.8" line from "gemfile".
|
1761
|
-
* Remove "exclude" and simplify build matrix.
|
1762
|
-
* Suggested by agrimm in https://github.com/bioruby/bioruby/pull/91
|
1763
|
-
|
1764
|
-
.travis.yml | 27 +++++----------------------
|
1765
|
-
1 file changed, 5 insertions(+), 22 deletions(-)
|
1766
|
-
|
1767
|
-
commit 80966bc875cc6e01978b6c9272f6ddd8f344aa62
|
1768
|
-
Author: Brynjar Smari Bjarnason <binni@binnisb.com>
|
1769
|
-
Date: Mon Dec 9 14:57:42 2013 +0100
|
1770
|
-
|
1771
|
-
Bug fix: Only do gsub on bio_ref.reference.authors if it exists.
|
1772
|
-
|
1773
|
-
* Bug fix: Only do gsub on bio_ref.reference.authors if it exists.
|
1774
|
-
Fix https://github.com/bioruby/bioruby/issues/89
|
1775
|
-
|
1776
|
-
lib/bio/db/biosql/sequence.rb | 2 +-
|
1777
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
1778
|
-
|
1779
|
-
commit 3337bbd3be2affcef44202a0c924b3e22dafd856
|
1780
|
-
Author: Brynjar Smari Bjarnason <binni@binnisb.com>
|
1781
|
-
Date: Mon Dec 9 14:55:24 2013 +0100
|
1782
|
-
|
1783
|
-
Bug fix: Missing require when generating genbank output for BioSQL sequence
|
1784
|
-
|
1785
|
-
* Bug fix: Missing require when generating genbank output for BioSQL
|
1786
|
-
sequence. Partly fix https://github.com/bioruby/bioruby/issues/89
|
1787
|
-
|
1788
|
-
lib/bio/db/biosql/biosql_to_biosequence.rb | 1 +
|
1789
|
-
1 file changed, 1 insertion(+)
|
1790
|
-
|
1791
|
-
commit 1f829ae8e8c89c5c24e7bc7aa8ed5fa25e8ef6c2
|
1792
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1793
|
-
Date: Sat Nov 23 18:17:43 2013 +0900
|
1794
|
-
|
1795
|
-
Benchmark example1-seqnos.aln in addition to example1.aln
|
1796
|
-
|
1797
|
-
* sample/benchmark_clustalw_report.rb: Benchmark parsing speed of
|
1798
|
-
example1-seqnos.aln in addition to example1.aln.
|
1799
|
-
|
1800
|
-
sample/benchmark_clustalw_report.rb | 28 ++++++++++++++++++++++------
|
1801
|
-
1 file changed, 22 insertions(+), 6 deletions(-)
|
1802
|
-
|
1803
|
-
commit c5d3e761859fa72c18f9301d84c31070f35e733e
|
1804
|
-
Author: Andrew Grimm <andrew.j.grimm@gmail.com>
|
1805
|
-
Date: Tue Sep 17 21:15:56 2013 +1000
|
1806
|
-
|
1807
|
-
Add benchmark script for Bio::ClustalW::Report.
|
1808
|
-
|
1809
|
-
sample/benchmark_clustalw_report.rb | 31 +++++++++++++++++++++++++++++++
|
1810
|
-
1 file changed, 31 insertions(+)
|
1811
|
-
create mode 100644 sample/benchmark_clustalw_report.rb
|
1812
|
-
|
1813
|
-
commit 07c14e94cdb94cf9ba8a2bf050572ae1cbf24cff
|
1814
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1815
|
-
Date: Sat Nov 23 17:49:54 2013 +0900
|
1816
|
-
|
1817
|
-
Bio::ClustalW::Report#do_parse speed optimization
|
1818
|
-
|
1819
|
-
* Bio::ClustalW::Report#do_parse speed optimization. Thanks to
|
1820
|
-
Andrew Grimm who indicates the optimization point.
|
1821
|
-
(https://github.com/bioruby/bioruby/pull/86 )
|
1822
|
-
* "$" in the regular expression is changed to "\z". In this context,
|
1823
|
-
the "$" was intended to be matched with only the end of the string.
|
1824
|
-
|
1825
|
-
lib/bio/appl/clustalw/report.rb | 4 +++-
|
1826
|
-
1 file changed, 3 insertions(+), 1 deletion(-)
|
1827
|
-
|
1828
|
-
commit 6a78028d4f595ecb5b4600d0f238b07a2d80bdd5
|
1829
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1830
|
-
Date: Sat Nov 23 15:52:15 2013 +0900
|
1831
|
-
|
1832
|
-
New test data: ClustalW with -SEQNOS=ON option
|
1833
|
-
|
1834
|
-
* test/data/clustalw/example1-seqnos.aln: New test data: ClustalW
|
1835
|
-
running with -SEQNOS=ON option.
|
1836
|
-
* Bio::TestClustalWReport::TestClustalWReportSeqnos: new test class
|
1837
|
-
that parses the above data.
|
1838
|
-
|
1839
|
-
test/data/clustalw/example1-seqnos.aln | 58 ++++++++++++++++++++++++++++++
|
1840
|
-
test/unit/bio/appl/clustalw/test_report.rb | 11 ++++++
|
1841
|
-
2 files changed, 69 insertions(+)
|
1842
|
-
create mode 100644 test/data/clustalw/example1-seqnos.aln
|
1843
|
-
|
1844
|
-
commit f5da0bbb4b1639616bb8c63ff8c58840e140ef8b
|
1845
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1846
|
-
Date: Sat Nov 23 15:35:31 2013 +0900
|
1847
|
-
|
1848
|
-
Simplify test data path in setup
|
1849
|
-
|
1850
|
-
* Bio::TestClustalWReport::TestClustalWReport#setup: simplify test data
|
1851
|
-
filename path.
|
1852
|
-
* Modify indentes and void lines.
|
1853
|
-
|
1854
|
-
test/unit/bio/appl/clustalw/test_report.rb | 10 +++-------
|
1855
|
-
1 file changed, 3 insertions(+), 7 deletions(-)
|
1856
|
-
|
1857
|
-
commit 8f0bea1d3252d0de9e2d91dc31ef8a9552c2d758
|
1858
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1859
|
-
Date: Sat Nov 23 15:21:38 2013 +0900
|
1860
|
-
|
1861
|
-
Common test methods are moved to a module
|
1862
|
-
|
1863
|
-
* New namespace module Bio::TestClustalWReport.
|
1864
|
-
* Common test methods are moved to CommonTestMethods,
|
1865
|
-
and test classes using the methods include it.
|
1866
|
-
* The test_sequences method is split into two methods
|
1867
|
-
CommonTestMethods#test_sequence0 and test_sequence1.
|
1868
|
-
|
1869
|
-
test/unit/bio/appl/clustalw/test_report.rb | 97 ++++++++++++++++--------------
|
1870
|
-
1 file changed, 53 insertions(+), 44 deletions(-)
|
1871
|
-
|
1872
|
-
commit edda65b8fb32c2eee6b0652074981c31aa68b0eb
|
1873
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1874
|
-
Date: Fri Aug 23 23:51:59 2013 +0900
|
1875
|
-
|
1876
|
-
Test bug fix: Read test file with binary mode to avoid encoding error
|
1877
|
-
|
1878
|
-
* Test bug fix: Read test file with binary mode to avoid string encoding
|
1879
|
-
error. Thanks to nieder (github.com/nieder) who reports the bug.
|
1880
|
-
(https://github.com/bioruby/bioruby/issues/84)
|
1881
|
-
|
1882
|
-
test/unit/bio/db/test_phyloxml.rb | 2 +-
|
1883
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
1884
|
-
|
1885
|
-
commit 011d6fe5f016408891c5da3143c83e2564ccbf27
|
1886
|
-
Author: meso_cacase <y-naito@dbcls.rois.ac.jp>
|
1887
|
-
Date: Fri Apr 5 01:13:27 2013 +0900
|
1888
|
-
|
1889
|
-
Modified siRNA design rules by Ui-Tei and Reynolds
|
1890
|
-
|
1891
|
-
* Ui-Tei rule: Avoided contiguous GCs 10 nt or more.
|
1892
|
-
* Reynolds rule: Total score of eight criteria is calculated.
|
1893
|
-
* Returns numerical score for functional siRNA instead of returning 'true'.
|
1894
|
-
* Returns 'false' for non-functional siRNA, as usual.
|
1895
|
-
* Unit tests are modified to reflect these changes.
|
1896
|
-
|
1897
|
-
lib/bio/util/sirna.rb | 92 +++++++++++++++++++++++++++++++++-------
|
1898
|
-
test/unit/bio/util/test_sirna.rb | 44 +++++++++----------
|
1899
|
-
2 files changed, 98 insertions(+), 38 deletions(-)
|
1900
|
-
|
1901
|
-
commit b6e7953108ebf34d61bc79ee4bdae1092cfe339f
|
1902
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1903
|
-
Date: Fri Jun 28 15:40:57 2013 +0900
|
1904
|
-
|
1905
|
-
Use Bio::UniProtKB instead of Bio::UniProt
|
1906
|
-
|
1907
|
-
* Use Bio::UniProtKB instead of Bio::UniProt.
|
1908
|
-
* Test class names are also changed from UniProt to UniProtKB.
|
1909
|
-
|
1910
|
-
test/unit/bio/db/embl/test_uniprotkb_new_part.rb | 22 +++++++++++-----------
|
1911
|
-
1 file changed, 11 insertions(+), 11 deletions(-)
|
1912
|
-
|
1913
|
-
commit cddd35cf8d64abfff8bd6a8372d019fc4c32848c
|
1914
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1915
|
-
Date: Fri Jun 28 15:26:20 2013 +0900
|
1916
|
-
|
1917
|
-
rename test/unit/bio/db/embl/test_uniprot_new_part.rb to test_uniprotkb_new_part.rb
|
1918
|
-
|
1919
|
-
test/unit/bio/db/embl/test_uniprot_new_part.rb | 208 -----------------------
|
1920
|
-
test/unit/bio/db/embl/test_uniprotkb_new_part.rb | 208 +++++++++++++++++++++++
|
1921
|
-
2 files changed, 208 insertions(+), 208 deletions(-)
|
1922
|
-
delete mode 100644 test/unit/bio/db/embl/test_uniprot_new_part.rb
|
1923
|
-
create mode 100644 test/unit/bio/db/embl/test_uniprotkb_new_part.rb
|
1924
|
-
|
1925
|
-
commit 1b51d0940712a6f144f8268dc77048bc7ec7d983
|
1926
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1927
|
-
Date: Fri Jun 28 15:21:36 2013 +0900
|
1928
|
-
|
1929
|
-
Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB.
|
1930
|
-
|
1931
|
-
* Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB.
|
1932
|
-
* Test class names are also changed.
|
1933
|
-
|
1934
|
-
test/unit/bio/db/embl/test_uniprotkb.rb | 223 ++++++++++++++++----------------
|
1935
|
-
1 file changed, 111 insertions(+), 112 deletions(-)
|
1936
|
-
|
1937
|
-
commit 68494aa862c3495def713e6cad6fc478f223416f
|
1938
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1939
|
-
Date: Fri Jun 28 15:01:15 2013 +0900
|
1940
|
-
|
1941
|
-
test_sptr.rb is renamed to test_uniprotkb.rb
|
1942
|
-
|
1943
|
-
test/unit/bio/db/embl/test_sptr.rb | 1807 -------------------------------
|
1944
|
-
test/unit/bio/db/embl/test_uniprotkb.rb | 1807 +++++++++++++++++++++++++++++++
|
1945
|
-
2 files changed, 1807 insertions(+), 1807 deletions(-)
|
1946
|
-
delete mode 100644 test/unit/bio/db/embl/test_sptr.rb
|
1947
|
-
create mode 100644 test/unit/bio/db/embl/test_uniprotkb.rb
|
1948
|
-
|
1949
|
-
commit e1ed7fab4c0350e6866dd420a93e950c53063f38
|
1950
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1951
|
-
Date: Fri Jun 28 14:52:08 2013 +0900
|
1952
|
-
|
1953
|
-
Add autoload of Bio::UniProtKB, and modify comments of deprecated classes.
|
1954
|
-
|
1955
|
-
lib/bio.rb | 18 ++++++++++--------
|
1956
|
-
1 file changed, 10 insertions(+), 8 deletions(-)
|
1957
|
-
|
1958
|
-
commit 7c78cb1b275a845e215f9a6da67026836efc5807
|
1959
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1960
|
-
Date: Fri Jun 28 14:28:02 2013 +0900
|
1961
|
-
|
1962
|
-
Bio::SwissProt and Bio::TrEMBL are deprecated
|
1963
|
-
|
1964
|
-
* Bio::SwissProt and Bio::TrEMBL are deprecated.
|
1965
|
-
* Show warning messages when using these classes.
|
1966
|
-
|
1967
|
-
lib/bio/db/embl/swissprot.rb | 41 ++++++++++++-----------------------------
|
1968
|
-
lib/bio/db/embl/trembl.rb | 43 +++++++++++++------------------------------
|
1969
|
-
2 files changed, 25 insertions(+), 59 deletions(-)
|
1970
|
-
|
1971
|
-
commit b998ad13849ff7f1d69ed0c640a2e1bafe3fc957
|
1972
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1973
|
-
Date: Fri Jun 28 14:27:36 2013 +0900
|
1974
|
-
|
1975
|
-
Bio::UniProt is changed to be an alias of Bio::UniProtKB.
|
1976
|
-
|
1977
|
-
lib/bio/db/embl/uniprot.rb | 41 ++++++++++++-----------------------------
|
1978
|
-
1 file changed, 12 insertions(+), 29 deletions(-)
|
1979
|
-
|
1980
|
-
commit f46324e2fb6a2bc3e4680c8064dc0fc3d89e6f24
|
1981
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1982
|
-
Date: Fri Jun 28 14:21:56 2013 +0900
|
1983
|
-
|
1984
|
-
Bio::SPTR is renamed as Bio::UniProtKB and changed to an alias
|
1985
|
-
|
1986
|
-
* Bio::SPTR is renamed to Bio::UniProtKB.
|
1987
|
-
* For older programs which use Bio::SPTR, set Bio::SPTR as an alias of
|
1988
|
-
Bio::UniProtKB.
|
1989
|
-
|
1990
|
-
lib/bio/db/embl/sptr.rb | 20 ++++++
|
1991
|
-
lib/bio/db/embl/uniprotkb.rb | 147 +++++++++++++++++++++----------------------
|
1992
|
-
2 files changed, 93 insertions(+), 74 deletions(-)
|
1993
|
-
create mode 100644 lib/bio/db/embl/sptr.rb
|
1994
|
-
|
1995
|
-
commit 70816d90a6ef290c7ca7f50d492e7c4f836aadd8
|
1996
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
1997
|
-
Date: Thu Jun 27 18:16:38 2013 +0900
|
1998
|
-
|
1999
|
-
Rename lib/bio/db/embl/sptr.rb to uniprotkb.rb
|
2000
|
-
|
2001
|
-
lib/bio/db/embl/sptr.rb | 1456 ------------------------------------------
|
2002
|
-
lib/bio/db/embl/uniprotkb.rb | 1456 ++++++++++++++++++++++++++++++++++++++++++
|
2003
|
-
2 files changed, 1456 insertions(+), 1456 deletions(-)
|
2004
|
-
delete mode 100644 lib/bio/db/embl/sptr.rb
|
2005
|
-
create mode 100644 lib/bio/db/embl/uniprotkb.rb
|
2006
|
-
|
2007
|
-
commit 2a10ded8e1502e0db5ec3b2e060f658ee53aafd0
|
2008
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2009
|
-
Date: Thu Jun 27 16:36:58 2013 +0900
|
2010
|
-
|
2011
|
-
Bio::RefSeq and Bio::DDBJ are deprecated. Show warnings.
|
2012
|
-
|
2013
|
-
* Bio::RefSeq and Bio::DDBJ are deprecated because they were only
|
2014
|
-
an alias of Bio::GenBank. Please use Bio::GenBank instead.
|
2015
|
-
* Show warning message when loading the classes and initializing
|
2016
|
-
a new instance.
|
2017
|
-
* Changed to require genbank.rb only when GenBank is not defined.
|
2018
|
-
This might reduce the possibility of circular require.
|
2019
|
-
|
2020
|
-
lib/bio/db/genbank/ddbj.rb | 11 +++++++++--
|
2021
|
-
lib/bio/db/genbank/refseq.rb | 14 +++++++++++---
|
2022
|
-
2 files changed, 20 insertions(+), 5 deletions(-)
|
2023
|
-
|
2024
|
-
commit 118d0bff58b48f69505eef5dcc2f961ac6e0d9de
|
2025
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2026
|
-
Date: Thu Jun 27 16:08:55 2013 +0900
|
2027
|
-
|
2028
|
-
Remove descriptions about DDBJ Web API (WABI)
|
2029
|
-
|
2030
|
-
KNOWN_ISSUES.rdoc | 8 --------
|
2031
|
-
1 file changed, 8 deletions(-)
|
2032
|
-
|
2033
|
-
commit fe8f976c7ced4d525a4eabd728269f71326cf001
|
2034
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2035
|
-
Date: Thu Jun 27 13:41:19 2013 +0900
|
2036
|
-
|
2037
|
-
Remove ddbjsoap method that uses Bio::DDBJ::XML
|
2038
|
-
|
2039
|
-
lib/bio/shell/plugin/soap.rb | 28 ----------------------------
|
2040
|
-
1 file changed, 28 deletions(-)
|
2041
|
-
|
2042
|
-
commit 54bef3fc48bb48eb198537a9fba6379f33f036cc
|
2043
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2044
|
-
Date: Thu Jun 27 13:39:42 2013 +0900
|
2045
|
-
|
2046
|
-
Remove Bio::Blast::Remote::DDBJ from the comment line
|
2047
|
-
|
2048
|
-
test/network/bio/appl/blast/test_remote.rb | 2 +-
|
2049
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
2050
|
-
|
2051
|
-
commit a7c5a656dab1bb8ada6b36ec003a89aec9e26671
|
2052
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2053
|
-
Date: Tue Jun 25 18:34:46 2013 +0900
|
2054
|
-
|
2055
|
-
Delete sample/demo_ddbjxml.rb which uses Bio::DDBJ::XML
|
2056
|
-
|
2057
|
-
sample/demo_ddbjxml.rb | 212 -------------------------------------------------
|
2058
|
-
1 file changed, 212 deletions(-)
|
2059
|
-
delete mode 100644 sample/demo_ddbjxml.rb
|
2060
|
-
|
2061
|
-
commit e55293b67d305382cfb30b45aa30af82a574b580
|
2062
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2063
|
-
Date: Tue Jun 25 18:29:54 2013 +0900
|
2064
|
-
|
2065
|
-
Remove Bio::Blast::Remote::DDBJ, Bio::Blast.ddbj and related components
|
2066
|
-
|
2067
|
-
* Remove Bio::Blast::Remote::DDBJ, Bio::Blast.ddbj and related components
|
2068
|
-
which use Bio::DDBJ::XML or Bio::DDBJ::REST.
|
2069
|
-
|
2070
|
-
lib/bio/appl/blast/ddbj.rb | 131 -----------------------------
|
2071
|
-
lib/bio/appl/blast/remote.rb | 9 --
|
2072
|
-
test/network/bio/appl/blast/test_remote.rb | 14 ---
|
2073
|
-
test/network/bio/appl/test_blast.rb | 12 ---
|
2074
|
-
4 files changed, 166 deletions(-)
|
2075
|
-
delete mode 100644 lib/bio/appl/blast/ddbj.rb
|
2076
|
-
|
2077
|
-
commit 19a5c992096a68a26f8684ee2ae128d17f2a49fd
|
2078
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2079
|
-
Date: Tue Jun 25 16:52:05 2013 +0900
|
2080
|
-
|
2081
|
-
Remove Bio::DDBJ::XML and REST due to suspension of DDBJ Web API (WABI)
|
2082
|
-
|
2083
|
-
* Remove Bio::DDBJ::XML and Bio::DDBJ::REST due to suspension of
|
2084
|
-
DDBJ Web API (WABI). DDBJ says that it is now under reconstruction
|
2085
|
-
and the API will be completely changed. Thus, I've decided to throw
|
2086
|
-
away current API client in Ruby and to implement new one with the new
|
2087
|
-
API.
|
2088
|
-
* Autoload lines in lib/bio/db/genbank/ddbj.rb are removed.
|
2089
|
-
* Tests are also removed.
|
2090
|
-
|
2091
|
-
lib/bio/db/genbank/ddbj.rb | 3 -
|
2092
|
-
lib/bio/io/ddbjrest.rb | 344 --------------------------
|
2093
|
-
lib/bio/io/ddbjxml.rb | 458 -----------------------------------
|
2094
|
-
test/network/bio/io/test_ddbjrest.rb | 47 ----
|
2095
|
-
test/unit/bio/io/test_ddbjxml.rb | 81 -------
|
2096
|
-
5 files changed, 933 deletions(-)
|
2097
|
-
delete mode 100644 lib/bio/io/ddbjrest.rb
|
2098
|
-
delete mode 100644 lib/bio/io/ddbjxml.rb
|
2099
|
-
delete mode 100644 test/network/bio/io/test_ddbjrest.rb
|
2100
|
-
delete mode 100644 test/unit/bio/io/test_ddbjxml.rb
|
2101
|
-
|
2102
|
-
commit 1f852e0bf3c830aaa40dc7fc2bd535418af8dfd1
|
2103
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2104
|
-
Date: Sat May 25 03:00:08 2013 +0900
|
2105
|
-
|
2106
|
-
regenerate bioruby.gemspec with rake regemspec
|
2107
|
-
|
2108
|
-
bioruby.gemspec | 2 --
|
2109
|
-
1 file changed, 2 deletions(-)
|
2110
|
-
|
2111
|
-
commit 5b90959ab399f961823a7c4453392c75cf971333
|
2112
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2113
|
-
Date: Sat May 25 02:58:50 2013 +0900
|
2114
|
-
|
2115
|
-
Update files and directories used to create package without git
|
2116
|
-
|
2117
|
-
bioruby.gemspec.erb | 6 ++++--
|
2118
|
-
1 file changed, 4 insertions(+), 2 deletions(-)
|
2119
|
-
|
2120
|
-
commit df29f057ded6ac73fbdce7ae04a70ead28f4cc9f
|
2121
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2122
|
-
Date: Sat May 25 02:46:32 2013 +0900
|
2123
|
-
|
2124
|
-
Ruby 2.0 support: not to add ChangeLog and LEGAL to rdoc_files
|
2125
|
-
|
2126
|
-
* Ruby 2.0 support: not to add ChangeLog and LEGAL to rdoc_files.
|
2127
|
-
Because ChangeLog is not rdoc format, rdoc bundled with Ruby 2.0
|
2128
|
-
raises error during parsing.
|
2129
|
-
|
2130
|
-
bioruby.gemspec.erb | 4 ++--
|
2131
|
-
1 file changed, 2 insertions(+), 2 deletions(-)
|
2132
|
-
|
2133
|
-
commit 930a5fcf5e38ae2bdfeee62eed9a46db1c519fae
|
2134
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2135
|
-
Date: Thu Apr 4 17:29:33 2013 +0900
|
2136
|
-
|
2137
|
-
Remove unused variable in lib/bio/util/contingency_table.rb
|
2138
|
-
|
2139
|
-
This commit removes below interpreter warning.
|
2140
|
-
|
2141
|
-
* warning: assigned but unused variable
|
2142
|
-
|
2143
|
-
lib/bio/util/contingency_table.rb | 2 --
|
2144
|
-
1 file changed, 2 deletions(-)
|
2145
|
-
|
2146
|
-
commit 490b3f7ca3b987c1a17852b641aad3125fc565cd
|
2147
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2148
|
-
Date: Thu Apr 4 17:28:30 2013 +0900
|
2149
|
-
|
2150
|
-
Rename unused variable in lib/bio/tree.rb
|
2151
|
-
|
2152
|
-
This commit removes below interpreter warning.
|
2153
|
-
|
2154
|
-
* warning: assigned but unused variable
|
2155
|
-
|
2156
|
-
lib/bio/tree.rb | 4 ++--
|
2157
|
-
1 file changed, 2 insertions(+), 2 deletions(-)
|
2158
|
-
|
2159
|
-
commit c024fb972edb52e213165149273fc7ac4bec2f6e
|
2160
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2161
|
-
Date: Thu May 16 21:26:44 2013 +0900
|
2162
|
-
|
2163
|
-
Refactoring to suppress "warning: assigned but unused variable"
|
2164
|
-
|
2165
|
-
lib/bio/pathway.rb | 2 +-
|
2166
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
2167
|
-
|
2168
|
-
commit b3b2a268d6118307eed88fce1d805a61c6fb843d
|
2169
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2170
|
-
Date: Thu Apr 4 17:18:44 2013 +0900
|
2171
|
-
|
2172
|
-
Remove unused variable in lib/bio/db/transfac.rb
|
2173
|
-
|
2174
|
-
This commit removes below interpreter warning.
|
2175
|
-
|
2176
|
-
* warning: assigned but unused variable
|
2177
|
-
|
2178
|
-
lib/bio/db/transfac.rb | 2 +-
|
2179
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
2180
|
-
|
2181
|
-
commit dd8abf1f95af4a70cf0b86b0e719e3dcfd8abecf
|
2182
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2183
|
-
Date: Thu May 16 21:13:34 2013 +0900
|
2184
|
-
|
2185
|
-
Refactoring to suppress warnings "assigned but unused variable"
|
2186
|
-
|
2187
|
-
lib/bio/db/nexus.rb | 5 +++--
|
2188
|
-
1 file changed, 3 insertions(+), 2 deletions(-)
|
2189
|
-
|
2190
|
-
commit b37512fb8028cf30bb2f813928aed49a5b39dce3
|
2191
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2192
|
-
Date: Thu Apr 4 17:15:59 2013 +0900
|
2193
|
-
|
2194
|
-
Rename unused variable in lib/bio/db/kegg/reaction.rb
|
2195
|
-
|
2196
|
-
This commit removes below interpreter warning.
|
2197
|
-
|
2198
|
-
* warning: assigned but unused variable
|
2199
|
-
|
2200
|
-
lib/bio/db/kegg/reaction.rb | 2 +-
|
2201
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
2202
|
-
|
2203
|
-
commit a81fca3b1247ae4a3e05bfa912c8181efdfca81b
|
2204
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2205
|
-
Date: Thu Apr 4 17:15:09 2013 +0900
|
2206
|
-
|
2207
|
-
Remove unused variable in lib/bio/db/go.rb
|
2208
|
-
|
2209
|
-
This commit removes below interpreter warning.
|
2210
|
-
|
2211
|
-
* warning: assigned but unused variable
|
2212
|
-
|
2213
|
-
lib/bio/db/go.rb | 6 +++---
|
2214
|
-
1 file changed, 3 insertions(+), 3 deletions(-)
|
2215
|
-
|
2216
|
-
commit 69b0c433e76faffba6a48dfc38dcc2b1444ce2b7
|
2217
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2218
|
-
Date: Thu Apr 4 17:13:24 2013 +0900
|
2219
|
-
|
2220
|
-
Rename unused variable in lib/bio/db/gff.rb
|
2221
|
-
|
2222
|
-
This commit removes below interpreter warning.
|
2223
|
-
|
2224
|
-
* warning: assigned but unused variable
|
2225
|
-
|
2226
|
-
lib/bio/db/gff.rb | 2 +-
|
2227
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
2228
|
-
|
2229
|
-
commit 88c214fe3183c161cda94a3a4cda442b3a769965
|
2230
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2231
|
-
Date: Thu May 9 23:46:28 2013 +0900
|
2232
|
-
|
2233
|
-
add a dummy line to suppress "warning: assigned but unused variable"
|
2234
|
-
|
2235
|
-
lib/bio/db/embl/sptr.rb | 1 +
|
2236
|
-
1 file changed, 1 insertion(+)
|
2237
|
-
|
2238
|
-
commit 1ead12f9c951a983c6775f79ca1b6944f95a61b9
|
2239
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2240
|
-
Date: Thu May 9 23:41:54 2013 +0900
|
2241
|
-
|
2242
|
-
Refactoring to suppress warnings "assigned but unused variable"
|
2243
|
-
|
2244
|
-
lib/bio/db/embl/embl.rb | 7 ++++---
|
2245
|
-
1 file changed, 4 insertions(+), 3 deletions(-)
|
2246
|
-
|
2247
|
-
commit 8d0eb5105eb2f419f5b4f4fbb191b8fb2032664b
|
2248
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2249
|
-
Date: Thu Apr 4 17:01:27 2013 +0900
|
2250
|
-
|
2251
|
-
Remove unused variable in lib/bio/appl/paml/common
|
2252
|
-
|
2253
|
-
This commit removes below interpreter warning.
|
2254
|
-
|
2255
|
-
* warning: assigned but unused variable
|
2256
|
-
|
2257
|
-
lib/bio/appl/paml/common.rb | 2 +-
|
2258
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
2259
|
-
|
2260
|
-
commit c6cf0d2e2a3a0b9062f9464dba0e363f460d04e4
|
2261
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2262
|
-
Date: Thu May 9 23:27:54 2013 +0900
|
2263
|
-
|
2264
|
-
suppress warning "assigned but unused variable"
|
2265
|
-
|
2266
|
-
lib/bio/appl/paml/codeml/report.rb | 1 +
|
2267
|
-
1 file changed, 1 insertion(+)
|
2268
|
-
|
2269
|
-
commit 8834d50544b03a92a3ca816704b179e4333d1dfc
|
2270
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2271
|
-
Date: Thu Apr 4 16:59:18 2013 +0900
|
2272
|
-
|
2273
|
-
Remove unused variable in lib/bio/appl/meme/mast/report
|
2274
|
-
|
2275
|
-
This commit removes below interpreter warning.
|
2276
|
-
|
2277
|
-
* warning: assigned but unused variable
|
2278
|
-
|
2279
|
-
lib/bio/appl/meme/mast/report.rb | 2 +-
|
2280
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
2281
|
-
|
2282
|
-
commit fe51a49ee68c41a3ce0c48c39db6e8a28d1689ee
|
2283
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2284
|
-
Date: Thu Apr 4 16:57:44 2013 +0900
|
2285
|
-
|
2286
|
-
Remove unused variable in lib/bio/appl/blast/report
|
2287
|
-
|
2288
|
-
This commit removes below interpreter warning.
|
2289
|
-
|
2290
|
-
* warning: assigned but unused variable
|
2291
|
-
|
2292
|
-
lib/bio/appl/blast/report.rb | 2 +-
|
2293
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
2294
|
-
|
2295
|
-
commit 622497ff309412fb986c5315d55d41c3ca48d362
|
2296
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2297
|
-
Date: Thu Apr 4 17:25:29 2013 +0900
|
2298
|
-
|
2299
|
-
Fix indent in lib/bio/map
|
2300
|
-
|
2301
|
-
This commit removes below interpreter warning.
|
2302
|
-
|
2303
|
-
* warning: mismatched indentations at ...
|
2304
|
-
|
2305
|
-
lib/bio/map.rb | 2 +-
|
2306
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
2307
|
-
|
2308
|
-
commit 3ea6bcaf229fd1a71a0192253cc47e817bb64b82
|
2309
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2310
|
-
Date: Thu Apr 4 18:05:04 2013 +0900
|
2311
|
-
|
2312
|
-
Remove unused variable in test/unit/bio/appl/blast/test_report
|
2313
|
-
|
2314
|
-
This commit removes below interpreter warning.
|
2315
|
-
|
2316
|
-
* warning: assigned but unused variable
|
2317
|
-
|
2318
|
-
test/unit/bio/appl/blast/test_report.rb | 2 --
|
2319
|
-
1 file changed, 2 deletions(-)
|
2320
|
-
|
2321
|
-
commit 178ca9e5244cc3aa7f0507c7d5528bb57b0858be
|
2322
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2323
|
-
Date: Thu Apr 4 18:03:46 2013 +0900
|
2324
|
-
|
2325
|
-
Remove unused variable in test/unit/bio/appl/bl2seq/test_report
|
2326
|
-
|
2327
|
-
This commit removes below interpreter warning.
|
2328
|
-
|
2329
|
-
* warning: assigned but unused variable
|
2330
|
-
|
2331
|
-
test/unit/bio/appl/bl2seq/test_report.rb | 1 -
|
2332
|
-
1 file changed, 1 deletion(-)
|
2333
|
-
|
2334
|
-
commit b8a5c1cb9f54d9199200b406f77e8152eef96f02
|
2335
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2336
|
-
Date: Thu May 9 21:20:10 2013 +0900
|
2337
|
-
|
2338
|
-
Add assertions and suppress "unused variable" warnings
|
2339
|
-
|
2340
|
-
* Add assertions to check object id returned by forward_complement
|
2341
|
-
and reverse_complement methods. This change also aims to suppress
|
2342
|
-
"assigned but unused variable" warnings.
|
2343
|
-
|
2344
|
-
test/unit/bio/sequence/test_na.rb | 4 +++-
|
2345
|
-
1 file changed, 3 insertions(+), 1 deletion(-)
|
2346
|
-
|
2347
|
-
commit bd8fc9b197c54c108d74fea9161c8f0dd3b041fc
|
2348
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2349
|
-
Date: Thu Apr 4 17:59:09 2013 +0900
|
2350
|
-
|
2351
|
-
Remove unused variable in test/unit/bio/io/flatfile/test_splitter
|
2352
|
-
|
2353
|
-
This commit removes below interpreter warning.
|
2354
|
-
|
2355
|
-
* warning: assigned but unused variable
|
2356
|
-
|
2357
|
-
test/unit/bio/io/flatfile/test_splitter.rb | 2 +-
|
2358
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
2359
|
-
|
2360
|
-
commit 0a87c9e265c4560453faf84fc009b60319c75416
|
2361
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2362
|
-
Date: Thu Apr 4 17:57:51 2013 +0900
|
2363
|
-
|
2364
|
-
Remove unused variable in test/unit/bio/db/test_phyloxml_writer
|
2365
|
-
|
2366
|
-
This commit removes below interpreter warning.
|
2367
|
-
|
2368
|
-
* warning: assigned but unused variable
|
2369
|
-
|
2370
|
-
test/unit/bio/db/test_phyloxml_writer.rb | 4 ++--
|
2371
|
-
1 file changed, 2 insertions(+), 2 deletions(-)
|
2372
|
-
|
2373
|
-
commit 95b2614eb32eb12428df29360d0c1f146f39a469
|
2374
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2375
|
-
Date: Thu May 9 20:56:43 2013 +0900
|
2376
|
-
|
2377
|
-
Comment out some lines to suppress "unused variable" warnings
|
2378
|
-
|
2379
|
-
test/unit/bio/db/test_gff.rb | 4 ++--
|
2380
|
-
1 file changed, 2 insertions(+), 2 deletions(-)
|
2381
|
-
|
2382
|
-
commit b8917841559fbd506c73fdf374a8097f23a1bc37
|
2383
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2384
|
-
Date: Thu Apr 4 17:51:11 2013 +0900
|
2385
|
-
|
2386
|
-
Remove unused variable in test/unit/bio/db/embl/test_sptr.rb
|
2387
|
-
|
2388
|
-
* Remove warnings "warning: assigned but unused variable"
|
2389
|
-
* Note that the sequence in TestSPTRUniProtRel7_6#test_10000aa is
|
2390
|
-
a fragment of human p53 protein, and is not related with Q09165.
|
2391
|
-
|
2392
|
-
test/unit/bio/db/embl/test_sptr.rb | 3 ---
|
2393
|
-
1 file changed, 3 deletions(-)
|
2394
|
-
|
2395
|
-
commit 6b46d324a545f509bbd238ae7ec009d586469314
|
2396
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2397
|
-
Date: Thu Apr 4 17:45:47 2013 +0900
|
2398
|
-
|
2399
|
-
Remove unused variable in test/unit/bio/db/embl/test_embl_rel89
|
2400
|
-
|
2401
|
-
This commit removes below interpreter warning.
|
2402
|
-
|
2403
|
-
* warning: assigned but unused variable
|
2404
|
-
|
2405
|
-
test/unit/bio/db/embl/test_embl_rel89.rb | 1 -
|
2406
|
-
1 file changed, 1 deletion(-)
|
2407
|
-
|
2408
|
-
commit f36eeb0107e7a8315c66888ec8292ed33bd959cc
|
2409
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2410
|
-
Date: Thu Apr 4 17:45:21 2013 +0900
|
2411
|
-
|
2412
|
-
Remove unused variable in test/unit/bio/db/embl/test_embl
|
2413
|
-
|
2414
|
-
This commit removes below interpreter warning.
|
2415
|
-
|
2416
|
-
* warning: assigned but unused variable
|
2417
|
-
|
2418
|
-
test/unit/bio/db/embl/test_embl.rb | 1 -
|
2419
|
-
1 file changed, 1 deletion(-)
|
2420
|
-
|
2421
|
-
commit a1a2ad9b963d9bb2da8d07ae7b182bd339bea88e
|
2422
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2423
|
-
Date: Thu Apr 4 17:36:59 2013 +0900
|
2424
|
-
|
2425
|
-
Fix indent in test/unit/bio/sequence/test_dblink
|
2426
|
-
|
2427
|
-
This commit removes below interpreter warning.
|
2428
|
-
|
2429
|
-
* warning: mismatched indentations at ...
|
2430
|
-
|
2431
|
-
test/unit/bio/sequence/test_dblink.rb | 2 +-
|
2432
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
2433
|
-
|
2434
|
-
commit 345a8eb4408ca241c13c410a578490c905eb7391
|
2435
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2436
|
-
Date: Thu Apr 4 17:36:21 2013 +0900
|
2437
|
-
|
2438
|
-
Fix indent in test/unit/bio/db/test_phyloxml
|
2439
|
-
|
2440
|
-
This commit removes below interpreter warning.
|
2441
|
-
|
2442
|
-
* warning: mismatched indentations at ...
|
2443
|
-
|
2444
|
-
test/unit/bio/db/test_phyloxml.rb | 58 +++++++++++++++++++--------------------
|
2445
|
-
1 file changed, 29 insertions(+), 29 deletions(-)
|
2446
|
-
|
2447
|
-
commit ae8c7a6705a30c0c18c57df9869979a968aa63ac
|
2448
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2449
|
-
Date: Thu Apr 4 17:35:07 2013 +0900
|
2450
|
-
|
2451
|
-
Fix indent in test/unit/bio/db/genbank/test_genbank
|
2452
|
-
|
2453
|
-
This commit removes below interpreter warning.
|
2454
|
-
|
2455
|
-
* warning: mismatched indentations at ...
|
2456
|
-
|
2457
|
-
test/unit/bio/db/genbank/test_genbank.rb | 2 +-
|
2458
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
2459
|
-
|
2460
|
-
commit 872d8954e1351251fbace20e331035251ae5f806
|
2461
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2462
|
-
Date: Thu Apr 4 17:33:23 2013 +0900
|
2463
|
-
|
2464
|
-
Fix indent in test/unit/bio/appl/test_blast
|
2465
|
-
|
2466
|
-
This commit removes below interpreter warning.
|
2467
|
-
|
2468
|
-
* warning: mismatched indentations at ...
|
2469
|
-
|
2470
|
-
test/unit/bio/appl/test_blast.rb | 4 ++--
|
1355
|
+
RELEASE_NOTES.rdoc | 4 ++--
|
2471
1356
|
1 file changed, 2 insertions(+), 2 deletions(-)
|
2472
|
-
|
2473
|
-
commit bd973e084695c4d777c8ecf6d566788838158165
|
2474
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2475
|
-
Date: Wed Mar 27 03:03:49 2013 +0900
|
2476
|
-
|
2477
|
-
.travis.yml: rbx-18mode is moved to allow_failures
|
2478
|
-
|
2479
|
-
.travis.yml | 8 +++++---
|
2480
|
-
1 file changed, 5 insertions(+), 3 deletions(-)
|
2481
|
-
|
2482
|
-
commit 63e93faba74a8143a0be9595fdf87329f3015745
|
2483
|
-
Author: Andrew Grimm <andrew.j.grimm@gmail.com>
|
2484
|
-
Date: Tue Mar 26 20:20:11 2013 +1100
|
2485
|
-
|
2486
|
-
Squash warning in alignment.rb: assigned but unused variable - oldkeys
|
2487
|
-
|
2488
|
-
lib/bio/alignment.rb | 1 -
|
2489
|
-
1 file changed, 1 deletion(-)
|
2490
|
-
|
2491
|
-
commit bd735d6f9d6edfd1550a4279167ac06b372f847a
|
2492
|
-
Author: Andrew Grimm <andrew.j.grimm@gmail.com>
|
2493
|
-
Date: Tue Mar 26 20:14:46 2013 +1100
|
2494
|
-
|
2495
|
-
Squash warning in alignment.rb: assigned but unused variable - lines
|
2496
|
-
|
2497
|
-
lib/bio/alignment.rb | 2 +-
|
2498
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
2499
|
-
|
2500
|
-
commit 3e7b27f96a901a3abfc338572f98d60a9e3be498
|
2501
|
-
Author: Andrew Grimm <andrew.j.grimm@gmail.com>
|
2502
|
-
Date: Tue Mar 26 19:44:49 2013 +1100
|
2503
|
-
|
2504
|
-
Squash warning in defline.rb: assigned but unused variable - idtype
|
2505
|
-
|
2506
|
-
lib/bio/db/fasta/defline.rb | 1 -
|
2507
|
-
1 file changed, 1 deletion(-)
|
2508
|
-
|
2509
|
-
commit aafc03330fa79243cfa4097d356a7c304ddb7980
|
2510
|
-
Author: Kenichi Kamiya <kachick1@gmail.com>
|
2511
|
-
Date: Sat Feb 16 21:22:55 2013 +0900
|
2512
|
-
|
2513
|
-
Simplify some regular expressions
|
2514
|
-
|
2515
|
-
* /\w/ including /\d/
|
2516
|
-
* /\s/ including [/\r/, /\t/, /\n/]
|
2517
|
-
|
2518
|
-
lib/bio/appl/blast/format0.rb | 2 +-
|
2519
|
-
lib/bio/db/embl/common.rb | 2 +-
|
2520
|
-
lib/bio/db/embl/embl.rb | 2 +-
|
2521
|
-
lib/bio/db/embl/sptr.rb | 2 +-
|
2522
|
-
lib/bio/db/gff.rb | 2 +-
|
2523
|
-
5 files changed, 5 insertions(+), 5 deletions(-)
|
2524
|
-
|
2525
|
-
commit 623ad4011fa8b56f3c9f50a859d1fa26f6570700
|
2526
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2527
|
-
Date: Fri Jan 11 16:41:12 2013 +0900
|
2528
|
-
|
2529
|
-
Improvement of parameter checks and error output
|
2530
|
-
|
2531
|
-
* Improvement of parameter checks
|
2532
|
-
* To avoid potential XSS in old MSIE which ignores content-type,
|
2533
|
-
always do CGI.escapeHTML for parameters in error messages
|
2534
|
-
|
2535
|
-
sample/biofetch.rb | 91 +++++++++++++++++++++++++++++++++++++-----------------
|
2536
|
-
1 file changed, 63 insertions(+), 28 deletions(-)
|
2537
|
-
|
2538
|
-
commit 03d48c43f1de7ebc9104b9aa972f226774a0bf49
|
2539
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2540
|
-
Date: Fri Jan 11 15:32:05 2013 +0900
|
2541
|
-
|
2542
|
-
Add metadata cache
|
2543
|
-
|
2544
|
-
* Add metadata cache. It caches the list of databases and a list of
|
2545
|
-
available formats for each database. Database entries are not cached.
|
2546
|
-
* charset=utf-8 in CGI header.
|
2547
|
-
|
2548
|
-
sample/biofetch.rb | 110 ++++++++++++++++++++++++++++++++++++++++++-----------
|
2549
|
-
1 file changed, 87 insertions(+), 23 deletions(-)
|
2550
|
-
|
2551
|
-
commit 114d29d4bdfc328f5e91adee9bea465622248e0d
|
2552
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2553
|
-
Date: Fri Jan 11 09:10:08 2013 +0900
|
2554
|
-
|
2555
|
-
remove excess double quotations in html part
|
2556
|
-
|
2557
|
-
sample/biofetch.rb | 8 ++++----
|
2558
|
-
1 file changed, 4 insertions(+), 4 deletions(-)
|
2559
|
-
|
2560
|
-
commit 949311648b92d51a2596f896fdae8d74ac0608a3
|
2561
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2562
|
-
Date: Fri Jan 11 08:59:18 2013 +0900
|
2563
|
-
|
2564
|
-
add magic comment: coding utf-8
|
2565
|
-
|
2566
|
-
sample/biofetch.rb | 1 +
|
2567
|
-
1 file changed, 1 insertion(+)
|
2568
|
-
|
2569
|
-
commit 4ae509273134c5deca7910847063ed07c56150db
|
2570
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2571
|
-
Date: Thu Jan 10 23:27:09 2013 +0900
|
2572
|
-
|
2573
|
-
Rewrite to use TogoWS REST API instead of SOAP-based KEGG API.
|
2574
|
-
|
2575
|
-
* Rewrite to use TogoWS REST API instead of deprecated SOAP-based
|
2576
|
-
KEGG API.
|
2577
|
-
* Examples are changed to fit with current TogoWS.
|
2578
|
-
* Now, the script does not depend on any non-standard libraries
|
2579
|
-
including BioRuby. This means that one can put this script on
|
2580
|
-
a server without installing BioRuby.
|
2581
|
-
* New constans SCRIPT_NAME and BASE_URL for easy customizing.
|
2582
|
-
* Many changes. See "git diff" for details.
|
2583
|
-
|
2584
|
-
sample/biofetch.rb | 265 ++++++++++++++++++++++++++---------------------------
|
2585
|
-
1 file changed, 131 insertions(+), 134 deletions(-)
|
2586
|
-
|
2587
|
-
commit bc98bc54c59be98425d66c64b19a3b9612993beb
|
2588
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2589
|
-
Date: Thu Jan 10 15:17:42 2013 +0900
|
2590
|
-
|
2591
|
-
Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
|
2592
|
-
|
2593
|
-
gemfiles/Gemfile.travis-ruby1.9 | 1 +
|
2594
|
-
1 file changed, 1 insertion(+)
|
2595
|
-
|
2596
|
-
commit dfe54b2fbe303f56a868404173fe346724b7aa4a
|
2597
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2598
|
-
Date: Thu Jan 10 14:06:45 2013 +0900
|
2599
|
-
|
2600
|
-
Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
|
2601
|
-
|
2602
|
-
gemfiles/Gemfile.travis-jruby1.8 | 1 +
|
2603
|
-
gemfiles/Gemfile.travis-jruby1.9 | 1 +
|
2604
|
-
2 files changed, 2 insertions(+)
|
2605
|
-
|
2606
|
-
commit f07ec6ac326d51c055496983abba54afd00c35d4
|
2607
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2608
|
-
Date: Thu Jan 10 01:38:00 2013 +0900
|
2609
|
-
|
2610
|
-
Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
|
2611
|
-
|
2612
|
-
gemfiles/Gemfile.travis-ruby1.8 | 1 +
|
2613
|
-
1 file changed, 1 insertion(+)
|
2614
|
-
|
2615
|
-
commit 4221d52055087f85daa1c23349d10ecdb4d01a31
|
2616
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2617
|
-
Date: Thu Jan 10 01:27:03 2013 +0900
|
2618
|
-
|
2619
|
-
Ruby 2.0 support: Set script encoding to US-ASCII for gff.rb.
|
2620
|
-
|
2621
|
-
lib/bio/db/gff.rb | 1 +
|
2622
|
-
1 file changed, 1 insertion(+)
|
2623
|
-
|
2624
|
-
commit 1526df8273e9d2283fd4a921d4cf8c0c664fe71c
|
2625
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2626
|
-
Date: Thu Jan 10 00:45:36 2013 +0900
|
2627
|
-
|
2628
|
-
Convert encoding of the Japanese tutorial files to UTF-8
|
2629
|
-
|
2630
|
-
doc/Tutorial.rd.ja | 1920 +++++++++++++++++++++++------------------------
|
2631
|
-
doc/Tutorial.rd.ja.html | 1918 +++++++++++++++++++++++-----------------------
|
2632
|
-
2 files changed, 1919 insertions(+), 1919 deletions(-)
|
2633
|
-
|
2634
|
-
commit 3215570185a46dd0d6c4cd96d583b2487636b483
|
2635
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2636
|
-
Date: Thu Jan 10 00:41:51 2013 +0900
|
2637
|
-
|
2638
|
-
updated doc/Tutorial.rd.html and doc/Tutorial.rd.ja.html
|
2639
|
-
|
2640
|
-
doc/Tutorial.rd.html | 19 ++---
|
2641
|
-
doc/Tutorial.rd.ja.html | 202 ++++++++++++++----------------------------------
|
2642
|
-
2 files changed, 63 insertions(+), 158 deletions(-)
|
2643
|
-
|
2644
|
-
commit 8db12935a9cc15bae92bdb7183476cfea9e1f819
|
2645
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2646
|
-
Date: Thu Jan 10 00:38:18 2013 +0900
|
2647
|
-
|
2648
|
-
Set html title when generating tutorial html
|
2649
|
-
|
2650
|
-
Rakefile | 3 ++-
|
2651
|
-
1 file changed, 2 insertions(+), 1 deletion(-)
|
2652
|
-
|
2653
|
-
commit 644d438decceb072475877a749435fba543ff8ea
|
2654
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2655
|
-
Date: Fri Jan 4 03:19:00 2013 +0900
|
2656
|
-
|
2657
|
-
regenerate bioruby.gemspec with rake regemspec
|
2658
|
-
|
2659
|
-
bioruby.gemspec | 6 ------
|
2660
|
-
1 file changed, 6 deletions(-)
|
2661
|
-
|
2662
|
-
commit 54dc9b9f68ee2de9ee005a772ce000277a073d97
|
2663
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2664
|
-
Date: Fri Jan 4 02:35:01 2013 +0900
|
2665
|
-
|
2666
|
-
Remove sample/psortplot_html.rb which depend on Bio::KEGG::API.
|
2667
|
-
|
2668
|
-
* Remove sample/psortplot_html.rb because it strongly depend on
|
2669
|
-
removed Bio::KEGG::API and discontinued SOAP-based KEGG API.
|
2670
|
-
It is hard to re-write by using new REST-based KEGG API because
|
2671
|
-
the new API seems to lack color_pathway_by_objects that returns
|
2672
|
-
image URL. Moreover, there is no one-by-one API migration guide.
|
2673
|
-
|
2674
|
-
sample/psortplot_html.rb | 214 -----------------------------------------------
|
2675
|
-
1 file changed, 214 deletions(-)
|
2676
|
-
delete mode 100644 sample/psortplot_html.rb
|
2677
|
-
|
2678
|
-
commit dbdf2dad3dec9d10141b891a481b9b05e1561708
|
2679
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2680
|
-
Date: Fri Jan 4 02:34:05 2013 +0900
|
2681
|
-
|
2682
|
-
Remove descriptions about KEGG API and Bio::KEGG::API.
|
2683
|
-
|
2684
|
-
doc/Tutorial.rd | 6 ---
|
2685
|
-
doc/Tutorial.rd.ja | 106 +----------------------------------------------------
|
2686
|
-
2 files changed, 1 insertion(+), 111 deletions(-)
|
2687
|
-
|
2688
|
-
commit 3ca725dc1e07f794344c9fcae43d4972ed2895da
|
2689
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2690
|
-
Date: Fri Jan 4 02:33:09 2013 +0900
|
2691
|
-
|
2692
|
-
Remove description about KEGG API and Bio::KEGG::API.
|
2693
|
-
|
2694
|
-
README.rdoc | 6 ++----
|
2695
|
-
1 file changed, 2 insertions(+), 4 deletions(-)
|
2696
|
-
|
2697
|
-
commit d4568788069f2d998a78ad72b1d906aae13e85f4
|
2698
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2699
|
-
Date: Thu Jan 3 23:55:58 2013 +0900
|
2700
|
-
|
2701
|
-
Remove KEGG API plugin of BioRuby Shell, due to the removal of Bio::KEGG::API.
|
2702
|
-
|
2703
|
-
lib/bio/shell.rb | 1 -
|
2704
|
-
lib/bio/shell/plugin/keggapi.rb | 181 ----------------------------------------
|
2705
|
-
2 files changed, 182 deletions(-)
|
2706
|
-
delete mode 100644 lib/bio/shell/plugin/keggapi.rb
|
2707
|
-
|
2708
|
-
commit 22c8f4945d622f8f22c08b262c6caf81a0261284
|
2709
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2710
|
-
Date: Thu Jan 3 23:52:36 2013 +0900
|
2711
|
-
|
2712
|
-
Delete autoload lines for removed Bio::KEGG::API
|
2713
|
-
|
2714
|
-
lib/bio.rb | 4 ----
|
2715
|
-
1 file changed, 4 deletions(-)
|
2716
|
-
|
2717
|
-
commit b56ec0984d5001c3a4d3b4f0ba8fbbbf79835747
|
2718
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2719
|
-
Date: Thu Jan 3 23:51:24 2013 +0900
|
2720
|
-
|
2721
|
-
Remove Bio::KEGG::API and its sample code and documentation files.
|
2722
|
-
|
2723
|
-
* Remove Bio::KEGG::API and its sample code and documentation files.
|
2724
|
-
* deleted: lib/bio/io/keggapi.rb
|
2725
|
-
* deleted: doc/KEGG_API.rd
|
2726
|
-
* deleted: doc/KEGG_API.rd.ja
|
2727
|
-
* deleted: sample/demo_keggapi.rb
|
2728
|
-
|
2729
|
-
doc/KEGG_API.rd | 1843 ------------------------------------------------
|
2730
|
-
doc/KEGG_API.rd.ja | 1834 -----------------------------------------------
|
2731
|
-
lib/bio/io/keggapi.rb | 363 ----------
|
2732
|
-
sample/demo_keggapi.rb | 502 -------------
|
2733
|
-
4 files changed, 4542 deletions(-)
|
2734
|
-
delete mode 100644 doc/KEGG_API.rd
|
2735
|
-
delete mode 100644 doc/KEGG_API.rd.ja
|
2736
|
-
delete mode 100644 lib/bio/io/keggapi.rb
|
2737
|
-
delete mode 100644 sample/demo_keggapi.rb
|
2738
|
-
|
2739
|
-
commit 63af413c122b4531193153fbfee034deaf0a9606
|
2740
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2741
|
-
Date: Mon Oct 1 21:11:14 2012 +0900
|
2742
|
-
|
2743
|
-
Bug fix: parse error when subject sequence contains spaces
|
2744
|
-
|
2745
|
-
* Bug fix: parse error when subject sequence contains spaces.
|
2746
|
-
Thanks to Edward Rice who reports the bug. (Bug #3385)
|
2747
|
-
(https://redmine.open-bio.org/issues/3385)
|
2748
|
-
|
2749
|
-
lib/bio/appl/blast/format0.rb | 38 +++++++++++++++++++-------------------
|
2750
|
-
1 file changed, 19 insertions(+), 19 deletions(-)
|
2751
|
-
|
2752
|
-
commit 9f2f682ec6624ff356bea7aca76365ba95d33549
|
2753
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2754
|
-
Date: Fri Sep 7 16:50:44 2012 +0900
|
2755
|
-
|
2756
|
-
add an env line to be recognized in allow_failures
|
2757
|
-
|
2758
|
-
.travis.yml | 1 +
|
2759
|
-
1 file changed, 1 insertion(+)
|
2760
|
-
|
2761
|
-
commit fead6dda526081db09c56c2262f111338b7d8cd7
|
2762
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2763
|
-
Date: Fri Sep 7 16:08:57 2012 +0900
|
2764
|
-
|
2765
|
-
environment variable TESTOPTS=-v for verbose output of rake test
|
2766
|
-
|
2767
|
-
.travis.yml | 22 ++++++++++++++--------
|
2768
|
-
1 file changed, 14 insertions(+), 8 deletions(-)
|
2769
|
-
|
2770
|
-
commit 3de19895140502898c77fc83d9ad6fae47331763
|
2771
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2772
|
-
Date: Thu Sep 6 18:17:22 2012 +0900
|
2773
|
-
|
2774
|
-
Remove Bio.method_missing because it is broken.
|
2775
|
-
|
2776
|
-
* Bio.method_missing, the hook of undefined methods, providing
|
2777
|
-
shortcut of Bio::Shell methods, is now removed, because it does
|
2778
|
-
not work correctly, and because the use of method_missing should
|
2779
|
-
normally be avoided unless it is really necessary. Alternatively,
|
2780
|
-
use Bio::Shell.xxxxx (xxxxx is a method name).
|
2781
|
-
|
2782
|
-
lib/bio.rb | 13 -------------
|
2783
|
-
1 file changed, 13 deletions(-)
|
2784
|
-
|
2785
|
-
commit a358584c4a76be6a38ab38a18e6dc66840030450
|
2786
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2787
|
-
Date: Thu Sep 6 16:48:51 2012 +0900
|
2788
|
-
|
2789
|
-
Delete autoload line of a removed class Bio::NCBI::SOAP.
|
2790
|
-
|
2791
|
-
lib/bio/io/ncbirest.rb | 1 -
|
2792
|
-
1 file changed, 1 deletion(-)
|
2793
|
-
|
2794
|
-
commit 340d665775b862da638e4d12751b84d2ccd83e82
|
2795
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2796
|
-
Date: Thu Sep 6 16:47:03 2012 +0900
|
2797
|
-
|
2798
|
-
Delete autoload lines of removed classes.
|
2799
|
-
|
2800
|
-
lib/bio.rb | 4 ----
|
2801
|
-
1 file changed, 4 deletions(-)
|
2802
|
-
|
2803
|
-
commit c7c29a672b38d2182cf4afc9a970b854af1149a7
|
2804
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2805
|
-
Date: Thu Sep 6 16:43:25 2012 +0900
|
2806
|
-
|
2807
|
-
regenerate bioruby.gemspec with rake regemspec
|
2808
|
-
|
2809
|
-
bioruby.gemspec | 3 ---
|
2810
|
-
1 file changed, 3 deletions(-)
|
2811
|
-
|
2812
|
-
commit 09bb4b8a8b7e01a36dbe0cf44a5c2a6a6b5750f1
|
2813
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2814
|
-
Date: Thu Sep 6 16:23:17 2012 +0900
|
2815
|
-
|
2816
|
-
Remove Bio::Shell#ncbisoap which uses removed Bio::NCBI::SOAP.
|
2817
|
-
|
2818
|
-
lib/bio/shell/plugin/soap.rb | 9 ---------
|
2819
|
-
1 file changed, 9 deletions(-)
|
2820
|
-
|
2821
|
-
commit a5e46acdaf06568bea6cb773200bbf3881b5670e
|
2822
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2823
|
-
Date: Thu Sep 6 16:02:32 2012 +0900
|
2824
|
-
|
2825
|
-
Remove issues about removed classes Bio::NCBI::SOAP and Bio::KEGG::Taxonomy
|
2826
|
-
|
2827
|
-
KNOWN_ISSUES.rdoc | 10 ----------
|
2828
|
-
1 file changed, 10 deletions(-)
|
2829
|
-
|
2830
|
-
commit 529815acb1b57486bd506b81eec6be80277cbae7
|
2831
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2832
|
-
Date: Wed Sep 5 11:33:27 2012 +0900
|
2833
|
-
|
2834
|
-
Remove Bio::KEGG::Taxonomy which is old and broken
|
2835
|
-
|
2836
|
-
* Remove Bio::KEGG::Taxonomy because it raises error or the data
|
2837
|
-
structure in the return value seems to be broken. In addition,
|
2838
|
-
running the sample script sample/demo_kegg_taxonomy.rb shows
|
2839
|
-
error or falls into infinite loop. Moreover, KEGG closes public
|
2840
|
-
FTP site and the target data file of the class ("taxonomy")
|
2841
|
-
can only be obtained by paid subscribers. From the above reasons,
|
2842
|
-
it seems there are no users of this class now.
|
2843
|
-
* Deleted files: lib/bio/db/kegg/taxonomy.rb,
|
2844
|
-
sample/demo_kegg_taxonomy.rb
|
2845
|
-
|
2846
|
-
lib/bio/db/kegg/taxonomy.rb | 280 -------------------------------------------
|
2847
|
-
sample/demo_kegg_taxonomy.rb | 92 --------------
|
2848
|
-
2 files changed, 372 deletions(-)
|
2849
|
-
delete mode 100644 lib/bio/db/kegg/taxonomy.rb
|
2850
|
-
delete mode 100644 sample/demo_kegg_taxonomy.rb
|
2851
|
-
|
2852
|
-
commit dc47fb46e86bba15ba43de31075eaba3cf811fa3
|
2853
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2854
|
-
Date: Wed Sep 5 11:26:00 2012 +0900
|
2855
|
-
|
2856
|
-
Remove Bio::NCBI::SOAP which is broken
|
2857
|
-
|
2858
|
-
* Remove Bio::NCBI::SOAP in lib/bio/io/ncbisoap.rb, because it always
|
2859
|
-
raises error during the parsing of WSDL files provided by NCBI, both
|
2860
|
-
with Ruby 1.8.X (with bundled SOAP4R) and Ruby 1.9.X (with
|
2861
|
-
soap4r-ruby1.9 gem). To solve the error, modifying SOAP4R may be
|
2862
|
-
needed, that seems very difficult. The alternative is Bio::NCBI::REST,
|
2863
|
-
REST client class for the NCBI EUtil web services.
|
2864
|
-
|
2865
|
-
lib/bio/io/ncbisoap.rb | 156 -------------------------------------------------
|
2866
|
-
1 file changed, 156 deletions(-)
|
2867
|
-
delete mode 100644 lib/bio/io/ncbisoap.rb
|
2868
|
-
|
2869
|
-
commit 314e06e54603bb238015c391904f414b3da48752
|
2870
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2871
|
-
Date: Tue Sep 4 11:13:47 2012 +0900
|
2872
|
-
|
2873
|
-
regenerate bioruby.gemspec with rake regemspec
|
2874
|
-
|
2875
|
-
bioruby.gemspec | 10 ++++------
|
2876
|
-
1 file changed, 4 insertions(+), 6 deletions(-)
|
2877
|
-
|
2878
|
-
commit e929d5d23a9b489ef42f30b33959f059baf1e185
|
2879
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2880
|
-
Date: Tue Sep 4 11:09:36 2012 +0900
|
2881
|
-
|
2882
|
-
Remove issues about removed classes Bio::Ensembl and Bio::DBGET.
|
2883
|
-
|
2884
|
-
KNOWN_ISSUES.rdoc | 16 ----------------
|
2885
|
-
1 file changed, 16 deletions(-)
|
2886
|
-
|
2887
|
-
commit 550a5440490012f73b6d38d84238cd498f2ebb02
|
2888
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2889
|
-
Date: Tue Sep 4 10:57:20 2012 +0900
|
2890
|
-
|
2891
|
-
Remove Bio::Ensembl because it does not work
|
2892
|
-
|
2893
|
-
* Remove Bio::Ensembl because it does not work after the renewal of
|
2894
|
-
the Ensembl web site in 2008.
|
2895
|
-
* Alternative is io-ensembl gem which supports current Ensembl API.
|
2896
|
-
http://rubygems.org/gems/bio-ensembl
|
2897
|
-
* Deleted files: lib/bio/io/ensembl.rb,
|
2898
|
-
test/network/bio/io/test_ensembl.rb, test/unit/bio/io/test_ensembl.rb.
|
2899
|
-
|
2900
|
-
lib/bio/io/ensembl.rb | 229 -----------------------------------
|
2901
|
-
test/network/bio/io/test_ensembl.rb | 230 ------------------------------------
|
2902
|
-
test/unit/bio/io/test_ensembl.rb | 111 -----------------
|
2903
|
-
3 files changed, 570 deletions(-)
|
2904
|
-
delete mode 100644 lib/bio/io/ensembl.rb
|
2905
|
-
delete mode 100644 test/network/bio/io/test_ensembl.rb
|
2906
|
-
delete mode 100644 test/unit/bio/io/test_ensembl.rb
|
2907
|
-
|
2908
|
-
commit 61301a8ec252f3623f994edd59f597360f73448b
|
2909
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2910
|
-
Date: Tue Sep 4 10:47:52 2012 +0900
|
2911
|
-
|
2912
|
-
Remove obsolete Bio::DBGET
|
2913
|
-
|
2914
|
-
* Remove Bio::DBGET because it uses old original protocol that was
|
2915
|
-
discontinued about 8 years ago.
|
2916
|
-
* Remove lib/bio/io/dbget.rb and sample/dbget.
|
2917
|
-
|
2918
|
-
lib/bio/io/dbget.rb | 194 ----------------------------------------------------
|
2919
|
-
sample/dbget | 37 ----------
|
2920
|
-
2 files changed, 231 deletions(-)
|
2921
|
-
delete mode 100644 lib/bio/io/dbget.rb
|
2922
|
-
delete mode 100755 sample/dbget
|
2923
|
-
|
2924
|
-
commit 3c5e288a8685ba3279a3ba73f1b31056c1b6f7a8
|
2925
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2926
|
-
Date: Thu Aug 23 00:25:43 2012 +0900
|
2927
|
-
|
2928
|
-
Refresh ChangeLog, showing changes after 1.4.3 release.
|
2929
|
-
|
2930
|
-
* Refresh to the new ChangeLog, showing changes after 1.4.3 release.
|
2931
|
-
For the changes before 1.4.3, see doc/ChangeLog-1.4.3.
|
2932
|
-
For the changes before 1.4.2, see doc/ChangeLog-before-1.4.2.
|
2933
|
-
For the changes before 1.3.1, see doc/ChangeLog-before-1.3.1.
|
2934
|
-
|
2935
|
-
ChangeLog | 61 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|
2936
|
-
1 file changed, 61 insertions(+)
|
2937
|
-
create mode 100644 ChangeLog
|
2938
|
-
|
2939
|
-
commit 63c13ad8516b9dcacbe001137666c3468968542b
|
2940
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2941
|
-
Date: Thu Aug 23 00:25:07 2012 +0900
|
2942
|
-
|
2943
|
-
Rakefile: Update hardcoded git tag name for updating of ChangeLog.
|
2944
|
-
|
2945
|
-
Rakefile | 2 +-
|
2946
|
-
1 file changed, 1 insertion(+), 1 deletion(-)
|
2947
|
-
|
2948
|
-
commit b10c7ad2db24d88726ffb8c63078baa217aeac43
|
2949
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2950
|
-
Date: Thu Aug 23 00:20:01 2012 +0900
|
2951
|
-
|
2952
|
-
renamed ChangeLog to doc/ChangeLog-1.4.3
|
2953
|
-
|
2954
|
-
ChangeLog | 1478 ---------------------------------------------------
|
2955
|
-
doc/ChangeLog-1.4.3 | 1478 +++++++++++++++++++++++++++++++++++++++++++++++++++
|
2956
|
-
2 files changed, 1478 insertions(+), 1478 deletions(-)
|
2957
|
-
delete mode 100644 ChangeLog
|
2958
|
-
create mode 100644 doc/ChangeLog-1.4.3
|
2959
|
-
|
2960
|
-
commit 0c20cb62ba6b253098e7198c14de1829f72474f5
|
2961
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2962
|
-
Date: Thu Aug 23 00:18:50 2012 +0900
|
2963
|
-
|
2964
|
-
ChangeLog updated: add log about 1.4.3 release.
|
2965
|
-
|
2966
|
-
ChangeLog | 9 +++++++++
|
2967
|
-
1 file changed, 9 insertions(+)
|
2968
|
-
|
2969
|
-
commit 5e88ccbe0fefdd4d57f144aaf9073f5e7d93281c
|
2970
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2971
|
-
Date: Thu Aug 23 00:16:25 2012 +0900
|
2972
|
-
|
2973
|
-
New RELEASE_NOTES.rdoc for the next release version.
|
2974
|
-
|
2975
|
-
RELEASE_NOTES.rdoc | 47 +++++++++++++++++++++++++++++++++++++++++++++++
|
2976
|
-
1 file changed, 47 insertions(+)
|
2977
|
-
create mode 100644 RELEASE_NOTES.rdoc
|
2978
|
-
|
2979
|
-
commit e3d40b90d88ab0d0a91d8e32ebf97c16097f0996
|
2980
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2981
|
-
Date: Thu Aug 23 00:12:40 2012 +0900
|
2982
|
-
|
2983
|
-
Renamed RELEASE_NOTES.rdoc to doc/RELEASE_NOTES-1.4.3.rdoc
|
2984
|
-
|
2985
|
-
RELEASE_NOTES.rdoc | 204 -------------------------------------------
|
2986
|
-
doc/RELEASE_NOTES-1.4.3.rdoc | 204 +++++++++++++++++++++++++++++++++++++++++++
|
2987
|
-
2 files changed, 204 insertions(+), 204 deletions(-)
|
2988
|
-
delete mode 100644 RELEASE_NOTES.rdoc
|
2989
|
-
create mode 100644 doc/RELEASE_NOTES-1.4.3.rdoc
|
2990
|
-
|
2991
|
-
commit 08bcabecccb271385d38a0f807e8c408def5a128
|
2992
|
-
Author: Naohisa Goto <ng@bioruby.org>
|
2993
|
-
Date: Thu Aug 23 00:00:15 2012 +0900
|
2994
|
-
|
2995
|
-
Bio::BIORUBY_EXTRA_VERSION set to ".5000" (unstable version).
|
2996
|
-
|
2997
|
-
bioruby.gemspec | 2 +-
|
2998
|
-
lib/bio/version.rb | 2 +-
|
2999
|
-
2 files changed, 2 insertions(+), 2 deletions(-)
|