bio 1.6.0.pre.20181210 → 2.0.3

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Files changed (48) hide show
  1. checksums.yaml +4 -4
  2. data/.travis.yml +32 -34
  3. data/ChangeLog +1462 -8
  4. data/Gemfile +0 -2
  5. data/KNOWN_ISSUES.rdoc +4 -10
  6. data/LEGAL +0 -10
  7. data/README.rdoc +31 -80
  8. data/README_DEV.rdoc +5 -5
  9. data/RELEASE_NOTES.rdoc +171 -18
  10. data/Rakefile +0 -34
  11. data/appveyor.yml +15 -7
  12. data/bioruby.gemspec +13 -4
  13. data/bioruby.gemspec.erb +0 -1
  14. data/gemfiles/Gemfile.travis-rbx +0 -2
  15. data/gemfiles/Gemfile.travis-ruby1.8 +0 -2
  16. data/gemfiles/Gemfile.travis-ruby1.9 +0 -2
  17. data/gemfiles/Gemfile.windows +6 -0
  18. data/lib/bio/appl/blast/report.rb +40 -8
  19. data/lib/bio/appl/iprscan/report.rb +3 -3
  20. data/lib/bio/appl/sosui/report.rb +1 -1
  21. data/lib/bio/db/embl/uniprotkb.rb +1 -1
  22. data/lib/bio/db/gff.rb +3 -1
  23. data/lib/bio/db/go.rb +2 -2
  24. data/lib/bio/db/kegg/common.rb +14 -0
  25. data/lib/bio/db/kegg/genes.rb +26 -0
  26. data/lib/bio/db/kegg/pathway.rb +5 -11
  27. data/lib/bio/sequence/common.rb +112 -0
  28. data/lib/bio/sequence/format.rb +1 -0
  29. data/lib/bio/tree.rb +1 -1
  30. data/lib/bio/version.rb +3 -3
  31. data/sample/color_scheme_aa.rb +82 -0
  32. data/sample/color_scheme_na.rb +5 -6
  33. data/sample/fastq2html.cwl +23 -0
  34. data/sample/fastq2html.rb +94 -0
  35. data/sample/fastq2html.testdata.yaml +5 -0
  36. data/sample/na2aa.cwl +23 -0
  37. data/sample/na2aa.rb +11 -25
  38. data/sample/na2aa.testdata.yaml +7 -0
  39. data/sample/rev_comp.cwl +23 -0
  40. data/sample/rev_comp.rb +20 -0
  41. data/sample/rev_comp.testdata.yaml +7 -0
  42. data/test/network/bio/db/kegg/test_genes_hsa7422.rb +91 -0
  43. data/test/unit/bio/appl/blast/test_report.rb +4 -4
  44. data/test/unit/bio/db/test_gff.rb +5 -0
  45. data/test/unit/bio/sequence/test_ruby3.rb +462 -0
  46. metadata +17 -8
  47. data/lib/bio/appl/blast/xmlparser.rb +0 -236
  48. data/setup.rb +0 -1600
data/Gemfile CHANGED
@@ -4,5 +4,3 @@ gem "rake"
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4
  gem "rdoc"
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  gem "test-unit"
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- gem "xmlparser"
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-
data/KNOWN_ISSUES.rdoc CHANGED
@@ -1,5 +1,5 @@
1
1
  = KNOWN_ISSUES.rdoc - Known issues and bugs in BioRuby
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- Copyright:: Copyright (C) 2009-2012 Naohisa Goto <ng@bioruby.org>
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+ Copyright:: Copyright (C) 2009-2020 Naohisa Goto <ng@bioruby.org>
3
3
  License:: The Ruby License
4
4
 
5
5
  = Known issues and bugs in BioRuby
@@ -12,11 +12,6 @@ they are not BioRuby's issues and/or it is very difficult to fix them.
12
12
 
13
13
  == 1. Ruby version specific issues
14
14
 
15
- === Ruby 1.9.1 or later
16
-
17
- Some classes/modules/methods still may not work or may return incorrect
18
- results in Ruby 1.9.X, especially those not covered by the unit tests.
19
-
20
15
  ==== String encodings
21
16
 
22
17
  Currently, BioRuby do not care string encodings. In some cases,
@@ -28,12 +23,11 @@ Encoding::CompatibilityError or "ArgumentError: invalid byte sequence in
28
23
  ==== Ruby 1.9.0
29
24
 
30
25
  (WONT_FIX) Ruby 1.9.0 is NOT supported because it isn't a stable release.
31
- Use Ruby 1.9.1 or later.
32
26
 
33
- ==== Ruby 1.8.6 or earlier
27
+ ==== Ruby 1.9.1 or earlier (including Ruby 1.8.7)
34
28
 
35
- (WONT_FIX) Problems observed only with Ruby 1.8.6 or earlier will not be
36
- fixed. Note that Ruby 1.8.6 or earlier is no longer supported, as described
29
+ (WONT_FIX) Problems observed only with Ruby 1.9.1 or earlier will not be
30
+ fixed. Note that Ruby 1.9.1 or earlier is no longer supported, as described
37
31
  in README.rdoc.
38
32
 
39
33
  ==== Ruby 1.8.2 or earlier
data/LEGAL CHANGED
@@ -6,15 +6,6 @@ license (see the file COPYING) or public-domain except some files
6
6
  mentioned below.
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7
 
8
8
 
9
- setup.rb:
10
-
11
- Copyright (c) 2000-2006 Minero Aoki
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-
13
- This program is free software.
14
- You can distribute/modify this program under the terms of
15
- the GNU LGPL, Lesser General Public License version 2.1.
16
-
17
-
18
9
  sample/any2fasta.rb:
19
10
 
20
11
  Copyright (C) 2006 Pjotr Prins <p@bioruby.org>
@@ -68,7 +59,6 @@ sample/vs-genes.rb:
68
59
 
69
60
  sample/fastagrep.rb:
70
61
  sample/fastasort.rb:
71
- sample/na2aa.rb:
72
62
 
73
63
  Copyright (C) 2008 KATAYAMA Toshiaki <k@bioruby.org> & Pjotr Prins
74
64
 
data/README.rdoc CHANGED
@@ -2,7 +2,7 @@
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2
  = README.rdoc - README for BioRuby
3
3
  Copyright:: Copyright (C) 2001-2007 Toshiaki Katayama <k@bioruby.org>,
4
4
  Copyright (C) 2008 Jan Aerts <jandot@bioruby.org>
5
- Copyright (C) 2011-2015 Naohisa Goto <ng@bioruby.org>
5
+ Copyright (C) 2011-2019 Naohisa Goto <ng@bioruby.org>
6
6
  License:: The Ruby License
7
7
  * The above statement is limited to this file. See below about BioRuby's
8
8
  copyright and license.
@@ -10,7 +10,7 @@ License:: The Ruby License
10
10
 
11
11
  = BioRuby
12
12
 
13
- Copyright (C) 2001-2012 Toshiaki Katayama <k@bioruby.org>
13
+ Copyright (C) 2001-2019 Toshiaki Katayama <k@bioruby.org>
14
14
 
15
15
  BioRuby is an open source Ruby library for developing bioinformatics
16
16
  software. Object oriented scripting language Ruby has many features
@@ -45,10 +45,7 @@ See RELEASE_NOTES.rdoc for news and important changes in this version.
45
45
  README.rdoc:: This file. General information and installation procedure.
46
46
  RELEASE_NOTES.rdoc:: News and important changes in this release.
47
47
  KNOWN_ISSUES.rdoc:: Known issues and bugs in BioRuby.
48
- doc/RELEASE_NOTES-1.4.3.rdoc:: News and incompatible changes from 1.4.2 to 1.4.3.
49
- doc/RELEASE_NOTES-1.4.2.rdoc:: News and incompatible changes from 1.4.1 to 1.4.2.
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- doc/RELEASE_NOTES-1.4.1.rdoc:: News and incompatible changes from 1.4.0 to 1.4.1.
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- doc/RELEASE_NOTES-1.4.0.rdoc:: News and incompatible changes from 1.3.1 to 1.4.0.
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+ doc/RELEASE_NOTES-*.rdoc:: Release notes for old versions.
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  doc/Changes-1.3.rdoc:: News and incompatible changes from 1.2.1 to 1.3.0.
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50
  doc/Changes-0.7.rd:: News and incompatible changes from 0.6.4 to 1.2.1.
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51
 
@@ -60,7 +57,7 @@ doc/Tutorial.rd.html:: HTML version of Tutorial.rd.
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57
  ==== BioRuby development
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58
 
62
59
  ChangeLog:: History of changes.
63
- doc/ChangeLog-1.4.3:: changes from 1.4.2 to 1.4.3.
60
+ doc/ChangeLog-*:: ChangeLog for old versions.
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61
  doc/ChangeLog-before-1.4.2:: changes before 1.4.2.
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62
  doc/ChangeLog-before-1.3.1:: changes before 1.3.1.
66
63
  README_DEV.rdoc:: Describes ways to contribute to the BioRuby project, including coding styles and documentation guidelines.
@@ -114,9 +111,8 @@ and can be obtained by the following procedure:
114
111
 
115
112
  == REQUIREMENTS
116
113
 
117
- * Ruby 1.8.7 or later (except Ruby 1.9.0) -- http://www.ruby-lang.org/
118
- * Ruby 2.1.6 or later, or Ruby 2.2.2 or later is recommended.
119
- * This is the final version running on Ruby 1.8, tested with Ruby1.8.7-p374.
114
+ * Ruby 2.0.0 or later -- http://www.ruby-lang.org/
115
+ * Ruby 2.4.6, 2.5.5, 2.6.3 or later is recommended.
120
116
  * See KNOWN_ISSUES.rdoc for Ruby version specific problems.
121
117
 
122
118
 
@@ -126,14 +122,6 @@ Some optional libraries can be utilized to extend BioRuby's functionality.
126
122
  If your needs meets the following conditions, install them by using RubyGems,
127
123
  or download and install from the following web sites.
128
124
 
129
- For faster parsing of the BLAST XML output format:
130
-
131
- * {xmlparser}[https://rubygems.org/gems/xmlparser]
132
- * For Ruby 1.8: {gem install xmlparser}[http://rubygems.org/gems/xmlparser]
133
- * For Ruby 1.9 or later: http://www.yoshidam.net/Ruby.html#xmlparser
134
- * In both cases, {The Expat XML Parser}[http://expat.sourceforge.net/]
135
- and C compiler will be required.
136
-
137
125
  Creating faster flatfile index using Berkley DB:
138
126
 
139
127
  * {GitHub:ruby-bdb}[https://github.com/knu/ruby-bdb]
@@ -153,40 +141,6 @@ If you are using RubyGems, just type
153
141
  Alternatively, manually download bio-X.X.X.gem from
154
142
  http://bioruby.org/archive/ and install it by using gems command.
155
143
 
156
- RubyGems is bundled with Ruby 1.9.1 or later. For Ruby 1.8.7 or earlier,
157
- download and install RubyGems from http://rubygems.org/ .
158
-
159
- === INSTALL without RubyGems
160
-
161
- In the bioruby source directory (such as bioruby-x.x.x/), run setup.rb
162
- as follows:
163
-
164
- % su
165
- # ruby setup.rb
166
-
167
- These simple step installs this program under the default location of
168
- Ruby libraries. You can also install files into your favorite directory
169
- by supplying setup.rb some options. Try "ruby setup.rb --help".
170
-
171
- If your operating system supports 'sudo' command (such as Mac OS X),
172
- try the following procedure instead of the above.
173
-
174
- % sudo ruby setup.rb
175
-
176
- For older version users: "install.rb" is now renamed to "setup.rb".
177
- The options "config", "setup", and "install" are still available.
178
-
179
- % ruby setup.rb config
180
- % ruby setup.rb setup
181
- % su
182
- # ruby setup.rb install
183
-
184
- You can run
185
-
186
- % ruby setup.rb --help
187
-
188
- for more details.
189
-
190
144
 
191
145
  === Running self-test
192
146
 
@@ -197,19 +151,6 @@ To run tests,
197
151
 
198
152
  % ruby test/runner.rb
199
153
 
200
- If you are using Ruby 1.8.x and you want to use components installed by using
201
- RubyGems, explicit loading of RubyGems may be needed.
202
-
203
- % ruby -rubygems test/runner.rb
204
-
205
- Alternatively, testrb, the test runner command of ruby, can be used.
206
-
207
- % testrb test/
208
-
209
- With testrb, you can select tests to run, for example,
210
-
211
- % testrb test/unit
212
-
213
154
  For those familiar with Rake,
214
155
 
215
156
  % rake test
@@ -253,15 +194,6 @@ You can also read other documentation in the 'doc' directory.
253
194
 
254
195
  bioruby-x.x.x/doc/
255
196
 
256
- === RubyGems on Ruby 1.8.x
257
-
258
- With RubyGems on Ruby 1.8.x, you may need to load 'rubygems' library before
259
- using 'bio'. This may not be needed, depending on settings of Ruby.
260
-
261
- #!/usr/bin/env ruby
262
- require 'rubygems'
263
- require 'bio'
264
-
265
197
 
266
198
  == PLUGIN (Biogem)
267
199
 
@@ -274,26 +206,45 @@ Plugins (Biogems) listed below had been included in BioRuby in former days,
274
206
  and were split to separate packages to reduce complexity and external
275
207
  dependencies.
276
208
 
277
- * {bioruby-phyloxml}[http://rubygems.org/gems/bioruby-phyloxml]
209
+ * {bio-shell}[https://rubygems.org/gems/bio-shell]
210
+ * {bio-executables}[https://rubygems.org/gems/bio-executables]
211
+ * {bio-blast-xmlparser}[https://rubygems.org/gems/bio-blast-xmlparser]
212
+ * {bioruby-phyloxml}[https://rubygems.org/gems/bioruby-phyloxml]
278
213
  * NOTE: Please uninstall bio-phyloxml, that have been created as a
279
214
  preliminary trial of splitting a module in 2012 and have not been
280
215
  maintained after that.
281
- * {bio-biosql}[http://rubygems.org/gems/bio-biosql]
216
+ * {bio-biosql}[https://rubygems.org/gems/bio-biosql]
217
+
218
+ Plugins (Biogems) listed below may be useful for running existing codes.
219
+
220
+ * {bio-old-biofetch-emulator}[https://rubygems.org/gems/bio-old-biofetch-emulator] -- Emulates deprecated BioRuby's BioFetch server by using other existing web services.
282
221
 
283
222
  To develop your own plugin, see "Plugins" pages of BioRuby Wiki.
284
223
 
285
224
  * http://bioruby.open-bio.org/wiki/Plugins
286
225
 
226
+ === Recommended Plugins (gems)
227
+
228
+ For existing BioRuby users, it is recommended to install the following gems:
229
+
230
+ bio-shell :: If you use the BioRuby Shell.
231
+ bio-executables :: If you use br_bio* commands.
232
+ bio-old-biofetch-emulator :: If you run existing codes using BioFetch, including sample and demo codes in sample/.
233
+ bio-blast-xmlparser :: If you treat BLAST XML result files and Expat XML parser (with development files) is installed in your system.
234
+ bioruby-phyloxml :: If you use Bio::PhyloXML and Libxml2 (with developemnt files) is installed in your system.
235
+
236
+ Note that it is NOT recommended to install bio-biosql unless you have
237
+ really used Bio::SQL, because it depends on older version of ActiveRecords
238
+ and ActiveSupport that may not be run on recent Ruby versions.
239
+
240
+
287
241
  == LICENSE
288
242
 
289
243
  BioRuby can be freely distributed under the same terms as Ruby.
290
244
  See the file COPYING (or COPYING.ja written in Japanese).
291
245
 
292
246
  As written in the file COPYING, see the file LEGAL for files distributed
293
- under different license. For example, setup.rb which comes from "setup"
294
- developed by Minero Aoki (http://i.loveruby.net/en/projects/setup/) is
295
- licensed under LGPL 2.1.
296
-
247
+ under different license.
297
248
 
298
249
  == REFERENCE
299
250
 
data/README_DEV.rdoc CHANGED
@@ -2,7 +2,7 @@
2
2
 
3
3
  Copyright:: Copyright (C) 2005, 2006 Toshiaki Katayama <k@bioruby.org>
4
4
  Copyright:: Copyright (C) 2006, 2008 Jan Aerts <jandot@bioruby.org>
5
- Copyright:: Copyright (C) 2011 Naohisa Goto <ng@bioruby.org>
5
+ Copyright:: Copyright (C) 2011, 2019 Naohisa Goto <ng@bioruby.org>
6
6
 
7
7
  = HOW TO CONTRIBUTE TO THE BIORUBY PROJECT?
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8
 
@@ -360,16 +360,16 @@ We are mainly using Ruby MRI (Matz' Ruby Implementation, or Matz' Ruby
360
360
  Interpreter). Please confirm that your code is running on current stable
361
361
  release versions of Ruby MRI.
362
362
 
363
- We are very happy if your code can run on both Ruby 1.8.x and 1.9.x.
364
- Note that Ruby 1.9.0 should be ignored because it was discontinued.
365
- Ruby 1.8.5 or earlier versions can also be ignored. See README.rdoc and
366
- RELEASE_NOTES.rdoc for recommended Ruby versions.
363
+ See README.rdoc and RELEASE_NOTES.rdoc for recommended Ruby versions.
367
364
 
368
365
  It is welcome to support JRuby, Rubinius, etc, in addition to Ruby MRI.
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366
 
370
367
  Of course, it is strongly encouraged to write code that is not affected by
371
368
  differences between Ruby versions and/or implementations, as far as possible.
372
369
 
370
+ Although we no longer support Ruby 1.8, it might be useful if your code
371
+ could also run on Ruby 1.8.7 in addition to supported Ruby versions.
372
+
373
373
  = OS and ARCHITECTURE
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374
 
375
375
  We hope BioRuby can be run on both UNIX (and UNIX-like OS) and Microsoft
data/RELEASE_NOTES.rdoc CHANGED
@@ -1,32 +1,176 @@
1
- = BioRuby 1.5.1 RELEASE NOTES
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+ = BioRuby 2.0.3 RELEASE NOTES
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2
 
3
- A lot of changes have been made to the BioRuby 1.5.1 after the version 1.5.0
3
+ Some bug fixes have been made in BioRuby 2.0.3 after the release of 2.0.2.
4
+
5
+ == Bug fixes
6
+
7
+ * Fix Ruby 3.0.0 Bio::Sequence::* issue.
8
+ (https://github.com/bioruby/bioruby/issues/137 )
9
+ * Fix typo (https://github.com/bioruby/bioruby/pull/145 )
10
+
11
+ == Incompatible changes
12
+
13
+ === Bio::Sequence::* incompatible changes since Ruby 3.0.0
14
+
15
+ Since Ruby 3.0.0, the following methods in Bio::Sequence::NA,
16
+ Bio::Sequence::AA, and Bio::Sequence::Generic return or yield
17
+ String instance, instead of the Bio::Sequence::* instance.
18
+
19
+ * dump
20
+ * scrub
21
+
22
+ For details about Ruby 3.0.0 incompatible changes, see
23
+ {News for Ruby 3.0.0}[https://github.com/ruby/ruby/blob/v3_0_0/NEWS.md].
24
+
25
+
26
+
27
+ = BioRuby 2.0.2 RELEASE NOTES
28
+
29
+ Some bugs fixes have been made in BioRuby 2.0.2 after the release of 2.0.1.
30
+
31
+ == Bug fixes
32
+
33
+ * Fix NameError in Bio::Sequence#output(:embl)
34
+ (https://github.com/bioruby/bioruby/issues/135 )
35
+ * Suppress warning: Gem::Specification#has_rdoc= is deprecated
36
+ (https://github.com/bioruby/bioruby/issues/138 )
37
+ * Fix misspelling URL in README.rdoc
38
+
39
+ == Known issues
40
+
41
+ A known issue about Ruby 3.0 is added to KNOWN_ISSUES.rdoc.
42
+ The issue will be fixed in the near future.
43
+
44
+
45
+
46
+ = BioRuby 2.0.1 RELEASE NOTES
47
+
48
+ Some bug fixes and improvements have been made to the BioRuby 2.0.1 after
49
+ the version 2.0.0 is released.
50
+
51
+ == Bug fixes
52
+
53
+ * Bio::GFF::GFF2::Record.parse did not return correct object.
54
+
55
+ == Improvement of sample scripts
56
+
57
+ The following scripts in the sample/ directiry are newly added.
58
+
59
+ * color_scheme_aa.rb: Example of Bio::ColorScheme for an amino acid sequence.
60
+ * fastq2html.rb: Visualization of FASTQ sequences, colored by quality scores.
61
+ * rev_comp.rb: Shows reverse-complement sequences of the given sequences.
62
+
63
+ The floowing scripts are modified to fix bug and/or to improve features.
64
+
65
+ * na2aa.rb: Completely rewritten to fix bug. Shows translated sequences.
66
+ * color_scheme_na.rb: Added support for various sequence formats.
67
+
68
+ === CWL (Common Workflow Language) workflow files are added
69
+
70
+ CWL (Common Workflow Language) workflow files are added for some sample
71
+ scripts. The usage of each sample script will be clarified with the CWL
72
+ workflow files.
73
+
74
+ Two type of files are prepared for CWL workflow engine. *.cwl is a workflow
75
+ definition file for each sample script. *.testdata.yaml describes sample
76
+ input data for each CWL workflow.
77
+
78
+ In this version, cwl files for the 3 sample scripts are added.
79
+
80
+ * fastq2html.rb: fastq2html.cwl with fastq2html.testdata.yaml
81
+ * na2aa.rb: na2aa.cwl with na2aa.testdata.yaml
82
+ * rev_comp.rb: rev_comp.cwl with rev_comp.testdata.yaml
83
+
84
+
85
+
86
+ = BioRuby 2.0.0 RELEASE NOTES
87
+
88
+ A lot of changes have been made to the BioRuby 2.0.0 after the version 1.5.x
4
89
  is released. This document describes important and/or incompatible changes
5
90
  since the BioRuby 1.5.0 release.
6
91
 
7
92
  For known problems, see KNOWN_ISSUES.rdoc.
8
93
 
9
- == New features
94
+ == Features moved to separete gems
10
95
 
11
- === (tbd)
96
+ Some features are moved to separate gems because of reducing complexity
97
+ and/or to avoid external library dependency of BioRuby core.
12
98
 
13
- (paragraph)
99
+ === BioRuby Shell is moved to "bio-shell"
14
100
 
15
- === Other new features
101
+ BioRuby Shell is split to "bio-shell" gem.
16
102
 
17
- * (tbd)
18
- * (tbd)
103
+ === Executable files are moved to "bio-executables"
19
104
 
20
- == Bug fixes
105
+ To avoid unexpected loading of executable files by some Rails software,
106
+ all executable commands are moved to "bio-executables" gem
107
+ (except the "bioruby" command that is included in the above "bio-shell" gem).
108
+
109
+ === Fast BLAST XML result parser by using Expat XML Parser is moved to "bio-blast-xmlparser"
110
+
111
+ Fast BLAST XML result parser by using Expat XML Parser is split to
112
+ "bio-blast-xmlparser" gem, because of external C library dependency.
113
+ Please install "bio-blast-xmlparser" gem if possible.
114
+ If it is installed, BioRuby automatically use it.
115
+
116
+ === Bio::PhyloXML is moved to "bioruby-phyloxml"
117
+
118
+ Bio::PhyloXML is split to "bioruby-phyloxml" gem.
119
+
120
+ NOTE: Please uninstall "bio-phyloxml" gem, that have been created as a
121
+ preliminary trial of splitting a module in 2012 and have not been
122
+ maintained after that.
123
+
124
+ === Bio::SQL is moved to "bio-biosql"
125
+
126
+ Bio::SQL is split to "bio-biosql" gem.
21
127
 
22
- === (tbd)
23
128
 
24
- (paragraph)
129
+ == New features and improvements
25
130
 
26
- === Other bug fixes
131
+ === HTTPS is used to access NCBI web services
132
+
133
+ As you may know, NCBI announced that all HTTP resources will be switched
134
+ to HTTPS on September 30, 2016. To follow the transition, all URLs for
135
+ accessing NCBI E-utilities in BioRuby are changed to use HTTPS.
136
+
137
+ In BioRuby, the following classes/modules are affected.
138
+
139
+ * Bio::NCBI::REST and descending classes
140
+ * Bio::PubMed
141
+
142
+ In some rare cases (especially when building Ruby and/or OpenSSL by yourself
143
+ from source code), Ruby does not include SSL/TLS support, or Ruby fails to
144
+ detect SSL root certificates. In such cases, you may need to reinstall or
145
+ upgrade Ruby, OpenSSL (or alternatives), and/or SSL root certificates with
146
+ appropriate configuration options. Alternatively, installing binary packages
147
+ is generally a good idea.
148
+
149
+ === KEGG::GENES#diseases and related methods are added
150
+
151
+ The following methods are added to KEGG::GENES, contributed by @kojix2.
152
+
153
+ * networks_as_strings
154
+ * diseases_as_strings
155
+ * diseases_as_hash
156
+ * diseases
157
+ * drug_targets_as_strings
158
+
159
+ === Pre-calculated ambiguity codon tables in Bio::CodonTable
160
+
161
+ Pre-calculated ambiguity codon tables are added, contributed by
162
+ Tomoaki NISHIYAMA.
163
+
164
+
165
+ == Bug fixes
166
+
167
+ * Fixed a parser bug in Bio::Fasta::Report, FASTA output (-m 10) parser,
168
+ contributed by William Van Etten and Mark Wilkinson via GitHub.
169
+ * HTTPS is used to access GenomeNet BLAST web service, contributed
170
+ by @ramadis via GitHub.
171
+ * Bio::AAindex documentation fix, suggested by @kojix2 via GitHub.
172
+ * Suppress warning messages in Ruby 2.4 and later.
27
173
 
28
- * Fixed: (...)
29
- * Fixed: (...)
30
174
 
31
175
  == Incompatible changes
32
176
 
@@ -51,18 +195,27 @@ Bio::PhyloXML::Taxonomy or adding the following monkey patch may be needed.
51
195
  In the future, Bio::Taxonomy might be added as general taxonomy data class.
52
196
  The new Bio::Taxonomy might be incompatible with the current Bio::Taxonmy.
53
197
 
54
- === (tbd)
198
+ === Some features are moved to separete gems
55
199
 
56
- (paragraph)
200
+ Some features are split to separete gems and removed from this "bio" gem.
201
+ See the above "Features moved to separete gems" topics for details.
57
202
 
58
203
  == Known issues
59
204
 
60
205
  The following issues are added or updated. See KNOWN_ISSUES.rdoc for other
61
206
  already known issues.
62
207
 
63
- * (tbd)
64
208
 
65
209
  == Other important news
66
210
 
67
- (tbd)
211
+ === Ruby 1.8 is no longer supported
212
+
213
+ Ruby 1.8.x is no longer supported. Though unsupported, some components
214
+ may still run on Ruby 1.8.7. Please use Ruby 1.8.7 at your own risk
215
+ with this version of BioRuby.
216
+
217
+ === Installation without RubyGems is no longer supported
218
+
219
+ Installation by using setup.rb without RubyGems is no longer supported,
220
+ and setup.rb is no longer included in BioRuby distribution.
68
221
 
data/Rakefile CHANGED
@@ -272,36 +272,6 @@ task :"see-env" do
272
272
  end
273
273
  end
274
274
 
275
- desc "DANGER: build tar and install (GNU tar needed)"
276
- task :"tar-install" => [ :package ] do
277
- pwd = Dir.pwd
278
- work_in_another_directory do |dirname|
279
- begin
280
- # remove tar file in direname
281
- FileUtils.remove_entry_secure(tar_filename, true)
282
- # chdir to old pwd
283
- chdir_with_message(pwd)
284
- # copy (or link) tar file
285
- safe_ln(tar_pkg_filepath, dirname)
286
- # chdir to dirname again
287
- chdir_with_message(dirname)
288
- # remove a directory the tar file will contain
289
- FileUtils.remove_entry_secure(tar_basename, true)
290
- # extract tar
291
- sh("tar zxvf #{tar_filename}")
292
- # chdir to the directory
293
- chdir_with_message(tar_basename)
294
- # run tests
295
- ruby("setup.rb")
296
- ensure
297
- # cleanup
298
- chdir_with_message(dirname)
299
- FileUtils.remove_entry_secure(tar_basename, true)
300
- FileUtils.remove_entry_secure(tar_filename, true)
301
- end
302
- end
303
- end
304
-
305
275
  desc "test installed bioruby on system"
306
276
  task :"installed-test" do
307
277
  data_path = File.join(Dir.pwd, "test/data")
@@ -318,10 +288,6 @@ task :"installed-test" do
318
288
  end
319
289
  end
320
290
 
321
- desc "DANGER: build tar, install and run test"
322
- task :"tar-integration-test" => [ :"tar-install",
323
- :"installed-test" ]
324
-
325
291
  desc "test installed bioruby gem version #{spec.version.to_s}"
326
292
  task :"gem-test" do
327
293
  data_path = File.join(Dir.pwd, "test/data")
data/appveyor.yml CHANGED
@@ -6,16 +6,24 @@ branches:
6
6
  clone_depth: 10
7
7
  install:
8
8
  - SET PATH=C:\Ruby%ruby_version%\bin;%PATH%
9
+ - SET BUNDLE_GEMFILE=gemfiles/Gemfile.windows
10
+ - bundle install
11
+ - bundle exec rake regemspec
12
+ - bundle exec rake gem
13
+ - bundle exec gem install pkg/bio-*.gem
14
+ - echo gem "bio" >> gemfiles\Gemfile.windows
15
+ build: off
16
+ before_test:
9
17
  - ruby --version
10
18
  - gem --version
11
- - gem build bioruby.gemspec
12
- - gem install *.gem
13
- build: off
19
+ - bundle --version
20
+ test_script:
21
+ - bundle exec rake gem-test
14
22
  environment:
15
23
  matrix:
16
- - ruby_version: "21"
17
- - ruby_version: "21-x64"
18
- - ruby_version: "22"
19
- - ruby_version: "22-x64"
20
24
  - ruby_version: "23"
21
25
  - ruby_version: "23-x64"
26
+ - ruby_version: "24"
27
+ - ruby_version: "24-x64"
28
+ - ruby_version: "25"
29
+ - ruby_version: "25-x64"
data/bioruby.gemspec CHANGED
@@ -3,7 +3,7 @@
3
3
  #
4
4
  Gem::Specification.new do |s|
5
5
  s.name = 'bio'
6
- s.version = "1.6.0.pre.20181211"
6
+ s.version = "2.0.3"
7
7
 
8
8
  s.author = "BioRuby project"
9
9
  s.email = "staff@bioruby.org"
@@ -54,6 +54,7 @@ Gem::Specification.new do |s|
54
54
  "gemfiles/Gemfile.travis-rbx",
55
55
  "gemfiles/Gemfile.travis-ruby1.8",
56
56
  "gemfiles/Gemfile.travis-ruby1.9",
57
+ "gemfiles/Gemfile.windows",
57
58
  "gemfiles/modify-Gemfile.rb",
58
59
  "gemfiles/prepare-gemspec.rb",
59
60
  "lib/bio.rb",
@@ -69,7 +70,6 @@ Gem::Specification.new do |s|
69
70
  "lib/bio/appl/blast/rexml.rb",
70
71
  "lib/bio/appl/blast/rpsblast.rb",
71
72
  "lib/bio/appl/blast/wublast.rb",
72
- "lib/bio/appl/blast/xmlparser.rb",
73
73
  "lib/bio/appl/blat/report.rb",
74
74
  "lib/bio/appl/clustalw.rb",
75
75
  "lib/bio/appl/clustalw/report.rb",
@@ -258,6 +258,7 @@ Gem::Specification.new do |s|
258
258
  "sample/any2fasta.rb",
259
259
  "sample/benchmark_clustalw_report.rb",
260
260
  "sample/biofetch.rb",
261
+ "sample/color_scheme_aa.rb",
261
262
  "sample/color_scheme_na.rb",
262
263
  "sample/demo_aaindex.rb",
263
264
  "sample/demo_aminoacid.rb",
@@ -296,6 +297,9 @@ Gem::Specification.new do |s|
296
297
  "sample/fasta2tab.rb",
297
298
  "sample/fastagrep.rb",
298
299
  "sample/fastasort.rb",
300
+ "sample/fastq2html.cwl",
301
+ "sample/fastq2html.rb",
302
+ "sample/fastq2html.testdata.yaml",
299
303
  "sample/fsplit.rb",
300
304
  "sample/gb2fasta.rb",
301
305
  "sample/gb2tab.rb",
@@ -307,16 +311,20 @@ Gem::Specification.new do |s|
307
311
  "sample/genome2tab.rb",
308
312
  "sample/goslim.rb",
309
313
  "sample/gt2fasta.rb",
314
+ "sample/na2aa.cwl",
310
315
  "sample/na2aa.rb",
316
+ "sample/na2aa.testdata.yaml",
311
317
  "sample/pmfetch.rb",
312
318
  "sample/pmsearch.rb",
319
+ "sample/rev_comp.cwl",
320
+ "sample/rev_comp.rb",
321
+ "sample/rev_comp.testdata.yaml",
313
322
  "sample/seqdatabase.ini",
314
323
  "sample/ssearch2tab.rb",
315
324
  "sample/tdiary.rb",
316
325
  "sample/test_restriction_enzyme_long.rb",
317
326
  "sample/tfastx2tab.rb",
318
327
  "sample/vs-genes.rb",
319
- "setup.rb",
320
328
  "test/bioruby_test_helper.rb",
321
329
  "test/data/HMMER/hmmpfam.out",
322
330
  "test/data/HMMER/hmmsearch.out",
@@ -452,6 +460,7 @@ Gem::Specification.new do |s|
452
460
  "test/network/bio/appl/blast/test_remote.rb",
453
461
  "test/network/bio/appl/test_blast.rb",
454
462
  "test/network/bio/appl/test_pts1.rb",
463
+ "test/network/bio/db/kegg/test_genes_hsa7422.rb",
455
464
  "test/network/bio/io/test_pubmed.rb",
456
465
  "test/network/bio/io/test_togows.rb",
457
466
  "test/network/bio/test_command.rb",
@@ -537,6 +546,7 @@ Gem::Specification.new do |s|
537
546
  "test/unit/bio/sequence/test_dblink.rb",
538
547
  "test/unit/bio/sequence/test_na.rb",
539
548
  "test/unit/bio/sequence/test_quality_score.rb",
549
+ "test/unit/bio/sequence/test_ruby3.rb",
540
550
  "test/unit/bio/sequence/test_sequence_masker.rb",
541
551
  "test/unit/bio/test_alignment.rb",
542
552
  "test/unit/bio/test_command.rb",
@@ -571,7 +581,6 @@ Gem::Specification.new do |s|
571
581
  "test/unit/bio/util/test_sirna.rb"
572
582
  ]
573
583
 
574
- s.has_rdoc = true
575
584
  s.extra_rdoc_files = [
576
585
  "KNOWN_ISSUES.rdoc",
577
586
  "README.rdoc",
data/bioruby.gemspec.erb CHANGED
@@ -63,7 +63,6 @@ Gem::Specification.new do |s|
63
63
  %>
64
64
  ]
65
65
 
66
- s.has_rdoc = true
67
66
  s.extra_rdoc_files = [
68
67
  <%= ###### Below is executed in ERB environment ######
69
68
  # Files whose suffix are .rdoc are selected.