ngoto-bio 1.2.9.9501 → 1.3.0

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data/ChangeLog CHANGED
@@ -1,3 +1,196 @@
1
+ 2009-02-20 Naohisa Goto <ng@bioruby.org>
2
+
3
+ * BioRuby 1.3.0 is released.
4
+
5
+ 2009-02-19 Naohisa Goto <ng@bioruby.org>
6
+
7
+ * lib/bio/version.rb
8
+
9
+ Preparation for bioruby-1.3.0 release.
10
+ (commit fd7fc9f78bc5f4d9a10b3c0d457d9781c9ec2e49)
11
+
12
+ * bioruby.gemspec.erb
13
+
14
+ Fixed a logic to determine whether in git repository, and file
15
+ lists are changed to be sorted.
16
+ (commit ede0c0d7aeab078b6183c4e0e7c74faec32739f7)
17
+
18
+ 2009-02-18 Naohisa Goto <ng@bioruby.org>
19
+
20
+ * README.rdoc
21
+
22
+ Added list of document files bundled in the BioRuby distribution.
23
+ (commit 92748f848e4708766e44c22b2f02ac662491971f)
24
+
25
+ 2009-02-10 Naohisa Goto <ng@bioruby.org>
26
+
27
+ * KNOWN_ISSUES.rdoc
28
+
29
+ Added details about the text mode issue on mswin32/mingw32/bccwin32
30
+ and about non-UNIX/Windows systems.
31
+ (commit 342a167a23d3b078bd77b3f16f0ceb1aa071df66)
32
+
33
+ 2009-02-09 Naohisa Goto <ng@bioruby.org>
34
+
35
+ * test/unit/bio/db/test_gff.rb
36
+
37
+ Test bug fix: test_gff.rb failed in some environment (e.g. Windows)
38
+ because the default formatting rule of Float#to_s depends on the
39
+ libc implementation.
40
+ (commit f39bf88ed6a41bd328372ee7de7a23902235f833)
41
+
42
+
43
+ 2009-02-06 Naohisa Goto <ng@bioruby.org>
44
+
45
+ * lib/bio/db/gff.rb, test/unit/bio/db/test_gff.rb
46
+
47
+ * Bug fix: Bio::GFF::GFF3::Record#id and #id= should be changed
48
+ to follow the previous incompatible change of @attributes.
49
+ Thanks to Tomoaki NISHIYAMA who reports the bug ([BioRuby]
50
+ GFF3 status (possible bug?)).
51
+ * Unit tests are added.
52
+ (commit 5258d88ef98a12fd7829eb86aa8664a18a672a43)
53
+ (commit c0c7708b3e91b0d2f2d0d50a4a0ba36928057cc8)
54
+
55
+ 2009-02-05 Naohisa Goto <ng@bioruby.org>
56
+
57
+ * Rakefile
58
+
59
+ New task "tutorial2html" to generate html from doc/Tutorial.rd
60
+ and doc/Tutorial.rd.ja.
61
+ (commit 8d66fae59477f01f12b2fa3509ea34c371102725)
62
+
63
+ * doc/Tutorial.rd.html, doc/Tutorial.rd.ja.html
64
+
65
+ Automatically generated tutorial html from RD formatted documents.
66
+ (commit 90c4a23eea08b06dd758aaa0a53bea789602d252)
67
+
68
+ * doc/bioruby.css
69
+
70
+ Newly added stylesheet for the tutorial html files. The bioruby.css
71
+ have been used in http://bioruby.org/ and have been maintained by
72
+ Toshiaki Katayama.
73
+ (commit b69dc243787525de065bdf2e6b7da68d6079ab91)
74
+
75
+ * test/runner.rb
76
+
77
+ Added workaroud for test-unit-2.0.x.
78
+ (commit 475ac6a6b38e8df30de3d9bf4c7e810759ab023d)
79
+
80
+ 2009-02-04 Naohisa Goto <ng@bioruby.org>
81
+
82
+ * lib/bio/appl/blast/format0.rb
83
+
84
+ Bug fix: a null line can be inserted after query name lines.
85
+ (commit bea9ce35b4177f407575ed0752c36bba8a50f502)
86
+
87
+ 2009-02-03 Naohisa Goto <ng@bioruby.org>
88
+
89
+ * Tutorial.rd.ja
90
+
91
+ * Document bug: BioRuby shell commands seq, ent, obj were renamed to
92
+ getseq, getent, getobj, respectively. Thanks to Hiroyuki Mishima
93
+ who reports the issue ([BioRuby-ja]).
94
+ * Changes of returned value of getseq are also reflected to the
95
+ document.
96
+ * Recommended Ruby version and installation procedure are also
97
+ changed.
98
+ (commit 916e96ca549db71a550e7a5d3bd49a3149614313)
99
+
100
+ * doc/Changes-0.7.rd
101
+
102
+ Documentation forgotten in 1.1.0: rename of BioRuby shell commands.
103
+ (commit 64113314caac3453b4cc3b80ece9b5fb5841e069)
104
+
105
+ 2009-01-30 Naohisa Goto <ng@bioruby.org>
106
+
107
+ * lib/bio/appl/blast/format0.rb
108
+
109
+ Bug fix: incorrect parsing of hit sequence's whole length.
110
+ (commit 98e6f57630b2c3394a9403f58e76b102346c56ef)
111
+
112
+ Bug fix: Whole length of a hit sequence is mistakenly parsed when
113
+ it contains ",". WU-BLAST parser is also affected in addition to
114
+ NCBI BLAST parser.
115
+
116
+ * lib/bio/db/lasergene.rb, lib/bio/db/soft.rb,
117
+ lib/bio/util/color_scheme.rb, lib/bio/util/contingency_table.rb,
118
+ lib/bio/util/restriction_enzyme.rb
119
+
120
+ Removed ":nodoc:" in in "module Bio" which prevents RDoc of the
121
+ Bio module.
122
+ (commit 458db79b467d40ed02db0d085218f611e7dd5e04)
123
+
124
+ 2009-01-29 Naohisa Goto <ng@bioruby.org>
125
+
126
+ * doc/Changes-1.3.rdoc
127
+
128
+ Added documents about Bio::TogoWS and Bio::BIORUBY_VERSION.
129
+
130
+ * lib/bio/shell/plugin/entry.rb
131
+
132
+ getent (BioRuby shell command) is changed to use EBI Dbfetch or
133
+ TogoWS in addition to NCBI or KEGG API.
134
+ (commit 0e172590f60dd5a5f27a24ecd230037a7909224c)
135
+
136
+ * lib/bio/shell/plugin/togows.rb, lib/bio/shell.rb
137
+
138
+ Added new shell plugin providing accesses to TogoWS REST services.
139
+ (commit 03f6720b90e90703c23536a11b3f12c8155550ff)
140
+
141
+ * lib/bio.rb
142
+
143
+ Added autoload of Bio::TogoWS.
144
+ (commit f8605e1234164a7aa7f236b4e96a4299229753d7)
145
+
146
+ * test/functional/bio/io/test_togows.rb,
147
+ test/unit/bio/io/test_togows.rb
148
+
149
+ Newly added functional and unit tests for Bio::TogoWS::REST.
150
+ (commit f04152b80d07f44f146fa3fa0729facede865aac)
151
+
152
+ * lib/bio/io/togows.rb
153
+
154
+ New class Bio::TogoWS::REST, a REST client for the TogoWS web
155
+ service (http://togows.dbcls.jp/site/en/rest.html).
156
+ (commit 652d2534163675182b9ce30cbb1dd5efff45cd60)
157
+
158
+ * bin/br_pmfetch.rb
159
+
160
+ Changed to use Bio::BIORUBY_VERSION_ID instead of CVS version ID.
161
+ (commit f69d538ffa9ded00eb68dd306e65505d03b6c656)
162
+
163
+ * lib/bio/shell/core.rb
164
+
165
+ Changed to use BIORUBY_VERSION_ID.
166
+ (commit 4ce11656a205e85cae64eca27cef7cd94eb80930)
167
+
168
+ * bioruby.gemspec.erb
169
+
170
+ Gem version is now determined from lib/bio/version.rb or
171
+ BIORUBY_GEM_VERSION environment variable.
172
+ (commit 1811e845e60bc2847ea5717ef936bad93f9f2c87)
173
+
174
+ * Rakefile
175
+
176
+ * Changed to use lib/bio/version.rb.
177
+ * Environment variable BIORUBY_EXTRAVERSION is renamed to
178
+ BIORUBY_EXTRA_VERSION.
179
+ * Added dependency on lib/bio/version.rb to bioruby.gemspec.
180
+ (commit fb27eaa584cda1bb4cb75e10085996503361c98a)
181
+
182
+ * lib/bio.rb, lib/bio/version.rb
183
+
184
+ Bio::BIORUBY_VERSION is split into lib/bio/version.rb.
185
+ (commit 9779398c3fa0e9405a875b754a5243e0d6922c32)
186
+
187
+ * New file lib/bio/version.rb contains BioRuby version information.
188
+ * New constants: Bio::BIORUBY_EXTRA_VERSION stores extra version
189
+ string (e.g. "-pre1") and Bio::BIORUBY_VERSION_ID stores BioRuby
190
+ version string (e.g. "1.3.0-pre1").
191
+ * Bio::BIORUBY_VERSION is changed to be frozen. Above two constants
192
+ also store frozen values.
193
+
1
194
  2009-01-26 Naohisa Goto <ng@bioruby.org>
2
195
 
3
196
  * KNOWN_ISSUES.rdoc
@@ -5,21 +198,25 @@
5
198
  Newly added KNOWN_ISSUES.rdoc that describes known issues and
6
199
  bugs in current BioRuby.
7
200
  (commit 06b10262be0bf797a3b133e4697e9b0955408944)
201
+ (commit a65ad8b42613e46b0b4bb0650d6301da0dcc88c9)
8
202
 
9
203
  * lib/bio/shell/plugin/ncbirest.rb, lib/bio/shell.rb
10
204
 
11
205
  New shell plugin lib/bio/shell/plugin/ncbirest.rb, providing
12
206
  "efetch", "einfo", "esearch", and "esearch_count" methods.
13
207
  They act the same as those defined in Bio::NCBI::REST, except
14
- that efetch automatically selects databases if no options
15
- are given and only 1 id is given.
208
+ that "efetch" fetches entries with pre-defined databases
209
+ depending on arguments.
16
210
  (commit c482e1864aa0dbca3727b1059d4fe3d0aefb3917)
211
+ (commit 3360b8905fdbcd4ca050470fdb2f02a7387e8bb9)
17
212
 
18
213
  * lib/bio/shell/plugin/entry.rb
19
214
 
20
- A shell command "getobj" is changed to use "efetch" method
21
- when "gb" or some variant is specified as the database.
215
+ Shell commands "getent" and "getseq" are changed to use
216
+ "efetch" method when "gb" or some variant is specified as
217
+ the database.
22
218
  (commit c482e1864aa0dbca3727b1059d4fe3d0aefb3917)
219
+ (commit 3360b8905fdbcd4ca050470fdb2f02a7387e8bb9)
23
220
 
24
221
  * bioruby.gemspec.erb, bioruby.gemspec
25
222
 
data/KNOWN_ISSUES.rdoc CHANGED
@@ -38,20 +38,42 @@ SOAP4R (SOAP and WSDL implementation) is no longer bundled with Ruby 1.9.
38
38
  In addition, because of the API changes in recent SOAP4R, some
39
39
  classes/modules using SOAP4R may not work.
40
40
 
41
+ === Problem with REXML DoS vulnerability patch before 09-Nov-2008
42
+
43
+ (WONT_FIX) If you have applied a patch taken from
44
+ http://www.ruby-lang.org/en/news/2008/08/23/dos-vulnerability-in-rexml/
45
+ before 09 Nov 2008 12:40 +0900, because of the bug in the patch,
46
+ parsing of Blast XML results with REXML parser may fail. The bug is already
47
+ fixed and new patch is available on the above URL. Note that some Linux
48
+ distributions would have incorporated the patch in their manners, and may
49
+ have the same problem.
50
+
41
51
  == 2. OS and/or architecture-dependent issues
42
52
 
43
53
  === Microsoft Windows
44
54
 
45
- Following 4 tests failed because of the processing of file contents in the
46
- text mode.
55
+ ==== Text mode issues
56
+
57
+ Following 4 tests failed on mswin32 (and maybe on mingw32 and bccwin32)
58
+ because of the conversion of line feed codes in the text mode.
47
59
 
48
60
  * test_ended_pos and test_start_pos in test/unit/bio/io/test_flatfile.rb
49
61
  * test_pos in test/unit/bio/io/flatfile/test_buffer.rb
50
62
  * test_entry_pos in test/unit/bio/appl/blast/test_rpsblast.rb
51
63
 
64
+ This indicates that br_bioflat.rb and Bio::FlatFileIndex may create
65
+ incorrect indexes on mswin32, mingw32, and bccwin32. In addition,
66
+ Bio::FlatFile may return incorrect data.
67
+
68
+ ==== Windows 95/98/98SE/ME
69
+
52
70
  (WONT_FIX) Some methods that call external programs may not work in
53
71
  Windows 95/98/98SE/ME because of the limitation of COMMAND.COM.
54
72
 
73
+ === OpenVMS, BeOS, OS/2, djgpp, Windows CE
74
+
75
+ (WONT_FIX) BioRuby may not work on these platforms.
76
+
55
77
  == 3. Known issues and bugs in BioRuby
56
78
 
57
79
  === Bio::Ensembl
data/README.rdoc CHANGED
@@ -35,6 +35,35 @@ services including KEGG API can be easily utilized by BioRuby.
35
35
 
36
36
  == FOR MORE INFORMATION
37
37
 
38
+ === Documents in this distribution
39
+
40
+ ==== General information
41
+
42
+ README.rdoc:: This file. General information and installation procedure.
43
+ KNOWN_ISSUES.rdoc:: Known issues and bugs in BioRuby.
44
+ doc/Changes-1.3.rdoc:: News and incompatible changes from 1.2.1 to 1.3.0.
45
+ doc/Changes-0.7.rd:: News and incompatible changes from 0.6.4 to 1.2.1.
46
+
47
+ ==== Tutorials and other useful information
48
+
49
+ doc/Tutorial.rd:: BioRuby Tutorial.
50
+ doc/Tutorial.rd.html:: HTML version of Tutorial.rd.
51
+ doc/KEGG_API.rd:: Documents about KEGG API, including usage of Bio::KEGG::API.
52
+
53
+ ==== BioRuby development
54
+
55
+ ChangeLog:: History of changes.
56
+ README_DEV.rdoc:: Describes ways to contribute to the BioRuby project, including coding styles and documentation guidelines.
57
+
58
+ ==== Documents written in Japanese
59
+
60
+ doc/Tutorial.rd.ja:: BioRuby Tutorial written in Japanese.
61
+ doc/Tutorial.rd.ja.html:: HTML version of Tutorial.rd.ja.
62
+ doc/KEGG_API.rd.ja:: Japanese translation of KEGG_API.rd.
63
+
64
+
65
+ === WWW
66
+
38
67
  BioRuby's official website is at http://bioruby.org/.
39
68
  You will find links to related resources including downloads,
40
69
  mailing lists, Wiki documentation etc. in the top page.
data/Rakefile CHANGED
@@ -11,17 +11,19 @@ require 'rake/testtask'
11
11
  require 'rake/packagetask'
12
12
  require 'rake/gempackagetask'
13
13
  require 'rake/rdoctask'
14
- load "./lib/bio.rb"
14
+
15
+ load "./lib/bio/version.rb"
16
+ BIO_VERSION_RB_LOADED = true
15
17
 
16
18
  # Version string for tar.gz, tar.bz2, or zip archive.
17
19
  # If nil, use the value in lib/bio.rb
18
20
  # Note that gem version is always determined from bioruby.gemspec.erb.
19
21
  version = ENV['BIORUBY_VERSION'] || Bio::BIORUBY_VERSION.join(".")
20
22
  version = nil if version.to_s.empty?
21
- extraversion = ENV['BIORUBY_EXTRAVERSION']
23
+ extraversion = ENV['BIORUBY_EXTRA_VERSION'] || Bio::BIORUBY_EXTRA_VERSION
22
24
  extraversion = nil if extraversion.to_s.empty?
23
- version += extraversion.to_s if version and extraversion
24
25
  BIORUBY_VERSION = version
26
+ BIORUBY_EXTRA_VERSION = extraversion
25
27
 
26
28
  task :default => "test"
27
29
 
@@ -63,7 +65,8 @@ task :regemspec do
63
65
  end
64
66
 
65
67
  desc "Update #{GEM_SPEC_FILE}"
66
- file GEM_SPEC_FILE => [ GEM_SPEC_TEMPLATE_FILE, 'Rakefile' ] do |t|
68
+ file GEM_SPEC_FILE => [ GEM_SPEC_TEMPLATE_FILE, 'Rakefile',
69
+ 'lib/bio/version.rb' ] do |t|
67
70
  puts "creates #{GEM_SPEC_FILE}"
68
71
  File.open(t.name, 'w') do |w|
69
72
  w.print gem_spec_string
@@ -79,7 +82,7 @@ Rake::PackageTask.new("bioruby") do |pkg|
79
82
  pkg.need_tar_gz = true
80
83
  pkg.package_files.import(spec.files)
81
84
  pkg.package_files.include(*tar_additional_files)
82
- pkg.version = BIORUBY_VERSION || spec.version
85
+ pkg.version = (BIORUBY_VERSION || spec.version) + BIORUBY_EXTRA_VERSION.to_s
83
86
  end
84
87
 
85
88
  Rake::GemPackageTask.new(spec) do |pkg|
@@ -102,3 +105,39 @@ Rake::RDocTask.new do |r|
102
105
  r.main = main
103
106
  r.options = opts
104
107
  end
108
+
109
+ # Tutorial files
110
+ TUTORIAL_RD = 'doc/Tutorial.rd'
111
+ TUTORIAL_RD_JA = 'doc/Tutorial.rd.ja'
112
+
113
+ TUTORIAL_RD_HTML = TUTORIAL_RD + '.html'
114
+ TUTORIAL_RD_JA_HTML = TUTORIAL_RD_JA + '.html'
115
+
116
+ HTMLFILES_TUTORIAL = [ TUTORIAL_RD_HTML, TUTORIAL_RD_JA_HTML ]
117
+
118
+ # Formatting RD to html.
119
+ def rd2html(src, dst)
120
+ sh "rd2 -r rd/rd2html-lib.rb --with-css=bioruby.css #{src} > #{dst}"
121
+ end
122
+
123
+ # Tutorial.rd to Tutorial.rd.html
124
+ file TUTORIAL_RD_HTML => TUTORIAL_RD do |t|
125
+ rd2html(t.prerequisites[0], t.name)
126
+ end
127
+
128
+ # Tutorial.rd.ja to Tutorial.html.ja
129
+ file TUTORIAL_RD_JA_HTML => TUTORIAL_RD_JA do |t|
130
+ rd2html(t.prerequisites[0], t.name)
131
+ end
132
+
133
+ desc "Update doc/Tutorial*.html"
134
+ task :tutorial2html => HTMLFILES_TUTORIAL
135
+
136
+ desc "Force update doc/Tutorial*.html"
137
+ task :retutorial2html do
138
+ # safe_unlink HTMLFILES_TUTORIAL
139
+ HTMLFILES_TUTORIAL.each do |x|
140
+ Rake::Task[x].execute
141
+ end
142
+ end
143
+
data/bin/br_pmfetch.rb CHANGED
@@ -6,15 +6,16 @@
6
6
  # Toshiaki Katayama <k@bioruby.org>
7
7
  # License:: The Ruby License
8
8
  #
9
- # $Id: br_pmfetch.rb,v 1.7 2007/04/05 23:35:39 trevor Exp $
9
+ # $Id:$
10
10
  #
11
11
 
12
- PROG_VER = '$Id: br_pmfetch.rb,v 1.7 2007/04/05 23:35:39 trevor Exp $'
12
+ require 'bio'
13
+
14
+ PROG_VER = "Powered by BioRuby #{Bio::BIORUBY_VERSION_ID}"
13
15
  PROG_NAME = File.basename($0)
14
16
 
15
17
 
16
18
  require 'getoptlong'
17
- require 'bio'
18
19
 
19
20
 
20
21
  ### formatting
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 = "1.2.9.9501"
6
+ s.version = "1.3.0"
7
7
 
8
8
  s.author = "BioRuby project"
9
9
  s.email = "staff@bioruby.org"
@@ -31,7 +31,10 @@ Gem::Specification.new do |s|
31
31
  "doc/KEGG_API.rd",
32
32
  "doc/KEGG_API.rd.ja",
33
33
  "doc/Tutorial.rd",
34
+ "doc/Tutorial.rd.html",
34
35
  "doc/Tutorial.rd.ja",
36
+ "doc/Tutorial.rd.ja.html",
37
+ "doc/bioruby.css",
35
38
  "etc/bioinformatics/seqdatabase.ini",
36
39
  "extconf.rb",
37
40
  "lib/bio.rb",
@@ -202,6 +205,7 @@ Gem::Specification.new do |s|
202
205
  "lib/bio/io/registry.rb",
203
206
  "lib/bio/io/soapwsdl.rb",
204
207
  "lib/bio/io/sql.rb",
208
+ "lib/bio/io/togows.rb",
205
209
  "lib/bio/location.rb",
206
210
  "lib/bio/map.rb",
207
211
  "lib/bio/pathway.rb",
@@ -235,6 +239,7 @@ Gem::Specification.new do |s|
235
239
  "lib/bio/shell/plugin/psort.rb",
236
240
  "lib/bio/shell/plugin/seq.rb",
237
241
  "lib/bio/shell/plugin/soap.rb",
242
+ "lib/bio/shell/plugin/togows.rb",
238
243
  "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb",
239
244
  "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml",
240
245
  "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml",
@@ -290,6 +295,7 @@ Gem::Specification.new do |s|
290
295
  "lib/bio/util/restriction_enzyme/single_strand_complement.rb",
291
296
  "lib/bio/util/restriction_enzyme/string_formatting.rb",
292
297
  "lib/bio/util/sirna.rb",
298
+ "lib/bio/version.rb",
293
299
  "rdoc.zsh",
294
300
  "sample/any2fasta.rb",
295
301
  "sample/biofetch.rb",
@@ -354,6 +360,7 @@ Gem::Specification.new do |s|
354
360
  "test/functional/bio/appl/test_pts1.rb",
355
361
  "test/functional/bio/io/test_ensembl.rb",
356
362
  "test/functional/bio/io/test_soapwsdl.rb",
363
+ "test/functional/bio/io/test_togows.rb",
357
364
  "test/functional/bio/sequence/test_output_embl.rb",
358
365
  "test/functional/bio/test_command.rb",
359
366
  "test/runner.rb",
@@ -403,6 +410,7 @@ Gem::Specification.new do |s|
403
410
  "test/unit/bio/io/test_fastacmd.rb",
404
411
  "test/unit/bio/io/test_flatfile.rb",
405
412
  "test/unit/bio/io/test_soapwsdl.rb",
413
+ "test/unit/bio/io/test_togows.rb",
406
414
  "test/unit/bio/sequence/test_aa.rb",
407
415
  "test/unit/bio/sequence/test_common.rb",
408
416
  "test/unit/bio/sequence/test_compat.rb",
@@ -443,11 +451,11 @@ Gem::Specification.new do |s|
443
451
 
444
452
  s.has_rdoc = true
445
453
  s.extra_rdoc_files = [
454
+ "ChangeLog",
446
455
  "KNOWN_ISSUES.rdoc",
447
456
  "README.rdoc",
448
457
  "README_DEV.rdoc",
449
- "doc/Changes-1.3.rdoc",
450
- "ChangeLog"
458
+ "doc/Changes-1.3.rdoc"
451
459
  ]
452
460
  s.rdoc_options << '--main' << 'README.rdoc'
453
461
  s.rdoc_options << '--title' << 'BioRuby API documentation'
data/bioruby.gemspec.erb CHANGED
@@ -1,6 +1,41 @@
1
1
  Gem::Specification.new do |s|
2
2
  s.name = 'bio'
3
- s.version = "1.2.9.9501"
3
+ s.version = "<% ###### Below is executed in ERB environment ######
4
+ # Version can be specified by the environment variable
5
+ env_ver = ENV['BIORUBY_GEM_VERSION']
6
+ env_ver = nil if env_ver.to_s.strip.empty?
7
+
8
+ # By default, determined from lib/bio/version.rb
9
+ load "./lib/bio/version.rb" unless defined?(BIO_VERSION_RB_LOADED)
10
+ case Bio::BIORUBY_EXTRA_VERSION
11
+ when nil
12
+ suffix = nil
13
+ when /\A\.(\d+)\z/
14
+ suffix = $1
15
+ when /\-alpha(\d+)/
16
+ decrement = true
17
+ suffix = 9000 + $1.to_i
18
+ when /\-pre(\d+)/
19
+ decrement = true
20
+ suffix = 9500 + $1.to_i
21
+ when /\-rc(\d+)/
22
+ decrement = true
23
+ suffix = 9900 + $1.to_i
24
+ else
25
+ suffix = "0000"
26
+ end
27
+ ver = Bio::BIORUBY_VERSION.reverse.collect do |i|
28
+ if decrement then
29
+ i -= 1
30
+ i < 0 ? (i += 10) : decrement = false
31
+ end
32
+ i
33
+ end.reverse
34
+ ver.push suffix if suffix
35
+ %><%=
36
+ (env_ver || ver.join('.'))
37
+ ###### Above is executed in ERB environment ######
38
+ %>"
4
39
 
5
40
  s.author = "BioRuby project"
6
41
  s.email = "staff@bioruby.org"
@@ -16,7 +51,7 @@ Gem::Specification.new do |s|
16
51
  files = (`git ls-files` rescue nil).to_s.split(/\r?\n/)
17
52
  files.delete_if { |x| x.empty? }
18
53
  # When git-ls-files isn't available, creates a list from current files.
19
- unless $?.success? or files.size <= 0 then
54
+ if !($?.success?) or files.size <= 0 then
20
55
  files =
21
56
  [ "README.rdoc", "README_DEV.rdoc",
22
57
  "ChangeLog", "KNOWN_ISSUES.rdoc",
@@ -33,7 +68,7 @@ Gem::Specification.new do |s|
33
68
  end
34
69
  end
35
70
  %><%=
36
- files.collect { |x| x.dump }.join(",\n ")
71
+ files.sort.collect { |x| x.dump }.join(",\n ")
37
72
  ###### Above is executed in ERB environment ######
38
73
  %>
39
74
  ]
@@ -49,7 +84,7 @@ Gem::Specification.new do |s|
49
84
  'doc/Changes-1.3.rdoc' ]
50
85
  end
51
86
  rdoc_files.push "ChangeLog" unless rdoc_files.include?("ChangeLog")
52
- rdoc_files.collect { |x| x.dump }.join(",\n ")
87
+ rdoc_files.sort.collect { |x| x.dump }.join(",\n ")
53
88
  ###### Above is executed in ERB environment ######
54
89
  %>
55
90
  ]
@@ -74,7 +109,7 @@ Gem::Specification.new do |s|
74
109
  if exec_files.empty? then
75
110
  exec_files = [ "bioruby", "br_biofetch.rb", "br_biogetseq.rb", "br_bioflat.rb", "br_pmfetch.rb" ]
76
111
  end
77
- exec_files.collect { |x| x.dump }.join(",\n ")
112
+ exec_files.sort.collect { |x| x.dump }.join(",\n ")
78
113
  ###### Above is executed in ERB environment ######
79
114
  %>
80
115
  ]
data/doc/Changes-0.7.rd CHANGED
@@ -338,6 +338,13 @@ In 1.1.0:
338
338
  instead of a string or nil: score, percent_identity, percent_positive,
339
339
  percent_gaps.
340
340
 
341
+ --- BioRuby Shell
342
+
343
+ In 1.1.0:
344
+
345
+ * Shell commands seq, ent, obj are renamed to getseq, getent, getobj,
346
+ respectively.
347
+
341
348
  === Deleted files
342
349
 
343
350
  : lib/bio/db/genbank.rb
data/doc/Changes-1.3.rdoc CHANGED
@@ -58,6 +58,11 @@ particular use cases.
58
58
 
59
59
  New method Bio::Locations#to_s is added to support output of features.
60
60
 
61
+ === Bio::TogoWS::REST
62
+
63
+ TogoWS REST client class is newly added. Information about TogoWS REST service
64
+ can be found on http://togows.dbcls.jp/site/en/rest.html.
65
+
61
66
  == Deprecated classes
62
67
 
63
68
  === Bio::Features
@@ -74,6 +79,18 @@ will soon be removed in the future.
74
79
 
75
80
  == Incompatible changes
76
81
 
82
+ === Bio::BIORUBY_VERSION
83
+
84
+ Definition of the constant Bio::BIORUBY_VERSION is moved from lib/bio.rb to
85
+ lib/bio/version.rb. Normally, the autoload mechanism of Ruby correctly loads
86
+ the version.rb, but special scripts directly using bio.rb may be needed to
87
+ be changed.
88
+
89
+ Bio::BIORUBY_VERSION is changed to be frozen.
90
+
91
+ New constants Bio::BIORUBY_EXTRA_VERSION and Bio::BIORUBY_VERSION_ID are
92
+ added. See their RDoc for details.
93
+
77
94
  === Bio::Sequence
78
95
 
79
96
  Bio::Sequence#date is removed. Alternatively, date_created or date_modified