bel 0.3.0.beta2 → 0.3.0.beta3
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- checksums.yaml +7 -0
- data/bel.gemspec +3 -5
- data/lib/bel.rb +1 -0
- data/lib/bel/version.rb +3 -0
- data/lib/libbel.rb +48 -9
- metadata +73 -94
checksums.yaml
ADDED
@@ -0,0 +1,7 @@
|
|
1
|
+
---
|
2
|
+
SHA1:
|
3
|
+
metadata.gz: 1e2c14f81c221242a5a14c473220410c36a4af27
|
4
|
+
data.tar.gz: 83b4cd6dea6ccadc861d1e708106a3b4fde574f6
|
5
|
+
SHA512:
|
6
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+
metadata.gz: 2f8bb3efbd5c10f13f80e786aa8fc935607c42dac905923c13e085f456ad2b952b30fee1e436a4add5aa4787ab52863427848867cffb72659ec998aa81816f89
|
7
|
+
data.tar.gz: dac427227db2d9fc47b1fb13c9dbc055eca3ac7a8fc28c1929c1d0a8cc56ca5ecfe44e9fe614f5351089710867ba4c0260badc3c821e9926ba6f88087088e322
|
data/bel.gemspec
CHANGED
@@ -1,6 +1,6 @@
|
|
1
1
|
Gem::Specification.new do |spec|
|
2
2
|
spec.name = 'bel'
|
3
|
-
spec.version = '0.3.0.
|
3
|
+
spec.version = '0.3.0.beta3'
|
4
4
|
spec.summary = '''
|
5
5
|
Process BEL with ruby.
|
6
6
|
'''.gsub(%r{^\s+}, ' ').gsub(%r{\n}, '')
|
@@ -48,9 +48,7 @@ Gem::Specification.new do |spec|
|
|
48
48
|
spec.required_ruby_version = '>= 1.9.2'
|
49
49
|
|
50
50
|
# runtime
|
51
|
-
|
52
|
-
# - before upgrading check each platform gem is present in the new version
|
53
|
-
spec.add_dependency 'ffi', '1.9.6'
|
51
|
+
spec.add_dependency 'ffi', '1.9.8'
|
54
52
|
|
55
53
|
# test rdf functionality
|
56
54
|
spec.add_development_dependency 'uuid', '~> 2.3'
|
@@ -61,9 +59,9 @@ Gem::Specification.new do |spec|
|
|
61
59
|
spec.add_development_dependency 'bundler', '~> 1.7'
|
62
60
|
spec.add_development_dependency 'rake', '~> 10.4'
|
63
61
|
spec.add_development_dependency 'rake-compiler', '~> 0.9'
|
62
|
+
spec.add_development_dependency 'rdoc', '~> 4.2'
|
64
63
|
spec.add_development_dependency 'rspec', '~> 3.2'
|
65
64
|
spec.add_development_dependency 'yard', '~> 0.8'
|
66
|
-
spec.add_development_dependency 'rdoc', '~> 4.2'
|
67
65
|
end
|
68
66
|
# vim: ts=2 sw=2:
|
69
67
|
# encoding: utf-8
|
data/lib/bel.rb
CHANGED
data/lib/bel/version.rb
ADDED
data/lib/libbel.rb
CHANGED
@@ -6,6 +6,34 @@ module LibBEL
|
|
6
6
|
defined?(RUBY_ENGINE) && ("rbx" == RUBY_ENGINE)
|
7
7
|
end
|
8
8
|
|
9
|
+
# @api_private
|
10
|
+
# Determines the correct extension path for your ruby version
|
11
|
+
def extension_path(ruby_version = RUBY_VERSION)
|
12
|
+
version =
|
13
|
+
case ruby_version
|
14
|
+
when %r{1\.9}
|
15
|
+
'1.9'
|
16
|
+
when %r{2\.0}
|
17
|
+
'2.0'
|
18
|
+
when %r{2\.1}
|
19
|
+
'2.1'
|
20
|
+
when %r{2\.2}
|
21
|
+
'2.1' # 2.2 is compatible with 2.1, but cannot cross compile 2.2
|
22
|
+
else
|
23
|
+
fail RuntimeError.new("Do not support Ruby #{RUBY_VERSION}.")
|
24
|
+
end
|
25
|
+
extension_path = File.join(
|
26
|
+
File.expand_path(File.dirname(__FILE__)),
|
27
|
+
version
|
28
|
+
)
|
29
|
+
if !File.readable?(extension_path)
|
30
|
+
msg = "Extension path cannot be read: #{extension_path}"
|
31
|
+
fail IOError.new(msg)
|
32
|
+
end
|
33
|
+
|
34
|
+
extension_path
|
35
|
+
end
|
36
|
+
|
9
37
|
# @api_private
|
10
38
|
# Determine FFI constant for this ruby engine.
|
11
39
|
def find_ffi
|
@@ -29,7 +57,7 @@ module LibBEL
|
|
29
57
|
end
|
30
58
|
|
31
59
|
# @api_private
|
32
|
-
# Loads the
|
60
|
+
# Loads the libbel shared library.
|
33
61
|
def load_libBEL
|
34
62
|
ffi_module = find_ffi
|
35
63
|
extend ffi_module::Library
|
@@ -38,17 +66,28 @@ module LibBEL
|
|
38
66
|
# libbel.bundle: Mac OSX
|
39
67
|
messages = []
|
40
68
|
library_loaded = ['libbel.so', 'libbel.bundle'].map { |library_file|
|
41
|
-
|
42
|
-
|
43
|
-
|
44
|
-
|
45
|
-
|
69
|
+
[
|
70
|
+
library_file,
|
71
|
+
File.join(
|
72
|
+
File.expand_path(File.dirname(__FILE__)),
|
73
|
+
library_file
|
74
|
+
)
|
75
|
+
]
|
76
|
+
}.any? do |library_file, library_path|
|
77
|
+
# Try loading top-level shared library.
|
46
78
|
begin
|
47
79
|
ffi_lib library_path
|
48
80
|
true
|
49
|
-
rescue LoadError =>
|
50
|
-
|
51
|
-
|
81
|
+
rescue LoadError => exception1
|
82
|
+
# Try loading version-specific shared library.
|
83
|
+
begin
|
84
|
+
ffi_lib File.join(extension_path, library_file)
|
85
|
+
true
|
86
|
+
rescue LoadError => exception2
|
87
|
+
messages << exception1.to_s
|
88
|
+
messages << exception2.to_s
|
89
|
+
false
|
90
|
+
end
|
52
91
|
end
|
53
92
|
end
|
54
93
|
|
metadata
CHANGED
@@ -1,8 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: bel
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.3.0.
|
5
|
-
prerelease: 6
|
4
|
+
version: 0.3.0.beta3
|
6
5
|
platform: ruby
|
7
6
|
authors:
|
8
7
|
- Anthony Bargnesi
|
@@ -12,170 +11,150 @@ authors:
|
|
12
11
|
autorequire:
|
13
12
|
bindir: bin
|
14
13
|
cert_chain: []
|
15
|
-
date: 2015-03-
|
14
|
+
date: 2015-03-16 00:00:00.000000000 Z
|
16
15
|
dependencies:
|
17
16
|
- !ruby/object:Gem::Dependency
|
18
17
|
name: ffi
|
19
18
|
requirement: !ruby/object:Gem::Requirement
|
20
|
-
none: false
|
21
19
|
requirements:
|
22
20
|
- - '='
|
23
21
|
- !ruby/object:Gem::Version
|
24
|
-
version: 1.9.
|
22
|
+
version: 1.9.8
|
25
23
|
type: :runtime
|
26
24
|
prerelease: false
|
27
25
|
version_requirements: !ruby/object:Gem::Requirement
|
28
|
-
none: false
|
29
26
|
requirements:
|
30
27
|
- - '='
|
31
28
|
- !ruby/object:Gem::Version
|
32
|
-
version: 1.9.
|
29
|
+
version: 1.9.8
|
33
30
|
- !ruby/object:Gem::Dependency
|
34
31
|
name: uuid
|
35
32
|
requirement: !ruby/object:Gem::Requirement
|
36
|
-
none: false
|
37
33
|
requirements:
|
38
|
-
- - ~>
|
34
|
+
- - "~>"
|
39
35
|
- !ruby/object:Gem::Version
|
40
36
|
version: '2.3'
|
41
37
|
type: :development
|
42
38
|
prerelease: false
|
43
39
|
version_requirements: !ruby/object:Gem::Requirement
|
44
|
-
none: false
|
45
40
|
requirements:
|
46
|
-
- - ~>
|
41
|
+
- - "~>"
|
47
42
|
- !ruby/object:Gem::Version
|
48
43
|
version: '2.3'
|
49
44
|
- !ruby/object:Gem::Dependency
|
50
45
|
name: addressable
|
51
46
|
requirement: !ruby/object:Gem::Requirement
|
52
|
-
none: false
|
53
47
|
requirements:
|
54
|
-
- - ~>
|
48
|
+
- - "~>"
|
55
49
|
- !ruby/object:Gem::Version
|
56
50
|
version: '2.3'
|
57
51
|
type: :development
|
58
52
|
prerelease: false
|
59
53
|
version_requirements: !ruby/object:Gem::Requirement
|
60
|
-
none: false
|
61
54
|
requirements:
|
62
|
-
- - ~>
|
55
|
+
- - "~>"
|
63
56
|
- !ruby/object:Gem::Version
|
64
57
|
version: '2.3'
|
65
58
|
- !ruby/object:Gem::Dependency
|
66
59
|
name: rdf
|
67
60
|
requirement: !ruby/object:Gem::Requirement
|
68
|
-
none: false
|
69
61
|
requirements:
|
70
|
-
- - ~>
|
62
|
+
- - "~>"
|
71
63
|
- !ruby/object:Gem::Version
|
72
64
|
version: '1.1'
|
73
65
|
type: :development
|
74
66
|
prerelease: false
|
75
67
|
version_requirements: !ruby/object:Gem::Requirement
|
76
|
-
none: false
|
77
68
|
requirements:
|
78
|
-
- - ~>
|
69
|
+
- - "~>"
|
79
70
|
- !ruby/object:Gem::Version
|
80
71
|
version: '1.1'
|
81
72
|
- !ruby/object:Gem::Dependency
|
82
73
|
name: bundler
|
83
74
|
requirement: !ruby/object:Gem::Requirement
|
84
|
-
none: false
|
85
75
|
requirements:
|
86
|
-
- - ~>
|
76
|
+
- - "~>"
|
87
77
|
- !ruby/object:Gem::Version
|
88
78
|
version: '1.7'
|
89
79
|
type: :development
|
90
80
|
prerelease: false
|
91
81
|
version_requirements: !ruby/object:Gem::Requirement
|
92
|
-
none: false
|
93
82
|
requirements:
|
94
|
-
- - ~>
|
83
|
+
- - "~>"
|
95
84
|
- !ruby/object:Gem::Version
|
96
85
|
version: '1.7'
|
97
86
|
- !ruby/object:Gem::Dependency
|
98
87
|
name: rake
|
99
88
|
requirement: !ruby/object:Gem::Requirement
|
100
|
-
none: false
|
101
89
|
requirements:
|
102
|
-
- - ~>
|
90
|
+
- - "~>"
|
103
91
|
- !ruby/object:Gem::Version
|
104
92
|
version: '10.4'
|
105
93
|
type: :development
|
106
94
|
prerelease: false
|
107
95
|
version_requirements: !ruby/object:Gem::Requirement
|
108
|
-
none: false
|
109
96
|
requirements:
|
110
|
-
- - ~>
|
97
|
+
- - "~>"
|
111
98
|
- !ruby/object:Gem::Version
|
112
99
|
version: '10.4'
|
113
100
|
- !ruby/object:Gem::Dependency
|
114
101
|
name: rake-compiler
|
115
102
|
requirement: !ruby/object:Gem::Requirement
|
116
|
-
none: false
|
117
103
|
requirements:
|
118
|
-
- - ~>
|
104
|
+
- - "~>"
|
119
105
|
- !ruby/object:Gem::Version
|
120
106
|
version: '0.9'
|
121
107
|
type: :development
|
122
108
|
prerelease: false
|
123
109
|
version_requirements: !ruby/object:Gem::Requirement
|
124
|
-
none: false
|
125
110
|
requirements:
|
126
|
-
- - ~>
|
111
|
+
- - "~>"
|
127
112
|
- !ruby/object:Gem::Version
|
128
113
|
version: '0.9'
|
129
114
|
- !ruby/object:Gem::Dependency
|
130
|
-
name:
|
115
|
+
name: rdoc
|
131
116
|
requirement: !ruby/object:Gem::Requirement
|
132
|
-
none: false
|
133
117
|
requirements:
|
134
|
-
- - ~>
|
118
|
+
- - "~>"
|
135
119
|
- !ruby/object:Gem::Version
|
136
|
-
version: '
|
120
|
+
version: '4.2'
|
137
121
|
type: :development
|
138
122
|
prerelease: false
|
139
123
|
version_requirements: !ruby/object:Gem::Requirement
|
140
|
-
none: false
|
141
124
|
requirements:
|
142
|
-
- - ~>
|
125
|
+
- - "~>"
|
143
126
|
- !ruby/object:Gem::Version
|
144
|
-
version: '
|
127
|
+
version: '4.2'
|
145
128
|
- !ruby/object:Gem::Dependency
|
146
|
-
name:
|
129
|
+
name: rspec
|
147
130
|
requirement: !ruby/object:Gem::Requirement
|
148
|
-
none: false
|
149
131
|
requirements:
|
150
|
-
- - ~>
|
132
|
+
- - "~>"
|
151
133
|
- !ruby/object:Gem::Version
|
152
|
-
version: '
|
134
|
+
version: '3.2'
|
153
135
|
type: :development
|
154
136
|
prerelease: false
|
155
137
|
version_requirements: !ruby/object:Gem::Requirement
|
156
|
-
none: false
|
157
138
|
requirements:
|
158
|
-
- - ~>
|
139
|
+
- - "~>"
|
159
140
|
- !ruby/object:Gem::Version
|
160
|
-
version: '
|
141
|
+
version: '3.2'
|
161
142
|
- !ruby/object:Gem::Dependency
|
162
|
-
name:
|
143
|
+
name: yard
|
163
144
|
requirement: !ruby/object:Gem::Requirement
|
164
|
-
none: false
|
165
145
|
requirements:
|
166
|
-
- - ~>
|
146
|
+
- - "~>"
|
167
147
|
- !ruby/object:Gem::Version
|
168
|
-
version: '
|
148
|
+
version: '0.8'
|
169
149
|
type: :development
|
170
150
|
prerelease: false
|
171
151
|
version_requirements: !ruby/object:Gem::Requirement
|
172
|
-
none: false
|
173
152
|
requirements:
|
174
|
-
- - ~>
|
153
|
+
- - "~>"
|
175
154
|
- !ruby/object:Gem::Version
|
176
|
-
version: '
|
177
|
-
description:
|
178
|
-
Expression Language) with a natural DSL.
|
155
|
+
version: '0.8'
|
156
|
+
description: " The BEL gem allows the reading, writing, and processing of BEL (Biological
|
157
|
+
Expression Language) with a natural DSL. "
|
179
158
|
email:
|
180
159
|
- abargnesi@selventa.com
|
181
160
|
- ncatlett@selventa.com
|
@@ -193,54 +172,56 @@ extensions:
|
|
193
172
|
- ext/mri/extconf.rb
|
194
173
|
extra_rdoc_files: []
|
195
174
|
files:
|
196
|
-
- lib/util.rb
|
197
|
-
- lib/libbel.rb
|
198
|
-
- lib/bel/quoting.rb
|
199
|
-
- lib/bel/rdf.rb
|
200
|
-
- lib/bel/completion.rb
|
201
|
-
- lib/bel/completion_rule.rb
|
202
|
-
- lib/bel/script.rb
|
203
|
-
- lib/bel/language.rb
|
204
|
-
- lib/bel/namespace.rb
|
205
|
-
- lib/features.rb
|
206
|
-
- lib/bel.rb
|
207
|
-
- ext/mri/bel-token.c
|
208
|
-
- ext/mri/bel-ast.c
|
209
|
-
- ext/mri/bel-tokenize-term.c
|
210
|
-
- ext/mri/libbel.c
|
211
|
-
- ext/mri/bel-parser.c
|
212
|
-
- ext/mri/bel-parse-statement.c
|
213
|
-
- ext/mri/bel-parse-term.c
|
214
|
-
- ext/mri/bel-node-stack.c
|
215
|
-
- ext/mri/bel-token.h
|
216
|
-
- ext/mri/bel-node-stack.h
|
217
|
-
- ext/mri/bel-parser.h
|
218
|
-
- ext/mri/bel-ast.h
|
219
|
-
- ext/mri/libbel.def
|
220
|
-
- bel.gemspec
|
221
|
-
- LICENSE
|
222
175
|
- INSTALL.md
|
223
176
|
- INSTALL_RUBY.md
|
177
|
+
- LICENSE
|
224
178
|
- README.md
|
225
|
-
-
|
226
|
-
- bin/bel_rdfschema
|
227
|
-
- bin/bel_upgrade_term
|
179
|
+
- bel.gemspec
|
228
180
|
- bin/bel2rdf
|
229
|
-
- bin/bel_parse
|
230
181
|
- bin/bel_compare
|
182
|
+
- bin/bel_parse
|
183
|
+
- bin/bel_rdfschema
|
184
|
+
- bin/bel_summarize
|
231
185
|
- bin/bel_upgrade
|
186
|
+
- bin/bel_upgrade_term
|
187
|
+
- ext/mri/bel-ast.c
|
188
|
+
- ext/mri/bel-ast.h
|
189
|
+
- ext/mri/bel-node-stack.c
|
190
|
+
- ext/mri/bel-node-stack.h
|
191
|
+
- ext/mri/bel-parse-statement.c
|
192
|
+
- ext/mri/bel-parse-term.c
|
193
|
+
- ext/mri/bel-parser.c
|
194
|
+
- ext/mri/bel-parser.h
|
195
|
+
- ext/mri/bel-token.c
|
196
|
+
- ext/mri/bel-token.h
|
197
|
+
- ext/mri/bel-tokenize-term.c
|
232
198
|
- ext/mri/extconf.rb
|
199
|
+
- ext/mri/libbel.c
|
200
|
+
- ext/mri/libbel.def
|
201
|
+
- lib/bel.rb
|
202
|
+
- lib/bel/completion.rb
|
203
|
+
- lib/bel/completion_rule.rb
|
204
|
+
- lib/bel/language.rb
|
205
|
+
- lib/bel/namespace.rb
|
206
|
+
- lib/bel/quoting.rb
|
207
|
+
- lib/bel/rdf.rb
|
208
|
+
- lib/bel/script.rb
|
209
|
+
- lib/bel/version.rb
|
210
|
+
- lib/features.rb
|
211
|
+
- lib/libbel.rb
|
212
|
+
- lib/util.rb
|
233
213
|
homepage: https://github.com/OpenBEL/bel.rb
|
234
214
|
licenses:
|
235
215
|
- Apache-2.0
|
216
|
+
metadata: {}
|
236
217
|
post_install_message:
|
237
218
|
rdoc_options:
|
238
|
-
- --title
|
219
|
+
- "--title"
|
239
220
|
- BEL Ruby Documentation
|
240
|
-
- --main
|
221
|
+
- "--main"
|
241
222
|
- README.md
|
242
|
-
- --line-numbers
|
243
|
-
- --exclude
|
223
|
+
- "--line-numbers"
|
224
|
+
- "--exclude"
|
244
225
|
- lib/bel/script.rb
|
245
226
|
- README.md
|
246
227
|
- INSTALL.md
|
@@ -249,22 +230,20 @@ rdoc_options:
|
|
249
230
|
require_paths:
|
250
231
|
- lib
|
251
232
|
required_ruby_version: !ruby/object:Gem::Requirement
|
252
|
-
none: false
|
253
233
|
requirements:
|
254
|
-
- -
|
234
|
+
- - ">="
|
255
235
|
- !ruby/object:Gem::Version
|
256
236
|
version: 1.9.2
|
257
237
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
258
|
-
none: false
|
259
238
|
requirements:
|
260
|
-
- -
|
239
|
+
- - ">"
|
261
240
|
- !ruby/object:Gem::Version
|
262
241
|
version: 1.3.1
|
263
242
|
requirements: []
|
264
243
|
rubyforge_project:
|
265
|
-
rubygems_version:
|
244
|
+
rubygems_version: 2.2.2
|
266
245
|
signing_key:
|
267
|
-
specification_version:
|
246
|
+
specification_version: 4
|
268
247
|
summary: Process BEL with ruby.
|
269
248
|
test_files: []
|
270
249
|
has_rdoc:
|