semin-ulla 0.9.7 → 0.9.8
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- data/History.txt +4 -0
- data/Rakefile +14 -21
- data/lib/ulla/cli.rb +4 -4
- data/lib/ulla.rb +1 -1
- data/ulla.gemspec +7 -10
- data/website/index.html +1 -1
- metadata +5 -16
data/History.txt
CHANGED
data/Rakefile
CHANGED
@@ -1,32 +1,25 @@
|
|
1
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-
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2
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-
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1
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+
require 'rubygems'
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2
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+
gem 'hoe', '>= 2.1.0'
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3
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+
require 'hoe'
|
4
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+
require 'fileutils'
|
5
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+
|
6
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+
Hoe.plugin :newgem
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7
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+
# Hoe.plugin :website
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8
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+
# Hoe.plugin :cucumberfeatures
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3
9
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|
4
10
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# Generate all the Rake tasks
|
5
11
|
# Run 'rake -T' to see list of generated tasks (from gem root directory)
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6
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-
$hoe = Hoe.
|
7
|
-
|
8
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-
|
9
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-
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10
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-
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11
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-
p.extra_deps = [
|
12
|
+
$hoe = Hoe.spec 'ulla' do
|
13
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+
self.developer 'Semin Lee', 'seminlee@gmail.com'
|
14
|
+
self.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
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15
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+
self.rubyforge_name = self.name # TODO this is default value
|
16
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+
self.extra_deps = [
|
12
17
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['narray', '>= 0.5.9.5'],
|
13
18
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['bio', '>= 1.2.1'],
|
14
19
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['facets', '>= 2.4.5'],
|
15
20
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['rmagick', '>= 2.9.1'],
|
16
21
|
]
|
17
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-
|
18
|
-
p.extra_dev_deps = [
|
19
|
-
['newgem', ">= #{::Newgem::VERSION}"]
|
20
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-
]
|
21
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-
|
22
|
-
p.clean_globs |= %w[**/.DS_Store tmp *.log *.swp]
|
23
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-
path = (p.rubyforge_name == p.name) ? p.rubyforge_name : "\#{p.rubyforge_name}/\#{p.name}"
|
24
|
-
p.remote_rdoc_dir = File.join(path.gsub(/^#{p.rubyforge_name}\/?/,''), 'rdoc')
|
25
|
-
p.rsync_args = '-av --delete --ignore-errors'
|
26
22
|
end
|
27
23
|
|
28
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-
require 'newgem/tasks'
|
24
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+
require 'newgem/tasks'
|
29
25
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Dir['tasks/**/*.rake'].each { |t| load t }
|
30
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-
|
31
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-
# TODO - want other tests/tasks run by default? Add them to the list
|
32
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-
# task :default => [:spec, :features]
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data/lib/ulla/cli.rb
CHANGED
@@ -384,7 +384,7 @@ Options:
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|
384
384
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|
385
385
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# if --cys option 2, then we don't care about 'J' (for both Cystine and Cystine)
|
386
386
|
if $cys == 2
|
387
|
-
$amino_acids = 'ACDEFGHIKLMNPQRSTVWY'.delete('J')
|
387
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+
$amino_acids = 'ACDEFGHIKLMNPQRSTVWY'.delete('J').split('')
|
388
388
|
end
|
389
389
|
|
390
390
|
# create an EnvironmentFeatureArray object for storing all environment
|
@@ -709,11 +709,11 @@ Options:
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|
709
709
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env_label2 = $environment == 1 ? aa2 + '-' + aa1[1..-1] : env_labels[id2][pos]
|
710
710
|
|
711
711
|
if $cst_features.empty?
|
712
|
-
$env_classes[env_label1].increase_residue_count(aa2[0].chr, jnt_cnt)
|
713
|
-
$env_classes[env_label2].increase_residue_count(aa1[0].chr, jnt_cnt)
|
712
|
+
$env_classes[env_label1].increase_residue_count(aa2[0].chr, jnt_cnt) #rescue $logger.error "Something wrong with #{tem_file}-#{id2}-#{pos}-#{aa2}-#{env_label2}"
|
713
|
+
$env_classes[env_label2].increase_residue_count(aa1[0].chr, jnt_cnt) #rescue $logger.error "Something wrong with #{tem_file}-#{id2}-#{pos}-#{aa2}-#{env_label2}"
|
714
714
|
elsif (env_labels[id1][pos].split('').values_at(*$cst_features) == env_labels[id2][pos].split('').values_at(*$cst_features))
|
715
715
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$env_classes[env_label1].increase_residue_count(aa2[0].chr, jnt_cnt)
|
716
|
-
$env_classes[env_label2].increase_residue_count(aa1[
|
716
|
+
$env_classes[env_label2].increase_residue_count(aa1[0].chr, jnt_cnt)
|
717
717
|
else
|
718
718
|
$logger.debug "Skipped #{id1}-#{pos}-#{aa1[0].chr} and #{id2}-#{pos}-#{aa2[0].chr} having different symbols for constrained environment features each other."
|
719
719
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next
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data/lib/ulla.rb
CHANGED
data/ulla.gemspec
CHANGED
@@ -2,16 +2,16 @@
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2
2
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3
3
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Gem::Specification.new do |s|
|
4
4
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s.name = %q{ulla}
|
5
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-
s.version = "0.9.
|
5
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+
s.version = "0.9.8"
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6
6
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|
7
7
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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8
8
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s.authors = ["Semin Lee"]
|
9
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-
s.date = %q{2009-
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9
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+
s.date = %q{2009-07-21}
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10
10
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s.default_executable = %q{ulla}
|
11
11
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s.description = %q{'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
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12
12
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s.email = ["seminlee@gmail.com"]
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13
13
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s.executables = ["ulla"]
|
14
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-
s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "
|
14
|
+
s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "website/index.txt"]
|
15
15
|
s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/ulla", "config/website.yml", "config/website.yml.sample", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "lib/string_extensions.rb", "lib/ulla.rb", "lib/ulla/cli.rb", "lib/ulla/environment.rb", "lib/ulla/environment_class_hash.rb", "lib/ulla/environment_feature.rb", "lib/ulla/environment_feature_array.rb", "lib/ulla/heatmap_array.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/test_helper.rb", "test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/test_ulla.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "ulla.gemspec", "website/index.html", "website/index.txt", "website/javascripts/rounded_corners_lite.inc.js", "website/stylesheets/screen.css", "website/template.html.erb"]
|
16
16
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s.homepage = %q{http://www-cryst.bioc.cam.ac.uk/ulla}
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17
17
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s.post_install_message = %q{PostInstall.txt}
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@@ -20,7 +20,7 @@ Gem::Specification.new do |s|
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20
20
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s.rubyforge_project = %q{ulla}
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21
21
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s.rubygems_version = %q{1.3.4}
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22
22
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s.summary = %q{'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
|
23
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-
s.test_files = ["test/
|
23
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+
s.test_files = ["test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "test/test_helper.rb", "test/test_ulla.rb"]
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24
24
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|
25
25
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if s.respond_to? :specification_version then
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26
26
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current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
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@@ -31,22 +31,19 @@ Gem::Specification.new do |s|
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31
31
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s.add_runtime_dependency(%q<bio>, [">= 1.2.1"])
|
32
32
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s.add_runtime_dependency(%q<facets>, [">= 2.4.5"])
|
33
33
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s.add_runtime_dependency(%q<rmagick>, [">= 2.9.1"])
|
34
|
-
s.add_development_dependency(%q<
|
35
|
-
s.add_development_dependency(%q<hoe>, [">= 1.8.0"])
|
34
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+
s.add_development_dependency(%q<hoe>, [">= 2.3.2"])
|
36
35
|
else
|
37
36
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s.add_dependency(%q<narray>, [">= 0.5.9.5"])
|
38
37
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s.add_dependency(%q<bio>, [">= 1.2.1"])
|
39
38
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s.add_dependency(%q<facets>, [">= 2.4.5"])
|
40
39
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s.add_dependency(%q<rmagick>, [">= 2.9.1"])
|
41
|
-
s.add_dependency(%q<
|
42
|
-
s.add_dependency(%q<hoe>, [">= 1.8.0"])
|
40
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+
s.add_dependency(%q<hoe>, [">= 2.3.2"])
|
43
41
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end
|
44
42
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else
|
45
43
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s.add_dependency(%q<narray>, [">= 0.5.9.5"])
|
46
44
|
s.add_dependency(%q<bio>, [">= 1.2.1"])
|
47
45
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s.add_dependency(%q<facets>, [">= 2.4.5"])
|
48
46
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s.add_dependency(%q<rmagick>, [">= 2.9.1"])
|
49
|
-
s.add_dependency(%q<
|
50
|
-
s.add_dependency(%q<hoe>, [">= 1.8.0"])
|
47
|
+
s.add_dependency(%q<hoe>, [">= 2.3.2"])
|
51
48
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end
|
52
49
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end
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data/website/index.html
CHANGED
@@ -4,7 +4,7 @@
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4
4
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<head>
|
5
5
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<meta http-equiv="Refresh" content="5; URL=http://github.com/semin/ulla">
|
6
6
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<title>
|
7
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-
|
7
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+
Ulla: a program for calculating environment-specific substitution tables
|
8
8
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</title>
|
9
9
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</head>
|
10
10
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<body>
|
metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: semin-ulla
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.9.
|
4
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+
version: 0.9.8
|
5
5
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platform: ruby
|
6
6
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authors:
|
7
7
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- Semin Lee
|
@@ -9,7 +9,7 @@ autorequire:
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|
9
9
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bindir: bin
|
10
10
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cert_chain: []
|
11
11
|
|
12
|
-
date: 2009-
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12
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+
date: 2009-07-21 00:00:00 -07:00
|
13
13
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default_executable: ulla
|
14
14
|
dependencies:
|
15
15
|
- !ruby/object:Gem::Dependency
|
@@ -52,16 +52,6 @@ dependencies:
|
|
52
52
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- !ruby/object:Gem::Version
|
53
53
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version: 2.9.1
|
54
54
|
version:
|
55
|
-
- !ruby/object:Gem::Dependency
|
56
|
-
name: newgem
|
57
|
-
type: :development
|
58
|
-
version_requirement:
|
59
|
-
version_requirements: !ruby/object:Gem::Requirement
|
60
|
-
requirements:
|
61
|
-
- - ">="
|
62
|
-
- !ruby/object:Gem::Version
|
63
|
-
version: 1.4.1
|
64
|
-
version:
|
65
55
|
- !ruby/object:Gem::Dependency
|
66
56
|
name: hoe
|
67
57
|
type: :development
|
@@ -70,7 +60,7 @@ dependencies:
|
|
70
60
|
requirements:
|
71
61
|
- - ">="
|
72
62
|
- !ruby/object:Gem::Version
|
73
|
-
version:
|
63
|
+
version: 2.3.2
|
74
64
|
version:
|
75
65
|
description: "'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes."
|
76
66
|
email:
|
@@ -83,7 +73,6 @@ extra_rdoc_files:
|
|
83
73
|
- History.txt
|
84
74
|
- Manifest.txt
|
85
75
|
- PostInstall.txt
|
86
|
-
- README.rdoc
|
87
76
|
- website/index.txt
|
88
77
|
files:
|
89
78
|
- History.txt
|
@@ -152,12 +141,12 @@ signing_key:
|
|
152
141
|
specification_version: 3
|
153
142
|
summary: "'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes."
|
154
143
|
test_files:
|
155
|
-
- test/test_helper.rb
|
156
144
|
- test/test_math_extensions.rb
|
157
145
|
- test/test_narray_extensions.rb
|
158
146
|
- test/test_nmatrix_extensions.rb
|
159
147
|
- test/test_string_extensions.rb
|
160
|
-
- test/test_ulla.rb
|
161
148
|
- test/ulla/test_cli.rb
|
162
149
|
- test/ulla/test_environment_class_hash.rb
|
163
150
|
- test/ulla/test_environment_feature.rb
|
151
|
+
- test/test_helper.rb
|
152
|
+
- test/test_ulla.rb
|