semin-ulla 0.9.7 → 0.9.8

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
data/History.txt CHANGED
@@ -1,3 +1,7 @@
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+ == 0.9.8 21/07/2009
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+
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+ * Fixed a bug in generating amino acids symbols when --cys 2 is set
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+
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  == 0.9.7 30/05/2009
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  * Added --environment option to consider not only substituted amino acids' environments but also substituting amino acids' environments
data/Rakefile CHANGED
@@ -1,32 +1,25 @@
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- %w[rubygems rake rake/clean fileutils newgem rubigen].each { |f| require f }
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- require File.dirname(__FILE__) + '/lib/ulla'
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+ require 'rubygems'
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+ gem 'hoe', '>= 2.1.0'
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+ require 'hoe'
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+ require 'fileutils'
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+
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+ Hoe.plugin :newgem
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+ # Hoe.plugin :website
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+ # Hoe.plugin :cucumberfeatures
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  # Generate all the Rake tasks
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  # Run 'rake -T' to see list of generated tasks (from gem root directory)
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- $hoe = Hoe.new('ulla', Ulla::VERSION) do |p|
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- p.developer('Semin Lee', 'seminlee@gmail.com')
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- p.changes = p.paragraphs_of("History.txt", 0..1).join("\n\n")
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- p.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
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- p.rubyforge_name = p.name # TODO this is default value
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- p.extra_deps = [
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+ $hoe = Hoe.spec 'ulla' do
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+ self.developer 'Semin Lee', 'seminlee@gmail.com'
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+ self.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
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+ self.rubyforge_name = self.name # TODO this is default value
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+ self.extra_deps = [
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  ['narray', '>= 0.5.9.5'],
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  ['bio', '>= 1.2.1'],
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  ['facets', '>= 2.4.5'],
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  ['rmagick', '>= 2.9.1'],
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  ]
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-
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- p.extra_dev_deps = [
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- ['newgem', ">= #{::Newgem::VERSION}"]
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- ]
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-
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- p.clean_globs |= %w[**/.DS_Store tmp *.log *.swp]
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- path = (p.rubyforge_name == p.name) ? p.rubyforge_name : "\#{p.rubyforge_name}/\#{p.name}"
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- p.remote_rdoc_dir = File.join(path.gsub(/^#{p.rubyforge_name}\/?/,''), 'rdoc')
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- p.rsync_args = '-av --delete --ignore-errors'
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  end
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- require 'newgem/tasks' # load /tasks/*.rake
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+ require 'newgem/tasks'
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  Dir['tasks/**/*.rake'].each { |t| load t }
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-
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- # TODO - want other tests/tasks run by default? Add them to the list
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- # task :default => [:spec, :features]
data/lib/ulla/cli.rb CHANGED
@@ -384,7 +384,7 @@ Options:
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  # if --cys option 2, then we don't care about 'J' (for both Cystine and Cystine)
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  if $cys == 2
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- $amino_acids = 'ACDEFGHIKLMNPQRSTVWY'.delete('J')
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+ $amino_acids = 'ACDEFGHIKLMNPQRSTVWY'.delete('J').split('')
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  end
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  # create an EnvironmentFeatureArray object for storing all environment
@@ -709,11 +709,11 @@ Options:
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  env_label2 = $environment == 1 ? aa2 + '-' + aa1[1..-1] : env_labels[id2][pos]
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  if $cst_features.empty?
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- $env_classes[env_label1].increase_residue_count(aa2[0].chr, jnt_cnt)
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- $env_classes[env_label2].increase_residue_count(aa1[0].chr, jnt_cnt)
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+ $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}"
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+ $env_classes[env_label2].increase_residue_count(aa1[0].chr, jnt_cnt) #rescue $logger.error "Something wrong with #{tem_file}-#{id2}-#{pos}-#{aa2}-#{env_label2}"
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  elsif (env_labels[id1][pos].split('').values_at(*$cst_features) == env_labels[id2][pos].split('').values_at(*$cst_features))
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  $env_classes[env_label1].increase_residue_count(aa2[0].chr, jnt_cnt)
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- $env_classes[env_label2].increase_residue_count(aa1[1].chr, jnt_cnt)
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+ $env_classes[env_label2].increase_residue_count(aa1[0].chr, jnt_cnt)
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  else
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  $logger.debug "Skipped #{id1}-#{pos}-#{aa1[0].chr} and #{id2}-#{pos}-#{aa2[0].chr} having different symbols for constrained environment features each other."
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  next
data/lib/ulla.rb CHANGED
@@ -2,5 +2,5 @@ $:.unshift(File.dirname(__FILE__)) unless
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  $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
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  module Ulla
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- VERSION = '0.9.7'
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+ VERSION = '0.9.8'
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  end
data/ulla.gemspec CHANGED
@@ -2,16 +2,16 @@
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  Gem::Specification.new do |s|
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  s.name = %q{ulla}
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- s.version = "0.9.7"
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+ s.version = "0.9.8"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = ["Semin Lee"]
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- s.date = %q{2009-06-11}
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+ s.date = %q{2009-07-21}
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  s.default_executable = %q{ulla}
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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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  s.email = ["seminlee@gmail.com"]
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  s.executables = ["ulla"]
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- s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "website/index.txt"]
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+ s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "website/index.txt"]
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  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"]
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  s.homepage = %q{http://www-cryst.bioc.cam.ac.uk/ulla}
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  s.post_install_message = %q{PostInstall.txt}
@@ -20,7 +20,7 @@ Gem::Specification.new do |s|
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  s.rubyforge_project = %q{ulla}
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  s.rubygems_version = %q{1.3.4}
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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.}
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- s.test_files = ["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"]
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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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  if s.respond_to? :specification_version then
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  current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
@@ -31,22 +31,19 @@ Gem::Specification.new do |s|
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  s.add_runtime_dependency(%q<bio>, [">= 1.2.1"])
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  s.add_runtime_dependency(%q<facets>, [">= 2.4.5"])
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  s.add_runtime_dependency(%q<rmagick>, [">= 2.9.1"])
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- s.add_development_dependency(%q<newgem>, [">= 1.4.1"])
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- s.add_development_dependency(%q<hoe>, [">= 1.8.0"])
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+ s.add_development_dependency(%q<hoe>, [">= 2.3.2"])
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  else
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  s.add_dependency(%q<narray>, [">= 0.5.9.5"])
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  s.add_dependency(%q<bio>, [">= 1.2.1"])
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  s.add_dependency(%q<facets>, [">= 2.4.5"])
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  s.add_dependency(%q<rmagick>, [">= 2.9.1"])
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- s.add_dependency(%q<newgem>, [">= 1.4.1"])
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- s.add_dependency(%q<hoe>, [">= 1.8.0"])
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+ s.add_dependency(%q<hoe>, [">= 2.3.2"])
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  end
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  else
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  s.add_dependency(%q<narray>, [">= 0.5.9.5"])
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  s.add_dependency(%q<bio>, [">= 1.2.1"])
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  s.add_dependency(%q<facets>, [">= 2.4.5"])
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  s.add_dependency(%q<rmagick>, [">= 2.9.1"])
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- s.add_dependency(%q<newgem>, [">= 1.4.1"])
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- s.add_dependency(%q<hoe>, [">= 1.8.0"])
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+ s.add_dependency(%q<hoe>, [">= 2.3.2"])
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  end
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  end
data/website/index.html CHANGED
@@ -4,7 +4,7 @@
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  <head>
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  <meta http-equiv="Refresh" content="5; URL=http://github.com/semin/ulla">
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  <title>
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- ulla: a program for calculating environment-specific substitution tables
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+ Ulla: a program for calculating environment-specific substitution tables
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  </title>
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  </head>
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  <body>
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: semin-ulla
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  version: !ruby/object:Gem::Version
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- version: 0.9.7
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+ version: 0.9.8
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  platform: ruby
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  authors:
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  - Semin Lee
@@ -9,7 +9,7 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2009-06-11 00:00:00 -07:00
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+ date: 2009-07-21 00:00:00 -07:00
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  default_executable: ulla
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  dependencies:
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  - !ruby/object:Gem::Dependency
@@ -52,16 +52,6 @@ dependencies:
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  - !ruby/object:Gem::Version
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  version: 2.9.1
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  version:
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- - !ruby/object:Gem::Dependency
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- name: newgem
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- type: :development
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- version_requirement:
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- version_requirements: !ruby/object:Gem::Requirement
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- requirements:
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- - - ">="
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- - !ruby/object:Gem::Version
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- version: 1.4.1
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- version:
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  - !ruby/object:Gem::Dependency
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  name: hoe
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  type: :development
@@ -70,7 +60,7 @@ dependencies:
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  requirements:
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 1.8.0
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+ version: 2.3.2
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  version:
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  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."
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  email:
@@ -83,7 +73,6 @@ extra_rdoc_files:
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  - History.txt
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  - Manifest.txt
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  - PostInstall.txt
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- - README.rdoc
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  - website/index.txt
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  files:
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  - History.txt
@@ -152,12 +141,12 @@ signing_key:
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  specification_version: 3
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  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."
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  test_files:
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- - test/test_helper.rb
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  - test/test_math_extensions.rb
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  - test/test_narray_extensions.rb
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  - test/test_nmatrix_extensions.rb
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  - test/test_string_extensions.rb
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- - test/test_ulla.rb
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  - test/ulla/test_cli.rb
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  - test/ulla/test_environment_class_hash.rb
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  - test/ulla/test_environment_feature.rb
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+ - test/test_helper.rb
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+ - test/test_ulla.rb