bives 0.10 → 1.0

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data/.ruby-version

@@ -1 +1 @@
-ruby-1.9.3-p484
+ruby-2.1.6

data/.travis.yml

@@ -0,0 +1,11 @@
+language: ruby
+
+rvm:
+  - 2.1.6
+
+env:
+   - SUITE="rake test"
+   - SUITE="rake build"
+
+script: bundle exec $SUITE
+

data/Gemfile

@@ -2,6 +2,3 @@ source 'https://rubygems.org'
 
 # Specify your gem's dependencies in bevis.gemspec
 gemspec
-
-gem "open4","1.3.0"
-gem "minitest"

data/LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2013, University of Manchester and University of Rostock
+Copyright (c) 2013-2015, University of Manchester and University of Rostock
 
                                  Apache License
                            Version 2.0, January 2004

data/README.rdoc

@@ -0,0 +1,41 @@
+= BiVeS Ruby Gem
+
+{<img src="https://codeclimate.com/github/SysMO-DB/bives.svg" />}[https://codeclimate.com/github/SysMO-DB/bives]
+{<img src="https://travis-ci.org/SysMO-DB/bives.svg?branch=update" alt="Build Status" />}[https://travis-ci.org/SysMO-DB/bives]
+
+Authors::     Stuart Owen, Martin Scharm
+Contact::     http://fair-dom.org/contact
+Homepage::    http://fair-dom.org
+Source code:: https://github.com/SysMO-DB/bives
+Licence::     Apache 2.0 (See Licence file or http://opensource.org/licenses/Apache-2.0)
+Copyright::   (c) 2014, 2015 The University of Manchester, UK
+
+
+== Synopsis
+
+This is a Ruby Gem which wraps the BiVeS java tool.
+
+Its purpose is to produce and comparison of difference between two SBML models, based on the XyDiff algorithm.
+
+BiVeS is developed at SEMS, Rostock, Germany, and more information can be found at https://sems.uni-rostock.de/projects/bives/ .
+
+BiVeS is used as part of the {Seek4Science}[http://seek4science.org] project, but is a standalone library.
+
+
+== Usage
+
+include the gem in your Gemfile with:
+
+  gem 'bives'
+
+then to use in your code
+
+  include Bives
+  compare(file1,file2)
+
+where file1 and file2 are File objects.
+
+The result is a HTML report of the differences.
+
+You can see an example in our {Tests}[https://github.com/SysMO-DB/bives/blob/master/test/bives_test.rb]
+

data/Rakefile

@@ -1 +1,10 @@
 require "bundler/gem_tasks"
+require 'rake/testtask'
+
+Rake::TestTask.new do |t|
+  t.libs << 'lib/bives'
+  t.test_files = FileList['test/*_test.rb']
+  t.verbose = true
+end
+
+task :default => :test

data/bives.gemspec

@@ -1,16 +1,8 @@
-# coding: utf-8
-lib = File.expand_path('../lib', __FILE__)
-$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
-require 'bives/version'
-require "bundler/gem_tasks"
+# -*- encoding: utf-8 -*-
+$:.push File.expand_path("../lib", __FILE__)
 
-require 'rake/testtask'
+require 'bives/version'
 
-Rake::TestTask.new do |t|
-  t.libs << 'lib/bives'
-  t.test_files = FileList['test/*_test.rb']
-  t.verbose = true
-end
 
 Gem::Specification.new do |spec|
   spec.name          = "bives"
@@ -20,15 +12,18 @@ Gem::Specification.new do |spec|
   spec.description   = %q{Ruby wrapper for the BiVeS model version comparison tool}
   spec.summary       = %q{Ruby wrapper to interface with the BiVeS model version comparison tool - http://sems.uni-rostock.de/projects/bives/}
   spec.homepage      = ""
-  spec.license       = "MIT"
+  spec.license       = "Apache 2.0"
 
   spec.files         = `git ls-files`.split($/)
   spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
   spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
   spec.require_paths = ["lib"]
 
-  spec.add_development_dependency "bundler", "~> 1.3"
   spec.add_development_dependency "rake"
+  spec.add_development_dependency "test-unit", "~> 3.0"
+
+  spec.add_runtime_dependency "open4","~>1.3.0"
+
 end
 
 

data/lib/bives/version.rb

@@ -1,3 +1,3 @@
 module Bives
-  VERSION = "0.10"
+  VERSION = "1.0"
 end

data/lib/bives.rb

@@ -10,7 +10,7 @@ module Bives
 
   end
 
-  JAR_FILENAME = "BiVeS-1.1.3-SNAPSHOT-fat.jar"
+  JAR_FILENAME = "BiVeS-1.3.12-jar-with-dependencies.jar"
   JAR_FILEPATH = File.join File.dirname(__FILE__),"jars","#{JAR_FILENAME}"
 
   def self.included(mod)

metadata

@@ -1,43 +1,57 @@
 --- !ruby/object:Gem::Specification
 name: bives
 version: !ruby/object:Gem::Version
-  version: '0.10'
+  version: '1.0'
 platform: ruby
 authors:
 - Stuart Owen
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-12-20 00:00:00.000000000 Z
+date: 2015-06-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: bundler
+  name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: '0'
 - !ruby/object:Gem::Dependency
-  name: rake
+  name: test-unit
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '3.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: open4
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.3.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.3.0
 description: Ruby wrapper for the BiVeS model version comparison tool
 email:
 - stuart.owen@manchester.ac.uk
@@ -45,23 +59,24 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
-- .gitignore
-- .ruby-gemset
-- .ruby-version
+- ".gitignore"
+- ".ruby-gemset"
+- ".ruby-version"
+- ".travis.yml"
 - Gemfile
 - LICENSE
-- README.md
+- README.rdoc
 - Rakefile
 - bives.gemspec
 - lib/bives.rb
 - lib/bives/version.rb
-- lib/jars/BiVeS-1.1.3-SNAPSHOT-fat.jar
+- lib/jars/BiVeS-1.3.12-jar-with-dependencies.jar
 - test/bives_test.rb
 - test/models/potato1.xml
 - test/models/potato2.xml
 homepage: ''
 licenses:
-- MIT
+- Apache 2.0
 metadata: {}
 post_install_message: 
 rdoc_options: []
@@ -69,17 +84,17 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.1.11
+rubygems_version: 2.2.3
 signing_key: 
 specification_version: 4
 summary: Ruby wrapper to interface with the BiVeS model version comparison tool -

data/README.md

@@ -1,9 +0,0 @@
-# Bivis
-
-
-## Installation
-
-Add this line to your application's Gemfile:
-
-    gem 'bives'
-