nimbus 2.2.1 → 2.3.0

data/spec/training_set_spec.rb

@@ -9,8 +9,8 @@ describe Nimbus::TrainingSet do
     i3 = Nimbus::Individual.new 3, 33.0, [0,2,1,0]
     @training_set = Nimbus::TrainingSet.new [i1, i3], {i1.id => 11.0, i3.id => 33.0}
 
-    @training_set.individuals.should   == [i1, i3]
-    @training_set.ids_fenotypes.should == {i1.id => 11.0, i3.id => 33.0}
+    expect(@training_set.individuals).to eq [i1, i3]
+    expect(@training_set.ids_fenotypes).to eq ({i1.id => 11.0, i3.id => 33.0})
   end
 
   it "keeps track of ids of all individuals in the training set" do
@@ -19,7 +19,7 @@ describe Nimbus::TrainingSet do
     i3 = Nimbus::Individual.new 3, 33.0, [0,2,1,0]
     @training_set = Nimbus::TrainingSet.new [i1, i3], {i1.id => 11.0, i3.id => 33.0}
 
-    @training_set.all_ids.should == [1,3]
+    expect(@training_set.all_ids).to eq [1,3]
   end
 
 end

data/spec/tree_spec.rb

@@ -5,15 +5,15 @@ describe Nimbus::Tree do
 
   before(:each) do
     @config = Nimbus::Configuration.new
-    @config.load fixture_file('regression_config.yml')
+    @config.load fixture_file('regression/config.yml')
 
     @tree = Nimbus::Tree.new @config.tree
   end
 
   it "is initialized with tree config info" do
-    @tree.snp_total_count.should == 200
-    @tree.snp_sample_size.should == 60
-    @tree.node_min_size.should   == 5
+    expect(@tree.snp_total_count).to eq 200
+    expect(@tree.snp_sample_size).to eq 60
+    expect(@tree.node_min_size).to eq 5
   end
 
 end

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: nimbus
 version: !ruby/object:Gem::Version
-  version: 2.2.1
-  prerelease: 
+  version: 2.3.0
 platform: ruby
 authors:
 - Juanjo Bazán
@@ -10,19 +9,22 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-30 00:00:00.000000000 Z
+date: 2017-07-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2161078680 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 2.11.0
+        version: 3.6.0
   type: :development
   prerelease: false
-  version_requirements: *2161078680
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.6.0
 description: Nimbus is a Ruby gem to implement Random Forest in a genomic selection
   context.
 email:
@@ -32,8 +34,12 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
+- CODE_OF_CONDUCT.md
+- CONTRIBUTING.md
 - MIT-LICENSE.txt
 - README.md
+- bin/nimbus
+- lib/nimbus.rb
 - lib/nimbus/application.rb
 - lib/nimbus/classification_tree.rb
 - lib/nimbus/configuration.rb
@@ -45,17 +51,16 @@ files:
 - lib/nimbus/training_set.rb
 - lib/nimbus/tree.rb
 - lib/nimbus/version.rb
-- lib/nimbus.rb
 - spec/classification_tree_spec.rb
 - spec/configuration_spec.rb
-- spec/fixtures/classification_config.yml
-- spec/fixtures/classification_random_forest.yml
-- spec/fixtures/classification_testing.data
-- spec/fixtures/classification_training.data
-- spec/fixtures/regression_config.yml
-- spec/fixtures/regression_random_forest.yml
-- spec/fixtures/regression_testing.data
-- spec/fixtures/regression_training.data
+- spec/fixtures/classification/config.yml
+- spec/fixtures/classification/random_forest.yml
+- spec/fixtures/classification/testing.data
+- spec/fixtures/classification/training.data
+- spec/fixtures/regression/config.yml
+- spec/fixtures/regression/random_forest.yml
+- spec/fixtures/regression/testing.data
+- spec/fixtures/regression/training.data
 - spec/forest_spec.rb
 - spec/individual_spec.rb
 - spec/loss_functions_spec.rb
@@ -64,45 +69,43 @@ files:
 - spec/spec_helper.rb
 - spec/training_set_spec.rb
 - spec/tree_spec.rb
-- bin/nimbus
 homepage: http://nimbusgem.org
 licenses: []
+metadata: {}
 post_install_message: 
 rdoc_options:
-- --main
+- "--main"
 - README.rdoc
-- --charset=UTF-8
+- "--charset=UTF-8"
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.15
+rubygems_version: 2.6.12
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Random Forest algorithm for Genomics
 test_files:
 - spec/classification_tree_spec.rb
 - spec/configuration_spec.rb
-- spec/fixtures/classification_config.yml
-- spec/fixtures/classification_random_forest.yml
-- spec/fixtures/classification_testing.data
-- spec/fixtures/classification_training.data
-- spec/fixtures/regression_config.yml
-- spec/fixtures/regression_random_forest.yml
-- spec/fixtures/regression_testing.data
-- spec/fixtures/regression_training.data
+- spec/fixtures/classification/config.yml
+- spec/fixtures/classification/random_forest.yml
+- spec/fixtures/classification/testing.data
+- spec/fixtures/classification/training.data
+- spec/fixtures/regression/config.yml
+- spec/fixtures/regression/random_forest.yml
+- spec/fixtures/regression/testing.data
+- spec/fixtures/regression/training.data
 - spec/forest_spec.rb
 - spec/individual_spec.rb
 - spec/loss_functions_spec.rb

data/spec/fixtures/classification_random_forest.yml

@@ -1,922 +0,0 @@
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