nimbus 2.0.0 → 2.0.1

data/README.md

@@ -76,7 +76,7 @@ The `config.yml` has the following structure and parameters:
       training: training_regression.data
       testing: testing_regression.data
       forest: my_forest.yml
-      classes: [0,1]
+      classes: [0, 1]
 
     #Forest parameters
     forest:
@@ -90,7 +90,7 @@ Under the input chapter:
  * `training`: specify the path to the training data file (optional, if specified `nimbus` will create a random forest).
  * `testing`: specify the path to the testing data file (optional, if specified `nimbus` will traverse this dat through a random forest).
  * `forest`: specify the path to a file containing a random forest structure (optional, if there is also testing file, this will be the forest used for the testing).
- * `classes`: **optional (needed only for classification problems)**. Specify the list of classes in the input files as a comma separated list between squared brackets, e.g.:`[A,B]`.
+ * `classes`: **optional (needed only for classification problems)**. Specify the list of classes in the input files as a comma separated list between squared brackets, e.g.:`[A, B]`.
 
 Under the forest chapter:
 
@@ -110,7 +110,7 @@ The three input files you can use with Nimbus should have proper format:
 1. A column with the ID of the individual
 1. M columns (where M = SNP_total_count in `config.yml`) with values 0, 1 or 2, representing the genotype of the individual.
 
-**The training file** has any number of rows, each representing data for an individual, similar to the training file but without the fenotype column:
+**The testing file** has any number of rows, each representing data for an individual, similar to the training file but without the fenotype column:
 
 1. A column with the ID of the individual
 1. M columns (where M = SNP_total_count in `config.yml`) with values 0, 1 or 2, representing the genotype of the individual.

data/bin/nimbus

@@ -1,7 +1,7 @@
 #!/usr/bin/env ruby
 
 #--
-# Copyright (c) 2011 Juanjo Bazan
+# Copyright (c) 2011-2013 Juanjo Bazan
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to

data/lib/nimbus.rb

@@ -1,4 +1,4 @@
-require 'yaml'
+require 'psych'
 require 'nimbus/exceptions'
 require 'nimbus/training_set'
 require 'nimbus/configuration'

data/lib/nimbus/configuration.rb

@@ -106,7 +106,7 @@ module Nimbus
       if File.exists?(File.expand_path(config_file, Dir.pwd))
         begin
           config_file_path = File.expand_path config_file, Dir.pwd
-          user_config_params = YAML.load(File.open(config_file_path))
+          user_config_params = Psych.load(File.open(config_file_path))
           dirname = File.dirname config_file_path
         rescue ArgumentError => e
           raise Nimbus::WrongFormatFileError, "It was not posible to parse the config file (#{config_file}): \r\n#{e.message} "
@@ -184,10 +184,12 @@ module Nimbus
       trees = []
       if File.exists?(@forest_file)
         begin
-          trees = YAML.load(File.open @forest_file)
+          trees = Psych.load(File.open @forest_file)
         rescue ArgumentError => e
           raise Nimbus::WrongFormatFileError, "It was not posible to parse the random forest file (#{@forest_file}): \r\n#{e.message} "
         end
+      else
+        raise Nimbus::InputFileError, "Forest file not found (#{@forest_file})"
       end
       forest = Nimbus::Forest.new self
       forest.trees = trees

data/lib/nimbus/version.rb

@@ -1,3 +1,3 @@
 module Nimbus
-  VERSION = "2.0.0"
+  VERSION = "2.0.1"
 end

data/spec/classification_tree_spec.rb

@@ -116,7 +116,7 @@ describe Nimbus::ClassificationTree do
   end
 
   it 'get prediction for an individual pushing it down a tree structure' do
-    tree_structure = YAML.load(File.open fixture_file('classification_random_forest.yml')).first
+    tree_structure = Psych.load(File.open fixture_file('classification_random_forest.yml')).first
     individual_data = [0]*100
     prediction = Nimbus::Tree.traverse tree_structure, individual_data
     prediction.should == '1'

data/spec/configuration_spec.rb

@@ -105,7 +105,7 @@ describe Nimbus::Configuration do
     config = Nimbus::Configuration.new
     config.load fixture_file('regression_config.yml')
 
-    trees = YAML.load(File.open fixture_file('regression_random_forest.yml'))
+    trees = Psych.load(File.open fixture_file('regression_random_forest.yml'))
     trees.first.keys.first.should == 189
     trees.size.should == 3
 

data/spec/forest_spec.rb

@@ -38,7 +38,7 @@ describe Nimbus::Forest do
       @forest = @config.load_forest
       @forest.predictions.should == {}
 
-      tree_structure = YAML.load(File.open fixture_file('regression_random_forest.yml'))
+      tree_structure = Psych.load(File.open fixture_file('regression_random_forest.yml'))
       expected_predictions = {}
       @config.read_testing_data{|individual|
         individual_prediction = 0.0
@@ -54,7 +54,7 @@ describe Nimbus::Forest do
 
     it 'can output forest structure in YAML format' do
       @forest = @config.load_forest
-      YAML.load(File.open fixture_file('regression_random_forest.yml')) == YAML.load(@forest.to_yaml)
+      Psych.load(File.open fixture_file('regression_random_forest.yml')) == Psych.load(@forest.to_yaml)
     end
   end
 
@@ -94,7 +94,7 @@ describe Nimbus::Forest do
       @forest = @config.load_forest
       @forest.predictions.should == {}
 
-      tree_structure = YAML.load(File.open fixture_file('classification_random_forest.yml'))
+      tree_structure = Psych.load(File.open fixture_file('classification_random_forest.yml'))
       expected_predictions = {}
       @config.read_testing_data{|individual|
         individual_prediction = []
@@ -110,7 +110,7 @@ describe Nimbus::Forest do
 
     it 'can output forest structure in YAML format' do
       @forest = @config.load_forest
-      YAML.load(File.open fixture_file('classification_random_forest.yml')) == YAML.load(@forest.to_yaml)
+      Psych.load(File.open fixture_file('classification_random_forest.yml')) == Psych.load(@forest.to_yaml)
     end
   end
 end

data/spec/regression_tree_spec.rb

@@ -113,7 +113,7 @@ describe Nimbus::RegressionTree do
   end
 
   it 'get prediction for an individual pushing it down a tree structure' do
-    tree_structure = YAML.load(File.open fixture_file('regression_random_forest.yml')).first
+    tree_structure = Psych.load(File.open fixture_file('regression_random_forest.yml')).first
     individual_data = [0]*200
     prediction = Nimbus::Tree.traverse tree_structure, individual_data
     prediction.should == 0.25043

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: nimbus
 version: !ruby/object:Gem::Version
-  version: 2.0.0
+  version: 2.0.1
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-26 00:00:00.000000000 Z
+date: 2012-07-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2156549180 !ruby/object:Gem::Requirement
+  requirement: &2160657580 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,7 +22,7 @@ dependencies:
         version: 2.11.0
   type: :development
   prerelease: false
-  version_requirements: *2156549180
+  version_requirements: *2160657580
 description: Nimbus is a Ruby gem to implement Random Forest in a genomic selection
   context.
 email: