nimbus 2.3.0 → 2.4.0

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data/MIT-LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2017 Juanjo Bazán & Oscar González Recio
+Copyright (c) 2017-2019 Juanjo Bazán & Oscar González Recio
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/README.md

@@ -1,12 +1,14 @@
 # Nimbus
 Random Forest algorithm for genomic selection.
 
-[![Build Status](https://secure.travis-ci.org/xuanxu/nimbus.png?branch=master)](http://travis-ci.org/xuanxu/nimbus)
+[![Build Status](https://github.com/xuanxu/nimbus/actions/workflows/tests.yml/badge.svg)](https://github.com/xuanxu/nimbus/actions/workflows/tests.yml)
 [![Gem Version](https://badge.fury.io/rb/nimbus.png)](http://badge.fury.io/rb/nimbus)
+[![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://github.com/xuanxu/nimbus/blob/master/MIT-LICENSE.txt)
+[![DOI](http://joss.theoj.org/papers/10.21105/joss.00351/status.svg)](https://doi.org/10.21105/joss.00351)
 
 ## Random Forest
 
-The [random forest algorithm](http://en.wikipedia.org/wiki/Random_forest) is a classifier consisting in many random decision trees. It is based on choosing random subsets of variables for each tree and using the most frequent, or the averaged tree output as the overall classification. In machine learning terms, it is an ensembler classifier, so it uses multiple models to obtain better predictive performance than could be obtained from any of the constituent models.
+The [random forest algorithm](http://en.wikipedia.org/wiki/Random_forest) is a classifier consisting in many random decision trees. It is based on choosing random subsets of variables for each tree and using the most frequent, or the averaged tree output as the overall classification. In machine learning terms, it is an ensemble classifier, so it uses multiple models to obtain better predictive performance than could be obtained from any of the constituent models.
 
 The forest outputs the class that is the mean or the mode (in regression problems) or the majority class (in classification problems) of the node's output by individual trees.
 
@@ -56,7 +58,7 @@ You can disable this behaviour (and speed up the training process) by setting th
 
 ## Installation
 
-You need to have [Ruby](https://www.ruby-lang.org) (2.1 or higher) with Rubygems installed in your computer. Then install Nimbus with:
+You need to have [Ruby](https://www.ruby-lang.org) (2.6 or higher) with Rubygems installed in your computer. Then install Nimbus with:
 
 ````shell
 > gem install nimbus
@@ -229,7 +231,7 @@ It should output a `testing_file_predictions.txt` file with the resulting predic
 
 ## Test suite
 
-Nimbus includes a test suite located in the `spec` directory. You can run the specs if you clone the code to your local machine and run the default rake task:
+Nimbus includes a test suite located in the `spec` directory. The current state of the build is [publicly tracked by Travis CI](https://travis-ci.org/xuanxu/nimbus). You can run the specs locally if you clone the code to your local machine and run the default rake task:
 
 ````shell
 > git clone git://github.com/xuanxu/nimbus.git
@@ -256,11 +258,18 @@ Contributions are welcome. We encourage you to contribute to the Nimbus codebase
 Please read the [CONTRIBUTING](CONTRIBUTING.md) file.
 
 
-## Credits
+## Credits and DOI
+
+If you use Nimbus, please cite our [JOSS paper: http://dx.doi.org/10.21105/joss.00351](http://dx.doi.org/10.21105/joss.00351)
+
+You can find the citation info in [Bibtex format here](CITATION.bib).
+
+**Cite as:**  
+*Bazán et al, (2017), Nimbus: a Ruby gem to implement Random Forest algorithms in a genomic selection context, Journal of Open Source Software, 2(16), 351, doi:10.21105/joss.0035*
 
 Nimbus was developed by [Juanjo Bazán](http://twitter.com/xuanxu) in collaboration with Oscar González-Recio.
 
 
 ## LICENSE
 
-Copyright © 2017 Juanjo Bazán, released under the [MIT license](MIT-LICENSE.txt)
+Copyright © Juanjo Bazán, released under the [MIT license](MIT-LICENSE.txt)

data/bin/nimbus

@@ -1,7 +1,7 @@
 #!/usr/bin/env ruby
 
 #--
-# Copyright (c) 2011-2017 Juanjo Bazan
+# Copyright (c) 2011-2019 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/configuration.rb

@@ -105,7 +105,7 @@ module Nimbus
     def load(config_file = DEFAULTS[:config_file])
       user_config_params = {}
       dirname = Dir.pwd
-      if File.exists?(File.expand_path(config_file, Dir.pwd))
+      if File.exist?(File.expand_path(config_file, Dir.pwd))
         begin
           config_file_path = File.expand_path config_file, Dir.pwd
           user_config_params = Psych.load(File.open(config_file_path))
@@ -121,9 +121,9 @@ module Nimbus
         @forest_file   = File.expand_path(user_config_params['input']['forest'  ], dirname) if user_config_params['input']['forest']
         @classes       = user_config_params['input']['classes'] if user_config_params['input']['classes']
       else
-        @training_file = File.expand_path(DEFAULTS[:training_file], Dir.pwd) if File.exists? File.expand_path(DEFAULTS[:training_file], Dir.pwd)
-        @testing_file  = File.expand_path(DEFAULTS[:testing_file ], Dir.pwd) if File.exists? File.expand_path(DEFAULTS[:testing_file ], Dir.pwd)
-        @forest_file   = File.expand_path(DEFAULTS[:forest_file  ], Dir.pwd) if File.exists? File.expand_path(DEFAULTS[:forest_file  ], Dir.pwd)
+        @training_file = File.expand_path(DEFAULTS[:training_file], Dir.pwd) if File.exist? File.expand_path(DEFAULTS[:training_file], Dir.pwd)
+        @testing_file  = File.expand_path(DEFAULTS[:testing_file ], Dir.pwd) if File.exist? File.expand_path(DEFAULTS[:testing_file ], Dir.pwd)
+        @forest_file   = File.expand_path(DEFAULTS[:forest_file  ], Dir.pwd) if File.exist? File.expand_path(DEFAULTS[:forest_file  ], Dir.pwd)
       end
 
       @do_training = true unless @training_file.nil?
@@ -186,7 +186,7 @@ module Nimbus
     # The format of the input file should be the same as the forest output data of a Nimbus Application.
     def load_forest
       trees = []
-      if File.exists?(@forest_file)
+      if File.exist?(@forest_file)
         begin
           trees = Psych.load(File.open @forest_file)
         rescue ArgumentError => e

data/lib/nimbus/version.rb

@@ -1,3 +1,3 @@
 module Nimbus
-  VERSION = "2.3.0"
+  VERSION = "2.4.0"
 end

metadata

@@ -1,30 +1,30 @@
 --- !ruby/object:Gem::Specification
 name: nimbus
 version: !ruby/object:Gem::Version
-  version: 2.3.0
+  version: 2.4.0
 platform: ruby
 authors:
 - Juanjo Bazán
 - Oscar González Recio
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2017-07-12 00:00:00.000000000 Z
+date: 2023-03-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 3.6.0
+        version: '3.12'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 3.6.0
+        version: '3.12'
 description: Nimbus is a Ruby gem to implement Random Forest in a genomic selection
   context.
 email:
@@ -70,9 +70,10 @@ files:
 - spec/training_set_spec.rb
 - spec/tree_spec.rb
 homepage: http://nimbusgem.org
-licenses: []
+licenses:
+- MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options:
 - "--main"
 - README.rdoc
@@ -90,9 +91,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.6.12
-signing_key: 
+rubygems_version: 3.4.6
+signing_key:
 specification_version: 4
 summary: Random Forest algorithm for Genomics
 test_files: