weka 0.5.0-java → 0.7.3-java

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitignore

@@ -1,10 +1,11 @@
-/.bundle/
-/.yardoc
-/Gemfile.lock
-/_yardoc/
-/coverage/
-/doc/
-/pkg/
-/spec/reports/
-/tmp/
+.bundle
+.yardoc
+Gemfile.lock
+_yardoc
+coverage
+doc
+pkg
+spec/reports
+tmp
 jars
+lib/*_jars.rb

data/.rubocop.yml

@@ -5,6 +5,7 @@ AllCops:
     - '*.gemspec'
     - 'Gemfile'
     - 'Gemfile.lock'
+    - 'lib/weka_jars.rb'
 
 Style/Copyright:
   Enabled: false
@@ -13,7 +14,10 @@ Style/Documentation:
   Enabled: false
 
 Metrics/LineLength:
-  Max: 80
+  Max: 105
+
+Metrics/ClassLength:
+  Max: 250
 
 Layout/MultilineMethodCallIndentation:
   EnforcedStyle: indented
@@ -28,3 +32,28 @@ Metrics/ModuleLength:
 Metrics/BlockLength:
   Exclude:
     - "**/*_spec.rb"
+
+Lint/ConstantDefinitionInBlock:
+  Exclude:
+    - "**/*_spec.rb"
+
+Layout/EmptyLineBetweenDefs:
+  Enabled: false
+
+Layout/HashAlignment:
+  Enabled: false
+
+Lint/BooleanSymbol:
+  Enabled: false
+
+Style/HashEachMethods:
+  Exclude:
+    - lib/weka/core/instances.rb
+    - spec/classifiers/evaluation_spec.rb
+
+Naming/PredicateName:
+  Exclude:
+    - lib/weka/core/instances.rb
+
+Metrics/CyclomaticComplexity:
+  Max: 8

data/CHANGELOG.md

@@ -0,0 +1,104 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.7.3] – 2021-01-21
+### Changed
+- Update Weka Jar dependency to weka-dev v3.9.5  
+  Please also refer to the weka changelog for included updates & fixes:  
+  https://www.cs.waikato.ac.nz/~ml/weka/CHANGELOG-3-9-5
+- Update dev dependencies
+
+## [0.7.2] – 2020-03-20
+### Changed
+- Update Weka Jar dependency to weka-dev v3.9.4  
+  Please also refer to the weka changelog for included updates & fixes:  
+  https://www.cs.waikato.ac.nz/~ml/weka/CHANGELOG-3-9-4
+- Drop shoulda-matchers as dev-dependency
+
+## [0.7.1] – 2018-11-09
+### Changed
+- Update Weka Jar dependency to weka-dev v3.9.3
+- Update rake to \~>12.0, jar-dependencies to \~>0.4
+
+### Fixed
+- Float::NAN check in Weka::Core::Attributes#internal_value_of
+
+## [0.7.0] – 2018-01-01
+### Added
+- Add new unsupervised attribute filters added in weka-dev v3.9.2
+- Make classes from weka.filters module available
+- Make WeightedInstancesHandlerWrapper available in Weka::Classifiers::Meta
+- Make FilteredClusterer & MakeDensityBasedClusterer available in Weka::Clusterers
+
+### Changed
+- Update Weka Jar dependency to weka-dev v3.9.2
+
+## [0.6.0] – 2017-12-17
+### Added
+- #copy method for Weka::Core::Instances
+
+### Changed
+- Load Jars with jar-dependencies instead of lock_jar gem
+- Make Weka::Core::Instances#instance_from public
+
+### Fixed
+- Weka::UnassignedTrainingInstancesError when running #classify/#cluster and
+  #distribution_for on deserialized classfiers and clusterers
+
+
+## [0.5.0] – 2017-06-17
+### Added
+- #to_m (to Matrix) method for Weka::Core::Instances
+- Curve classes in Weka::Classifiers::Evaluation module
+- Allow including additional modules on class building
+- Rubocop config for project
+
+### Changed
+- Allow passing a hash to Weka::Core::Instances#add_instance
+
+### Removed
+- Block argument in Weka::Core::Instances#initialize
+
+
+## [0.4.0] – 2016-12-22
+### Added
+- C45 converters
+- Full support for string attributes
+
+### Removed
+- ActiveSupport as dependency
+
+
+## [0.3.0] – 2016-02-10
+### Added
+- Allow adding Instances with missing values
+- Allow creating DenseInstances with missing values
+- #merge method for Weka::Core:Instances
+
+
+## [0.2.0] – 2016-01-19
+### Added
+- Serialization/deserialization functionality
+- #apply_filters method for Weka::Core::Instances
+
+
+## [0.1.0] – 2015-12-26
+Initial release
+
+[Unreleased]: https://github.com/paulgoetze/weka-jruby/compare/v0.7.3...HEAD
+[0.7.3]: https://github.com/paulgoetze/weka-jruby/compare/v0.7.2...v0.7.3
+[0.7.2]: https://github.com/paulgoetze/weka-jruby/compare/v0.7.1...v0.7.2
+[0.7.1]: https://github.com/paulgoetze/weka-jruby/compare/v0.7.0...v0.7.1
+[0.7.0]: https://github.com/paulgoetze/weka-jruby/compare/v0.6.0...v0.7.0
+[0.6.0]: https://github.com/paulgoetze/weka-jruby/compare/v0.5.0...v0.6.0
+[0.5.0]: https://github.com/paulgoetze/weka-jruby/compare/v0.4.0...v0.5.0
+[0.4.0]: https://github.com/paulgoetze/weka-jruby/compare/v0.3.0...v0.4.0
+[0.3.0]: https://github.com/paulgoetze/weka-jruby/compare/v0.2.0...v0.3.0
+[0.2.0]: https://github.com/paulgoetze/weka-jruby/compare/v0.1.0...v0.2.0
+[0.1.0]: https://github.com/paulgoetze/weka-jruby/compare/ce6a985017c28ea755290a9baba4d81acddc2d20...v0.1.0

data/CODE_OF_CONDUCT.md

@@ -1,13 +1,76 @@
-# Contributor Code of Conduct
+# Contributor Covenant Code of Conduct
 
-As contributors and maintainers of this project, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.
+## Our Pledge
 
-We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to make participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
 
-Examples of unacceptable behavior by participants include the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.
+## Our Standards
 
-Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed from the project team.
+Examples of behavior that contributes to creating a positive environment
+include:
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers.
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
 
-This Code of Conduct is adapted from the [Contributor Covenant](http://contributor-covenant.org), version 1.0.0, available at [http://contributor-covenant.org/version/1/0/0/](http://contributor-covenant.org/version/1/0/0/)
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies within all project spaces, and it also applies when
+an individual is representing the project or its community in public spaces.
+Examples of representing a project or community include using an official
+project e-mail address, posting via an official social media account, or acting
+as an appointed representative at an online or offline event. Representation of
+a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at paul.christoph.goetze@gmail.com. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

data/MIT-LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2015 Paul Götze
+Copyright (c) 2015-2021 Paul Götze
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

data/README.md

@@ -1,8 +1,9 @@
 # Weka
 
 [![Gem Version](https://badge.fury.io/rb/weka.svg)](http://badge.fury.io/rb/weka)
-[![Travis Build](https://travis-ci.org/paulgoetze/weka-jruby.svg)](https://travis-ci.org/paulgoetze/weka-jruby)
+[![Build Status](https://github.com/paulgoetze/weka-jruby/workflows/JRuby%20CI/badge.svg)](https://github.com/paulgoetze/weka-jruby/workflows/JRuby%20CI/badge.svg)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/9634a6709ef545198e079a8daddff100)](https://www.codacy.com/app/paul-christoph-goetze/weka-jruby?utm_source=github.com&utm_medium=referral&utm_content=paulgoetze/weka-jruby&utm_campaign=Badge_Grade)
+[![Open Source Helpers](https://www.codetriage.com/paulgoetze/weka-jruby/badges/users.svg)](https://www.codetriage.com/paulgoetze/weka-jruby)
 
 Machine Learning & Data Mining with JRuby based on the [Weka](http://www.cs.waikato.ac.nz/~ml/weka/index.html) Java library.
 
@@ -39,26 +40,30 @@ detailed information about how to use weka with JRuby and some examplary code sn
 
 ## Development
 
-After checking out the repo, run `bin/setup` to install dependencies.
-To install this gem onto your local machine, run `bundle exec rake install`.
+1. Check out the repo with `git clone git@github.com:paulgoetze/weka-jruby.git`.
+2. Set a local environment variable `export JARS_VENDOR=false`.
+   This will prevent
+   compiling the jars into your repo’s /lib directory and will load them from your local maven repository instead.
+   See the  [jar-dependencies README](https://github.com/mkristian/jar-dependencies#for-development-you-do-not-need-to-vendor-the-jars-at-all) for more information.
+3. Run `bin/setup` or `bundle install` to install the dependencies.
 
 Then, run `rake spec` to run the tests. You can also run `bin/console` or `rake irb` for an interactive prompt that will allow you to experiment.
 
 ## Contributing
 
-Bug reports and pull requests are welcome on GitHub at https://github.com/paulgoetze/weka-jruby. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant code of conduct](http://contributor-covenant.org/version/1/2/0).
+Bug reports and pull requests are welcome on GitHub at https://github.com/paulgoetze/weka-jruby. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant Code of Conduct](https://github.com/paulgoetze/weka-jruby/blob/main/CODE_OF_CONDUCT.md).
 
 For development we use the [git branching model](http://nvie.com/posts/a-successful-git-branching-model/) described by [nvie](https://github.com/nvie).
 
 Here’s how to contribute:
 
-1. Fork it ( https://github.com/paulgoetze/weka-jruby/fork )
+1. Fork it (https://github.com/paulgoetze/weka-jruby/fork)
 2. Create your feature branch (`git checkout -b feature/my-new-feature develop`)
 3. Commit your changes (`git commit -am 'Add some feature'`)
 4. Push to the branch (`git push origin feature/my-new-feature`)
 5. Create a new Pull Request
 
-Please try to add RSpec tests along with your new features. This will ensure that your code does not break existing functionality and that your feature is working as expected.
+Please try to add RSpec tests along with your new feature. This will ensure that your code does not break existing functionality and that your feature is working as expected.
 
 We use [Rubocop](https://github.com/bbatsov/rubocop) for code style recommendations.
 Please make sure your contributions comply with the project’s Rubocop config.
@@ -69,4 +74,4 @@ The original ideas for wrapping Weka in JRuby come from [@arrigonialberto86](htt
 
 ## License
 
-The gem is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).
+The gem is available as open source under the terms of the [MIT License](https://github.com/paulgoetze/weka-jruby/blob/main/MIT-LICENSE.txt).

data/Rakefile

@@ -3,17 +3,7 @@ require 'rspec/core/rake_task'
 
 RSpec::Core::RakeTask.new(:spec)
 
-task default: :prepare
-task install: :prepare
-
-desc 'Install weka jars & dependencies'
-task :prepare do
-  require 'lock_jar'
-  lib_path = File.expand_path('.', File.dirname(__FILE__))
-  jars_dir = File.join(lib_path, 'jars')
-
-  LockJar.install('Jarfile.lock', local_repo: jars_dir)
-end
+task default: :spec
 
 desc 'Start an irb session with the gem loaded'
 task :irb do

data/lib/weka.rb

@@ -1,11 +1,9 @@
 require 'java'
-require 'weka/jars'
 require 'weka/version'
 require 'weka/exceptions'
+require Dir[File.join(File.dirname(__FILE__), '*_jars.rb')].first
 
 module Weka
-  include Jars
-
   class << self
     def require_all(type)
       files        = Dir[File.expand_path("../weka/#{type}/**/*.rb", __FILE__)]

data/lib/weka/class_builder.rb

@@ -88,6 +88,7 @@ module Weka
 
       def include_utils
         return unless utils_defined?
+
         "include #{utils}"
       end
 
@@ -103,7 +104,7 @@ module Weka
       end
 
       def constantize(module_names)
-        Object.module_eval("::#{module_names}")
+        Object.module_eval("::#{module_names}", __FILE__, __LINE__)
       end
 
       def utils
@@ -116,6 +117,7 @@ module Weka
 
       def downcase_first_char(string)
         return if string.nil? || string.empty?
+
         string[0].downcase + string[1..-1]
       end
     end

data/lib/weka/classifiers/evaluation.rb

@@ -1,4 +1,5 @@
 require 'weka/class_builder'
+require 'weka/concerns'
 
 module Weka
   module Classifiers
@@ -6,6 +7,7 @@ module Weka
 
     class Evaluation
       include ClassBuilder
+      include Weka::Concerns::Persistent
 
       # Use both nomenclatures f_measure and fmeasure for consistency
       # due to jruby's auto method generation of 'fMeasure' to 'f_measure' and

data/lib/weka/classifiers/meta.rb

@@ -23,7 +23,8 @@ module Weka
                     :RandomSubSpace,
                     :RegressionByDiscretization,
                     :Stacking,
-                    :Vote
+                    :Vote,
+                    :WeightedInstancesHandlerWrapper
     end
   end
 end

data/lib/weka/classifiers/utils.rb

@@ -19,7 +19,7 @@ module Weka
 
           error   = 'Class attribute is not assigned for Instances.'
           hint    = 'You can assign a class attribute with #class_attribute=.'
-          message = "#{error} #{hint}"
+          message = "#{error}\n#{hint}"
 
           raise UnassignedClassError, message
         end
@@ -29,27 +29,49 @@ module Weka
 
           error   = 'Classifier is not trained with Instances.'
           hint    = 'You can set the training instances with #train_with_instances.'
-          message = "#{error} #{hint}"
+          message = "#{error}\n#{hint}"
 
           raise UnassignedTrainingInstancesError, message
         end
+
+        def ensure_valid_instances_structure!(instances)
+          unless instances.is_a?(Weka::Core::Instances)
+            message = 'Instances has to be a Weka::Core::Instances object.'
+            raise ArgumentError, message
+          end
+
+          return if training_instances.nil?
+          return if instances.equal_headers(training_instances)
+
+          message = 'The passed instances need to have the same structure as ' \
+                    'the classifier’s training instances.'
+
+          raise InvalidInstancesStructureError, message
+        end
+
+        def ensure_instances_structure_available!
+          return unless instances_structure.nil?
+
+          error   = 'Classifier does not have any instances structure info.'
+          hint    = 'You probably tried to classify values with a ' \
+                    'classifier that is untrained or doesn’t have an ' \
+                    'instances_structure set. Please run ' \
+                    '#train_with_instances, try serializing and ' \
+                    'deserializing your classifier again in case you used a ' \
+                    'deserialized classifier or set its instances_structure.'
+          message = "#{error}\n#{hint}"
+
+          raise MissingInstancesStructureError, message
+        end
       end
 
       module Transformers
         private
 
         def classifiable_instance_from(instance_or_values)
-          attributes = training_instances.attributes
-          instances  = Weka::Core::Instances.new(attributes: attributes)
+          ensure_instances_structure_available!
 
-          class_attribute = training_instances.class_attribute
-          class_index     = training_instances.class_index
-          instances.insert_attribute_at(class_attribute, class_index)
-
-          instances.class_index = training_instances.class_index
-          instances.add_instance(instance_or_values)
-
-          instance = instances.first
+          instance = instances_structure.instance_from(instance_or_values)
           instance.set_class_missing
           instance
         end
@@ -59,17 +81,24 @@ module Weka
         java_import 'java.util.Random'
         include Checks
 
-        attr_reader :training_instances
+        attr_reader :training_instances, :instances_structure
 
         def train_with_instances(instances)
           ensure_class_attribute_assigned!(instances)
 
           @training_instances = instances
+          @instances_structure = instances.string_free_structure
+
           build_classifier(instances)
 
           self
         end
 
+        def instances_structure=(instances)
+          ensure_valid_instances_structure!(instances)
+          @instances_structure = instances.string_free_structure
+        end
+
         def cross_validate(folds: 3)
           ensure_trained_with_instances!
 
@@ -101,8 +130,6 @@ module Weka
         include Transformers
 
         def classify(instance_or_values)
-          ensure_trained_with_instances!
-
           instance = classifiable_instance_from(instance_or_values)
           index    = classify_instance(instance)
 
@@ -112,7 +139,7 @@ module Weka
         private
 
         def class_value_of_index(index)
-          training_instances.class_attribute.value(index)
+          instances_structure.class_attribute.value(index)
         end
       end
 
@@ -136,8 +163,6 @@ module Weka
         include Transformers
 
         def distribution_for(instance_or_values)
-          ensure_trained_with_instances!
-
           instance      = classifiable_instance_from(instance_or_values)
           distributions = distribution_for_instance(instance)
 
@@ -147,7 +172,7 @@ module Weka
         private
 
         def class_distributions_from(distributions)
-          class_values = training_instances.class_attribute.values
+          class_values = instances_structure.class_attribute.values
 
           distributions.each_with_object({}).with_index do |(distribution, result), index|
             class_value = class_values[index]

data/lib/weka/clusterers.rb

@@ -10,7 +10,9 @@ module Weka
                   :Cobweb,
                   :EM,
                   :FarthestFirst,
+                  :FilteredClusterer,
                   :HierarchicalClusterer,
+                  :MakeDensityBasedClusterer,
                   :SimpleKMeans
   end
 end

data/lib/weka/clusterers/cluster_evaluation.rb

@@ -1,12 +1,14 @@
+require 'weka/concerns'
+
 module Weka
   module Clusterers
     java_import 'weka.clusterers.ClusterEvaluation'
 
     class ClusterEvaluation
+      include Concerns::Persistent
+
       alias summary        cluster_results_to_string
       alias clusters_count num_clusters
     end
-
-    Java::WekaClusterers::ClusterEvaluation.__persistent__ = true
   end
 end

data/lib/weka/clusterers/utils.rb

@@ -27,36 +27,61 @@ module Weka
 
           error   = 'Clusterer is not trained with Instances.'
           hint    = 'You can set the training instances with #train_with_instances.'
-          message = "#{error} #{hint}"
+          message = "#{error}\n#{hint}"
 
           raise UnassignedTrainingInstancesError, message
         end
-      end
 
-      module Transformers
-        private
+        def ensure_valid_instances_structure!(instances)
+          unless instances.is_a?(Weka::Core::Instances)
+            message = 'Instances has to be a Weka::Core::Instances object.'
+            raise ArgumentError, message
+          end
+
+          return if training_instances.nil?
+          return if instances.equal_headers(training_instances)
 
-        def clusterable_instance_from(instance_or_values)
-          attributes = training_instances.attributes
-          instances  = Weka::Core::Instances.new(attributes: attributes)
+          message = 'The passed instances need to have the same structure as ' \
+                    'the clusterers training instances.'
 
-          instances.add_instance(instance_or_values)
-          instances.first
+          raise InvalidInstancesStructureError, message
+        end
+
+        def ensure_instances_structure_available!
+          return unless instances_structure.nil?
+
+          error   = 'Clusterer does not have any instances structure info.'
+          hint    = 'You probably tried to cluster values with a clusterer ' \
+                    'that is untrained or doesn’t have an ' \
+                    'instances_structure set. Please run ' \
+                    '#train_with_instances, try serializing and ' \
+                    'deserializing your clusterer again in case you used a ' \
+                    'deserialized clusterer or set its instances_structure.'
+          message = "#{error}\n#{hint}"
+
+          raise MissingInstancesStructureError, message
         end
       end
 
       module Buildable
         include Checks
 
-        attr_reader :training_instances
+        attr_reader :training_instances, :instances_structure
 
         def train_with_instances(instances)
           @training_instances = instances
+          @instances_structure = instances.string_free_structure
+
           build_clusterer(instances)
 
           self
         end
 
+        def instances_structure=(instances)
+          ensure_valid_instances_structure!(instances)
+          @instances_structure = instances.string_free_structure
+        end
+
         def evaluate(test_instances)
           ensure_trained_with_instances!
 
@@ -85,12 +110,11 @@ module Weka
 
       module Clusterable
         include Checks
-        include Transformers
 
         def cluster(instance_or_values)
-          ensure_trained_with_instances!
+          ensure_instances_structure_available!
 
-          instance = clusterable_instance_from(instance_or_values)
+          instance = instances_structure.instance_from(instance_or_values)
           cluster_instance(instance)
         end
       end
@@ -112,12 +136,11 @@ module Weka
 
       module Distributable
         include Checks
-        include Transformers
 
         def distribution_for(instance_or_values)
-          ensure_trained_with_instances!
+          ensure_instances_structure_available!
 
-          instance = clusterable_instance_from(instance_or_values)
+          instance = instances_structure.instance_from(instance_or_values)
           distribution_for_instance(instance).to_a
         end
       end

data/lib/weka/core/attribute.rb

@@ -71,7 +71,7 @@ module Weka
       # The order of the if statements is important here, because a date is also
       # a numeric.
       def internal_value_of(value)
-        return value                      if value === Float::NAN
+        return value                      if value.respond_to?(:nan?) && value.nan?
         return Float::NAN                 if [nil, '?'].include?(value)
         return parse_date(value.to_s)     if date?
         return value.to_f                 if numeric?

data/lib/weka/core/dense_instance.rb

@@ -18,17 +18,19 @@ module Weka
         enumerate_attributes.to_a
       end
 
-      def each_attribute
+      def each_attribute(&block)
         if block_given?
-          enumerate_attributes.each { |attribute| yield(attribute) }
+          enumerate_attributes.each(&block)
         else
           enumerate_attributes
         end
       end
 
-      def each_attribute_with_index
-        enumerate_attributes.each_with_index do |attribute, index|
-          yield(attribute, index) if block_given?
+      def each_attribute_with_index(&block)
+        if block_given?
+          enumerate_attributes.each_with_index(&block)
+        else
+          enumerate_attributes
         end
       end
 

data/lib/weka/core/instances.rb

@@ -47,6 +47,11 @@ module Weka
         super(relation_name.to_s, attribute_list, 0)
       end
 
+      def copy
+        constructor = Instances.java_class.declared_constructor(Instances)
+        constructor.new_instance(self).to_java(Instances)
+      end
+
       def instances
         enumerate_instances.to_a
       end
@@ -54,9 +59,8 @@ module Weka
       def attributes(include_class_attribute: false)
         attrs = enumerate_attributes.to_a
 
-        if include_class_attribute && class_attribute_defined?
-          attrs.insert(class_index, class_attribute)
-        end
+        class_available = include_class_attribute && class_attribute_defined?
+        attrs.insert(class_index, class_attribute) if class_available
 
         attrs
       end
@@ -94,31 +98,35 @@ module Weka
         check_for_attribute_type(type)
       end
 
-      def each
+      def each(&block)
         if block_given?
-          enumerate_instances.each { |instance| yield(instance) }
+          enumerate_instances.each(&block)
         else
           enumerate_instances
         end
       end
 
-      def each_with_index
-        enumerate_instances.each_with_index do |instance, index|
-          yield(instance, index) if block_given?
+      def each_with_index(&block)
+        if block_given?
+          enumerate_instances.each_with_index(&block)
+        else
+          enumerate_instances
         end
       end
 
-      def each_attribute
+      def each_attribute(&block)
         if block_given?
-          enumerate_attributes.each { |attribute| yield(attribute) }
+          enumerate_attributes.each(&block)
         else
           enumerate_attributes
         end
       end
 
-      def each_attribute_with_index
-        enumerate_attributes.each_with_index do |attribute, index|
-          yield(attribute, index) if block_given?
+      def each_attribute_with_index(&block)
+        if block_given?
+          enumerate_attributes.each_with_index(&block)
+        else
+          enumerate_attributes
         end
       end
 
@@ -267,6 +275,33 @@ module Weka
         Matrix[*instances.map(&:values)]
       end
 
+      # Wrap the attribute values for the instance to be added with
+      #   an Instance object, if needed. The Instance object is
+      #   assigned with the given weight.
+      #
+      # @param [Instance, Array, Hash] instance_or_values either the
+      #   instance object to be added or the attribute values for it.
+      #   For the latter case, it accepts an array or a hash.
+      #
+      # @param [Float] weight the weight for the Instance to be added
+      #
+      # @return [Instance] the object that contains the given
+      #   attribute values.
+      def instance_from(instance_or_values, weight: 1.0)
+        dataset = string_free_structure
+
+        if instance_or_values.is_a?(Java::WekaCore::Instance)
+          instance = instance_or_values
+          instance.weight = weight
+        else
+          data = instance_data(instance_or_values)
+          instance = DenseInstance.new(data, weight: weight)
+        end
+
+        dataset.add(instance)
+        dataset.first
+      end
+
       private
 
       def add_attribute(attribute)
@@ -274,9 +309,7 @@ module Weka
       end
 
       def ensure_attribute_defined!(name)
-        if attribute_names(include_class_attribute: true).include?(name.to_s)
-          return
-        end
+        return if attribute_names(include_class_attribute: true).include?(name.to_s)
 
         error   = "\"#{name}\" is not defined."
         hint    = 'Only defined attributes can be used as class attribute!'
@@ -291,42 +324,19 @@ module Weka
         end
       end
 
-      # Wrap the attribute values for the instance to be added with
-      #   an Instance object, if needed. The Instance object is
-      #   assigned with the given weight.
-      #
-      # @param [Instance, Array, Hash] instance_or_values either the
-      #   instance object to be added or the attribute values for it.
-      #   For the latter case, it accepts an array or a hash.
-      #
-      # @param [Float] weight the weight for the Instance to be added
-      #
-      # @return [Instance] the object that contains the given
-      #   attribute values.
-      def instance_from(instance_or_values, weight:)
-        if instance_or_values.is_a?(Java::WekaCore::Instance)
-          instance_or_values.weight = weight
-          instance_or_values
-        else
-          if instance_or_values.is_a?(Hash)
-            instance_or_values = attribute_values_from_hash(instance_or_values)
-          end
-
-          data = internal_values_of(instance_or_values)
-
-          if has_string_attribute?
-            data = check_string_attributes(data, instance_or_values)
-          end
-
-          DenseInstance.new(data, weight: weight)
-        end
-      end
-
       def map_attribute_type(type)
         return -1 unless Attribute::TYPES.include?(type.downcase.to_sym)
+
         Attribute.const_get(type.upcase)
       end
 
+      def instance_data(values)
+        values = attribute_values_from_hash(values) if values.is_a?(Hash)
+        data = internal_values_of(values)
+        data = check_string_attributes(data, values) if has_string_attribute?
+        data
+      end
+
       # Convert a hash whose keys are attribute names and values are attribute
       #   values into an array containing attribute values in the order
       #   of the Instances attributes.

data/lib/weka/core/serialization_helper.rb

@@ -3,9 +3,47 @@ module Weka
     java_import 'weka.core.SerializationHelper'
 
     class SerializationHelper
+      STRUCTURE_FILE_EXTENSION = 'structure'.freeze
+
       class << self
+        original_read = instance_method(:read)
+        original_write = instance_method(:write)
+
+        define_method(:read) do |filename|
+          object = original_read.bind(self).call(filename)
+
+          structure_filename = structure_file(filename)
+          structure_needed = object.respond_to?(:instances_structure)
+          structure_available = File.exist?(structure_filename)
+
+          if structure_needed && structure_available
+            structure = original_read.bind(self).call(structure_filename)
+            object.instances_structure = structure
+          end
+
+          object
+        end
+
+        define_method(:write) do |filename, object|
+          structure_needed = object.respond_to?(:instances_structure)
+
+          if structure_needed && object.instances_structure
+            structure_filename = structure_file(filename)
+            structure = object.instances_structure
+            original_write.bind(self).call(structure_filename, structure)
+          end
+
+          original_write.bind(self).call(filename, object)
+        end
+
         alias deserialize read
         alias serialize   write
+
+        private
+
+        def structure_file(filename)
+          "#{filename}.#{STRUCTURE_FILE_EXTENSION}"
+        end
       end
     end
   end

data/lib/weka/exceptions.rb

@@ -3,4 +3,6 @@ module Weka
 
   class UnassignedClassError < Error; end
   class UnassignedTrainingInstancesError < Error; end
+  class MissingInstancesStructureError < Error; end
+  class InvalidInstancesStructureError < Error; end
 end

data/lib/weka/filters.rb

@@ -1 +1,17 @@
 Weka.require_all :filters
+
+require 'weka/class_builder'
+
+module Weka
+  module Filters
+    include ClassBuilder
+
+    build_classes :CheckSource,
+                  :Filter,
+                  :MultiFilter,
+                  :RenameRelation,
+                  :SimpleBatchFilter,
+                  :SimpleFilter,
+                  :SimpleStreamFilter
+  end
+end

data/lib/weka/filters/unsupervised/attribute.rb

@@ -15,13 +15,16 @@ module Weka
                       :AddUserFields,
                       :AddUserFieldsBeanInfo,
                       :AddValues,
+                      :CartesianProduct,
                       :Center,
                       :ChangeDateFormat,
                       :ClassAssigner,
                       :ClusterMembership,
                       :Copy,
                       :Discretize,
+                      :DateToNumeric,
                       :FirstOrder,
+                      :FixedDictionaryStringToWordVector,
                       :InterquartileRange,
                       :KernelFilter,
                       :MakeIndicator,
@@ -34,9 +37,11 @@ module Weka
                       :Normalize,
                       :NumericCleaner,
                       :NumericToBinary,
+                      :NumericToDate,
                       :NumericToNominal,
                       :NumericTransform,
                       :Obfuscate,
+                      :OrdinalToNumeric,
                       :PartitionedMultiFilter,
                       :PKIDiscretize,
                       :PotentialClassIgnorer,

data/lib/weka/version.rb

@@ -1,3 +1,3 @@
 module Weka
-  VERSION = '0.5.0'.freeze
+  VERSION = '0.7.3'.freeze
 end

data/weka.gemspec

@@ -18,15 +18,15 @@ Gem::Specification.new do |spec|
   spec.platform               = 'java'
   spec.required_ruby_version  = '~> 2.0'
 
-  spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  spec.files         = Dir['**/{.*,*}'].reject { |f| f.match(%r{^((spec|jars|pkg)/|.*\.lock|lib/.*_jars\.rb)}) || File.directory?(f) }
   spec.bindir        = 'bin'
   spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
   spec.require_paths = ['lib']
 
-  spec.add_runtime_dependency     'lock_jar',         '~> 0.13'
+  spec.add_development_dependency 'bundler',          '~> 2.0'
+  spec.add_development_dependency 'rake',             '~> 13.0'
+  spec.add_development_dependency 'rspec',            '~> 3.10'
 
-  spec.add_development_dependency 'bundler',          '~> 1.6'
-  spec.add_development_dependency 'rake',             '~> 10.0'
-  spec.add_development_dependency 'rspec',            '~> 3.0'
-  spec.add_development_dependency 'shoulda-matchers', '~> 3.0'
+  spec.add_runtime_dependency 'jar-dependencies', '~> 0.4.1'
+  spec.requirements << 'jar nz.ac.waikato.cms.weka, weka-dev, 3.9.5'
 end

metadata

@@ -1,85 +1,71 @@
 --- !ruby/object:Gem::Specification
 name: weka
 version: !ruby/object:Gem::Version
-  version: 0.5.0
+  version: 0.7.3
 platform: java
 authors:
 - Paul Götze
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2017-06-17 00:00:00.000000000 Z
+date: 2021-01-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.13'
-  name: lock_jar
-  prerelease: false
-  type: :runtime
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.13'
-- !ruby/object:Gem::Dependency
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '2.0'
   name: bundler
-  prerelease: false
   type: :development
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '2.0'
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: '13.0'
   name: rake
-  prerelease: false
   type: :development
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: '13.0'
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.0'
+        version: '3.10'
   name: rspec
-  prerelease: false
   type: :development
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.0'
+        version: '3.10'
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.0'
-  name: shoulda-matchers
+        version: 0.4.1
+  name: jar-dependencies
+  type: :runtime
   prerelease: false
-  type: :development
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.0'
+        version: 0.4.1
 description: A JRuby wrapper for the Weka library (http://www.cs.waikato.ac.nz/ml/weka/)
 email:
 - paul.christoph.goetze@gmail.com
@@ -92,11 +78,9 @@ files:
 - ".gitignore"
 - ".rspec"
 - ".rubocop.yml"
-- ".travis.yml"
+- CHANGELOG.md
 - CODE_OF_CONDUCT.md
 - Gemfile
-- Jarfile
-- Jarfile.lock
 - MIT-LICENSE.txt
 - README.md
 - Rakefile
@@ -142,7 +126,6 @@ files:
 - lib/weka/filters/unsupervised/attribute.rb
 - lib/weka/filters/unsupervised/instance.rb
 - lib/weka/filters/utils.rb
-- lib/weka/jars.rb
 - lib/weka/version.rb
 - weka.gemspec
 homepage: https://github.com/paulgoetze/weka-jruby
@@ -163,9 +146,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
-requirements: []
-rubyforge_project:
-rubygems_version: 2.6.11
+requirements:
+- jar nz.ac.waikato.cms.weka, weka-dev, 3.9.5
+rubygems_version: 3.0.6
 signing_key:
 specification_version: 4
 summary: Machine Learning & Data Mining with JRuby.

data/.travis.yml

@@ -1,15 +0,0 @@
-sudo: false
-language: ruby
-
-rvm:
-  - jruby-9000
-
-cache:
-  - bundler
-
-before_install:
-  - rvm get head
-  - rvm use jruby-9.0.1.0 --install
-  - gem install bundler
-
-script: bundle exec rake spec

data/Jarfile

@@ -1 +0,0 @@
-jar 'nz.ac.waikato.cms.weka:weka-dev:jar:3.7.13'

data/Jarfile.lock

@@ -1,17 +0,0 @@
----
-version: 0.13.0
-groups:
-  default:
-    dependencies:
-    - nz.ac.waikato.cms.weka.thirdparty:java-cup-11b-runtime:jar:2015.03.26
-    - nz.ac.waikato.cms.weka.thirdparty:java-cup-11b:jar:2015.03.26
-    - nz.ac.waikato.cms.weka:weka-dev:jar:3.7.13
-    - org.pentaho.pentaho-commons:pentaho-package-manager:jar:1.0.11
-    artifacts:
-    - jar:nz.ac.waikato.cms.weka:weka-dev:jar:3.7.13:
-        transitive:
-          nz.ac.waikato.cms.weka.thirdparty:java-cup-11b:jar:2015.03.26: {}
-          org.pentaho.pentaho-commons:pentaho-package-manager:jar:1.0.11: {}
-          nz.ac.waikato.cms.weka.thirdparty:java-cup-11b-runtime:jar:2015.03.26: {}
-remote_repositories:
-- http://repo1.maven.org/maven2/

data/lib/weka/jars.rb

@@ -1,16 +0,0 @@
-module Weka
-  module Jars
-    def self.included(base)
-      base.class_eval do
-        require 'lock_jar'
-
-        lib_path = File.expand_path('../../', File.dirname(__FILE__))
-        lockfile = File.join(lib_path, 'Jarfile.lock')
-        jars_dir = File.join(lib_path, 'jars')
-
-        LockJar.install(lockfile, local_repo: jars_dir)
-        LockJar.load(lockfile, local_repo: jars_dir)
-      end
-    end
-  end
-end