libsvmloader 0.1.1 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: e72c3f971474f334d77a6cc023177234df573134
+SHA256:
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+  data.tar.gz: e4b83b0e4afc8c3760bd54b79349d8e5920a2cf7503194ee5a223bfec2517fd8
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data/.coveralls.yml

@@ -0,0 +1 @@
+service_name: github-ci

data/.github/workflows/build.yml

@@ -0,0 +1,22 @@
+name: build
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-20.04
+    strategy:
+      fail-fast: false
+      matrix:
+        ruby: [ '2.6', '2.7', '3.0' ]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Ruby ${{ matrix.ruby }}
+        uses: actions/setup-ruby@v1
+        with:
+          ruby-version: ${{ matrix.ruby }}
+      - name: Build and test with Rake
+        run: |
+          gem install --no-document bundler
+          bundle install --jobs 4 --retry 3
+          bundle exec rake

data/.github/workflows/coverage.yml

@@ -0,0 +1,26 @@
+name: coverage
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  coverage:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Ruby 2.7
+        uses: actions/setup-ruby@v1
+        with:
+          ruby-version: '2.7'
+      - name: Build and test with Rake
+        run: |
+          gem install bundler
+          bundle install
+          bundle exec rake
+      - name: Coveralls GitHub Action
+        uses: coverallsapp/github-action@v1.1.2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}

data/.gitignore

@@ -8,5 +8,14 @@
 /spec/reports/
 /tmp/
 
+
 # rspec failure tracking
 .rspec_status
+
+*.swp
+.DS_Store
+.ruby-version
+/spec/dump_cmp.t
+/spec/dump_dbl.t
+/spec/dump_int.t
+/spec/dump_zb.t

data/.rubocop.yml

@@ -0,0 +1,20 @@
+require:
+  - rubocop-performance
+
+AllCops:
+  NewCops: enable
+
+Metrics/LineLength:
+  Max: 120
+
+Metrics/ModuleLength:
+  Max: 200
+
+Metrics/ClassLength:
+  Max: 200
+
+Metrics/MethodLength:
+  Max: 40
+
+Style/FormatStringToken:
+  Enabled: false

data/CHANGELOG.md

@@ -0,0 +1,27 @@
+# 0.3.0
+- Add type declaration file: sig/libsvmloader.rbs
+- Refactor to avoid returning nil on array access.
+- Fix some configuration files.
+
+# 0.2.1
+- Fixed the bug that failed to load if there is a space at the end of the line.
+
+# 0.2.0
+## Breaking changes
+
+LibSVMLoader has been modified to return the samples and labels of dataset as Ruby Array.
+Thus, LibSVMLoader does not require NMatrix.
+
+# 0.1.3
+- Changed the visibility of protected methods to the private.
+- Fixed the description in the gemspec file.
+
+# 0.1.2
+- Changed the way to read a file.
+
+# 0.1.1
+- Fixed to fail reading zero vectors.
+
+# 0.1.0
+- Added basic class.
+- Added the methods that read and write a file with libsvm format.

data/Gemfile

@@ -4,3 +4,11 @@ git_source(:github) {|repo_name| "https://github.com/#{repo_name}" }
 
 # Specify your gem's dependencies in libsvmloader.gemspec
 gemspec
+
+gem 'bundler', '~> 2.0'
+gem 'rake', '~> 13.0'
+gem 'rspec', '~> 3.0'
+gem 'simplecov', '~> 0.19'
+gem 'simplecov-lcov', '~> 0.8'
+gem 'rbs', '~> 1.2'
+gem 'steep', '~> 0.44'

data/LICENSE.txt

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2017 yoshoku
+Copyright (c) 2017-2021 yoshoku
 
 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

@@ -1,5 +1,10 @@
 # LibSVMLoader
 
+[![Build Status](https://github.com/yoshoku/LibSVMLoader/workflows/build/badge.svg)](https://github.com/yoshoku/LibSVMLoader/actions?query=workflow%3Abuild)
+[![Coverage Status](https://coveralls.io/repos/github/yoshoku/LibSVMLoader/badge.svg?branch=main)](https://coveralls.io/github/yoshoku/LibSVMLoader?branch=main)
+[![Gem Version](https://badge.fury.io/rb/libsvmloader.svg)](https://badge.fury.io/rb/libsvmloader)
+[![MIT License](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/yoshoku/LibSVMLoader/blob/main/LICENSE.txt)
+
 LibSVMLoader loads (and dumps) dataset file with the libsvm file format.
 
 ## Installation
@@ -28,15 +33,37 @@ samples, labels = LibSVMLoader.load_libsvm_file('foo.t')
 LibSVMLoader.dump_libsvm_file(samples, labels, 'bar.t')
 
 # for regression task
-samples, target_variables = LibSVMLoader.load_libsvm_file('foo.t', label_dtype: :float64)
+samples, target_variables = LibSVMLoader.load_libsvm_file('foo.t', label_dtype: 'float')
 LibSVMLoader.dump_libsvm_file(samples, target_variables, 'bar.t')
 ```
 
-## Development
+When using with Numo::NArray:
+
+```ruby
+require 'libsvmloader'
+require 'numo/narray'
+
+samples, labels = LibSVMLoader.load_libsvm_file('foo.t')
+
+samples_na = Numo::NArray[*samples]
+labels_na = Numo::NArray[*labels]
+
+LibSVMLoader.dump_libsvm_file(samples_na.to_a, labels_na.to_a, 'bar.t')
+```
+
+When using with NMatrix:
+
+```ruby
+require 'libsvmloader'
+require 'nmatrix/nmatrix'
+
+samples, labels = LibSVMLoader.load_libsvm_file('foo.t')
 
-After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+samples_nm = N[*samples]
+labels_nm = N[*labels]
 
-To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+LibSVMLoader.dump_libsvm_file(samples_nm.to_a, labels_nm.to_a, 'bar.t')
+```
 
 ## Contributing
 

data/Steepfile

@@ -0,0 +1,20 @@
+target :lib do
+  signature "sig"
+#
+  check "lib"                       # Directory name
+#   check "Gemfile"                   # File name
+#   check "app/models/**/*.rb"        # Glob
+#   # ignore "lib/templates/*.rb"
+#
+#   # library "pathname", "set"       # Standard libraries
+#   # library "strong_json"           # Gems
+end
+
+# target :spec do
+#   signature "sig", "sig-private"
+#
+#   check "spec"
+#
+#   # library "pathname", "set"       # Standard libraries
+#   # library "rspec"
+# end

data/lib/libsvmloader.rb

@@ -1,95 +1,116 @@
+# frozen_string_literal: true
 
 require 'libsvmloader/version'
-require 'nmatrix/nmatrix'
+require 'csv'
 
 # LibSVMLoader loads (and dumps) dataset file with the libsvm file format.
 class LibSVMLoader
   class << self
-    # Load a dataset with the libsvm file format into NMatrix.
+    # Load a dataset with the libsvm file format.
     #
-    # @param filename    [String]  A path to a dataset file.
+    # @param filename    [String]  Path to a dataset file.
     # @param zero_based  [Boolean] Whether the column index starts from 0 (true) or 1 (false).
-    # @param stype       [Symbol]  The strorage type of the nmatrix consisting of feature vectors.
-    # @param label_dtype [Symbol]  The data type of the NMatrix consisting of labels or target values.
-    # @param value_dtype [Symbol]  The data type of the NMatrix consisting of feature vectors.
+    # @param label_dtype [String]  Data type of labels or target values ('int', 'float', 'complex').
+    # @param value_dtype [String]  Data type of feature vectors ('int', 'float', 'complex').
     #
-    # @return [Array<NMatrix>]
+    # @return [Array<Array>]
     #   Returns array containing the (n_samples x n_features) matrix for feature vectors
-    #   and (n_samples x 1) matrix for labels or target values.
-    def load_libsvm_file(filename, zero_based: false, stype: :yale,
-                         label_dtype: :int32, value_dtype: :float64)
-      ftvecs = []
+    #   and (n_samples) vector for labels or target values.
+    def load_libsvm_file(filename, zero_based: false, label_dtype: 'int', value_dtype: 'float')
       labels = []
-      n_features = 0
-      File.open(filename, 'r') do |file|
-        file.each_line do |line|
-          label, ftvec, max_idx = parse_libsvm_line(line, zero_based)
-          labels.push(label)
-          ftvecs.push(ftvec)
-          n_features = [n_features, max_idx].max
-        end
+      ftvecs = []
+      maxids = []
+      label_class = parse_dtype(label_dtype)
+      value_class = parse_dtype(value_dtype)
+      CSV.foreach(filename, col_sep: "\s", headers: false) do |row|
+        label, ftvec, maxid = parse_libsvm_row(row, zero_based, label_class, value_class)
+        labels.push(label)
+        ftvecs.push(ftvec)
+        maxids.push(maxid)
       end
-      [convert_to_nmatrix(ftvecs, n_features, value_dtype, stype),
-       NMatrix.new([labels.size, 1], labels, dtype: label_dtype)]
+      [convert_to_matrix(ftvecs, maxids.max + 1, value_class), labels]
     end
 
     # Dump the dataset with the libsvm file format.
     #
-    # @param data       [NMatrix] (n_samples x n_features) matrix consisting of feature vectors.
-    # @param labels     [NMatrix] (n_samples x 1) matrix consisting of labels or target values.
-    # @param filename   [String]  A path to the output libsvm file.
+    # @param data       [Array] (n_samples x n_features) matrix consisting of feature vectors.
+    # @param labels     [Array] (n_samples) vector consisting of labels or target values.
+    # @param filename   [String]  Path to the output libsvm file.
     # @param zero_based [Boolean] Whether the column index starts from 0 (true) or 1 (false).
     def dump_libsvm_file(data, labels, filename, zero_based: false)
-      n_samples = [data.rows, labels.rows].min
-      label_type = detect_dtype(labels)
-      value_type = detect_dtype(data)
+      n_samples = data.size < labels.size ? data.size : labels.size
+      label_format = detect_format(labels[0])
+      value_format = detect_format(data.flatten[0])
       File.open(filename, 'w') do |file|
-        n_samples.times do |n|
-          file.puts(dump_libsvm_line(labels[n], data.row(n),
-                                     label_type, value_type, zero_based))
-        end
+        n_samples.times { |n| file.puts(dump_libsvm_line(labels[n], data[n], label_format, value_format, zero_based)) }
       end
     end
 
-    protected
+    private
 
-    def parse_libsvm_line(line, zero_based)
-      tokens = line.split
-      label = tokens.shift.to_f
-      ftvec = tokens.map do |el|
+    def parse_libsvm_row(row, zero_based, label_type, value_type)
+      label = convert_type(row.shift, label_type)
+      adj_idx = zero_based == false ? 1 : 0
+      max_idx = -1
+      ftvec = []
+      while (el = row.shift)
         idx, val = el.split(':')
-        idx = idx.to_i - (zero_based == false ? 1 : 0)
-        [idx, val.to_f]
+        idx = idx.to_i - adj_idx
+        max_idx = idx if max_idx < idx
+        ftvec.push([idx, convert_type(val, value_type)])
       end
-      max_idx = ftvec.map { |el| el[0] }.max
-      max_idx ||= 0
       [label, ftvec, max_idx]
     end
 
-    def convert_to_nmatrix(data, n_features, value_dtype, stype)
-      n_samples = data.size
-      mat = NMatrix.zeros([n_samples, n_features + 1],
-                          dtype: value_dtype, stype: stype)
-      data.each_with_index do |ftvec, n|
-        ftvec.each do |el|
-          mat[n, el[0]] = el[1]
-        end
+    def parse_dtype(dtype)
+      case dtype.to_s
+      when /^(int)/i
+        :int
+      when /^(float)/i
+        :float
+      when /^(complex)/i
+        :complex
+      else
+        :string
+      end
+    end
+
+    def convert_type(value, dtype)
+      case dtype
+      when :int
+        value.to_i
+      when :float
+        value.to_f
+      when :complex
+        value.to_c
+      else
+        value
+      end
+    end
+
+    def convert_to_matrix(data, n_features, value_type)
+      z = convert_type(0, value_type)
+      data.map do |ft|
+        vec = Array.new(n_features) { z }
+        ft.each { |idx, val| vec[idx] = val }
+        vec
       end
-      mat
     end
 
-    def detect_dtype(data)
+    def detect_format(data)
       type = '%s'
-      type = '%d' if %i[int8 int16 int32 int64].include?(data.dtype)
-      type = '%.10g' if %i[float32 float64].include?(data.dtype)
+      type = '%d' if data.is_a?(Integer)
+      type = '%.10g' if data.is_a?(Float)
       type
     end
 
-    def dump_libsvm_line(label, ftvec, label_type, value_type, zero_based)
-      line = format(label_type.to_s, label)
-      ftvec.to_a.each_with_index do |val, n|
-        idx = n + (zero_based == false ? 1 : 0)
-        line += format(" %d:#{value_type}", idx, val) if val != 0.0
+    def dump_libsvm_line(label, ftvec, label_format, value_format, zero_based)
+      line = format(label_format, label)
+      ftvec.each_with_index do |val, n|
+        unless val.zero?
+          idx = n + (zero_based == false ? 1 : 0)
+          line += format(" %d:#{value_format}", idx, val)
+        end
       end
       line
     end

data/lib/libsvmloader/version.rb

@@ -1,11 +1,5 @@
-#module LibSVMLoader
-#  VERSION = "0.1.0"
-#end
+# frozen_string_literal: true
+
 class LibSVMLoader
-  module VERSION
-    MAJOR = 0
-    MINOR = 1
-    TINY = 1
-    STRING = [MAJOR, MINOR, TINY].compact.join('.')
-  end
+  VERSION = '0.3.0'
 end

data/libsvmloader.gemspec

@@ -1,27 +1,28 @@
 # coding: utf-8
-lib = File.expand_path("../lib", __FILE__)
+lib = File.expand_path('../lib', __FILE__)
 $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
-require "libsvmloader/version"
+require 'libsvmloader/version'
 
 Gem::Specification.new do |spec|
-  spec.name          = "libsvmloader"
-  spec.version       = LibSVMLoader::VERSION::STRING
-  spec.authors       = ["yoshoku"]
-  spec.email         = ["yoshoku@outlook.com"]
+  spec.name          = 'libsvmloader'
+  spec.version       = LibSVMLoader::VERSION
+  spec.authors       = ['yoshoku']
+  spec.email         = ['yoshoku@outlook.com']
 
-  spec.summary       = %q{LibSVMLoader loads (and dumps) dataset file with the libsvm file format.}
-  spec.homepage      = "https://github.com/yoshoku/libsvmloader"
-  spec.license       = "MIT"
+  spec.summary       = <<MSG
+LibSVMLoader loads (and dumps) dataset file with the libsvm file format.
+MSG
+  spec.description   = <<MSG
+LibSVMLoader is a class that loads (and dumps) dataset file with the libsvm file format.
+The feature vectors and labels of dataset are represented by Ruby Array.
+MSG
+  spec.homepage      = 'https://github.com/yoshoku/libsvmloader'
+  spec.license       = 'MIT'
 
   spec.files         = `git ls-files -z`.split("\x0").reject do |f|
     f.match(%r{^(test|spec|features)/})
   end
-  spec.bindir        = "exe"
+  spec.bindir        = 'exe'
   spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
-  spec.require_paths = ["lib"]
-
-  spec.add_development_dependency "bundler", "~> 1.15"
-  spec.add_development_dependency "rake", "~> 10.0"
-  spec.add_development_dependency "rspec", "~> 3.0"
-  spec.add_development_dependency "nmatrix", "~> 0.2.3"
+  spec.require_paths = ['lib']
 end

data/sig/libsvmloader.rbs

@@ -0,0 +1,18 @@
+# LibSVMLoader loads (and dumps) dataset file with the libsvm file format.
+class LibSVMLoader
+  VERSION: String
+
+  def self.load_libsvm_file: (String filename, ?zero_based: bool zero_based,
+                              ?label_dtype: String label_dtype, ?value_dtype: String value_dtype) -> Array[Array[untyped]]
+  def self.dump_libsvm_file: (Array[Array[untyped]] data, Array[Numeric | String] labels, String filename,
+                              ?zero_based: bool zero_based) -> void
+
+  private
+
+  def self.parse_libsvm_row: (Array[String] row, bool zero_based, Symbol label_type, Symbol value_type) -> Array[untyped]
+  def self.parse_dtype: (String | Symbol dtype) -> Symbol
+  def self.convert_type: (untyped value, Symbol dtype) -> untyped
+  def self.convert_to_matrix: (Array[untyped] data, Integer n_features, Symbol value_type) -> Array[Array[untyped]]
+  def self.detect_format: (untyped data) -> String
+  def self.dump_libsvm_line: (Numeric | String label, Array[untyped] ftvec, String label_format, String value_format, bool zero_based) -> String
+end

metadata

@@ -1,93 +1,41 @@
 --- !ruby/object:Gem::Specification
 name: libsvmloader
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.3.0
 platform: ruby
 authors:
 - yoshoku
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2017-09-11 00:00:00.000000000 Z
-dependencies:
-- !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.15'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.15'
-- !ruby/object:Gem::Dependency
-  name: rake
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '10.0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '10.0'
-- !ruby/object:Gem::Dependency
-  name: rspec
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.0'
-- !ruby/object:Gem::Dependency
-  name: nmatrix
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 0.2.3
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 0.2.3
-description: 
+date: 2021-06-12 00:00:00.000000000 Z
+dependencies: []
+description: |
+  LibSVMLoader is a class that loads (and dumps) dataset file with the libsvm file format.
+  The feature vectors and labels of dataset are represented by Ruby Array.
 email:
 - yoshoku@outlook.com
-executables:
-- libsvmloader
+executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- ".coveralls.yml"
+- ".github/workflows/build.yml"
+- ".github/workflows/coverage.yml"
 - ".gitignore"
 - ".rspec"
-- ".travis.yml"
+- ".rubocop.yml"
+- CHANGELOG.md
 - CODE_OF_CONDUCT.md
 - Gemfile
 - LICENSE.txt
 - README.md
 - Rakefile
-- bin/console
-- bin/setup
-- exe/libsvmloader
+- Steepfile
 - lib/libsvmloader.rb
 - lib/libsvmloader/version.rb
 - libsvmloader.gemspec
+- sig/libsvmloader.rbs
 homepage: https://github.com/yoshoku/libsvmloader
 licenses:
 - MIT
@@ -107,8 +55,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.6.13
+rubygems_version: 3.1.6
 signing_key: 
 specification_version: 4
 summary: LibSVMLoader loads (and dumps) dataset file with the libsvm file format.

data/.travis.yml

@@ -1,5 +0,0 @@
-sudo: false
-language: ruby
-rvm:
-  - 2.4.1
-before_install: gem install bundler -v 1.15.3

data/bin/console

@@ -1,14 +0,0 @@
-#!/usr/bin/env ruby
-
-require "bundler/setup"
-require "libsvmloader"
-
-# You can add fixtures and/or initialization code here to make experimenting
-# with your gem easier. You can also use a different console, if you like.
-
-# (If you use this, don't forget to add pry to your Gemfile!)
-# require "pry"
-# Pry.start
-
-require "irb"
-IRB.start(__FILE__)

data/bin/setup

@@ -1,8 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-IFS=$'\n\t'
-set -vx
-
-bundle install
-
-# Do any other automated setup that you need to do here

data/exe/libsvmloader

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-
-require "libsvmloader"