numo-libsvm 1.0.2 → 2.0.0

data/ext/numo/libsvm/src/COPYRIGHT

@@ -0,0 +1,31 @@
+
+Copyright (c) 2000-2019 Chih-Chung Chang and Chih-Jen Lin
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+
+1. Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+3. Neither name of copyright holders nor the names of its contributors
+may be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE REGENTS OR
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

data/lib/numo/libsvm/version.rb

@@ -3,6 +3,6 @@
 module Numo
   module Libsvm
     # The version of Numo::Libsvm you are using.
-    VERSION = '1.0.2'
+    VERSION = '2.0.0'
   end
 end

data/sig/numo/libsvm.rbs

@@ -0,0 +1,65 @@
+module Numo
+  module Libsvm
+    module SvmType
+      C_SVC: Integer
+      NU_SVC: Integer
+      ONE_CLASS: Integer
+      EPSILON_SVR: Integer
+      NU_SVR: Integer
+    end
+
+    module KenelType
+      LINEAR: Integer
+      POLY: Integer
+      RBF: Integer
+      SIGMOID: Integer
+      PRECOMPUTED: Integer
+    end
+
+    LIBSVM_VERSION: Integer
+    VERSION: String
+
+    type model = {
+      nr_class: Integer,
+      l: Integer,
+      SV: Numo::DFloat,
+      sv_coef: Numo::DFloat,
+      rho: Numo::DFloat,
+      probA: Numo::DFloat,
+      probB: Numo::DFloat,
+      sv_indices: Numo::Int32,
+      label: Numo::Int32,
+      nSV: Numo::Int32,
+      free_sv: Integer
+    }
+
+    type param = {
+      svm_type: Integer?,
+      kernel_type: Integer?,
+      degree: Integer?,
+      gamma: Float?,
+      coef0: Float?,
+      cache_size: Float?,
+      eps: Float?,
+      C: Float?,
+      nr_weight: Integer?,
+      weight_label: Numo::Int32?,
+      weight: Numo::DFloat?,
+      nu: Float?,
+      p: Float?,
+      shrinking: bool?,
+      probability: bool?,
+      verbose: bool?,
+      random_seed: Integer?
+    }
+
+    def self?.cv: (Numo::DFloat x, Numo::DFloat y, param, Integer n_folds) -> Numo::DFloat
+    def self?.train: (Numo::DFloat x, Numo::DFloat y, param) -> model
+    def self?.predict: (Numo::DFloat x, param, model) -> Numo::DFloat
+    def self?.predict_proba: (Numo::DFloat x, param, model) -> Numo::DFloat
+    def self?.decision_function: (Numo::DFloat x, param, model) -> Numo::DFloat
+    def self?.save_svm_model: (String filename, param, model) -> bool
+    def self?.load_svm_model: (String filename) -> [param, model]
+  end
+end
+

metadata

@@ -1,85 +1,29 @@
 --- !ruby/object:Gem::Specification
 name: numo-libsvm
 version: !ruby/object:Gem::Version
-  version: 1.0.2
+  version: 2.0.0
 platform: ruby
 authors:
 - yoshoku
 autorequire:
 bindir: exe
 cert_chain: []
-date: 2021-01-23 00:00:00.000000000 Z
+date: 2022-01-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: numo-narray
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.9.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.9.1
-- !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '2.0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '2.0'
-- !ruby/object:Gem::Dependency
-  name: rake
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '12.0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '12.0'
-- !ruby/object:Gem::Dependency
-  name: rake-compiler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.0'
-- !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'
 description: |
   Numo::Libsvm is a Ruby gem binding to the LIBSVM library.
   LIBSVM is one of the famous libraries that implemented Support Vector Machines,
@@ -92,36 +36,18 @@ extensions:
 - ext/numo/libsvm/extconf.rb
 extra_rdoc_files: []
 files:
-- ".github/workflows/build.yml"
-- ".gitignore"
-- ".gitmodules"
-- ".rspec"
 - CHANGELOG.md
-- CODE_OF_CONDUCT.md
-- Gemfile
 - LICENSE.txt
 - README.md
-- Rakefile
-- ext/numo/libsvm/converter.c
-- ext/numo/libsvm/converter.h
 - ext/numo/libsvm/extconf.rb
-- ext/numo/libsvm/kernel_type.c
-- ext/numo/libsvm/kernel_type.h
-- ext/numo/libsvm/libsvm/svm.cpp
-- ext/numo/libsvm/libsvm/svm.h
-- ext/numo/libsvm/libsvmext.c
-- ext/numo/libsvm/libsvmext.h
-- ext/numo/libsvm/svm_model.c
-- ext/numo/libsvm/svm_model.h
-- ext/numo/libsvm/svm_parameter.c
-- ext/numo/libsvm/svm_parameter.h
-- ext/numo/libsvm/svm_problem.c
-- ext/numo/libsvm/svm_problem.h
-- ext/numo/libsvm/svm_type.c
-- ext/numo/libsvm/svm_type.h
+- ext/numo/libsvm/libsvmext.cpp
+- ext/numo/libsvm/libsvmext.hpp
+- ext/numo/libsvm/src/COPYRIGHT
+- ext/numo/libsvm/src/svm.cpp
+- ext/numo/libsvm/src/svm.h
 - lib/numo/libsvm.rb
 - lib/numo/libsvm/version.rb
-- numo-libsvm.gemspec
+- sig/numo/libsvm.rbs
 homepage: https://github.com/yoshoku/numo-libsvm
 licenses:
 - BSD-3-Clause
@@ -144,7 +70,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.3
+rubygems_version: 3.3.3
 signing_key:
 specification_version: 4
 summary: Numo::Libsvm is a Ruby gem binding to the LIBSVM library. Numo::Libsvm makes

data/.github/workflows/build.yml

@@ -1,27 +0,0 @@
-name: build
-
-on: [push, pull_request]
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        ruby: [ '2.5', '2.6', '2.7' ]
-    steps:
-      - uses: actions/checkout@v2
-      - name: Checkout submodule
-        shell: bash
-        run: |
-          auth_header="$(git config --local --get http.https://github.com/.extraheader)"
-          git submodule sync --recursive
-          git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
-      - 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 bundler
-          bundle install --jobs 4 --retry 3
-          bundle exec rake

data/.gitignore

@@ -1,20 +0,0 @@
-/.bundle/
-/.yardoc
-/Gemfile.lock
-/_yardoc/
-/coverage/
-/doc/
-/pkg/
-/spec/reports/
-/tmp/
-/bin/
-
-# rspec failure tracking
-.rspec_status
-
-*.swp
-*.bundle
-mkmf.log
-tags
-.DS_Store
-.ruby-version

data/.gitmodules

@@ -1,3 +0,0 @@
-[submodule "ext/numo/libsvm/libsvm"]
-	path = ext/numo/libsvm/libsvm
-	url = https://github.com/cjlin1/libsvm.git

data/.rspec

@@ -1,3 +0,0 @@
---format documentation
---color
---require spec_helper

data/CODE_OF_CONDUCT.md

@@ -1,74 +0,0 @@
-# Contributor Covenant Code of Conduct
-
-## Our Pledge
-
-In the interest of fostering an open and welcoming environment, we as
-contributors and maintainers pledge to making participation in our project and
-our community a harassment-free experience for everyone, regardless of age, body
-size, disability, ethnicity, gender identity and expression, level of experience,
-nationality, personal appearance, race, religion, or sexual identity and
-orientation.
-
-## Our Standards
-
-Examples of behavior that contributes to creating a positive environment
-include:
-
-* 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
-
-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 both within project spaces and in public spaces
-when an individual is representing the project or its community. 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 yoshoku@outlook.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 [http://contributor-covenant.org/version/1/4][version]
-
-[homepage]: http://contributor-covenant.org
-[version]: http://contributor-covenant.org/version/1/4/

data/Gemfile

@@ -1,4 +0,0 @@
-source "https://rubygems.org"
-
-# Specify your gem's dependencies in numo-libsvm.gemspec
-gemspec

data/Rakefile

@@ -1,15 +0,0 @@
-require 'bundler/gem_tasks'
-require 'rspec/core/rake_task'
-
-RSpec::Core::RakeTask.new(:spec)
-
-require 'rake/extensiontask'
-
-task :build => :compile
-
-Rake::ExtensionTask.new('libsvmext') do |ext|
-  ext.ext_dir = 'ext/numo/libsvm'
-  ext.lib_dir = 'lib/numo/libsvm'
-end
-
-task :default => [:clobber, :compile, :spec]

data/ext/numo/libsvm/converter.c

@@ -1,204 +0,0 @@
-
-#include "converter.h"
-
-VALUE int_vec_to_nary(int* const arr, int const size)
-{
-  int i;
-  size_t shape[1] = { size };
-  VALUE v = rb_narray_new(numo_cInt32, 1, shape);
-  int32_t* vp = (int32_t*)na_get_pointer_for_write(v);
-  for (i = 0; i < size; i++) { vp[i] = (int32_t)arr[i]; }
-  return v;
-}
-
-int* nary_to_int_vec(VALUE vec_val)
-{
-  int i;
-  int n_elements;
-  narray_t* vec_nary;
-  int32_t* vec_pt;
-  int* vec;
-
-  if (vec_val == Qnil) return NULL;
-
-  GetNArray(vec_val, vec_nary);
-  n_elements = (int)NA_SHAPE(vec_nary)[0];
-
-  vec = ALLOC_N(int, n_elements);
-  vec_pt = (int32_t*)na_get_pointer_for_read(vec_val);
-  for (i = 0; i < n_elements; i++) { vec[i] = (int)vec_pt[i]; }
-
-  RB_GC_GUARD(vec_val);
-
-  return vec;
-}
-
-VALUE dbl_vec_to_nary(double* const arr, int const size)
-{
-  int i;
-  size_t shape[1] = { size };
-  VALUE v = rb_narray_new(numo_cDFloat, 1, shape);
-  double* vp = (double*)na_get_pointer_for_write(v);
-  for (i = 0; i < size; i++) { vp[i] = arr[i]; }
-  return v;
-}
-
-double* nary_to_dbl_vec(VALUE vec_val)
-{
-  int n_elements;
-  narray_t* vec_nary;
-  double* vec_pt;
-  double* vec;
-
-  if (vec_val == Qnil) return NULL;
-
-  GetNArray(vec_val, vec_nary);
-  n_elements = (int)NA_SHAPE(vec_nary)[0];
-
-  vec = ALLOC_N(double, n_elements);
-  vec_pt = (double*)na_get_pointer_for_read(vec_val);
-  memcpy(vec, vec_pt, n_elements * sizeof(double));
-
-  RB_GC_GUARD(vec_val);
-
-  return vec;
-}
-
-VALUE dbl_mat_to_nary(double** const mat, int const n_rows, int const n_cols)
-{
-  int i, j;
-  size_t shape[2] = { n_rows, n_cols };
-  VALUE v = rb_narray_new(numo_cDFloat, 2, shape);
-  double* vp = (double*)na_get_pointer_for_write(v);
-
-  for (i = 0; i < n_rows; i++) {
-    for (j = 0; j < n_cols; j++) {
-      vp[i * n_cols + j] = mat[i][j];
-    }
-  }
-
-  return v;
-}
-
-double** nary_to_dbl_mat(VALUE mat_val)
-{
-  int i, j;
-  int n_rows, n_cols;
-  narray_t* mat_nary;
-  double* mat_pt;
-  double** mat;
-
-  if (mat_val == Qnil) return NULL;
-
-  GetNArray(mat_val, mat_nary);
-  n_rows = (int)NA_SHAPE(mat_nary)[0];
-  n_cols = (int)NA_SHAPE(mat_nary)[1];
-
-  mat_pt = (double*)na_get_pointer_for_read(mat_val);
-  mat = ALLOC_N(double*, n_rows);
-  for (i = 0; i < n_rows; i++) {
-    mat[i] = ALLOC_N(double, n_cols);
-    for (j = 0; j < n_cols; j++) {
-      mat[i][j] = mat_pt[i * n_cols + j];
-    }
-  }
-
-  RB_GC_GUARD(mat_val);
-
-  return mat;
-}
-
-VALUE svm_nodes_to_nary(struct svm_node** const support_vecs, const int n_support_vecs)
-{
-  int i, j;
-  int n_dimensions = 0;
-  size_t shape[2] = { n_support_vecs, 1 };
-  VALUE v;
-  double* vp;
-
-  for (i = 0; i < n_support_vecs; i++) {
-    for (j = 0; support_vecs[i][j].index != -1; j++) {
-      if (n_dimensions < support_vecs[i][j].index) {
-        n_dimensions = support_vecs[i][j].index;
-      }
-    }
-  }
-
-  shape[1] = n_dimensions;
-  v = rb_narray_new(numo_cDFloat, 2, shape);
-  vp = (double*)na_get_pointer_for_write(v);
-  memset(vp, 0, n_support_vecs * n_dimensions * sizeof(double));
-
-  for (i = 0; i < n_support_vecs; i++) {
-    for (j = 0; support_vecs[i][j].index != -1; j++) {
-      vp[i * n_dimensions + support_vecs[i][j].index - 1] = support_vecs[i][j].value;
-    }
-  }
-
-  return v;
-}
-
-struct svm_node** nary_to_svm_nodes(VALUE nary_val)
-{
-  int i, j, k;
-  int n_rows, n_cols, n_nonzero_cols;
-  narray_t* nary;
-  double* nary_pt;
-  struct svm_node** support_vecs;
-
-  if (nary_val == Qnil) return NULL;
-
-  GetNArray(nary_val, nary);
-  n_rows = (int)NA_SHAPE(nary)[0];
-  n_cols = (int)NA_SHAPE(nary)[1];
-
-  nary_pt = (double*)na_get_pointer_for_read(nary_val);
-  support_vecs = ALLOC_N(struct svm_node*, n_rows);
-  for (i = 0; i < n_rows; i++) {
-    n_nonzero_cols = 0;
-    for (j = 0; j < n_cols; j++) {
-      if (nary_pt[i * n_cols + j] != 0) {
-        n_nonzero_cols++;
-      }
-    }
-    support_vecs[i] = ALLOC_N(struct svm_node, n_nonzero_cols + 1);
-    for (j = 0, k = 0; j < n_cols; j++) {
-      if (nary_pt[i * n_cols + j] != 0) {
-        support_vecs[i][k].index = j + 1;
-        support_vecs[i][k].value = nary_pt[i * n_cols + j];
-        k++;
-      }
-    }
-    support_vecs[i][n_nonzero_cols].index = -1;
-    support_vecs[i][n_nonzero_cols].value = 0.0;
-  }
-
-  RB_GC_GUARD(nary_val);
-
-  return support_vecs;
-}
-
-struct svm_node* dbl_vec_to_svm_node(double* const arr, int const size)
-{
-  int i, j;
-  int n_nonzero_elements;
-  struct svm_node* node;
-
-  n_nonzero_elements = 0;
-  for (i = 0; i < size; i++) {
-    if (arr[i] != 0.0) n_nonzero_elements++;
-  }
-
-  node = ALLOC_N(struct svm_node, n_nonzero_elements + 1);
-  for (i = 0, j = 0; i < size; i++) {
-    if (arr[i] != 0.0) {
-      node[j].index = i + 1;
-      node[j].value = arr[i];
-      j++;
-    }
-  }
-  node[n_nonzero_elements].index = -1;
-  node[n_nonzero_elements].value = 0.0;
-
-  return node;
-}

data/ext/numo/libsvm/converter.h

@@ -1,20 +0,0 @@
-#ifndef NUMO_LIBSVM_CONVERTER_H
-#define NUMO_LIBSVM_CONVERTER_H 1
-
-#include <string.h>
-#include <svm.h>
-#include <ruby.h>
-#include <numo/narray.h>
-#include <numo/template.h>
-
-VALUE int_vec_to_nary(int* const arr, int const size);
-int* nary_to_int_vec(VALUE vec_val);
-VALUE dbl_vec_to_nary(double* const arr, int const size);
-double* nary_to_dbl_vec(VALUE vec_val);
-VALUE dbl_mat_to_nary(double** const mat, int const n_rows, int const n_cols);
-double** nary_to_dbl_mat(VALUE mat_val);
-VALUE svm_nodes_to_nary(struct svm_node** const support_vecs, const int n_support_vecs);
-struct svm_node** nary_to_svm_nodes(VALUE nary_val);
-struct svm_node* dbl_vec_to_svm_node(double* const arr, int const size);
-
-#endif /* NUMO_LIBSVM_CONVERTER_H */

data/ext/numo/libsvm/kernel_type.c

@@ -1,22 +0,0 @@
-#include "kernel_type.h"
-
-RUBY_EXTERN VALUE mLibsvm;
-
-void rb_init_kernel_type_module()
-{
-  /**
-   * Document-module: Numo::Libsvm::KernelType
-   * The module consisting of constants for kernel type that used for parameter of LIBSVM.
-   */
-  VALUE mKernelType = rb_define_module_under(mLibsvm, "KernelType");
-  /* Linear kernel; u' * v */
-  rb_define_const(mKernelType, "LINEAR", INT2NUM(LINEAR));
-  /* Polynomial kernel; (gamma * u' * v + coef0)^degree */
-  rb_define_const(mKernelType, "POLY", INT2NUM(POLY));
-  /* RBF kernel; exp(-gamma * ||u - v||^2) */
-  rb_define_const(mKernelType, "RBF", INT2NUM(RBF));
-  /* Sigmoid kernel; tanh(gamma * u' * v + coef0) */
-  rb_define_const(mKernelType, "SIGMOID", INT2NUM(SIGMOID));
-  /* Precomputed kernel */
-  rb_define_const(mKernelType, "PRECOMPUTED", INT2NUM(PRECOMPUTED));
-}

data/ext/numo/libsvm/kernel_type.h

@@ -1,9 +0,0 @@
-#ifndef NUMO_LIBSVM_KERNEL_TYPE_H
-#define NUMO_LIBSVM_KERNEL_TYPE_H 1
-
-#include <svm.h>
-#include <ruby.h>
-
-void rb_init_kernel_type_module();
-
-#endif /* NUMO_LIBSVM_KERNEL_TYPE_H */