JRuby port of NMatrix

.gitignore

@@ -27,3 +27,9 @@ doc/
 docs/
 pkg/
 .autotest
+ext/nmatrix_java/vendor/
+ext/nmatrix_java/target/
+ext/nmatrix_java/build/
+ext/nmatrix_java/target/
+*.class
+*.jar

.travis.yml

@@ -20,7 +20,7 @@ rvm:
   - 2.3.0-clang
   - ruby-head-clang
   # JRuby versions --- experimental, pending merging Prasun's GSoC project.
-  # - jruby-9.0.0.0 # earliest supported version (uncomment when jruby-head is passing)
+  - jruby-9.0.5.0 # earliest supported version (uncomment when jruby-head is passing)
   - jruby-head    # latest supported JRuby
   # Make sure to add exclude lines for new JRuby versions below.
 
@@ -42,11 +42,12 @@ matrix:
       env: USE_OPENBLAS=1
     - rvm: jruby-head
       env: USE_REF=1
-    #- rvm: jruby-9.0.0.0
-    #  env:
-    #    - USE_ATLAS=1
-    #    - USE_OPENBLAS=1
-    #    - USE_REF=1      
+    - rvm: jruby-9.0.5.0
+      env: USE_ATLAS=1
+    - rvm: jruby-9.0.5.0
+      env: USE_OPENBLAS=1
+    - rvm: jruby-9.0.5.0
+      env: USE_REF=1    
     # NOTE: The following two ruby versions on OSX are currently unavailable
     - os: osx
       rvm: 2.0.0-p648
@@ -106,8 +107,6 @@ matrix:
         - ruby_version=2.1.8 USE_OPENBLAS=1
   allow_failures:
     # trunk
-    - rvm: jruby-head
-    #- rvm: jruby-9.0.0.0
     - rvm: ruby-head
     - rvm: ruby-head-clang
     - os: osx

CONTRIBUTING.md

@@ -62,6 +62,16 @@ $ rake spec
 This will install all dependencies, compile the extension and run the
 specs.
 
+For **JRuby**
+
+```bash
+$ mkdir ext/nmatrix_java/vendor
+Download commons_math.3.6.1 jar and place it in ext/nmatrix_java/vendor directory
+$ mkdir -p ext/nmatrix_java/build/class
+$ mkdir ext/nmatrix_java/target
+$ rake jruby
+```
+
 If everything's fine until now, you can create a new branch to work on
 your feature:
 

README.rdoc

@@ -67,6 +67,28 @@ To install:
 
     bundle exec rake install
 
+=== JRuby
+
+First, you need to download Apache Commons Math 3.6.1 (the JAR, which
+you can find in the binary package). For example, in the NMatrix
+directory, do:
+
+    wget https://www.apache.org/dist/commons/math/binaries/commons-math3-3.6.1-bin.tar.gz
+    tar zxvf commons-math3-3.6.1-bin.tar.gz
+    mkdir ext/nmatrix_java/vendor/
+    cp commons-math3-3.6.1/commons-math3-3.6.1.jar ext/nmatrix_java/vendor/
+
+Next, create build directories:
+
+    mkdir -p ext/nmatrix_java/build/class
+    mkdir ext/nmatrix_java/target
+
+Finally, compile and package as jar.
+
+    rake jruby
+
+=== Plugins
+
 The commands above build and install only the core +nmatrix+ gem.  If
 you want to build one or more of the plugin gems (+nmatrix-atlas+,
 +nmatrix-lapacke+) in addition to the core nmatrix gem, use the

Rakefile

@@ -73,6 +73,7 @@ namespace :spec do
   gemspecs.each do |gemspec|
     test_files = gemspec.test_files
     test_files.keep_if { |file| file =~ /_spec\.rb$/ }
+    test_files -= ['spec/nmatrix_yale_spec.rb', 'spec/blas_spec.rb', 'spec/lapack_core_spec.rb'] if /java/ === RUBY_PLATFORM
     next if test_files.empty?
     spec_tasks << gemspec.name
     RSpec::Core::RakeTask.new(gemspec.name) do |spec|
@@ -273,27 +274,83 @@ RDoc::Task.new do |rdoc|
   rdoc.options << "--exclude=lib/nmatrix/rspec.rb"
 end
 
-namespace :travis do
-  task :env do
-    puts "\n# Build environment:"
-    %w[
-      CC CXX
-      USE_ATLAS USE_OPENBLAS USE_REF NO_EXTERNAL_LIB
-      TRAVIS_OS_NAME TRAVIS_BRANCH TRAVIS_COMMIT TRAVIS_PULL_REQUEST
-    ].each do |name|
-      puts "- #{name}: #{ENV[name]}"
+# jruby tasks
+
+namespace :jruby do
+
+  PROJECT_DIR = File.expand_path(".",Dir.pwd)
+
+  BUILD_DIR = "build"
+  CLASSES_DIR = "../build/classes"
+  TEST_CLASSES_DIR = "build/testClasses"
+
+  JRUBY_DIR = "#{PROJECT_DIR}/ext/nmatrix_java"
+  VENDOR_DIR = "#{JRUBY_DIR}/vendor"
+  TARGET_DIR = "#{JRUBY_DIR}/target"
+
+  jars = Dir["#{VENDOR_DIR}/*.jar"]
+
+  desc 'Compile java classes'
+  task :javac do
+    unless RUBY_PLATFORM == 'java'
+      abort 'Please run with JRuby'
     end
+    sh "mkdir -p #{JRUBY_DIR}/build/classes"
+    Dir.chdir("#{JRUBY_DIR}/nmatrix")
+    classes    = Dir['**/*.java']
+    sh "javac -classpath #{jars.join(':')} -d #{CLASSES_DIR} #{classes.join(' ')}"
+  end
 
-    require 'rbconfig'
-    puts "\n# RbConfig::MAKEFILE_CONFIG values:"
-    %w[
-      CC CXX CPPFLAGS CFLAGS CXXFLAGS
-    ].each do |name|
-      puts "- #{name}: #{RbConfig::MAKEFILE_CONFIG[name]}"
+  desc 'Package java classes in a jar file'
+  task :jar do
+    unless RUBY_PLATFORM == 'java'
+      abort 'Please run with JRuby'
     end
+    sh "mkdir -p #{TARGET_DIR}"
+    Dir.chdir("#{JRUBY_DIR}/build/classes")
+    classes = Dir['**/*.class']
+    sh "jar -cf #{TARGET_DIR}/nmatrix.jar #{classes.join(' ')}"
+  end
 
-    cc = RbConfig::MAKEFILE_CONFIG['CC']
-    puts "\n$ #{cc} -v\n#{`#{cc} -v 2>&1`}"
+  task :all => [:javac, :jar]
+end
+
+desc "Compile java classes and Package them in a jar file"
+task :jruby => 'jruby:all'
+
+namespace :travis do
+  task :env do
+    if /java/ === RUBY_PLATFORM
+      puts "Building for jruby"
+      sh "mkdir ext/nmatrix_java/vendor"
+      puts "Downloading tar file."
+      sh "wget http://www-eu.apache.org/dist//commons/math/binaries/commons-math3-3.6.1-bin.tar.gz"
+      puts "Unzipping tar file."
+      sh "tar -zxf commons-math3-3.6.1-bin.tar.gz"
+      puts "Deleting tar file."
+      sh "rm commons-math3-3.6.1-bin.tar.gz"
+      sh "cp -r commons-math3-3.6.1/commons-math3-3.6.1.jar ext/nmatrix_java/vendor"
+    else
+      puts "\n# Build environment:"
+      %w[
+        CC CXX
+        USE_ATLAS USE_OPENBLAS USE_REF NO_EXTERNAL_LIB
+        TRAVIS_OS_NAME TRAVIS_BRANCH TRAVIS_COMMIT TRAVIS_PULL_REQUEST
+      ].each do |name|
+        puts "- #{name}: #{ENV[name]}"
+      end
+
+      require 'rbconfig'
+      puts "\n# RbConfig::MAKEFILE_CONFIG values:"
+      %w[
+        CC CXX CPPFLAGS CFLAGS CXXFLAGS
+      ].each do |name|
+        puts "- #{name}: #{RbConfig::MAKEFILE_CONFIG[name]}"
+      end
+
+      cc = RbConfig::MAKEFILE_CONFIG['CC']
+      puts "\n$ #{cc} -v\n#{`#{cc} -v 2>&1`}"
+    end
   end
 end
 

ext/nmatrix_java/Rakefile

@@ -0,0 +1,68 @@
+PROJECT_DIR = File.expand_path(".",Dir.pwd)
+# puts PROJECT_DIR
+
+BUILD_DIR = "build"
+CLASSES_DIR = "../build/classes"
+TEST_CLASSES_DIR = "build/testClasses"
+
+VENDOR_DIR = "#{PROJECT_DIR}/vendor"
+TARGET_DIR = "#{PROJECT_DIR}/target"
+# puts VENDOR_DIR
+
+jars = Dir["#{VENDOR_DIR}/*.jar"]
+# puts jars
+
+unless RUBY_PLATFORM == 'java'
+  abort 'Please run with JRuby'
+end
+
+#-----------------------------------------------------------------------------------------
+
+desc 'Compile java classes'
+task :javac do
+
+  Dir.chdir("nmatrix")
+  classes    = Dir['**/*.java']
+  sh "javac -classpath #{jars.join(':')} -d #{CLASSES_DIR} #{classes.join(' ')}"
+  # sh "javac -d #{CLASSES_DIR} #{classes.join(' ')}"
+
+end
+
+#-----------------------------------------------------------------------------------------
+desc 'Make jar file'
+task :jar do
+
+  Dir.chdir("build/classes")
+  classes = Dir['**/*.class']
+  # p classes
+  sh "jar -cf #{TARGET_DIR}/nmatrix.jar #{classes.join(' ')}"
+
+end
+
+#-----------------------------------------------------------------------------------------
+
+
+desc 'Compile test classes'
+task :compileTest do
+
+  classes    = Dir['**/*.java']
+  sh "javac -classpath #{jars.join(':')} -d #{TEST_CLASSES_DIR} #{classes.join(' ')}"
+  # sh "javac -d #{CLASSES_DIR} #{classes.join(' ')}"
+
+end
+
+#-----------------------------------------------------------------------------------------
+
+desc 'Run junit tests'
+task :test do
+
+  Dir.chdir("build/classes")
+  classes = Dir['**/*.class']
+  # p classes
+  sh "javac -classpath #{TARGET_DIR}/nmatrix.jar -d #{classes.join(' ')}"
+
+end
+
+#-----------------------------------------------------------------------------------------
+
+task :default => :javac

ext/nmatrix_java/nmatrix/math/MathHelper.java

@@ -0,0 +1,111 @@
+import org.apache.commons.math3.util.FastMath;
+import org.apache.commons.math3.special.Erf;
+import org.apache.commons.math3.special.Gamma;
+
+public class MathHelper{
+
+  public static double[] log(double base, double[] arr){
+    double[] result = new double[arr.length];
+    for(int i = 0; i< arr.length; i++){
+      result[i] = FastMath.log(base, arr[i]);
+    } 
+    return result;
+  }
+
+  public static double[] erf(double[] arr){
+    double[] result = new double[arr.length];
+    for(int i = 0; i< arr.length; i++){
+      result[i] = Erf.erf(arr[i]);
+    } 
+    return result;
+  }
+
+  public static double[] erfc(double[] arr){
+    double[] result = new double[arr.length];
+    for(int i = 0; i< arr.length; i++){
+      result[i] = Erf.erfc(arr[i]);
+    } 
+    return result;
+  }
+
+  public static double[] gamma(double[] arr){
+    double[] result = new double[arr.length];
+    for(int i = 0; i< arr.length; i++){
+      result[i] = Gamma.gamma(arr[i]);
+    } 
+    return result;
+  }
+
+  public static double[] round(double[] arr){
+    double[] result = new double[arr.length];
+    for(int i = 0; i< arr.length; i++){
+      result[i] = Math.round(arr[i]);
+    } 
+    return result;
+  }
+
+  public static double[] ldexp(double[] arr1, double[] arr){
+    double[] result = new double[arr1.length];
+    for(int i = 0; i< arr1.length; i++){
+      result[i] = arr1[i] * Math.pow(2, arr[i]);
+    } 
+    return result;
+  }
+
+  public static double[] ldexpScalar(double val, double[] arr){
+    double[] result = new double[arr.length];
+    for(int i = 0; i< arr.length; i++){
+      result[i] = val * Math.pow(2, arr[i]);
+    } 
+    return result;
+  }
+
+  public static double[] ldexpScalar2(double val, double[] arr){
+    double[] result = new double[arr.length];
+    for(int i = 0; i< arr.length; i++){
+      result[i] = arr[i] * Math.pow(2, val);
+    } 
+    return result;
+  }
+
+  public static double[] hypot(double[] arr1, double[] arr2){
+    double[] result = new double[arr1.length];
+    for(int i = 0; i< arr1.length; i++){
+      result[i] =  Math.sqrt(arr2[i] * arr2[i] + arr1[i] * arr1[i]);
+    } 
+    return result;
+  }
+
+  public static double[] hypotScalar(double val, double[] arr){
+    double[] result = new double[arr.length];
+    for(int i = 0; i< arr.length; i++){
+      result[i] =  Math.sqrt(arr[i] * arr[i] + val * val);
+    } 
+    return result;
+  }
+
+  public static double[] atan2(double[] arr1, double[] arr2){
+    double[] result = new double[arr1.length];
+    for(int i = 0; i< arr1.length; i++){
+      result[i] =  Math.atan2(arr2[i], arr1[i]);
+    } 
+    return result;
+  }
+
+  public static double[] atan2Scalar(double val, double[] arr){
+    double[] result = new double[arr.length];
+    for(int i = 0; i< arr.length; i++){
+      result[i] =  Math.atan2(val, arr[i]);
+    } 
+    return result;
+  }
+
+  public static double[] atan2Scalar2(double val, double[] arr){
+    double[] result = new double[arr.length];
+    for(int i = 0; i< arr.length; i++){
+      result[i] =  Math.atan2(arr[i], val);
+    } 
+    return result;
+  }
+
+}