nmatrix 0.0.4 → 0.0.5

data/spec/nmatrix_yale_spec.rb

@@ -70,6 +70,28 @@ describe NMatrix do
       n.yale_d.should == [0.2, 0.1]
     end
 
+    it "gets non-diagonal rows as hashes" do
+      n = NMatrix.new(:yale, [4,6], :float64)
+      n.extend(NMatrix::YaleFunctions)
+      n[0,0] = 0.1
+      n[0,2] = 0.2
+      n[0,3] = 0.3
+      n[1,5] = 0.4
+      h = n.yale_nd_row(0, :hash)
+      h.should == {2 => 0.2, 3 => 0.3}
+    end
+
+    it "gets non-diagonal occupied column indices for a given row" do
+      n = NMatrix.new(:yale, [4,6], :float64)
+      n.extend(NMatrix::YaleFunctions)
+      n[0,0] = 0.1
+      n[0,2] = 0.2
+      n[0,3] = 0.3
+      n[1,5] = 0.4
+      a = n.yale_nd_row(0, :array)
+      a.should == [2,3]
+    end
+
     it "does not resize until necessary" do
       n = NMatrix.new(:yale, [2,3], :float64)
       n.extend(NMatrix::YaleFunctions)
@@ -246,6 +268,39 @@ describe NMatrix do
 
     end
 
+    it "dots two vectors" do
+      n = NVector.new(:yale, [16,1], :int64)
+      m = NVector.new(:yale, [1,16], :int64)
+
+      n[0] = m[0] = 1
+      n[1] = m[1] = 2
+      n[2] = m[2] = 3
+      n[3] = m[3] = 4
+      n[4] = m[4] = 5
+      n[5] = m[5] = 6
+      n[6] = m[6] = 7
+      n[7] = m[7] = 8
+      n[8] = m[8] = 9
+      n[15] = m[15] = 16
+
+      nm = n.dot(m)
+
+      # Perform the same multiplication with dense
+      nmr = n.cast(:dense, :int64).dot(m.cast(:dense, :int64)).cast(:yale, :int64)
+
+      nm.extend(NMatrix::YaleFunctions)
+      nmr.extend(NMatrix::YaleFunctions)
+
+      # We want to do a structure comparison to ensure multiplication is occurring properly, but more importantly, to
+      # ensure that insertion sort is occurring as it should. If the row has more than four entries, it'll run quicksort
+      # instead. Quicksort calls insertion sort for small rows, so we test both with this particular multiplication.
+      nm.yale_ija[0...107].should == nmr.yale_ija[0...107]
+      nm.yale_a[0...107].should   == nmr.yale_a[0...107]
+
+      mn = m.dot(n)
+      mn[0,0].should == 541
+    end
+
     it "transposes" do
       a = NMatrix.new(:yale, 4, :float64)
       a[0,0] = 1.0

data/spec/nvector_spec.rb

@@ -25,13 +25,13 @@
 # Basic tests for NVector.
 #
 
-require "./lib/nmatrix"
+require File.dirname(__FILE__) + "/spec_helper.rb"
 
 describe NVector do
   it "initializes" do
     v = NVector.new(5, 0, :float64)
-    v.shape[0].should == 5
-    v.shape[1].should == 1
+    v.shape[0].should == 1
+    v.shape[1].should == 5
   end
 
   it "permits setting and getting contents" do
@@ -43,8 +43,8 @@ describe NVector do
   it "transpose() changes raw and column stored structure" do
     v = NVector.new 5, :float64
     v = v.transpose
-    v.shape[0].should == 1
-    v.shape[1].should == 5
+    v.shape[0].should == 5
+    v.shape[1].should == 1
     v[0] = 1.555
     v[0].should == 1.555
   end
@@ -52,28 +52,28 @@ describe NVector do
   it "transpose!() changes destructively its raw and column stored structure" do
     v = NVector.new 5, :float64
     v.transpose!
-    v.shape[0].should == 1
-    v.shape[1].should == 5
+    v.shape[0].should == 5
+    v.shape[1].should == 1
   end
 
-  it "multiply() multiples itself by another NVector" do
-    v1 = NVector.new 2, :float64
-    v2 = NVector.new 2, :float64
+  it "dot() multiples itself by another NVector" do
+    v1 = NVector.new(2, :float64)
+    v2 = NVector.new(2, :float64).transpose
     v1[0] = 1.5
     v1[1] = 2.3
     v2[0] = 1.3
     v2[1] = 2.5
-    v1.multiply(v2).should == 12.0
+    v1.dot(v2).should == 12.0
   end
 
-  it "multiply!() multiples destructively itself by another NVector" do
+  it "dot!() multiples itself destructively by another NVector" do
     v1 = NVector.new 2, :float64
-    v2 = NVector.new 2, :float64
+    v2 = NVector.new(2, :float64).transpose
     v1[0] = 1.5
     v1[1] = 2.3
     v2[0] = 1.3
     v2[1] = 2.5
-    v1.multiply!(v2)
+    v1.dot!(v2)
     v1.should == 12.0
   end
 
@@ -96,4 +96,23 @@ describe NVector do
     $stdout = STDOUT
     out.should == "0  0  0  0  0\n"
   end
+
+  [:dense, :list, :yale].each do |storage_type|
+    context "for #{storage_type}" do
+      before :each do
+        @m = create_vector(storage_type)
+      end
+
+      it "converts to an Array" do
+        a = @m.to_a
+        a.each.with_index { |v,idx| @m[idx].should equal(v) }
+      end
+
+      it "shuffles" do
+        n = @m.shuffle
+        n.to_a.hash.should_not == @m.to_a.hash
+        n.to_a.sort.hash.should equal(@m.to_a.sort.hash)
+      end
+    end
+  end
 end

data/spec/slice_spec.rb

@@ -66,12 +66,12 @@ describe "Slice operation" do
           @m[2,1].should eql(7)
         end
 
-        it 'should return a 1x2 matrix with refs to self elements' do
+        it 'should return a 1x2 vector with refs to self elements' do
           n = @m.slice(0,1..2)
           n.shape.should eql([1,2])
 
-          n[0,0].should == @m[0,1]
-          n[0,0] = -9
+          n[0].should == @m[0,1]
+          n[0] = -9
           @m[0,1].should eql(1)
         end
 
@@ -79,8 +79,8 @@ describe "Slice operation" do
           n = @m.slice(0..1,1)
           n.shape.should eql([2,1])
 
-          n[0,0].should == @m[0,1]
-          n[0,0] = -9
+          n[0].should == @m[0,1]
+          n[0] = -9
           @m[0,1].should eql(1)
         end
 
@@ -118,9 +118,9 @@ describe "Slice operation" do
           it "should correctly preserve zeros" do
             @m = NMatrix.new(:yale, 3, :int64)
             column_slice = @m.column(2, :copy)
-            column_slice[0,0].should == 0
-            column_slice[1,0].should == 0
-            column_slice[2,0].should == 0
+            column_slice[0].should == 0
+            column_slice[1].should == 0
+            column_slice[2].should == 0
           end
         end
       else
@@ -139,21 +139,21 @@ describe "Slice operation" do
             @m[1,0].should eql(-9)
           end
 
-          it 'should return a 1x2 matrix with refs to self elements' do
+          it 'should return a 1x2 vector with refs to self elements' do
             n = @m[0,1..2]
             n.shape.should eql([1,2])
 
-            n[0,0].should == @m[0,1]
-            n[0,0] = -9
+            n[0].should == @m[0,1]
+            n[0] = -9
             @m[0,1].should eql(-9)
           end
 
-          it 'should return a 2x1 matrix with refs to self elements' do
+          it 'should return a 2x1 vector with refs to self elements' do
             n = @m[0..1,1]
             n.shape.should eql([2,1])
 
-            n[0,0].should == @m[0,1]
-            n[0,0] = -9
+            n[0].should == @m[0,1]
+            n[0] = -9
             @m[0,1].should eql(-9)
           end
 
@@ -161,7 +161,7 @@ describe "Slice operation" do
 
           it 'should slice again' do
             n = @m[1..2, 1..2]
-            nm_eql(n[1,0..1], NMatrix.new([1,2], [7,8])).should be_true
+            nm_eql(n[1,0..1], NVector.new(2, [7,8], :int32).transpose).should be_true
           end
 
           it 'should be correct slice for range 0..2 and 0...3' do
@@ -293,7 +293,16 @@ describe "Slice operation" do
   def nm_eql(n, m) #:nodoc:
     if n.shape != m.shape
       false
-    else
+    elsif n.is_a?(NVector)
+      return false unless m.is_a?(NVector) # don't compare NV to NM
+      long_shape = n.shape[0] == 1 ? n.shape[1] : n.shape[0]
+      long_shape.times do |j|
+        if n[j] != m[j]
+          puts "n[#{j}] != m[#{j}] (#{n[j]} != #{m[j]})"
+          return false
+        end
+      end
+    else # NMatrix
       n.shape[0].times do |i|
         n.shape[1].times do |j|
           if n[i,j] != m[i,j]
@@ -302,7 +311,7 @@ describe "Slice operation" do
           end
         end
       end
-      true
     end
+    true
   end
 end

data/spec/spec_helper.rb

@@ -49,3 +49,20 @@ def create_matrix(stype) #:nodoc:
 
   m
 end
+
+def create_vector(stype) #:nodoc:
+  m = stype == :yale ? NVector.new(stype, 10, :int32) : NVector.new(stype, 10, 0, :int32)
+
+  m[0] = 1
+  m[1] = 2
+  m[2] = 3
+  m[3] = 4
+  m[4] = 5
+  m[5] = 6
+  m[6] = 7
+  m[7] = 8
+  m[8] = 9
+  m[9] = 10
+
+  m
+end

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: nmatrix
 version: !ruby/object:Gem::Version
-  version: 0.0.4
-  prerelease: 
+  version: 0.0.5
 platform: ruby
 authors:
 - John Woods
@@ -11,28 +10,25 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-05-17 00:00:00.000000000Z
+date: 2013-07-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 4.0.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 4.0.1
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -40,7 +36,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -48,23 +43,20 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -72,7 +64,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -80,7 +71,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: pry
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -88,7 +78,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -96,7 +85,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: guard-rspec
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -104,7 +92,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -112,7 +99,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: rake-compiler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -120,7 +106,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -151,7 +136,6 @@ files:
 - ext/nmatrix/data/rational.h
 - ext/nmatrix/data/ruby_object.h
 - ext/nmatrix/extconf.rb
-- ext/nmatrix/new_extconf.rb
 - ext/nmatrix/nmatrix.cpp
 - ext/nmatrix/nmatrix.h
 - ext/nmatrix/ruby_constants.cpp
@@ -187,6 +171,7 @@ files:
 - lib/nmatrix/nvector.rb
 - lib/nmatrix/shortcuts.rb
 - lib/nmatrix/version.rb
+- lib/nmatrix/yale_functions.rb
 - nmatrix.gemspec
 - scripts/mac-brew-gcc.sh
 - spec/2x2_dense_double.mat
@@ -196,6 +181,7 @@ files:
 - spec/elementwise_spec.rb
 - spec/io_spec.rb
 - spec/lapack_spec.rb
+- spec/leakcheck.rb
 - spec/math_spec.rb
 - spec/nmatrix_list_spec.rb
 - spec/nmatrix_spec.rb
@@ -208,42 +194,71 @@ files:
 - spec/utm5940.mtx
 homepage: http://sciruby.com
 licenses: []
-post_install_message: ! "***********************************************************\nWelcome
-  to SciRuby: Tools for Scientific Computing in Ruby!\n\n                     ***
-  WARNING ***\nPlease be aware that NMatrix is in ALPHA status. If you're\nthinking
-  of using NMatrix to write mission critical code,\nsuch as for driving a car or flying
-  a space shuttle, you\nmay wish to choose other software (for now).\n\nNMatrix requires
-  a C compiler, and has been tested only\nwith GCC 4.6+. We are happy to accept contributions\nwhich
-  improve the portability of this project.\n\nAlso required is ATLAS. Most Linux distributions
-  and Mac\nversions include ATLAS, but you may wish to compile it\nyourself. Rumor
-  has it that the Ubuntu/Debian apt package\nfor ATLAS WILL NOT WORK with NMatrix.
-  Please install it\nmanually if you are using apt.\n\nMore explicit instructions
-  for NMatrix and SciRuby should\nbe available on the SciRuby website, sciruby.com,
-  or\nthrough our mailing list (which can be found on our web-\nsite).\n\nThanks for
-  trying out NMatrix! Happy coding!\n\n***********************************************************\n"
+metadata: {}
+post_install_message: |
+  ***********************************************************
+  Welcome to SciRuby: Tools for Scientific Computing in Ruby!
+
+                       *** WARNING ***
+  Please be aware that NMatrix is in ALPHA status. If you're
+  thinking of using NMatrix to write mission critical code,
+  such as for driving a car or flying a space shuttle, you
+  may wish to choose other software (for now).
+
+  NMatrix requires a C compiler, and has been tested only
+  with GCC 4.6+. We are happy to accept contributions
+  which improve the portability of this project.
+
+  Also required is ATLAS. Most Linux distributions and Mac
+  versions include ATLAS, but you may wish to compile it
+  yourself. Rumor has it that the Ubuntu/Debian apt package
+  for ATLAS WILL NOT WORK with NMatrix. Please install it
+  manually if you are using apt.
+
+  More explicit instructions for NMatrix and SciRuby should
+  be available on the SciRuby website, sciruby.com, or
+  through our mailing list (which can be found on our web-
+  site).
+
+  Thanks for trying out NMatrix! Happy coding!
+
+  ***********************************************************
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: 1.9.2
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: 186187539
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.18
+rubygems_version: 2.0.2
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: NMatrix is an experimental linear algebra library for Ruby, written mostly
   in C.
-test_files: []
+test_files:
+- spec/2x2_dense_double.mat
+- spec/4x4_sparse.mat
+- spec/4x5_dense.mat
+- spec/blas_spec.rb
+- spec/elementwise_spec.rb
+- spec/io_spec.rb
+- spec/lapack_spec.rb
+- spec/leakcheck.rb
+- spec/math_spec.rb
+- spec/nmatrix_list_spec.rb
+- spec/nmatrix_spec.rb
+- spec/nmatrix_yale_resize_test_associations.yaml
+- spec/nmatrix_yale_spec.rb
+- spec/nvector_spec.rb
+- spec/shortcuts_spec.rb
+- spec/slice_spec.rb
+- spec/spec_helper.rb
+- spec/utm5940.mtx