nmatrix 0.0.8 → 0.0.9

data/spec/spec_helper.rb

@@ -22,7 +22,10 @@
 #
 # == spec_helper.rb
 #
-# Common data for testing. 
+# Common data and helper functions for testing.
+
+require "rspec/longrun"
+
 require "./lib/nmatrix"
 require "./lib/nmatrix/rspec"
 
@@ -36,7 +39,7 @@ RATIONAL_MATRIX43A_ARRAY = MATRIX43A_ARRAY.collect { |x| x.to_r }
 RATIONAL_MATRIX32A_ARRAY = MATRIX32A_ARRAY.collect { |x| x.to_r }
 
 def create_matrix(stype) #:nodoc:
-  m = stype == :yale ? NMatrix.new(stype, 3, :int32) : NMatrix.new(stype, [3,3], 0, :int32)
+  m = NMatrix.new([3,3], 0, dtype: :int32, stype: stype, default: 0)
 
   m[0,0] = 0
   m[0,1] = 1
@@ -51,6 +54,43 @@ def create_matrix(stype) #:nodoc:
   m
 end
 
+def create_rectangular_matrix(stype) #:nodoc:
+  m = NMatrix.new([5,6], 0, dtype: :int32, stype: stype, default: 0)
+
+  m[0,0] = 1
+  m[0,1] = 2
+  m[0,2] = 3
+  m[0,3] = 4
+  m[0,4] = 5
+  m[0,5] = 0
+
+  m[1,0] = 6
+  m[1,1] = 7
+  m[1,2] = 8
+  m[1,3] = 9
+  m[1,4] = 0
+  m[1,5] = 10
+
+  m[2,0] = 11
+  m[2,1] = 12
+  m[2,2] = 13
+  m[2,3] = 0
+  m[2,4] = 14
+  m[2,5] = 15
+
+  # skip row 3 -- all 0
+  m[3,0] = m[3,1] = m[3,2] = m[3,3] = m[3,4] = m[3,5] = 0
+
+  m[4,0] = 16
+  m[4,1] = 0
+  m[4,2] = 17
+  m[4,3] = 18
+  m[4,4] = 19
+  m[4,5] = 20
+
+  m
+end
+
 def create_vector(stype) #:nodoc:
   m = stype == :yale ? NVector.new(stype, 10, :int32) : NVector.new(stype, 10, 0, :int32)
 

data/spec/stat_spec.rb

@@ -0,0 +1,192 @@
+# = NMatrix
+#
+# A linear algebra library for scientific computation in Ruby.
+# NMatrix is part of SciRuby.
+#
+# NMatrix was originally inspired by and derived from NArray, by
+# Masahiro Tanaka: http://narray.rubyforge.org
+#
+# == Copyright Information
+#
+# SciRuby is Copyright (c) 2010 - 2012, Ruby Science Foundation
+# NMatrix is Copyright (c) 2012, Ruby Science Foundation
+#
+# Please see LICENSE.txt for additional copyright notices.
+#
+# == Contributing
+#
+# By contributing source code to SciRuby, you agree to be bound by
+# our Contributor Agreement:
+#
+# * https://github.com/SciRuby/sciruby/wiki/Contributor-Agreement
+#
+# == stat_spec.rb
+#
+# Tests for statistical functions in NMatrix.
+#
+
+# Can we use require_relative here instead?
+require File.join(File.dirname(__FILE__), "spec_helper.rb")
+require 'pry'
+
+describe "Statistical functions" do
+  context "mapping and reduction related functions" do
+
+    before :each do
+      @nm_1d = NMatrix[5.0,0.0,1.0,2.0,3.0]
+      @nm_2d = NMatrix[[0.0,1.0],[2.0,3.0]]
+    end
+
+    it "behaves like Enumerable#reduce with no argument to reduce" do
+      @nm_1d.reduce_along_dim(0) { |acc, el| acc + el }.to_f.should eq 11
+      @nm_2d.reduce_along_dim(1) { |acc, el| acc + el }.should eq NMatrix[[1, 5]]
+    end
+
+    it "should calculate the mean along the specified dimension" do
+      @nm_1d.mean.should eq NMatrix[2.2]
+      @nm_2d.mean.should eq NMatrix[[1.0,2.0]]
+    end
+
+    it "should calculate the minimum along the specified dimension" do
+      @nm_1d.min.should eq 0.0
+      @nm_2d.min.should eq NMatrix[[0.0, 1.0]]
+      @nm_2d.min(1).should eq NMatrix[[0.0], [2.0]]
+    end
+
+    it "should calculate the maximum along the specified dimension" do
+      @nm_1d.max.should eq 5.0
+      @nm_2d.max.should eq NMatrix[[2.0, 3.0]]
+    end
+
+    it "should calculate the variance along the specified dimension" do
+      @nm_1d.variance.should eq NMatrix[3.7]
+      @nm_2d.variance(1).should eq NMatrix[[0.5], [0.5]]
+    end
+
+    it "should calculate the sum along the specified dimension" do
+      @nm_1d.sum.should eq NMatrix[11]
+      @nm_2d.sum.should eq NMatrix[[2], [4]]
+    end
+
+    it "should calculate the standard deviation along the specified dimension" do
+      @nm_1d.std.should eq NMatrix[Math.sqrt(3.7)]
+      @nm_2d.std(1).should eq NMatrix[[Math.sqrt(0.5)], [Math.sqrt(0.5)]]
+    end
+
+    it "should raise an ArgumentError when any invalid dimension is provided" do
+      expect { @nm_1d.mean(3) }.to raise_exception(RangeError)
+    end
+
+    it "should convert to float if it contains only a single element" do
+      NMatrix[4.0].to_f.should eq 4.0
+      NMatrix[[[[4.0]]]].to_f.should eq 4.0
+    end
+
+    it "should raise an index error if it contains more than a single element" do
+      expect { @nm_1d.to_f }.to raise_error(IndexError)
+    end
+
+    it "should map a block to all elements" do
+      @nm_1d.map { |e| e ** 2 }.should eq NMatrix[25.0,0.0,1.0,4.0,9.0]
+      @nm_2d.map { |e| e ** 2 }.should eq NMatrix[[0.0,1.0],[4.0,9.0]]
+    end
+
+    it "should map! a block to all elements in place" do
+      fct = Proc.new { |e| e ** 2 }
+      expected1 = @nm_1d.map &fct
+      expected2 = @nm_2d.map &fct
+      @nm_1d.map! &fct
+      @nm_1d.should eq expected1
+      @nm_2d.map! &fct
+      @nm_2d.should eq expected2
+    end
+
+    it "should return an enumerator for map without a block" do
+      @nm_1d.map.should be_a Enumerator
+    end
+
+    it "should return an enumerator for reduce without a block" do
+      @nm_1d.reduce_along_dim(0).should be_a Enumerator
+    end
+
+    it "should return an enumerator for each_along_dim without a block" do
+      @nm_1d.each_along_dim(0).should be_a Enumerator
+    end
+
+    it "should iterate correctly for map without a block" do
+      en = @nm_1d.map
+      en.each { |e| e**2 }.should eq @nm_1d.map { |e| e**2 }
+      en = @nm_2d.map
+      en.each { |e| e**2 }.should eq @nm_2d.map { |e| e**2 }
+    end
+
+    it "should iterate correctly for reduce without a block" do
+      en = @nm_1d.reduce_along_dim(0, 1.0)
+      en.each { |a, e| a+e }.to_f.should eq 12
+      en = @nm_2d.reduce_along_dim(1, 1.0)
+      en.each { |a, e| a+e }.should eq NMatrix[[2.0],[6.0]]
+    end
+
+    it "should iterate correctly for each_along_dim without a block" do
+      res = NMatrix.zeros_like(@nm_1d[0...1])
+      en = @nm_1d.each_along_dim(0)
+      en.each { |e| res += e }
+      res.to_f.should eq 11
+
+      res = NMatrix.zeros_like (@nm_2d[0...2, 0])
+      en = @nm_2d.each_along_dim(1)
+      en.each { |e| res += e }
+      res.should eq NMatrix[[1.0], [5.0]]
+    end
+
+    it "should yield matrices of matching dtype for each_along_dim" do
+      m = NMatrix.new([2,3], [1,2,3,3,4,5], dtype: :complex128)
+      m.each_along_dim(1) do |sub_m|
+        sub_m.dtype.should eq :complex128
+      end
+    end
+
+    it "should reduce to a matrix of matching dtype for reduce_along_dim" do
+      m = NMatrix.new([2,3], [1,2,3,3,4,5], dtype: :complex128)
+      m.reduce_along_dim(1) do |acc, sub_m|
+        sub_m.dtype.should eq :complex128
+        acc
+      end
+
+      m = NMatrix.new([2,3], [1,2,3,3,4,5], dtype: :complex128)
+      m.reduce_along_dim(1, 0.0) do |acc, sub_m|
+        sub_m.dtype.should eq :complex128
+        acc
+      end
+    end
+
+    it "should allow overriding the dtype for reduce_along_dim" do
+      m = NMatrix[[1,2,3], [3,4,5], dtype: :complex128]
+      m.reduce_along_dim(1, 0.0, :float64) do |acc, sub_m|
+        acc.dtype.should eq :float64
+        acc
+      end
+
+      m = NMatrix[[1,2,3], [3,4,5], dtype: :complex128]
+      m.reduce_along_dim(1, nil, :float64) do |acc, sub_m|
+        acc.dtype.should eq :float64
+        acc
+      end
+    end
+
+    it "should convert integer dtypes to float when calculating mean" do
+      m = NMatrix[[1,2,3], [3,4,5], dtype: :int32]
+      m.mean(0).dtype.should eq :float64
+    end
+
+    it "should convert integer dtypes to float when calculating variance" do
+      m = NMatrix[[1,2,3], [3,4,5], dtype: :int32]
+      m.variance(0).dtype.should eq :float64
+    end
+
+    it "should convert integer dtypes to float when calculating standard deviation" do
+      m = NMatrix[[1,2,3], [3,4,5], dtype: :int32]
+      m.std(0).dtype.should eq :float64
+    end
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: nmatrix
 version: !ruby/object:Gem::Version
-  version: 0.0.8
+  version: 0.0.9
 platform: ruby
 authors:
 - John Woods
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-23 00:00:00.000000000 Z
+date: 2013-09-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
@@ -30,16 +30,16 @@ dependencies:
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - '>='
       - !ruby/object:Gem::Version
-        version: '0.9'
+        version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - '>='
       - !ruby/object:Gem::Version
-        version: '0.9'
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -58,18 +58,18 @@ dependencies:
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - '>='
       - !ruby/object:Gem::Version
-        version: 2.9.0
+        version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - '>='
       - !ruby/object:Gem::Version
-        version: 2.9.0
+        version: '0'
 - !ruby/object:Gem::Dependency
-  name: pry
+  name: rspec-longrun
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '>='
@@ -83,19 +83,19 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: guard-rspec
+  name: pry
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - '>='
       - !ruby/object:Gem::Version
-        version: 0.7.0
+        version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - '>='
       - !ruby/object:Gem::Version
-        version: 0.7.0
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rake-compiler
   requirement: !ruby/object:Gem::Requirement
@@ -121,6 +121,7 @@ extra_rdoc_files: []
 files:
 - .gitignore
 - .rspec
+- .travis.yml
 - CONTRIBUTING.md
 - Gemfile
 - Guardfile
@@ -133,6 +134,7 @@ files:
 - ext/nmatrix/data/complex.h
 - ext/nmatrix/data/data.cpp
 - ext/nmatrix/data/data.h
+- ext/nmatrix/data/meta.h
 - ext/nmatrix/data/rational.h
 - ext/nmatrix/data/ruby_object.h
 - ext/nmatrix/extconf.rb
@@ -164,6 +166,7 @@ files:
 - ext/nmatrix/nmatrix.h
 - ext/nmatrix/ruby_constants.cpp
 - ext/nmatrix/ruby_constants.h
+- ext/nmatrix/ruby_nmatrix.c
 - ext/nmatrix/storage/common.cpp
 - ext/nmatrix/storage/common.h
 - ext/nmatrix/storage/dense.cpp
@@ -172,8 +175,16 @@ files:
 - ext/nmatrix/storage/list.h
 - ext/nmatrix/storage/storage.cpp
 - ext/nmatrix/storage/storage.h
-- ext/nmatrix/storage/yale.cpp
-- ext/nmatrix/storage/yale.h
+- ext/nmatrix/storage/yale/class.h
+- ext/nmatrix/storage/yale/iterators/base.h
+- ext/nmatrix/storage/yale/iterators/iterator.h
+- ext/nmatrix/storage/yale/iterators/row.h
+- ext/nmatrix/storage/yale/iterators/row_stored.h
+- ext/nmatrix/storage/yale/iterators/row_stored_nd.h
+- ext/nmatrix/storage/yale/iterators/stored_diagonal.h
+- ext/nmatrix/storage/yale/math/transpose.h
+- ext/nmatrix/storage/yale/yale.cpp
+- ext/nmatrix/storage/yale/yale.h
 - ext/nmatrix/ttable_helper.rb
 - ext/nmatrix/types.h
 - ext/nmatrix/util/io.cpp
@@ -198,6 +209,9 @@ files:
 - lib/nmatrix/yale_functions.rb
 - nmatrix.gemspec
 - scripts/mac-brew-gcc.sh
+- spec/00_nmatrix_spec.rb
+- spec/01_enum_spec.rb
+- spec/02_slice_spec.rb
 - spec/2x2_dense_double.mat
 - spec/4x4_sparse.mat
 - spec/4x5_dense.mat
@@ -207,48 +221,30 @@ files:
 - 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/rspec_monkeys.rb
 - spec/rspec_spec.rb
 - spec/shortcuts_spec.rb
-- spec/slice_spec.rb
+- spec/slice_set_spec.rb
 - spec/spec_helper.rb
+- spec/stat_spec.rb
 - spec/utm5940.mtx
 homepage: http://sciruby.com
 licenses: []
 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!
-
-  ***********************************************************
+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. The Ubuntu/Debian
+  apt package for ATLAS WILL \nNOT WORK with NMatrix if LAPACK is also installed.\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"
 rdoc_options: []
 require_paths:
 - lib
@@ -256,7 +252,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - '>='
     - !ruby/object:Gem::Version
-      version: 1.9.2
+      version: '1.9'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - '>='
@@ -270,6 +266,9 @@ specification_version: 4
 summary: NMatrix is an experimental linear algebra library for Ruby, written mostly
   in C.
 test_files:
+- spec/00_nmatrix_spec.rb
+- spec/01_enum_spec.rb
+- spec/02_slice_spec.rb
 - spec/2x2_dense_double.mat
 - spec/4x4_sparse.mat
 - spec/4x5_dense.mat
@@ -279,14 +278,12 @@ test_files:
 - 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/rspec_monkeys.rb
 - spec/rspec_spec.rb
 - spec/shortcuts_spec.rb
-- spec/slice_spec.rb
+- spec/slice_set_spec.rb
 - spec/spec_helper.rb
+- spec/stat_spec.rb
 - spec/utm5940.mtx