nmatrix 0.0.6 → 0.0.7

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitignore

@@ -28,3 +28,5 @@ ext/nmatrix/**/*.o
 ext/nmatrix/Makefile
 ext/nmatrix/**/Makefile
 ext/nmatrix/nmatrix_config.h
+pkg/
+.autotest

data/Gemfile

@@ -3,3 +3,8 @@ source 'http://rubygems.org'
 gemspec
 
 gem 'packable', ">= 1.3.5"  # for Matlab IO
+
+group :development do
+  gem 'pry'
+  #gem 'pry-debugger'
+end

data/History.txt

@@ -281,3 +281,100 @@
 
   * Repaired list matrix element-wise functions
 
+=== 0.0.7 / 2013-08-22
+
+* 6 major enhancements:
+
+  * Eliminated NVector in favor of NMatrix objects with
+    #effective_dim smaller than #dim; added NVector-like
+    functionality to NMatrix, sometimes with #respond_to? dependent
+    upon matrix dimensions; allowed for NVector.new to continue
+    to function as before, but now returns an NMatrix instead
+
+  * Began major re-factoring of headers for math.cpp
+
+  * Added two singular value decomposition functions for dense
+    NMatrix objects, #gesvd and #gesdd, for floating point and
+    complex dtypes
+
+  * Added additional slicing shorthand, which uses hashes (e.g.,
+    n[0=>3,2] for n[0..3,2]), which may eventually allow users to use
+    n[0:3,2] notation instead (needs Ruby core patch)
+
+  * #[] and #[]= calls no longer need index on those matrix shape
+    elements which are equal to 1 (e.g., vectors)
+
+  * Yale slicing-by-reference has been added
+
+* 18 minor enhancements:
+
+  * Added user-friendly NMatrix::LAPACK::laswp method
+
+  * Added NMatrix#permute_columns! and NMatrix#permute_columns
+
+  * Added NMatrix#abs to compute element-wise absolute values, and
+    #abs_dtype to determine the dtype returned by a call to #abs on a
+    given matrix (needed for RSpec)
+
+  * Added NMatrix#size to compute the total number of cells in an
+    NMatrix object (solely accounting for the shape, not sparsity)
+
+  * Added RSpec monkey patches for #be_within to work with NMatrix
+    objects; usable by requiring "nmatrix/rspec"
+
+  * Added experimental NMatrix::LAPACK::lapack_gesvd function (which
+    does NOT depend upon CLAPACK) (by @ryanmt and @mohawkjohn)
+
+  * Added experimental non-LAPACK-dependent function
+    NMatrix::LAPACK::lapack_gesdd
+
+  * Added NMatrix#supershape method for getting the shape of a
+    slice's parent or other ancestor, which may be useful for calling
+    ATLAS and LAPACK functions on slices
+
+  * Aliased NMatrix[] to function like N[] shortcut for matrix
+    creation (by @agarie)
+
+  * Added #layer for matrices with dimension greater than two
+    (corresponds to #row and #column)
+
+  * Added #rank and #each_rank generics for #row/#column/#layer and
+    #each_row/#each_column/#each_layer respectively (#each_rank
+    replaces #each_along_dim)
+
+  * Replaced #reduce_along_dim with #inject_rank
+
+  * NMatrix#to_a now works for up to two dimensional matrices; and
+    returns a flattened array for single-row matrices
+
+  * NMatrix#to_flat_a now returns a flattened array of all entries
+
+  * Re-organized NMatrix Ruby sources into multiple files: math.rb
+    for instance methods which are mathematical in nature or are
+    essentially ATLAS/LAPACK/BLAS calls, enumerate.rb for methods
+    involving enumeration; and existing shortcuts.rb for convenience
+    functions and shortcut constructors, and nmatrix.rb for core
+    functionality (#inspect, #to_h, #to_a, #to_s, #pretty_print,
+    and so on)
+
+  * Improved #pretty_print, which now also prints layers (the third
+    dimension in a 3D matrix)
+
+  * Re-factored some of dense slicing to remove some redundant code
+
+  * Added shortcut functions #list?, #dense?, #yale? for quickly
+    testing matrix storage type
+
+* 5 bug fixes:
+
+  * Fixed compilation problem involving <typeinfo> and <vector> STL
+    headers
+
+  * Fixed NMatrix#inverse problem with non-square matrices
+
+  * Fixed invalid read problem detected by Valgrind for
+    Yale element-wise subtraction in spec
+
+  * Fixed conversion from Ruby object to Complex and Rational
+
+  * Fixed memory leak in slicing

data/Manifest.txt

@@ -7,27 +7,32 @@ Rakefile
 Gemfile
 Guardfile
 nmatrix.gemspec
+spec/blas_spec.rb
+spec/elementwise_spec.rb
 spec/io_spec.rb
+spec/lapack_spec.rb
 spec/math_spec.rb
-spec/nmatrix_spec.rb
 spec/nmatrix_list_spec.rb
+spec/nmatrix_spec.rb
 spec/nmatrix_yale_spec.rb
 spec/nvector_spec.rb
-spec/slice_spec.rb
+spec/rspec_spec.rb
 spec/shortcuts_spec.rb
-spec/elementwise_spec.rb
-spec/blas_spec.rb
-spec/lapack_spec.rb
+spec/slice_spec.rb
 spec/spec_helper.rb
 lib/nmatrix.rb
+lib/nmatrix/rspec.rb
 lib/nmatrix/io/market.rb
 lib/nmatrix/io/mat5_reader.rb
 lib/nmatrix/io/mat_reader.rb
 lib/nmatrix/blas.rb
+lib/nmatrix/enumerate.rb
 lib/nmatrix/lapack.rb
+lib/nmatrix/math.rb
 lib/nmatrix/monkeys.rb
 lib/nmatrix/nmatrix.rb
 lib/nmatrix/nvector.rb
+lib/nmatrix/rspec.rb
 lib/nmatrix/shortcuts.rb
 lib/nmatrix/version.rb
 lib/nmatrix/yale_functions.rb
@@ -46,12 +51,34 @@ ext/nmatrix/storage/storage.cpp
 ext/nmatrix/storage/storage.h
 ext/nmatrix/storage/yale.cpp
 ext/nmatrix/storage/yale.h
-ext/nmatrix/util/math.cpp
-ext/nmatrix/util/math.h
 ext/nmatrix/util/sl_list.cpp
 ext/nmatrix/util/sl_list.h
 ext/nmatrix/util/util.h
 ext/nmatrix/util/lapack.h
+ext/nmatrix/math.cpp
+ext/nmatrix/math/asum.h
+ext/nmatrix/math/geev.h
+ext/nmatrix/math/gemm.h
+ext/nmatrix/math/gemv.h
+ext/nmatrix/math/ger.h
+ext/nmatrix/math/gesdd.h
+ext/nmatrix/math/gesvd.h
+ext/nmatrix/math/getf2.h
+ext/nmatrix/math/getrf.h
+ext/nmatrix/math/getri.h
+ext/nmatrix/math/getrs.h
+ext/nmatrix/math/idamax.h
+ext/nmatrix/math/lapack.h
+ext/nmatrix/math/laswp.h
+ext/nmatrix/math/long_dtype.h
+ext/nmatrix/math/math.h
+ext/nmatrix/math/nrm2.h
+ext/nmatrix/math/potrs.h
+ext/nmatrix/math/rot.h
+ext/nmatrix/math/rotg.h
+ext/nmatrix/math/scal.h
+ext/nmatrix/math/swap.h
+ext/nmatrix/math/trsm.h
 ext/nmatrix/nmatrix.cpp
 ext/nmatrix/nmatrix.h
 ext/nmatrix/ruby_constants.cpp

data/README.rdoc

@@ -79,17 +79,17 @@ Read the instructions in +CONTRIBUTING.md+ if you want to help NMatrix.
 
 == Features
 
-The following features exist in the current version of NMatrix (0.0.6):
+The following features exist in the current version of NMatrix (0.0.7):
 
 * Matrix and vector storage containers: dense, yale, list (more to come)
 * Data types: byte (uint8), int8, int16, int32, int64, float32, float64, complex64, complex128, rational64, rational128,
   Ruby object
-* Conversion between storage and data types (except from-complex, and from-float-to-rational)
+* Interconversion between storage and data types
 * Element-wise and right-hand-scalar operations and comparisons for all matrix types
 * Matrix-matrix multiplication for dense (with and without ATLAS) and yale
 * Matrix-vector multiplication for dense (with and without ATLAS)
-* Dense and list matrix slicing by copy and reference
-* Yale matrix slicing by copy
+* Lots of enumerators (each, each_with_indices, each_row, each_column, each_rank, map, etc.)
+* Matrix slicing by copy and reference (for dense, yale, and list)
 * Native reading and writing of dense and yale matrices
   * Optional compression for dense matrices with symmetry or triangularity: symmetric, skew, hermitian, upper, lower
 * Matlab .MAT v5 file input
@@ -106,6 +106,9 @@ The following features exist in the current version of NMatrix (0.0.6):
   * xGETRF
   * xLASWP, xSCAL
   * xLAUUM (no LAPACK needed, but BLAS dtypes only)
+* LAPACK (non-ATLAS) access:
+  * xGESVD, xGESDD (singular value decomposition)
+  * xGEEV (eigenvalue decomposition of a asymmetric square matrices)
 * LU decomposition
 * Matrix inversions (requires LAPACK; BLAS dtypes only)
 * Determinant calculation for BLAS dtypes
@@ -114,20 +117,17 @@ The following features exist in the current version of NMatrix (0.0.6):
 
 === Planned Features (Short-to-Medium Term)
 
-These are features planned for NMatrix 0.1.0, our first beta:
+We are nearly the release of NMatrix 0.1.0, our first beta.
 
-* Yale matrix slicing
-* calculation of determinant (LAPACK-free), trace, and eigenvalues (characteristic polynomial)
-* exponentials and square roots
-* matrix inversions (LAPACK-free)
-* matrix decomposition/factorization
-* calculation of additional norms
+These are features planned for NMatrix 0.2.0:
+
+* slice assignments (`x[1..3,0..4] = some_other_matrix`)
+* LAPACK-free calculation of determinant, trace, and eigenvalues (characteristic polynomial)
+* LAPACK-free matrix inversions
 * tensor products
 * principal component analysis (PCA)
 * improved file I/O
   * compression of yale symmetries in I/O
-* operation scheduling
-* parallelization of some types of operations
 * optimization of non-BLAS data types on BLAS-like operations (e.g., matrix multiplication for rational numbers)
 
 === Warning

data/Rakefile

@@ -33,7 +33,8 @@ require 'rspec/core/rake_task'
 require 'rspec/core'
 require 'rspec/core/rake_task'
 RSpec::Core::RakeTask.new(:spec) do |spec|
-  spec.pattern = FileList['spec/**/*_spec.rb']
+  # Load nmatrix_spec first.
+  spec.pattern = FileList['spec/nmatrix_spec.rb', 'spec/**/*_spec.rb'].uniq
 end
 
 BASEDIR = Pathname( __FILE__ ).dirname.relative_path_from( Pathname.pwd )
@@ -69,23 +70,31 @@ task :pry do |task|
   run *cmd
 end
 
-#namespace :console do
-#  CONSOLE_CMD = ['irb', "-r './lib/nmatrix.rb'"]
-#  desc "Run console under GDB."
-#  task :gdb => [ :compile ] do |task|
-#          cmd = [ 'gdb' ] + GDB_OPTIONS
-#          cmd += [ '--args' ]
-#          cmd += CONSOLE_CMD
-#          run( *cmd )
-#  end
-#
-#  desc "Run console under Valgrind."
-#  task :valgrind => [ :compile ] do |task|
-#          cmd = [ 'valgrind' ] + VALGRIND_OPTIONS
-#          cmd += CONSOLE_CMD
-#          run( *cmd )
-#  end
-#end
+namespace :pry do
+  task :valgrind => [ :compile ] do |task|
+    cmd  = [ 'valgrind' ] + VALGRIND_OPTIONS
+    cmd += ['ruby', '-Ilib:ext', "-r './lib/nmatrix.rb'", "-r 'pry'", "-e 'binding.pry'"]
+    run *cmd
+  end
+end
+
+namespace :console do
+  CONSOLE_CMD = ['irb', "-r './lib/nmatrix.rb'"]
+  desc "Run console under GDB."
+  task :gdb => [ :compile ] do |task|
+          cmd = [ 'gdb' ] + GDB_OPTIONS
+          cmd += [ '--args' ]
+          cmd += CONSOLE_CMD
+          run( *cmd )
+  end
+
+  desc "Run console under Valgrind."
+  task :valgrind => [ :compile ] do |task|
+          cmd = [ 'valgrind' ] + VALGRIND_OPTIONS
+          cmd += CONSOLE_CMD
+          run( *cmd )
+  end
+end
 
 task :default => :spec
 
@@ -98,7 +107,7 @@ namespace :spec do
   # spurious (and eminently ignorable) warnings from the ruby
   # interpreter
 
-  RSPEC_CMD = [ 'ruby', '-S', 'rspec', '-Ilib:ext', SPECDIR ]
+  RSPEC_CMD = [ 'ruby', '-S', 'rspec', '-Ilib:ext', "#{SPECDIR}/nmatrix_spec.rb #{SPECDIR}" ]
 
   #desc "Run the spec for generator.rb"
   #task :generator do |task|
@@ -107,7 +116,7 @@ namespace :spec do
 
   desc "Run specs under GDB."
   task :gdb => [ :compile ] do |task|
-    cmd = [ 'gdb' ] + GDB_OPTIONS
+          cmd = [ 'gdb' ] + GDB_OPTIONS
     cmd += [ '--args' ]
     cmd += RSPEC_CMD
     run( *cmd )
@@ -116,22 +125,23 @@ namespace :spec do
   desc "Run specs under cgdb."
   task :cgdb => [ :compile ] do |task|
     cmd = [ 'cgdb' ] + GDB_OPTIONS
-    cmd += [ '--args' ]
-    cmd += RSPEC_CMD
-    run( *cmd )
+          cmd += [ '--args' ]
+          cmd += RSPEC_CMD
+          run( *cmd )
   end
 
   desc "Run specs under Valgrind."
   task :valgrind => [ :compile ] do |task|
-    cmd = [ 'valgrind' ] + VALGRIND_OPTIONS
-    cmd += RSPEC_CMD
-    run( *cmd )
+          cmd = [ 'valgrind' ] + VALGRIND_OPTIONS
+          cmd += RSPEC_CMD
+          run( *cmd )
   end
 end
 
 
 LEAKCHECK_CMD = [ 'ruby', '-Ilib:ext', "#{SPECDIR}/leakcheck.rb" ]
 
+
 desc "Run leakcheck script."
 task :leakcheck => [ :compile ] do |task|
   cmd = [ 'valgrind' ] + VALGRIND_OPTIONS

data/ext/nmatrix/data/data.cpp

@@ -83,6 +83,8 @@ namespace nm {
       break;
     case T_FLOAT:
     case T_RATIONAL:
+    case T_FIXNUM:
+    case T_BIGNUM:
       r = NUM2DBL(other.rval);
       i = 0.0;
       break;
@@ -91,14 +93,16 @@ namespace nm {
     }
   }
 
+
   template <typename Type>
   Rational<Type>::Rational(const RubyObject& other) {
     switch (TYPE(other.rval)) {
     case T_RATIONAL:
-      n = NUM2LONG(rb_funcall(this->rval, rb_intern("numerator"), 0));
-      d = NUM2LONG(rb_funcall(this->rval, rb_intern("denominator"), 0));
+      n = NUM2LONG(rb_funcall(other.rval, rb_intern("numerator"), 0));
+      d = NUM2LONG(rb_funcall(other.rval, rb_intern("denominator"), 0));
       break;
     case T_FIXNUM:
+    case T_BIGNUM:
       n = NUM2LONG(other.rval);
       d = 1;
       break;
@@ -340,5 +344,14 @@ void* rubyobj_to_cval(VALUE val, nm::dtype_t dtype) {
   return ret_val;
 }
 
+void nm_init_data() {
+    nm::RubyObject obj(INT2FIX(1));
+    nm::Rational32 x(obj);
+    nm::Rational64 y(obj);
+    nm::Rational128 z(obj);
+    nm::Complex64 a(obj);
+    nm::Complex128 b(obj);
+}
+
 
 } // end of extern "C" block

data/ext/nmatrix/data/data.h

@@ -46,6 +46,8 @@
 #include "ruby_object.h"
 
 namespace nm {
+
+
   /*
    * Constants
    */
@@ -776,6 +778,8 @@ void  		  		rubyval_to_cval(VALUE val, nm::dtype_t dtype, void* loc);
 nm::RubyObject	rubyobj_from_cval(void* val, nm::dtype_t dtype);
 nm::RubyObject  rubyobj_from_cval_by_itype(void* val, nm::itype_t itype);
 
+void nm_init_data();
+
 } // end of extern "C" block
 
 #endif // DATA_H

data/ext/nmatrix/data/ruby_object.h

@@ -123,21 +123,12 @@ class RubyObject {
   inline operator double()   const { RETURN_OBJ2NUM(NUM2DBL)        }
   inline operator float()  const { RETURN_OBJ2NUM(NUM2DBL)          }
 
-  //template <typename IntType>
-  //inline operator Rational<typename std::enable_if<std::is_integral<IntType>::value, IntType>::type>() const { return this->to<Rational<IntType> >(); }
-
-  //template <typename IntType>
-  //inline operator Rational<typename std::enable_if<std::is_integral<IntType>::value, IntType>::type>&() const { static Rational<IntType> x = this->to<Rational<IntType> >(); return x; }
-  //inline operator Rational32() const { return this->to<Rational32>();   }
-  //inline operator Rational64() const { return this->to<Rational64>();   }
-  //inline operator Rational128() const { return this->to<Rational128>(); }
-
-  //template <typename FloatType>
-  //inline operator Complex<typename std::enable_if<std::is_floating_point<FloatType>::value, FloatType>::type>() const { return this->to<Complex<FloatType> >();    }
-
-  //template <typename FloatType>
-  //inline operator Complex<typename std::enable_if<std::is_floating_point<FloatType>::value, FloatType>::type>&() const { static Complex<FloatType> x = this->to<Complex<FloatType> >(); return x;    }
+  inline operator Rational32() const { return this->to<Rational32>();   }
+  inline operator Rational64() const { return this->to<Rational64>();   }
+  inline operator Rational128() const { return this->to<Rational128>(); }
 
+  inline operator Complex64() const { return this->to<Complex64>(); }
+  inline operator Complex128() const { return this->to<Complex128>(); }
   /*
 	 * Copy constructors.
 	 */