Disabled list stoage element-wise ops, fixed Mat5 dense loading, added debugging statements for list storage element-wise operations. Updated Manifest, History. Fixed it so VERSION shows up. Updated README

Author: translunar

History.txt

@@ -4,7 +4,7 @@
 
   * Initial alpha release
 
-=== 0.0.2 / 2012-08-??
+=== 0.0.2 / 2012-09-21
 
 * Numerous major enhancements
 
@@ -33,3 +33,7 @@
   * `==` operator now used for matrix equality, `=~` and `!~` for element-wise comparisons
 
   * Dense `each` returns an Enumerator when called without a block
+
+  * Sped up list storage item deletion, fixed bugs
+
+* Note: Element-wise list operations current disabled

Manifest.txt

@@ -11,7 +11,9 @@ spec/nmatrix_spec.rb
 spec/nmatrix_yale_spec.rb
 spec/nvector_spec.rb
 spec/slice_spec.rb
-spec/io_spec.rb
+spec/elementwise_spec.rb
+spec/blas_spec.rb
+spec/lapack_spec.rb
 spec/spec_helper.rb
 lib/nmatrix.rb
 lib/nmatrix/io/mat5_reader.rb
@@ -41,6 +43,7 @@ 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/nmatrix.cpp
 ext/nmatrix/nmatrix.h
 ext/nmatrix/ruby_constants.cpp

README.rdoc

@@ -27,8 +27,7 @@ are working on a {patch for Ruby/GSL}[https://github.com/SciRuby/rb-gsl].
 
 == Features
 
-The following features exist in the version of NMatrix (0.0.2) currently under development, and may or may not exist in
-0.0.1 (the current gem):
+The following features exist in the current version of NMatrix (0.0.2):
 
 * Matrix storage containers: dense, yale, list (more to come)
 * Data types: uint8, int8, int16, int32, int64, float32, float64, complex64, complex128, rational64, rational128
@@ -45,17 +44,9 @@ The following features exist in the version of NMatrix (0.0.2) currently under d
   * xTRSM
 * LAPACK ATLAS access:
   * xGETRF (experimental)
-
-=== Planned Features (Very Short Term)
-
-These features will exist in our second alpha release, 0.0.2 (incomplete, thus not yet available as a gem):
-
-* Yale matrix slicing and referencing
-* LU decomposition
 * LAPACK internal implementations (no library needed):
   * xGETRF
-
-The estimated release date for 0.0.2 is the end of August 2012.
+* LU decomposition
 
 === Planned Features (Short-to-Medium Term)
 
@@ -99,13 +90,14 @@ If you get errors about clapack.h or cblas.h, figure out where your ATLAS header
 Then, tell your system:
 
     export C_INCLUDE_PATH=/usr/local/atlas/include
+    export CPLUS_INCLUDE_PATH=/usr/local/atlas/include
 
 Finally, try compiling again.
 
 == REQUIREMENTS:
 
 * ATLAS and LAPACK, probably
-* GCC 4.2
+* GCC 4.3
 * Ruby 1.9
 
 == INSTALLATION:

ext/nmatrix/data/complex.h

@@ -33,6 +33,7 @@
  */
 
 #include <type_traits>
+#include <iostream>
 
 /*
  * Project Includes
@@ -352,6 +353,12 @@ inline bool operator>=(const NativeType left, const Complex<ComplexType>& right)
 	return Complex<ComplexType>(left) >= right;
 }
 
+template <typename Type>
+inline std::ostream& operator<<(std::ostream& out, const Complex<Type>& rhs) {
+  out << "(" << rhs.r << "," << rhs.i << "i)" << std::flush;
+  return out;
+}
+
 } // end of namespace nm
 
 namespace std {

ext/nmatrix/data/rational.h

@@ -34,6 +34,7 @@
 
 #include <type_traits>
 #include <ruby.h>
+#include <iostream>
 
 /*
  * Project Includes
@@ -401,6 +402,12 @@ inline bool operator>=(const NativeType left, const Rational<RationalType>& righ
 	return (left > right) or (left == right); 
 }
 
+template <typename Type>
+inline std::ostream& operator<<(std::ostream& out, const Rational<Type>& rhs) {
+  out << rhs.n << "/" << rhs.d << std::flush;
+  return out;
+}
+
 } // end of namespace nm
 
 namespace std {

ext/nmatrix/data/ruby_object.h

@@ -33,7 +33,7 @@
  */
 
 #include <ruby.h>
-
+#include <iostream>
 #include <type_traits>
 
 /*
@@ -430,6 +430,11 @@ inline bool operator>(const Rational<IntType>& left, const RubyObject& right) {
 	return RubyObject(left) > right;
 }
 
+inline std::ostream& operator<<(std::ostream& out, const RubyObject& rhs) {
+  out << "RUBYOBJECT" << std::flush; // FIXME: Try calling inspect or something on the Ruby object if we really need to debug it.
+  return out;
+}
+
 } // end of namespace nm
 
 namespace std {

ext/nmatrix/nmatrix.cpp

@@ -1118,7 +1118,7 @@ static VALUE nm_xslice(int argc, VALUE* argv, void* (*slice_func)(STORAGE*, SLIC
 
 static VALUE elementwise_op(nm::ewop_t op, VALUE left_val, VALUE right_val) {
 	STYPE_MARK_TABLE(mark);
-	
+
 	static STORAGE* (*ew_op[nm::NUM_STYPES])(nm::ewop_t, const STORAGE*, const STORAGE*) = {
 		nm_dense_storage_ew_op,
 		nm_list_storage_ew_op,

ext/nmatrix/storage/list.cpp

@@ -32,6 +32,7 @@
 
 #include <ruby.h>
 #include <algorithm> // std::min
+#include <iostream>
 
 /*
  * Project Includes
@@ -341,6 +342,8 @@ bool nm_list_storage_eqeq(const STORAGE* left, const STORAGE* right) {
  * Element-wise operations for list storage.
  */
 STORAGE* nm_list_storage_ew_op(nm::ewop_t op, const STORAGE* left, const STORAGE* right) {
+  rb_raise(rb_eNotImpError, "elementwise operations for list storage currently broken");
+
 	OP_LR_DTYPE_TEMPLATE_TABLE(nm::list_storage::ew_op, void*, LIST* dest, const LIST* left, const void* l_default, const LIST* right, const void* r_default, const size_t* shape, size_t dim);
 
   // We may need to upcast our arguments to the same type.
@@ -989,6 +992,7 @@ static void ew_op_prime(LIST* dest, LDType d_default, const LIST* left, LDType l
 
 				if (level == last_level) {
 				  tmp_result = ew_op_switch<op, LDType, RDType>(l_default, *reinterpret_cast<RDType*>(r_node->val));
+				  std::cerr << "1. tmp_result = " << tmp_result << std::endl;
 
 					if (tmp_result != d_default) {
 						dest_node = nm::list::insert_helper(dest, dest_node, index, tmp_result);
@@ -1013,6 +1017,7 @@ static void ew_op_prime(LIST* dest, LDType d_default, const LIST* left, LDType l
 
 				if (level == last_level) {
 				  tmp_result = ew_op_switch<op, LDType, RDType>(*reinterpret_cast<LDType*>(l_node->val), r_default);
+				  std::cerr << "2. tmp_result = " << tmp_result << std::endl;
 
 					if (tmp_result != d_default) {
 						dest_node = nm::list::insert_helper(dest, dest_node, index, tmp_result);
@@ -1038,6 +1043,7 @@ static void ew_op_prime(LIST* dest, LDType d_default, const LIST* left, LDType l
 
 					if (level == last_level) {
 					  tmp_result = ew_op_switch<op, LDType, RDType>(*reinterpret_cast<LDType*>(l_node->val),*reinterpret_cast<RDType*>(r_node->val));
+					  std::cerr << "3. tmp_result = " << tmp_result << std::endl;
 
 						if (tmp_result != d_default) {
 							dest_node = nm::list::insert_helper(dest, dest_node, index, tmp_result);

lib/nmatrix.rb

@@ -38,6 +38,7 @@
 # NMatrix
 
 require 'nmatrix/nmatrix.rb'
+require 'nmatrix/version.rb'
 require 'nmatrix/nvector.rb'
 require 'nmatrix/blas.rb'
 

lib/nmatrix/io/mat5_reader.rb

@@ -147,7 +147,8 @@ def unpacked_data real_mdtype=nil, imag_mdtype=nil
 
           unpacked_real.zip(unpacked_imag).flatten
         else
-          self.real_part.data.unpack(real_unpack_args)
+          length = self.dimensions.inject(1) { |a,b| a * b } # get the product
+          self.real_part.data.unpack(*(real_unpack_args*length))
         end
 
       end
@@ -252,11 +253,11 @@ def to_nm(dtype = nil)
           # MATLAB always uses :miINT32 for indices according to the spec
           ia_ja                     = repacked_indices(to_itype)
           data_str, repacked_dtype  = repacked_data(dtype)
-          NMatrix.new(:yale, self.dimensions, repacked_dtype, ia_ja[0], ia_ja[1], data_str, repacked_dtype)
+          NMatrix.new(:yale, self.dimensions.reverse, repacked_dtype, ia_ja[0], ia_ja[1], data_str, repacked_dtype)
 
         else
           # Call regular dense constructor.
-          NMatrix.new(:dense, self.dimensions, unpacked_data, dtype)
+          NMatrix.new(:dense, self.dimensions.reverse, unpacked_data, dtype).transpose
         end
       end