nmatrix 0.0.1 → 0.0.2

data/.gitignore

@@ -0,0 +1,27 @@
+.idea
+Gemfile.lock
+ext/nmatrix/dense/daxpy.c
+ext/nmatrix/dense/dgeco.c
+ext/nmatrix/dense/dgefa.c
+ext/nmatrix/dense/dgemm.c
+ext/nmatrix/dense/dgemv.c
+ext/nmatrix/dense/dscal.c
+ext/nmatrix/dense/idamax.c
+ext/nmatrix/dense/467.c
+ext/nmatrix/dense/*.f
+ext/nmatrix/dense/transpose.txt
+ext/nmatrix/yale/aicm.tex
+tmp/
+test.c
+spec/*.mtx
+*.so
+/tags
+*.gem
+
+ext/nmatrix/*.o
+ext/nmatrix/*.so
+ext/nmatrix/*.log
+ext/nmatrix/**/*.o
+ext/nmatrix/Makefile
+ext/nmatrix/**/Makefile
+ext/nmatrix/nmatrix_config.h

data/.rspec

@@ -0,0 +1,2 @@
+--color
+--format nested

data/Gemfile

@@ -1,7 +1,5 @@
 # Gemfile
+source "http://rubygems.org"
+gemspec
 
-gem "rake", "!= 0.9.0"
-
-group :development, :test do
-  gem "rspec"
-end
+gem 'packable' # for Matlab IO

data/Guardfile

@@ -0,0 +1,6 @@
+guard 'rspec' do
+  watch(%r{^spec/.+_spec\.rb$})
+  watch(%r{^lib/(.+)\.rb$}) { "spec" }
+  watch(%r{^ext/nmatrix/(.+)\.(c|cpp|h|rb)$}) { `rake compile | rake spec` }
+  watch('spec/spec_helper.rb')  { "spec" }
+end

data/History.txt

@@ -4,3 +4,36 @@
 
   * Initial alpha release
 
+=== 0.0.2 / 2012-09-21
+
+* Numerous major enhancements
+
+  * Second alpha release
+
+  * Rewrote NMatrix in C++0x and C++11 using templates, namespaces; removed Ruby generators and CAST parser
+
+  * Added preliminary C API
+
+  * Slicing and referencing support for dense and list matrices
+
+  * BLAS level-3 xTRSM algorithm added for rationals and BLAS types
+
+  * LAPACK support added, including partially working xGETRF subroutine
+
+  * Element-wise comparisons now return byte-matrices
+
+  * Element-wise operations on list matrices may alter the default value of the return matrix
+
+  * Element-wise division behaves like Ruby division
+
+  * Improved MATLAB .MAT v5 file reading
+
+  * clang support
+
+  * `==` 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

data/Manifest.txt

@@ -1,51 +1,54 @@
-.autotest
 History.txt
 Manifest.txt
 README.rdoc
 LICENSE.txt
 Rakefile
 Gemfile
+Guardfile
+spec/io_spec.rb
+spec/math_spec.rb
 spec/nmatrix_spec.rb
 spec/nmatrix_yale_spec.rb
 spec/nvector_spec.rb
-spec/syntax_tree_spec.rb
-lib/array.rb
+spec/slice_spec.rb
+spec/elementwise_spec.rb
+spec/blas_spec.rb
+spec/lapack_spec.rb
+spec/spec_helper.rb
 lib/nmatrix.rb
-lib/string.rb
-ext/nmatrix/cblas.c
-ext/nmatrix/dense.c
-ext/nmatrix/depend
-ext/nmatrix/extconf.rb
-ext/nmatrix/generator.rb
-ext/nmatrix/list.c
-ext/nmatrix/nmatrix.c
+lib/nmatrix/io/mat5_reader.rb
+lib/nmatrix/io/mat_reader.rb
+lib/nmatrix/blas.rb
+lib/nmatrix/monkeys.rb
+lib/nmatrix/nmatrix.rb
+lib/nmatrix/nvector.rb
+lib/nmatrix/version.rb
+ext/nmatrix/data/complex.h
+ext/nmatrix/data/data.cpp
+ext/nmatrix/data/data.h
+ext/nmatrix/data/rational.h
+ext/nmatrix/data/ruby_object.h
+ext/nmatrix/storage/common.cpp
+ext/nmatrix/storage/common.h
+ext/nmatrix/storage/dense.cpp
+ext/nmatrix/storage/dense.h
+ext/nmatrix/storage/list.cpp
+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/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/nmatrix.cpp
 ext/nmatrix/nmatrix.h
-ext/nmatrix/rational.c
-ext/nmatrix/yale.c
-ext/nmatrix/generator/syntax_tree.rb
-ext/nmatrix/dense/blas_header.template.c
-ext/nmatrix/dense/elementwise.template.c
-ext/nmatrix/dense/gemm.template.c
-ext/nmatrix/dense/gemv.template.c
-ext/nmatrix/dense/rationalmath.template.c
-ext/nmatrix/yale/smmp1.template.c
-ext/nmatrix/yale/smmp2.template.c
-ext/nmatrix/yale/smmp1_header.template.c
-ext/nmatrix/yale/smmp2_header.template.c
-ext/nmatrix/yale/sort_columns.template.c
-ext/nmatrix/yale/symbmm.template.c
-ext/nmatrix/yale/numbmm.template.c
-ext/nmatrix/yale/transp.template.c
-ext/nmatrix/yale/complexmath.template.c
-ext/nmatrix/yale/elementwise.template.c
-ext/nmatrix/yale/elementwise_op.template.c
-
-
-
-
-
-
-
-
+ext/nmatrix/ruby_constants.cpp
+ext/nmatrix/ruby_constants.h
+ext/nmatrix/types.h
+ext/nmatrix/extconf.rb
 
 

data/README.rdoc

@@ -8,7 +8,8 @@ http://sciruby.com
 
 == Description
 
-NMatrix is an experimental linear algebra library for Ruby, written mostly in C. It can be used with or without SciRuby, but is part of the SciRuby project.
+NMatrix is an experimental linear algebra library for Ruby, written mostly in C and C++. It can be used with or without
+SciRuby, but is part of the SciRuby project.
 
 NMatrix was inspired by and based heavily upon {NArray}[http://narray.rubyforge.org], by Masahiro Tanaka.
 
@@ -16,23 +17,90 @@ NMatrix was inspired by and based heavily upon {NArray}[http://narray.rubyforge.
 
 === WARNING:
 
-Please be aware that SciRuby and NMatrix are in *PRE-ALPHA* status. If you're thinking of using SciRuby/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).
+Please be aware that SciRuby and NMatrix are *ALPHA* status. If you're thinking of using SciRuby/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).
+
+You should also be aware that NMatrix and NArray are incompatible with one another; you should not try to require both
+at the same time. Unfortunately, that causes problems with Ruby/GSL, which currently depends upon NArray. As such, we
+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):
+
 * Matrix storage containers: dense, yale, list (more to come)
-* Data types: int8, int16, int32, int64, float32, float64, complex64, complex128, rational64, rational128 (incomplete)
-* Very basic algebra (more to come)
+* Data types: uint8, int8, int16, int32, int64, float32, float64, complex64, complex128, rational64, rational128
+  (incomplete)
+* Conversion between storage and data types (except from-complex, and from-float-to-rational)
+* Element-wise operations and comparisons
+* Matrix-matrix multiplication for dense (using ATLAS) and yale
+* Matrix-vector multiplication for dense (using ATLAS)
+* Dense and list matrix slicing and referencing
+* Matlab .MAT v5 file input
+* C and C++ API
+* Level 3 BLAS internal implementations (no library) and ATLAS (with library) access:
+  * xGEMM
+  * 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.
+
+=== Planned Features (Short-to-Medium Term)
+
+These are features planned for NMatrix 0.1.0, our first beta.
+
+* calculation of determinant, trace, and eigenvalues (characteristic polynomial) (0.1.0)
+* Gaussian elimination
+* exponentials and square roots
+* matrix inversions
+* matrix decomposition/factorization
+* calculation of norms
+* tensor products
+* principal component analysis (PCA)
+* improved file 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)
+* Ruby/GSL interoperability
 
 == SYNOPSIS:
 
-From the command line,
+For full instructions, please see sciruby.com/nmatrix. Generally, you should be able to do
+
+    gem install nmatrix
+
+However, you will need to install ATLAS with CBLAS first. Those directions can be found at our website.
+
+NOTE: The above command will not give you 0.0.2, which is not yet complete. To obtain 0.0.2, you should use the
+following sequence of commands:
+
+    git clone https://github.com/SciRuby/nmatrix.git
+    cd nmatrix/
+    rake compile
+    rake repackage
+    gem install pkg/nmatrix-0.0.2.gem
 
-    git clone git@github.com:mohawkjohn/nmatrix.git
-    cd nmatrix
-    rake console
+If you get errors about clapack.h or cblas.h, figure out where your ATLAS headers are using:
 
-Gem coming later.
+    locate clapack.h
+
+Then, tell your system:
+
+    export C_INCLUDE_PATH=/usr/local/atlas/include
+
+Finally, try compiling again.
 
 == REQUIREMENTS:
 
@@ -48,7 +116,13 @@ More detailed installation instructions are available at {here}[http://sciruby.c
 
 == DEVELOPERS:
 
-Before commiting any code, you *MUST* read our {Contributor Agreement}[http://github.com/SciRuby/sciruby/wiki/Contributor-Agreement].
+Code in the master branch of SciRuby/nmatrix on github should compile and link, but is not necessarily stable. You might
+also check out the dev branch if master hasn't been updated in some time.
+
+    git clone https://github.com/mohawkjohn/nmatrix.git
+
+Before commiting any code, you *MUST* read our
+{Contributor Agreement}[http://github.com/SciRuby/sciruby/wiki/Contributor-Agreement].
 
 == LICENSE:
 
@@ -56,8 +130,11 @@ Copyright (c) 2012, The Ruby Science Foundation.
 
 All rights reserved.
 
-NMatrix, along with SciRuby, is licensed under the BSD 2-clause license. See {LICENSE.txt}[https://github.com/SciRuby/sciruby/wiki/License] for details.
+NMatrix, along with SciRuby, is licensed under the BSD 2-clause license. See
+{LICENSE.txt}[https://github.com/SciRuby/sciruby/wiki/License] for details.
 
 == DONATIONS:
 
+Support a SciRuby Fellow:
+
 {<img src=https://www.pledgie.com/campaigns/15783.png?skin_name=chrome>}[http://www.pledgie.com/campaigns/15783]

data/Rakefile

@@ -1,28 +1,40 @@
 # -*- ruby -*-
 
 require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
 
-# Fix for problem described here: https://github.com/jbarnette/isolate/pull/39
-module Gem
-  Deprecate = Module.new do
-    include Deprecate
-  end
+require 'rake'
+require "rake/extensiontask"
+Rake::ExtensionTask.new do |ext|
+    ext.name = 'nmatrix'          
+    ext.ext_dir = 'ext/nmatrix' 
+    ext.lib_dir = 'lib/'             
+    ext.source_pattern = "**/*.{c,cpp, h}" 
 end
-require 'isolate/now'
-# End Fix
 
-require 'hoe'
-require 'pathname'
-require 'rspec/core/rake_task'
+gemspec = eval(IO.read("nmatrix.gemspec"))
+
+require "rake/gempackagetask"
+Rake::GemPackageTask.new(gemspec).define
+
+desc "install the gem locally"
+task :install => [:package] do
+  sh %{gem install pkg/nmatrix-#{NMatrix::VERSION}}
+end
 
-Hoe.plugin :compiler
-Hoe.plugin :bundler
-Hoe.plugin :git
-# Hoe.plugin :compiler
-# Hoe.plugin :gem_prelude_sucks
-# Hoe.plugin :inline
-# Hoe.plugin :racc
-# Hoe.plugin :rubyforge
+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']
+end
 
 BASEDIR = Pathname( __FILE__ ).dirname.relative_path_from( Pathname.pwd )
 SPECDIR = BASEDIR + 'spec'
@@ -42,41 +54,6 @@ VALGRIND_MEMORYFILL_OPTIONS = [
 GDB_OPTIONS = []
 
 
-h = Hoe.spec 'nmatrix' do
-  self.require_ruby_version ">=1.9"
-  self.developer('John Woods', 'john.o.woods@gmail.com')
-  self.post_install_message = <<-EOF
-***********************************************************
-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 4.6.1. 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.
-
-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!
-
-***********************************************************
-EOF
-  #self.need_rdoc = false
-  self.readme_file = 'README.rdoc'
-  # self.rubyforge_name = 'nmatrixx' # if different than 'nmatrix'
-end
-
 RSpec::Core::RakeTask.new(:spec)
 
 task :console do |task|
@@ -84,6 +61,11 @@ task :console do |task|
   run *cmd
 end
 
+task :pry do |task|
+  cmd = [ 'pry', "-r './lib/nmatrix.rb'" ]
+  run *cmd
+end
+
 #namespace :console do
 #  CONSOLE_CMD = ['irb', "-r './lib/nmatrix.rb'"]
 #  desc "Run console under GDB."