nmatrix 0.1.0 → 0.2.0

data/LICENSE.txt

@@ -1,23 +0,0 @@
-This version of NMatrix is licensed under the BSD 2-clause license.
-
-* http://sciruby.com
-* http://github.com/sciruby/sciruby/wiki/License
-
-You *must* read the Contributor Agreement before contributing code to the SciRuby Project. This is available online:
-
-* http://github.com/sciruby/sciruby/wiki/Contributor-Agreement
-
------
-
-Copyright (c) 2010 - 2015, John Woods and the Ruby Science Foundation
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-
-* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
-
-* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
-
-* Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

data/Manifest.txt

@@ -1,92 +0,0 @@
-History.txt
-Manifest.txt
-README.rdoc
-LICENSE.txt
-CONTRIBUTING.md
-Rakefile
-Gemfile
-Guardfile
-nmatrix.gemspec
-.travis.yml
-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/io/point_cloud.rb
-lib/nmatrix/io/fortran_format.rb
-lib/nmatrix/io/harwell_boeing.rb
-lib/nmatrix/blas.rb
-lib/nmatrix/enumerate.rb
-lib/nmatrix/homogeneous.rb
-lib/nmatrix/lapack.rb
-lib/nmatrix/math.rb
-lib/nmatrix/monkeys.rb
-lib/nmatrix/nmatrix.rb
-lib/nmatrix/rspec.rb
-lib/nmatrix/shortcuts.rb
-lib/nmatrix/version.rb
-lib/nmatrix/yale_functions.rb
-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/storage/common.cpp
-ext/nmatrix/storage/common.h
-ext/nmatrix/storage/storage.cpp
-ext/nmatrix/storage/storage.h
-ext/nmatrix/storage/dense/dense.cpp
-ext/nmatrix/storage/dense/dense.h
-ext/nmatrix/storage/list/list.cpp
-ext/nmatrix/storage/list/list.h
-ext/nmatrix/storage/yale/yale.cpp
-ext/nmatrix/storage/yale/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/util/io.cpp
-ext/nmatrix/util/io.h
-ext/nmatrix/util/sl_list.cpp
-ext/nmatrix/util/sl_list.h
-ext/nmatrix/util/util.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/imax.h
-ext/nmatrix/math/inc.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
-ext/nmatrix/ruby_constants.h
-ext/nmatrix/ruby_nmatrix.c
-ext/nmatrix/types.h
-ext/nmatrix/nm_memory.h
-ext/nmatrix/extconf.rb
-
-

data/README.rdoc

@@ -1,150 +0,0 @@
-= NMatrix
-
-Fast Numerical Linear Algebra Library for Ruby
-
-* {sciruby.com}[http://sciruby.com]
-* {Google+}[https://plus.google.com/109304769076178160953/posts]
-* {Google Group - Mailing List}[https://groups.google.com/forum/#!forum/sciruby-dev]
-* {NMatrix Installation wiki}[https://github.com/SciRuby/nmatrix/wiki/Installation]
-* {SciRuby Installation guide}[http://sciruby.com/docs#installation]
-
-{<img src=https://travis-ci.org/SciRuby/nmatrix.png>}[https://travis-ci.org/SciRuby/nmatrix]
-
-{<img src="https://codeclimate.com/github/SciRuby/nmatrix.png" />}[https://codeclimate.com/github/SciRuby/nmatrix]
-
-== Description
-
-NMatrix is a fast numerical linear algebra library for Ruby, with dense and sparse matrices, written mostly in C and
-C++. It is part of the SciRuby project.
-
-NMatrix was inspired by {NArray}[http://narray.rubyforge.org], by Masahiro Tanaka.
-
-== Installation
-
-To install the latest stable version:
-
-    gem install nmatrix --pre
-
-However, you will need to install {ATLAS}[http://math-atlas.sourceforge.net/] with CBLAS (C interface to
-{BLAS}[http://en.wikipedia.org/wiki/Basic_Linear_Algebra_Subprograms]) first. Detailed directions can be found
-{here}[https://github.com/SciRuby/nmatrix/wiki/Installation]. The requirements for NMatrix are:
-
-* ATLAS, preferably with CLAPACK ({see here for details}[https://github.com/SciRuby/nmatrix/wiki/Installation])
-* a version of GCC or clang which supports C++0x or C++11
-* Ruby 1.9.3+
-* {packable}[http://github.com/marcandre/packable] 1.3.5 (used for I/O)
-
-If you want to obtain the latest (development) code, you should generally do:
-
-    git clone https://github.com/SciRuby/nmatrix.git
-    cd nmatrix/
-    bundle install
-    bundle exec rake compile
-    bundle exec rake repackage
-    gem install pkg/nmatrix-0.1.0.rc5.gem
-
-Detailed instructions are available for {Mac}[https://github.com/SciRuby/nmatrix/wiki/Installation#mac-os-x] and {Linux}[https://github.com/SciRuby/nmatrix/wiki/Installation#linux].
-We are currently working on Mavericks (Mac OS X) installation instructions, but in general, you'll need Homebrew and should
-probably use +brew install gcc48+ instead of using the install script.
-
-== Documentation
-
-If you have a suggestion or want to add documentation for any class or method in NMatrix, please open an issue or send a pull request with the changes.
-
-You can find the complete API documentation {on our website}[http://sciruby.com/nmatrix/docs/].
-
-== Examples
-
-Create a new NMatrix from a ruby Array:
-
-    >> require 'nmatrix'
-    >> NMatrix.new([2, 3], [0, 1, 2, 3, 4, 5], dtype: :int64)
-    => [
-        [0, 1, 2],
-        [3, 4, 5]
-       ]
-
-Create a new NMatrix using the +N+ shortcut:
-
-    >> m = N[ [2, 3, 4], [7, 8, 9] ]
-    => [
-        [2, 3, 4],
-        [7, 8, 9]
-       ]
-    >> m.inspect
-    => #<NMatrix:0x007f8e121b6cf8shape:[2,3] dtype:int32 stype:dense>
-
-The above output requires that you have a pretty-print-enabled console such as Pry; otherwise, you'll
-see the output given by +inspect+.
-
-If you want to learn more about how to create a
-matrix, {read the guide in our wiki}[https://github.com/SciRuby/nmatrix/wiki/How-to-create-a-NMatrix].
-
-Again, you can find the complete API documentation {on our website}[http://sciruby.com/nmatrix/docs/].
-
-== Developers
-
-Read the instructions in +CONTRIBUTING.md+ if you want to help NMatrix.
-
-== Features
-
-The following features exist in the current version of NMatrix (0.1.0.rc1):
-
-* 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
-* 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)
-* 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
-* Input/output:
-  * Matlab .MAT v5 file input
-  * MatrixMarket file input/output
-  * Harwell-Boeing and Fortran file input
-  * Point Cloud Library PCD file input
-* C and C++ API
-* BLAS internal implementations (no library) and ATLAS (with library) access:
-  * Level 1: xROT, xROTG (BLAS dtypes only), xASUM, xNRM2, IxAMAX
-  * Level 2: xGEMV
-  * Level 3: xGEMM, xTRSM
-* LAPACK ATLAS access:
-  * xGETRF, xGETRI, xGETRS, xGESV (Gaussian elimination)
-  * xPOTRF, xPOTRI, xPOTRS, xPOSV (Cholesky factorization)
-  * xLASWP, xSCAL, xLAUUM
-* LAPACK-less internal implementations (no LAPACK needed and working on non-BLAS dtypes):
-  * 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
-* Determinant calculation for BLAS dtypes
-* Traces
-* Ruby/GSL interoperability (requires {SciRuby's fork of rb-gsl}[http://github.com/SciRuby/rb-gsl])
-* slice assignments, e.g.,
-    x[1..3,0..4] = some_other_matrix
-
-=== Planned Features (Short-to-Medium Term)
-
-See the issues tracker for a list of planned features or to request new ones.
-
-== License
-
-Copyright (c) 2012--15, John Woods and 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.
-
-== Donations
-
-Support a SciRuby Fellow:
-
-{<img src=http://pledgie.com/campaigns/15783.png?skin_name=chrome>}[http://www.pledgie.com/campaigns/15783]

data/Rakefile

@@ -1,216 +0,0 @@
-# -*- ruby -*-
-
-require 'rubygems'
-require 'rubygems/package_task'
-require 'bundler'
-
-Bundler::GemHelper.install_tasks
-
-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
-
-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
-
-gemspec = eval(IO.read("nmatrix.gemspec"))
-
-Gem::PackageTask.new(gemspec).define
-
-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'].uniq
-end
-
-
-BASEDIR = Pathname( __FILE__ ).dirname.relative_path_from( Pathname.pwd )
-SPECDIR = BASEDIR + 'spec'
-
-VALGRIND_OPTIONS = [
-    "--tool=memcheck",
-    #"--leak-check=yes",
-    "--num-callers=15",
-    #"--error-limit=no",
-    "--partial-loads-ok=yes",
-    "--undef-value-errors=no" #,
-    #"--dsymutil=yes"
-]
-
-CALLGRIND_OPTIONS = [
-    "--tool=callgrind",
-    "--dump-instr=yes",
-    "--simulate-cache=yes",
-    "--collect-jumps=yes"
-]
-
-VALGRIND_MEMORYFILL_OPTIONS = [
-    "--freelist-vol=100000000",
-    "--malloc-fill=6D",
-    "--free-fill=66 ",
-]
-
-GDB_OPTIONS = []
-
-
-task :console do |task|
-  cmd = [ 'irb', "-r './lib/nmatrix.rb'" ]
-  run *cmd
-end
-
-task :pry do |task|
-  cmd = [ 'pry', "-r './lib/nmatrix.rb'" ]
-  run *cmd
-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
-
-def run *cmd
-  sh(cmd.join(" "))
-end
-
-namespace :spec do
-  # partial-loads-ok and undef-value-errors necessary to ignore
-  # spurious (and eminently ignorable) warnings from the ruby
-  # interpreter
-
-  RSPEC_CMD = [ 'ruby', '-S', 'rspec', '-Ilib:ext', SPECDIR.to_s ]
-
-  #desc "Run the spec for generator.rb"
-  #task :generator do |task|
-  #  run 'rspec spec/generator_spec.rb'
-  #end
-
-  desc "Run specs under GDB."
-  task :gdb => [ :compile ] do |task|
-          cmd = [ 'gdb' ] + GDB_OPTIONS
-    cmd += [ '--args' ]
-    cmd += RSPEC_CMD
-    run( *cmd )
-  end
-
-  desc "Run specs under cgdb."
-  task :cgdb => [ :compile ] do |task|
-    cmd = [ 'cgdb' ] + GDB_OPTIONS
-    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 )
-  end
-
-  desc "Run specs under Callgrind."
-  task :callgrind => [ :compile ] do |task|
-    cmd = [ 'valgrind' ] + CALLGRIND_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
-  cmd += LEAKCHECK_CMD
-  run( *cmd )
-end
-
-namespace :clean do
-  task :so do |task|
-    tmp_path = "tmp/#{RUBY_PLATFORM}/nmatrix/#{RUBY_VERSION}"
-    chdir tmp_path do
-      if RUBY_PLATFORM =~ /mswin/
-        `nmake soclean`
-      else
-        mkcmd = ENV['MAKE'] || %w[gmake make].find { |c| system("#{c} -v >> /dev/null 2>&1") }
-        `#{mkcmd} soclean`
-      end
-    end
-  end
-end
-
-
-desc "Check the manifest for correctness"
-task :check_manifest do |task|
-  manifest_files  = File.read("Manifest.txt").split
-
-  git_files       = `git ls-files |grep -v 'spec/'`.split
-  ignore_files    = %w{.gitignore .rspec ext/nmatrix/binary_format.txt ext/nmatrix/ttable_helper.rb scripts/mac-brew-gcc.sh}
-
-  possible_files  = git_files - ignore_files
-
-  missing_files   = possible_files - manifest_files
-  extra_files     = manifest_files - possible_files
-
-  unless missing_files.empty?
-    STDERR.puts "The following files are in the git repo but not the Manifest:"
-    missing_files.each { |f| STDERR.puts " -- #{f}"}
-  end
-
-  unless extra_files.empty?
-    STDERR.puts "The following files are in the Manifest but may not be necessary:"
-    extra_files.each { |f| STDERR.puts " -- #{f}"}
-  end
-
-  if extra_files.empty? && missing_files.empty?
-    STDERR.puts "Manifest looks good!"
-  end
-
-end
-
-require "rdoc/task"
-RDoc::Task.new do |rdoc|
-  rdoc.main = "README.rdoc"
-  rdoc.rdoc_files.include(%w{README.rdoc History.txt LICENSE.txt CONTRIBUTING.md lib ext})
-  rdoc.options << "--exclude=ext/nmatrix/extconf.rb"
-  rdoc.options << "--exclude=ext/nmatrix/ttable_helper.rb"
-  rdoc.options << "--exclude=lib/nmatrix/rspec.rb"
-end
-
-# vim: syntax=ruby