sciruby 0.1.3 → 0.2.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 37ce1d623a33cf7dc0c398b8320869da55bc12c4
+  data.tar.gz: b03df5bc7e818d9f1d4d5aaf5af7dbf5bea6ada0
+SHA512:
+  metadata.gz: 09bedbb54cae59b4a6eeed4a74e12ff4a2112ed81af3e074103b6c678a7e877e3c8e6b3e93a4327ab2a3a7ac8f6f3d1ae9b2bf9ec9fea3eac6967f44cc886b61
+  data.tar.gz: 15624febecc8ba89cb3561109a878f9ffac687f7acca94affe60808b3ce8a3d307af456d4364aa53f0fbb8c24adbfce416edb014f6421bdc4ed534407df9b44b

data/.gitignore

@@ -0,0 +1,2 @@
+*.gem
+Gemfile.lock

data/CHANGES

@@ -0,0 +1,3 @@
+0.2.1 (2015-06-08)
+
+  * Initial release as a meta gem

data/CONTRIBUTING.md

@@ -0,0 +1,46 @@
+SciRuby is a collaborative effort to bring scientific computation to Ruby. If you want to help, please do so!
+
+This guide covers way in which you can contribute.
+
+## How to help
+
+There are various ways in which you can improve SciRuby. Coding and documentation are the two primary possibilities and participate in the [mailing list][mailing-list] -- suggesting ideas and changes is very important!
+
+Apart from adding features and functionality, you can also create tests (we use RSpec), guides on how to do something using SciRuby, document the libraries and help find and fix bugs.
+
+Start by visiting our [issue tracker](https://github.com/SciRuby/sciruby/issues?state=open) if you want to start contributing, there's probably something with which you can help.
+
+## Projects
+
+SciRuby is an umbrella for many other projects in Ruby. There's not much hierarchy or anything, but we believe that the most important one at the time is [NMatrix][nmatrix], as it's very hard to create some scientific library that doesn't need a good numerical linear algebra library to deal with vectors and matrices.
+
+So, the SciRuby subprojects are, in no particular order:
+
+- [NMatrix][nmatrix]: A fast numerical linear algebra library
+- [Statsample][statsample]: A suite for basic and advanced statistics
+- [Distribution][distribution]: Diverse statistical distributions. Uses C (statistics2/GSL) or Java extensions when available.
+- [Integration][integration]: Integration methods.
+- [Minimization][minimization]: Various minimization algorithms in pure Ruby.
+
+## Documentation
+
+Documentation is something most developers don't want to create, but everyone likes to use (well, most of the time). We can't possibly have a big community without proper guides and API docs.
+
+Our current idea is to write guides (that can be initially created as blog posts, for example) and put them into a single place -- the [sciruby.com][sciruby] website. This enables people to start using the library without much friction.
+
+For API documentation, we're using the [RDoc format][rdoc] in the source code. It works with both Ruby and C, so we should be able to have a very good coverage. We want to put the whole API documentation in one single place; again, the [sciruby.com][sciruby] website.
+
+If you solved a problem or created an application that uses SciRuby or its subprojects, please say so in our mailing list and send us a pull request!
+
+## Conclusion
+
+Before commiting any code, you *MUST* read our [Contributor Agreement](http://github.com/SciRuby/sciruby/wiki/Contributor-Agreement). This is meant to protect both us and the users of SciRuby, as there are lots of scientific packages (or code found in books) that aren't so "open" as we would like them to be.
+
+[mailing-list]: https://groups.google.com/forum/?fromgroups#!forum/sciruby-dev
+[sciruby]: http://sciruby.com
+[nmatrix]: https://github.com/sciruby/nmatrix
+[statsample]: https://github.com/SciRuby/statsample
+[distribution]: https://github.com/SciRuby/distribution
+[integration]: https://github.com/SciRuby/integration
+[minimization]: https://github.com/SciRuby/minimization
+[rdoc]: http://rdoc.rubyforge.org/

data/Gemfile

@@ -0,0 +1,34 @@
+# This file specifies all gems which are installed by the `sciruby-full` gem or recommended by the `sciruby` gem.
+
+source 'https://rubygems.org'
+
+gem 'nmatrix'
+gem 'gsl-nmatrix'
+
+gem 'rubyvis'
+gem 'nyaplot'
+gem 'plotrb'
+gem 'gnuplot'
+
+gem 'iruby'
+gem 'pry'
+gem 'awesome_print'
+
+gem 'daru'
+
+gem 'integration'
+gem 'minimization'
+gem 'distribution'
+
+gem 'statsample'
+gem 'statsample-glm'
+gem 'statsample-bivariate-extension'
+#gem 'statsample-timeseries' # currently not working because of activesupport dependency
+gem 'extendmatrix'
+
+gem 'publisci'
+
+gem 'ai4r'
+
+# from the bioruby project
+gem 'bio'

data/LICENSE.txt

@@ -0,0 +1,21 @@
+This version of SciRuby 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, 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.
+
+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/README.rdoc

@@ -0,0 +1,28 @@
+= SciRuby meta gem
+
+Tools for Scientific Computing in Ruby
+
+* {Installation}[https://github.com/SciRuby/sciruby/wiki/Installation]
+* {Website}[http://sciruby.com]
+* {Google+}[https://plus.google.com/109304769076178160953/posts]
+* {NMatrix}[http://github.com/SciRuby/nmatrix]
+
+== Description
+
+Ruby has for some time had no equivalent to the beautifully constructed numpy, scipy, and matplotlib libraries for Python. We believe that the time for a Ruby science and visualization package has come and gone. Sometimes when a solution of sugar and water becomes super-saturated, from it precipitates a pure, delicious, and diabetes-inducing crystal of sweetness, induced by no more than the tap of a finger. So it is, we believe, with the need for numeric and visualization libraries in Ruby.
+
+We are not the first with this idea, but we are trying to bring it to life.
+
+== License
+
+Copyright (c) 2010 onward, The Ruby Science Foundation.
+
+All rights reserved.
+
+SciRuby is licensed under the BSD 3-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/lib/sciruby/gems.rb

@@ -0,0 +1,27 @@
+module SciRuby
+  extend self
+
+  def all_gems
+    @all_gems ||= File.read(File.expand_path(File.join(__FILE__, '..', '..', '..', 'Gemfile'))).scan(/^(?!#.*)gem\s+'(.*?)'/).map(&:first)
+  end
+
+  def installed_gems
+    @installed_gems ||=
+      begin
+        require 'rubygems'
+        Hash[all_gems.map {|name| (v = gem_version(name)) && [name, v] }.compact]
+      end
+  end
+
+  def require!
+    installed_gems.each {|gem,_| require gem }
+  end
+
+  private
+
+  def gem_version(name)
+    Gem::Specification.find_by_name(name).version.to_s
+  rescue Exception
+    nil
+  end
+end

data/lib/sciruby/version.rb

@@ -0,0 +1,3 @@
+module SciRuby
+  VERSION = '0.2.1'
+end

data/lib/sciruby.rb

@@ -1,77 +1,2 @@
-# = sciruby.rb -
-# SciRuby - Ruby scientific visualization and computation.
-#
-# Copyright (C) 2011  SciRuby Development Team
-#  * John O. Woods
-#  * John T. Prince
-#  * Claudio Bustos
-#  * others
-#
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 3
-# of the License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
-#
-# Specific notices will be placed where they are appropriate.
-#
-
-require "rubygems"
-require "bundler/setup"
-
-module SciRuby
-  VERSION = '0.1.3'
-  DIR     = Pathname.new(__FILE__).realpath.dirname.to_s
-
-  require File.join(::SciRuby::DIR, 'ext', 'string.rb')
-  require File.join(::SciRuby::DIR, 'ext', 'csv.rb')
-
-  class << self
-    def plot script
-      SciRuby::Plotter.new script
-    end
-
-    def integrate *args, &block
-      require "integration"
-      ::Integration.integrate(*args, &block)
-    end
-
-    # Produce a list of datasets that can be loaded using the +dataset+ method
-    def dataset_search database, args = {}
-      "SciRuby::Data::#{database.to_s.camelize}".constantize.new(args).datasets.keys
-    end
-
-    # Load a dataset from a specific database. For a list of datasets, use `dataset_search(:guardian)`, for example.
-    def dataset database, source_id
-      begin
-        "SciRuby::Data::#{database.to_s.camelize}".constantize.new.dataset(source_id)
-      rescue DatabaseUnavailableError => e
-        warn "Database appears to be unavailable. Attempting to use cached version."
-        SciRuby::Data::Cacher.new.dataset(source_id, database)
-      end
-    end
-
-    # Shorthand for SciRuby::Analysis.store(*args, &block)
-    def analyze *args, &block
-      SciRuby::Analysis.store(*args, &block)
-    end
-  end
-
-  autoload(:Analysis, File.join(DIR, 'sciruby', 'analysis'))
-  autoload(:Config, File.join(DIR, 'sciruby', 'config'))
-  autoload(:Editor, File.join(DIR, 'sciruby', 'editor'))
-  autoload(:Plotter, File.join(DIR, 'sciruby', 'plotter'))
-  autoload(:Recommend, File.join(DIR, 'sciruby', 'recommend'))
-  autoload(:Validation, File.join(DIR, 'sciruby', 'validation'))
-  autoload(:Data, File.join(DIR, 'sciruby', 'data'))
-end
-
-autoload(:Shoes, File.join(SciRuby::DIR, 'ext', 'shoes'))
+require 'sciruby/version'
+require 'sciruby/gems'

data/sciruby.gemspec

@@ -0,0 +1,35 @@
+# coding: utf-8
+$: << File.join(File.dirname(__FILE__), 'lib')
+require 'sciruby'
+require 'date'
+
+SCIRUBY_FULL = false unless defined?(SCIRUBY_FULL)
+
+Gem::Specification.new do |s|
+  s.name        = SCIRUBY_FULL ? 'sciruby-full' : 'sciruby'
+  s.date        = Date.today.to_s
+  s.version     = SciRuby::VERSION
+  s.authors     = ['SciRuby Development Team']
+  s.email       = ['sciruby-dev@googlegroups.com']
+  s.license     = 'BSD'
+  s.homepage    = 'http://sciruby.com'
+  s.summary     =
+  s.description = "Scientific gems for Ruby#{SCIRUBY_FULL ? ' (Full installation)' : ''}"
+
+  s.require_paths = %w(lib)
+  s.files = `git ls-files`.split($/)
+
+  if SCIRUBY_FULL
+    s.files.delete 'sciruby.gemspec'
+    s.files.reject! {|f| f =~ /\Alib/ }
+
+    s.add_runtime_dependency 'sciruby', "= #{SciRuby::VERSION}"
+    SciRuby.all_gems.each {|gem| s.add_runtime_dependency gem }
+  else
+    s.files.delete 'sciruby-full.gemspec'
+
+    m = "Please consider installing 'sciruby-full' or the following gems:\n"
+    SciRuby.all_gems.each {|gem| m << "  * #{gem}\n" }
+    s.post_install_message = m << "\n"
+  end
+end