y_petri 2.2.4 → 2.3.2

data/test/transition_test.rb

@@ -1,6 +1,7 @@
 #! /usr/bin/ruby
 # encoding: utf-8
 
+gem 'minitest'
 require 'minitest/autorun'
 require 'y_support/typing'
 
@@ -63,13 +64,13 @@ describe ::YPetri::Transition do
       assert [@t1, @t2, @t3].all? { |t| t.s? }
       # Now let's flex them:
       @t1.fire!
-      [@p1.m, @p3.m].must_equal [3, 5]
+      [ @p1.marking, @p3.marking ].must_equal [3, 5]
       @t3.fire!
-      [@p1.m, @p3.m].must_equal [3.5, 5.5]
+      [ @p1.marking, @p3.marking ].must_equal [3.5, 5.5]
       @t2.fire!
-      [@p1.m, @p3.m].must_equal [7.0, 9.0]
-      @t1.codomain_marking.must_equal [@p1.m, @p3.m]
-      @t1.domain_marking.must_equal [@p2.m]
+      [ @p1.marking, @p3.marking ].must_equal [7.0, 9.0]
+      @t1.codomain_marking.must_equal [ @p1.marking, @p3.marking ]
+      @t1.domain_marking.must_equal [@p2.marking ]
       @t1.zero_action.must_equal [0, 0]
     end
   end
@@ -97,11 +98,11 @@ describe ::YPetri::Transition do
       @t2.s.must_equal( { @p5.object_id => -1, @p1.object_id => 1 } )
       @t1.domain.must_equal [@p5] # inferred domain
       @t2.domain.must_equal [] # domain is empty in functionless transitions!
-      [@p1.m, @p5.m].must_equal [1, 5]
+      [ @p1.marking, @p5.marking ].must_equal [1, 5]
       @t1.fire!
-      [@p1.m, @p5.m].must_equal [2, 4]
+      [ @p1.marking, @p5.marking ].must_equal [2, 4]
       @t2.fire!
-      [@p1.m, @p5.m].must_equal [3, 3]
+      [ @p1.marking, @p5.marking ].must_equal [3, 3]
     end
   end
 
@@ -117,10 +118,10 @@ describe ::YPetri::Transition do
       assert @t1.functional?
       assert @t1.timed?
       @t1.domain.must_equal [@p5]
-      [@p1.m, @p5.m].must_equal [1, 5]
+      [ @p1.marking, @p5.marking ].must_equal [1, 5]
       @t1.rate_closure.arity.must_equal 0
       @t1.fire! 0.5
-      [@p1.m, @p5.m].must_equal [1.5, 4.5]
+      [ @p1.marking, @p5.marking ].must_equal [1.5, 4.5]
     end
   end
 

data/test/world_test.rb

@@ -1,6 +1,7 @@
 #! /usr/bin/ruby
 # encoding: utf-8
 
+gem 'minitest'
 require 'minitest/autorun'
 require_relative '../lib/y_petri'     # tested component itself
 # require 'y_petri'
@@ -62,6 +63,7 @@ describe YPetri::World do
     @w.simulation.run!
     rec_csv = @w.simulation.recording.to_csv
     expected_rec_csv =
+      ":event,:AA,:BB,:CC\n" +
       "0.0,1.0,2.0,3.0\n" +
       "10.0,0.86102,0.86102,4.13898\n" +
       "20.0,1.29984,0.29984,4.70016\n"

data/test/y_petri_test.rb

@@ -1,6 +1,7 @@
 #! /usr/bin/ruby
-# encoding: utf-8
+#encoding: utf-8
 
+gem 'minitest'
 require 'minitest/autorun'
 require_relative '../lib/y_petri' # tested component itself
 # require 'y_petri'

data/y_petri.gemspec

@@ -1,21 +1,27 @@
-# -*- encoding: utf-8 -*-
-require File.expand_path('../lib/y_petri/version', __FILE__)
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'y_petri/version'
 
-Gem::Specification.new do |gem|
-  gem.authors       = ["boris"]
-  gem.email         = ["\"boris@iis.sinica.edu.tw\""]
-  gem.description   = %q{a Petri net domain model and simulator}
-  gem.summary       = %q{a Petri net domain model and simulator}
-  gem.homepage      = ""
+Gem::Specification.new do |spec|
+  spec.name          = "y_petri"
+  spec.version       = YPetri::VERSION
+  spec.authors       = ["boris"]
+  spec.email         = ["\"boris@iis.sinica.edu.tw\""]
+  spec.summary       = %q{Systems modelling and simulation gem, and a domain model of a special kind of Petri nets (YPetri nets) that can be used to model and simulate any kind of dynamic systems.}
+  spec.description   = %q{YPetri is a gem for modelling and simulation of dynamic systems. Wiring diagram of a dynamic system to be modelled is expressed as YPetri net, a specific kind of Petri net that unifies discrete/continous, deterministic/stochastic, timed/timeless and stoichiometric/nonstoichiometric dichotomies, thus enabling modelling and simulation of dynamic systems of any kind whatsoever. Like Petri nets themselves, YPetri was inspired by problems from the domain of chemistry, but its use is not limited to it.}
+  spec.homepage      = ""
+  spec.license       = "GPLv3"
 
-  gem.files         = `git ls-files`.split($\)
-  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
-  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
-  gem.name          = "y_petri"
-  gem.require_paths = ["lib"]
-  gem.version       = YPetri::VERSION
-  
-  gem.add_dependency "y_support"
-  gem.add_dependency "gnuplot"
-  gem.add_dependency "ruby-graphviz"
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.6"
+  spec.add_development_dependency "rake"
+  spec.add_dependency "y_support"
+  spec.add_dependency "gnuplot"
+  spec.add_dependency "ruby-graphviz"
+  spec.add_dependency "distribution"
 end

metadata

@@ -1,15 +1,43 @@
 --- !ruby/object:Gem::Specification
 name: y_petri
 version: !ruby/object:Gem::Version
-  version: 2.2.4
+  version: 2.3.2
 platform: ruby
 authors:
 - boris
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-22 00:00:00.000000000 Z
+date: 2014-04-23 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: y_support
   requirement: !ruby/object:Gem::Requirement
@@ -52,7 +80,27 @@ dependencies:
     - - '>='
       - !ruby/object:Gem::Version
         version: '0'
-description: a Petri net domain model and simulator
+- !ruby/object:Gem::Dependency
+  name: distribution
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: YPetri is a gem for modelling and simulation of dynamic systems. Wiring
+  diagram of a dynamic system to be modelled is expressed as YPetri net, a specific
+  kind of Petri net that unifies discrete/continous, deterministic/stochastic, timed/timeless
+  and stoichiometric/nonstoichiometric dichotomies, thus enabling modelling and simulation
+  of dynamic systems of any kind whatsoever. Like Petri nets themselves, YPetri was
+  inspired by problems from the domain of chemistry, but its use is not limited to
+  it.
 email:
 - '"boris@iis.sinica.edu.tw"'
 executables: []
@@ -61,32 +109,36 @@ extra_rdoc_files: []
 files:
 - .gitignore
 - Gemfile
-- LICENSE
+- LICENSE.txt
 - README.md
 - Rakefile
 - lib/y_petri.rb
 - lib/y_petri/agent.rb
 - lib/y_petri/agent/hash_key_pointer.rb
-- lib/y_petri/agent/petri_net_related.rb
+- lib/y_petri/agent/petri_net_aspect.rb
 - lib/y_petri/agent/selection.rb
-- lib/y_petri/agent/simulation_related.rb
+- lib/y_petri/agent/simulation_aspect.rb
 - lib/y_petri/core.rb
+- lib/y_petri/core/guarded.rb
 - lib/y_petri/core/timed.rb
 - lib/y_petri/core/timed/euler.rb
 - lib/y_petri/core/timed/gillespie.rb
+- lib/y_petri/core/timed/methods.rb
 - lib/y_petri/core/timed/pseudo_euler.rb
 - lib/y_petri/core/timed/quasi_euler.rb
 - lib/y_petri/core/timed/runge_kutta.rb
 - lib/y_petri/core/timeless.rb
+- lib/y_petri/core/timeless/methods.rb
 - lib/y_petri/core/timeless/pseudo_euler.rb
 - lib/y_petri/dsl.rb
 - lib/y_petri/fixed_assets.rb
 - lib/y_petri/net.rb
 - lib/y_petri/net/data_set.rb
-- lib/y_petri/net/element_access.rb
+- lib/y_petri/net/node_access.rb
 - lib/y_petri/net/own_state.rb
 - lib/y_petri/net/state.rb
 - lib/y_petri/net/state/feature.rb
+- lib/y_petri/net/state/feature/assignment.rb
 - lib/y_petri/net/state/feature/delta.rb
 - lib/y_petri/net/state/feature/firing.rb
 - lib/y_petri/net/state/feature/flux.rb
@@ -98,13 +150,11 @@ files:
 - lib/y_petri/net/visualization.rb
 - lib/y_petri/place.rb
 - lib/y_petri/place/arcs.rb
+- lib/y_petri/place/features.rb
 - lib/y_petri/place/guard.rb
 - lib/y_petri/place/guarded.rb
 - lib/y_petri/simulation.rb
 - lib/y_petri/simulation/dependency.rb
-- lib/y_petri/simulation/element_representation.rb
-- lib/y_petri/simulation/elements.rb
-- lib/y_petri/simulation/elements/access.rb
 - lib/y_petri/simulation/feature_set.rb
 - lib/y_petri/simulation/initial_marking.rb
 - lib/y_petri/simulation/initial_marking/access.rb
@@ -113,6 +163,9 @@ files:
 - lib/y_petri/simulation/marking_vector.rb
 - lib/y_petri/simulation/marking_vector/access.rb
 - lib/y_petri/simulation/matrix.rb
+- lib/y_petri/simulation/node_representation.rb
+- lib/y_petri/simulation/nodes.rb
+- lib/y_petri/simulation/nodes/access.rb
 - lib/y_petri/simulation/place_mapping.rb
 - lib/y_petri/simulation/place_representation.rb
 - lib/y_petri/simulation/places.rb
@@ -157,15 +210,13 @@ files:
 - lib/y_petri/transition/cocking.rb
 - lib/y_petri/transition/construction_convenience.rb
 - lib/y_petri/transition/t.rb
-- lib/y_petri/transition/type.rb
-- lib/y_petri/transition/type_information.rb
 - lib/y_petri/transition/types.rb
 - lib/y_petri/transition/usable_without_world.rb
 - lib/y_petri/version.rb
 - lib/y_petri/world.rb
 - lib/y_petri/world/dependency.rb
-- lib/y_petri/world/petri_net_related.rb
-- lib/y_petri/world/simulation_related.rb
+- lib/y_petri/world/petri_net_aspect.rb
+- lib/y_petri/world/simulation_aspect.rb
 - test/acceptance/basic_usage_test.rb
 - test/acceptance/simulation_test.rb
 - test/acceptance/simulation_with_physical_units_test.rb
@@ -189,7 +240,8 @@ files:
 - test/y_petri_test.rb
 - y_petri.gemspec
 homepage: ''
-licenses: []
+licenses:
+- GPLv3
 metadata: {}
 post_install_message: 
 rdoc_options: []
@@ -207,10 +259,12 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.3
+rubygems_version: 2.0.14
 signing_key: 
 specification_version: 4
-summary: a Petri net domain model and simulator
+summary: Systems modelling and simulation gem, and a domain model of a special kind
+  of Petri nets (YPetri nets) that can be used to model and simulate any kind of dynamic
+  systems.
 test_files:
 - test/acceptance/basic_usage_test.rb
 - test/acceptance/simulation_test.rb

data/LICENSE

@@ -1,22 +0,0 @@
-Copyright (c) 2012 boris
-
-MIT License
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/lib/y_petri/net/element_access.rb

@@ -1,239 +0,0 @@
-# Selections of various kinds of places / transitions (place names / transition
-# names) in a Petri net.
-# 
-module YPetri::Net::ElementAccess
-  # Does the net include a place?
-  # 
-  def includes_place? id
-    begin
-      place( id ) and true
-    rescue NameError, TypeError; false end
-  end
-  alias include_place? includes_place?
-
-  # Does the net include a transition?
-  # 
-  def includes_transition? id
-    begin; transition( id ) and true; rescue NameError, TypeError; false end
-  end
-  alias include_transition? includes_transition?
-
-  # Inquirer whether the net includes an element.
-  # 
-  def include? id
-    include_place?( id ) || include_transition?( id )
-  end
-  alias includes? include?
-
-  # Returns the net's place identified by the argument.
-  # 
-  def place id
-    ( super rescue Place().instance( id ) ).tap do |p|
-      fail TypeError, "No place #{id} in the net!" unless places.include? p
-    end
-  end
-
-  # Returns the net's transition identified by the argument.
-  # 
-  def transition id
-    ( super rescue Transition().instance( id ) ).tap do |t|
-      transitions.include? t or fail TypeError, "No transition #{id} in the net!"
-    end
-  end
-
-  # Returns the net's element identified by the argument
-  # 
-  def element id
-    begin; place( id ); rescue NameError, TypeError
-      begin; transition( id ); rescue NameError, TypeError
-        raise TypeError, "The net does not include place/transition #{id}!"
-      end
-    end
-  end
-
-  # Returns the net's elements identified by the argument's elements.
-  # 
-  def elements ids=nil
-    return @places + @transitions if ids.nil?
-    ids.map { |id| element id }
-  end
-
-  # Returns the names of the net's elements identified by the array.
-  # 
-  def en ids=nil
-    elements( ids ).names
-  end
-
-  # Returns the net's places identified by the argument's elements.
-  # 
-  def places ids=nil
-    return @places.dup if ids.nil?
-    ids.map { |id| place id }
-  end
-  alias pp places
-
-  # Returns the net's transitions identified by the argument's elements.
-  # 
-  def transitions ids=nil
-    return @transitions.dup if ids.nil?
-    ids.map { |id| transition id }
-  end
-  alias tt transitions
-
-  # Names of places in the net.
-  # 
-  def pn ids=nil
-    places( ids ).names
-  end
-
-  # Names of transitions in the net.
-  # 
-  def tn ids=nil
-    transitions( ids ).names
-  end
-
-  # *ts* transitions.
-  # 
-  def ts_transitions ids=nil
-    return transitions.select &:ts? if ids.nil?
-    transitions( ids ).aT_all "transition identifiers", "be ts", &:ts?
-  end
-  alias ts_tt ts_transitions
-
-  # Names of *ts* transitions.
-  # 
-  def nts ids=nil
-    ts_transitions( ids ).names
-  end
-
-  # *tS* transitions.
-  # 
-  def tS_transitions ids=nil
-    return transitions.select &:tS? if ids.nil?
-    transitions( ids ).aT_all "transition identifiers", "be tS", &:tS?
-  end
-  alias tS_tt tS_transitions
-
-  # Names of *tS* transitions.
-  # 
-  def ntS ids=nil
-    tS_transitions( ids ).names
-  end
-
-  # *Ts* transitions.
-  # 
-  def Ts_transitions ids=nil
-    return transitions.select &:Ts? if ids.nil?
-    transitions( ids ).aT_all "transition identifiers", "be Ts", &:Ts?
-  end
-  alias Ts_tt Ts_transitions
-
-  # Names of *Ts* transitions.
-  # 
-  def nTs ids=nil
-    Ts_transitions( ids ).names
-  end
-
-  # *TS* transitions.
-  # 
-  def TS_transitions ids=nil
-    return transitions.select &:TS? if ids.nil?
-    transitions( ids ).aT_all "transition identifiers", "be TS", &:TS?
-  end
-  alias TS_tt TS_transitions
-
-  # Names of *TS* transitions.
-  # 
-  def nTS ids=nil
-    TS_transitions( ids ).names
-  end
-
-  # *A* transitions.
-  # 
-  def A_transitions ids=nil
-    return transitions.select &:A? if ids.nil?
-    transitions( ids ).aT_all "transition identifiers", "be A", &:A?
-  end
-  alias A_tt A_transitions
-
-  # Names of *A* transitions.
-  # 
-  def nA ids=nil
-    A_transitions( ids ).names
-  end
-
-  # *a* transitions.
-  # 
-  def a_transitions ids=nil
-    return transitions.select &:a? if ids.nil?
-    transitions( ids ).aT_all "transition identifiers",
-                              "be a (non-assignment)", &:a?
-  end
-  alias a_tt a_transitions
-
-  # Names of *a* transitions.
-  # 
-  def na ids=nil
-    A_transitions( ids ).names
-  end
-
-  # *S* transitions.
-  # 
-  def S_transitions ids=nil
-    return transitions.select &:S? if ids.nil?
-    transitions( ids ).aT_all "transition identifiers",
-                              "be S (stoichiometric)", &:S?
-  end
-  alias S_tt S_transitions
-
-  # Names of *S* transitions.
-  # 
-  def nS ids=nil
-    S_transitions( ids ).names
-  end
-
-  # *s* transitions.
-  # 
-  def s_transitions ids=nil
-    return transitions.select &:s? if ids.nil?
-    transitions( ids ).aT_all "transition identifiers",
-                              "be s (non-stoichiometric)", &:s?
-  end
-  alias s_tt s_transitions
-
-  # Names of *s* transitions.
-  # 
-  def ns ids=nil
-    s_transitions( ids ).names
-  end
-
-  # *T* transitions.
-  #
-  def T_transitions ids=nil
-    return transitions.select &:T? if ids.nil?
-    transitions( ids ).aT_all "transition identifiers",
-                              "be T (timed)", &:T?
-  end
-  alias T_tt T_transitions
-
-  # Names of *T* transitions.
-  # 
-  def nT ids=nil
-    T_transitions( ids ).names
-  end
-
-  # *t* transitions.
-  # 
-  def t_transitions ids=nil
-    return transitions.select &:t? if ids.nil?
-    transitions( ids ).aT_all "transition identifiers",
-                              "be t (timeless)", &:t?
-  end
-  alias t_tt t_transitions
-
-  # Names of *t* transitions.
-  # 
-  def nt ids=nil
-    t_transitions( ids ).names
-  end  
-end # class YPetri::Net::ElementAccess

data/lib/y_petri/simulation/element_representation.rb

@@ -1,20 +0,0 @@
-#encoding: utf-8
-
-# Representation of a YPetri::Place inside a YPetri::Simulation instance.
-#
-class YPetri::Simulation
-  class ElementRepresentation
-    ★ NameMagic
-    ★ Dependency
-
-    attr_reader :source # source place
-
-    delegate :simulation, to: "self.class"
-
-    # Expect a single YPetri place as an argument.
-    # 
-    def initialize net_element_id
-      @source = net.element( net_element_id )
-    end
-  end # class ElementRepresentation
-end # class YPetri::Simulation

data/lib/y_petri/simulation/elements/access.rb

@@ -1,57 +0,0 @@
-#encoding: utf-8
-
-# Simulation mixin providing access to elements (an element is either a
-# place, or a transition -- see also mixins +Places::Access+ and
-# +Transitions::Access+.
-# 
-class YPetri::Simulation::Elements
-  module Access
-    # Does an element belong to the simulation?
-    # 
-    def includes?( id )
-      includes_place?( id ) || includes_transition?( id )
-    end
-    alias include? includes?
-
-    # Element of the simulation (belonging to the net).
-    # 
-    def e( id )
-      element( id ).source
-    end
-
-    # Elements of the simulation (belonging to the net).
-    # 
-    def ee( ids=nil )
-      elements( ids ).map &:source
-    end
-
-    # Names of the simulation's elements. Arguments, if any, are treated
-    # analogically to the +#elements+ method.
-    # 
-    def en ids=nil
-      elements( ids ).names
-    end
-
-    protected
-
-    # Element instance identification.
-    # 
-    def element( id )
-      if include_place? id
-        return place( id )
-      end
-      if include_transition? id
-        return transition( id )
-      end
-      fail TypeError, "No element #{id} in the simulation!"
-    end
-
-    # Without arguments, returns all the elements (places + transitions). If
-    # arguments are given, they are converted into elements.
-    # 
-    def elements ids=nil
-      return places + transitions if ids.nil?
-      ids.map { |id| element id }
-    end
-  end # module Access
-end # class YPetri::Simulation::Elements