y_petri 2.0.2 → 2.0.3

data/lib/y_petri/net.rb

@@ -28,9 +28,9 @@ class YPetri::Net
   # <em>false</em> if the place is already included in the net.
   # 
   def include_place! place
-    p = place( place )
-    return false if @places.include? p
-    @places << p
+    pl = place( place )
+    return false if @places.include? pl
+    @places << pl
     return true
   end
 
@@ -40,12 +40,12 @@ class YPetri::Net
   # already in the net.
   # 
   def include_transition! transition;
-    t = transition( transition )
-    return false if @transitions.include? t
-    raise TypeError, "Unable to include the transition #{t} in #{self}: " +
+    tr = transition( transition )
+    return false if @transitions.include? tr
+    raise TypeError, "Unable to include the transition #{tr} in #{self}: " +
       "It connects to one or more places outside the net." unless
-      t.arcs.all? { |p| include? p }
-    @transitions << t
+      tr.arcs.all? { |pl| include? pl }
+    @transitions << tr
     return true
   end
 
@@ -55,10 +55,10 @@ class YPetri::Net
   # net connect to it.
   # 
   def exclude_place! place
-    p = place( place )
-    raise "Unable to exclude #{p} from #{self}: One or more transitions" +
-      "depend on it" if transitions.any? { |t| t.arcs.include? p }
-    return true if @places.delete p
+    pl = place( place )
+    raise "Unable to exclude #{pl} from #{self}: One or more transitions" +
+      "depend on it" if transitions.any? { |tr| tr.arcs.include? pl }
+    return true if @places.delete pl
     return false
   end
 
@@ -66,8 +66,8 @@ class YPetri::Net
   # <em>false</em> if the transition was not found in the net.
   # 
   def exclude_transition! transition
-    t = transition( transition )
-    return true if @transitions.delete t
+    tr = transition( transition )
+    return true if @transitions.delete tr
     return false
   end
 
@@ -92,18 +92,18 @@ class YPetri::Net
   # Inquirer whether the net includes a place / transition.
   # 
   def include? place_or_transition
-    p = begin
-          place( place_or_transition )
-        rescue NameError
-          nil
-        end
-    return places.include? p if p
-    t = begin
-          transition( place_or_transition )
-        rescue NameError
-          nil
-        end
-    return transitions.include? t if t
+    pl = begin
+           place( place_or_transition )
+         rescue NameError
+           nil
+         end
+    return places.include? pl if pl
+    tr = begin
+           transition( place_or_transition )
+         rescue NameError
+           nil
+         end
+    return transitions.include? tr if tr
     return false
   end
 
@@ -336,94 +336,53 @@ class YPetri::Net
 
   def visualize
     require 'graphviz'
-    γ = GraphViz.new :G     # creating a new graph
-      
-    # main        = γ.add_nodes( "main", shape: "box" )
-    # parse       = γ.add_nodes( "parse", fillcolor: "yellow", style: "rounded,filled", shape: "diamond" )
-    # execute     = γ.add_nodes( "execute", shape: "record", label: "{ a | b | c }", style: "rounded" )
-    # init        = γ.add_nodes( "init", fillcolor: "yellow", style: "filled" )
-
-    # # set global node options
-    # g.node[:color] = "#ddaa66"
-    # g.node[:style] = "filled"
-    # g.node[:shape] = "box"
-    # g.node[:penwidth] = "1"
-    # g.node[:fontname] = "Trebuchet MS"
-    # g.node[:fontsize] = "8"
-    # g.node[:fillcolor] = "#ffeecc"
-    # g.node[:fontcolor] = "#775500"
-    # g.node[:margin] = "0.0"
-
-    # # set global edge options
-    # g.edge[:color] = "#999999"
-    # g.edge[:weight] = "1"
-    # g.edge[:fontsize] = "6"
-    # g.edge[:fontcolor] = "#444444"
-    # g.edge[:fontname] = "Verdana"
-    # g.edge[:dir] = "forward"
-    # g.edge[:arrowsize] = "0.5"
-
-    # add place nodes
-    place_nodes =
-      Hash[ places.zip places.map { |p|
-              γ.add_nodes p.name.to_s, fillcolor: 'lightgrey', color: 'grey', style: 'filled'
-            } ]
-
-    # add transition nodes
-    transition_nodes =
-      Hash[ transitions.zip transitions.map { |t|
-              γ.add_nodes( t.name.to_s,
-                           shape: 'box',
-                           fillcolor: if t.assignment? then 'yellow'
-                                      elsif t.basic_type == :SR then 'lightcyan'
-                                      else 'ghostwhite' end,
-                           color: if t.assignment? then 'goldenrod'
-                                  elsif t.basic_type == :SR then 'cyan'
-                                  else 'grey' end,
-                           style: 'filled'
-                           )
-              
-            } ]
-
-    # add edges
-    transition_nodes.each { |t, t_node|
-      if t.assignment? then
-        t.codomain.each { |p|
-          γ.add_edges t_node, place_nodes[p], color: 'goldenrod'
+    γ = GraphViz.new :G
+    # Add places and transitions.
+    place_nodes = places.map.with_object Hash.new do |pl, ꜧ|
+      ꜧ[pl] = γ.add_nodes pl.name.to_s,
+                          fillcolor: 'lightgrey',
+                          color: 'grey',
+                          style: 'filled'
+    end
+    transition_nodes = transitions.map.with_object Hash.new do |tr, ꜧ|
+      ꜧ[tr] = γ.add_nodes tr.name.to_s,
+                          shape: 'box',
+                          fillcolor: if tr.assignment? then 'yellow'
+                                     elsif tr.basic_type == :SR then 'lightcyan'
+                                     else 'ghostwhite' end,
+                          color: if tr.assignment? then 'goldenrod'
+                                 elsif tr.basic_type == :SR then 'cyan'
+                                 else 'grey' end,
+                          style: 'filled'
+    end
+    # Add Petri net arcs.
+    transition_nodes.each { |tr, tr_node|
+      if tr.assignment? then
+        tr.codomain.each { |pl|
+          γ.add_edges tr_node, place_nodes[pl], color: 'goldenrod'
         }
-        ( t.domain - t.codomain ).each { |p|
-          γ.add_edges t_node, place_nodes[p], color: 'grey', arrowhead: 'none'
+        ( tr.domain - tr.codomain ).each { |pl|
+          γ.add_edges tr_node, place_nodes[pl], color: 'grey', arrowhead: 'none'
         }
-      elsif t.basic_type == :SR then
-        t.codomain.each { |p|
-          if t.stoichio[p] > 0 then # producing arc
-            γ.add_edges t_node, place_nodes[p], color: 'cyan'
-          elsif t.stoichio[p] < 0 then # consuming arc
-            γ.add_edges place_nodes[p], t_node, color: 'cyan'
+      elsif tr.basic_type == :SR then
+        tr.codomain.each { |pl|
+          if tr.stoichio[pl] > 0 then # producing arc
+            γ.add_edges tr_node, place_nodes[pl], color: 'cyan'
+          elsif tr.stoichio[pl] < 0 then # consuming arc
+            γ.add_edges place_nodes[pl], tr_node, color: 'cyan'
           else
-            γ.add_edges place_nodes[p], t_node, color: 'grey', arrowhead: 'none'
+            γ.add_edges place_nodes[pl], tr_node, color: 'grey', arrowhead: 'none'
           end
         }
-        ( t.domain - t.codomain ).each { |p|
-          γ.add_edges t_node, place_nodes[p], color: 'grey', arrowhead: 'none'
+        ( tr.domain - tr.codomain ).each { |pl|
+          γ.add_edges tr_node, place_nodes[pl], color: 'grey', arrowhead: 'none'
         }
       end
     }
-
-    # place_collection.each { |place_name, place_label|
-    #   place_instance = place( place_name )
-    #   place_instance.upstream_places.each { |upstream_place|
-    #     node = nodes[ place_name ]
-    #     next unless set_of_places.map { |ɴ, _| ɴ }.include?( upstream_place.name )
-    #     next if upstream_place == place_instance
-    #     upstream_node = nodes[ upstream_place.name ]
-    #     node << upstream_node
-    #   }
-    # }
-
-    # Generate output image
-    γ.output png: "y_petri_graph.png"
-    YSupport::KDE.show_file_with_kioclient File.expand_path( '.', "y_petri_graph.png" )
+    # Generate output image.
+    γ.output png: File.expand_path( "~/y_petri_graph.png" )
+    # require 'y_support/kde'
+    YSupport::KDE.show_file_with_kioclient File.expand_path( "~/y_petri_graph.png" )
   end
 
   # Inspect string of the instance.

data/lib/y_petri/simulation.rb

@@ -30,6 +30,14 @@ class YPetri::Simulation
   attr_reader :recording
   alias :r :recording
 
+  # Zero marking vector.
+  # 
+  attr_reader :zero_ᴍ
+
+  # Zero gradient.
+  # 
+  attr_reader :zero_gradient
+
   # Simulation settings.
   # 
   def settings; {} end
@@ -141,13 +149,14 @@ class YPetri::Simulation
 
     @assignment_closures_for_A = create_assignment_closures_for_A
 
-    @zero_ᴍ = Matrix.zero( free_places.size, 1 )
-
     puts "other assets set up, about to reset" if YPetri::DEBUG
 
     # ----------- Reset -------------
     reset!
 
+    @zero_ᴍ = compute_initial_marking_vector_of_free_places.map { |e| e * 0 }
+    @zero_gradient = @zero_ᴍ.dup
+
     puts "reset complete" if YPetri::DEBUG
   end
 
@@ -777,7 +786,7 @@ class YPetri::Simulation
   # State differential for sR transitions.
   # 
   def gradient_for_sR
-    rate_closures_for_sR.map( &:call ).reduce( @zero_ᴍ, :+ )
+    rate_closures_for_sR.map( &:call ).reduce( @zero_gradient, :+ )
   end
 
   # State differential for sR transitions as a hash { place_name: ∂ / ∂ᴛ }.
@@ -1059,25 +1068,35 @@ class YPetri::Simulation
   # 
   def reset!
     puts "Starting #reset! method" if YPetri::DEBUG
-    # zero_vector = Matrix.column_vector( places.map { SY::ZERO rescue 0 } ) # Float zeros
-    zero_vector = Matrix.column_vector( places.map { 0 } ) # Float zeros
-    puts "zero vector prepared" if YPetri::DEBUG
+
     mv_clamped = compute_marking_vector_of_clamped_places
     puts "#reset! obtained marking vector of clamped places" if YPetri::DEBUG
     clamped_component = C2A() * mv_clamped
     puts "clamped component of marking vector prepared:\n#{clamped_component}" if YPetri::DEBUG
+
     mv_free = compute_initial_marking_vector_of_free_places
     puts "#reset! obtained initial marking vector of free places" if YPetri::DEBUG
     free_component = F2A() * mv_free
     puts "free component of marking vector prepared:\n#{free_component}" if YPetri::DEBUG
+    
+    # zero_vector = Matrix.column_vector( places.map { SY::ZERO rescue 0 } ) # Float zeros
+    zero_vector = Matrix.column_vector( places.map { 0 } ) # Float zeros
+    puts "zero vector prepared: #{zero_vector}" if YPetri::DEBUG
+
     free_component.aT { |v|
       qnt = v.first.quantity rescue :no_quantity
       unless qnt == :no_quantity
         v.all? { |e| e.quantity == qnt }
       else true end
-    }
-    puts "free component of marking vector prepared:\n#{free_component}" if YPetri::DEBUG
-    @marking_vector = zero_vector + clamped_component + free_component
+    } if YPetri::DEBUG
+    puts "free component of marking vector checked" if YPetri::DEBUG
+
+    @marking_vector = free_component + clamped_component
+    # Matrix
+    #   .column_vector( places.map.with_index do |_, i|
+    #                     clamped_component[i, 0] || free_component[i, 0]
+    #                   end )
+
     puts "marking vector assembled\n#{m}\n, about to reset recording" if YPetri::DEBUG
     reset_recording!
     puts "reset recording done, about to initiate sampling process" if YPetri::DEBUG

data/lib/y_petri/timed_simulation.rb

@@ -87,8 +87,9 @@ class YPetri::TimedSimulation < YPetri::Simulation
     @sampling_period = args.delete :sampling_period
     @target_time = args.delete :target_time
     @initial_time = args.delete( :initial_time ) ||
-      @target_time.nil? ? nil : @target_time.class.zero
+      @target_time.nil? ? nil : @sampling_period * 0 # @target_time.class.zero
     super args
+    @zero_gradient = @zero_ᴍ.map { |e| step_size.to_f / step_size * e }
   end
   # LATER: transition clamps
 
@@ -113,7 +114,12 @@ class YPetri::TimedSimulation < YPetri::Simulation
   # Scalar field gradient for free places.
   # 
   def gradient_for_free_places
-    S_for_SR() * flux_vector_for_SR + gradient_for_sR
+    g_sR = gradient_for_sR
+    if g_sR then
+      S_for_SR() * flux_vector_for_SR + g_sR
+    else
+      S_for_SR() * flux_vector_for_SR
+    end
   end
 
   # Gradient for free places as a hash { place_name: ∂ / ∂ᴛ }.
@@ -133,7 +139,8 @@ class YPetri::TimedSimulation < YPetri::Simulation
   # 
   def Δ_Euler_for_free_places( Δt=step_size )
     # Here, ∂ represents all R transitions, to which TSr and Tsr are added:
-    gradient_for_free_places * Δt + Δ_for_TSr( Δt ) + Δ_for_Tsr( Δt )
+    g_free = gradient_for_free_places * Δt
+    g_free + Δ_for_TSr( Δt ) + Δ_for_Tsr( Δt )
   end
   alias Δ_euler_for_free_places Δ_Euler_for_free_places
   alias ΔE Δ_Euler_for_free_places

data/lib/y_petri/transition.rb

@@ -375,25 +375,19 @@ module YPetri
     #                 rate: λ { |a| a * 0.5 } )
     #       
     def initialize *args
-      # do the big work of checking in the arguments
-      check_in_arguments *args
-      # Inform upstream and downstream places they have been connected:
-      inform_upstream_places
-      inform_downstream_places
-      @cocked = false    # transitions initialize uncocked
+      check_in_arguments *args       # the big work of checking in args
+      inform_upstream_places         # that they have been connected
+      inform_downstream_places       # that they have been connected
+      @cocked = false                # transitions initialize uncocked
     end
 
     # Marking of the domain places.
     # 
-    def domain_marking
-      domain.map &:marking
-    end
+    def domain_marking; domain.map &:marking end
 
     # Marking of the codomain places.
     # 
-    def codomain_marking
-      codomain.map &:marking
-    end
+    def codomain_marking; codomain.map &:marking end
 
     # Result of the transition's "function", regardless of the #enabled? status.
     # 
@@ -588,24 +582,15 @@ module YPetri
     # 
     def check_in_arguments *args
       oo = args.extract_options!
-      oo.may_have :stoichiometry, syn!: [ :stoichio,
-                                          :s ]
-      oo.may_have :codomain, syn!: [ :codomain_arcs,
-                                     :codomain_places,
+      oo.may_have :stoichiometry, syn!: [ :stoichio, :s ]
+      oo.may_have :codomain, syn!: [ :codomain_arcs, :codomain_places,
                                      :downstream,
-                                     :downstream_arcs,
-                                     :downstream_places,
+                                     :downstream_arcs, :downstream_places,
                                      :action_arcs ]
-      oo.may_have :domain, syn!: [ :domain_arcs,
-                                   :domain_places,
-                                   :upstream,
-                                   :upstream_arcs,
-                                   :upstream_places ]
-      oo.may_have :rate, syn!: [ :flux,
-                                 :propensity,
-                                 :rate_closure,
-                                 :flux_closure,
-                                 :propensity_closure ]
+      oo.may_have :domain, syn!: [ :domain_arcs, :domain_places,
+                                   :upstream, :upstream_arcs, :upstream_places ]
+      oo.may_have :rate, syn!: [ :rate_closure,
+                                 :propensity, :propensity_closure ]
       oo.may_have :action, syn!: :action_closure
       oo.may_have :timed
 

data/lib/y_petri/version.rb

@@ -1,3 +1,4 @@
 module YPetri
-  VERSION = "2.0.2"
+  VERSION = "2.0.3"
+  DEBUG = false
 end

data/lib/y_petri/workspace/petri_net_related_methods.rb

@@ -0,0 +1,88 @@
+# -*- coding: utf-8 -*-
+
+# Workspace instance methods related to Petri net itsef (places, transitions,
+# net instances).
+# 
+module YPetri::Workspace::PetriNetRelatedMethods
+  # Readers for @Place, @Transition, @Net instance variables, which should
+  # contain said classes, or their instance-specific subclasses.
+
+  # Parametrized Place class.
+  # 
+  attr_reader :Place
+
+  # Parametrized Transition class.
+  # 
+  attr_reader :Transition
+
+  # Parametrized Net class.
+  # 
+  attr_reader :Net
+
+  # Instance initialization.
+  # 
+  def initialize
+    set_up_Top_net # Sets up :Top net encompassing all places and transitions.
+    super
+  end
+
+  # Returns a place instance identified by the argument.
+  # 
+  def place which; Place().instance which end
+
+  # Returns a transition instance identified by the argument.
+  # 
+  def transition which; Transition().instance which end
+
+  # Returns a net instance identified by the argument.
+  # 
+  def net which; Net().instance which end
+
+  # Returns the name of a place identified by the argument.
+  # 
+  def pl which; place( which ).name end
+
+  # Returns the name of a transition identified by the argument.
+  # 
+  def tr which; transition( which ).name end
+
+  # Returns the name of a net identified by the argument.
+  # 
+  def ne which; net( which ).name end
+
+  # Place instances.
+  # 
+  def places; Place().instances end
+
+  # Transition instances.
+  # 
+  def transitions; Transition().instances end
+
+  # Net instances.
+  # 
+  def nets; Net().instances end
+
+  # Place names.
+  # 
+  def pp; places.map &:name end
+
+  # Transition names.
+  # 
+  def tt; transitions.map &:name end
+
+  # Net names.
+  # 
+  def nn; nets.map &:name end
+
+  private
+
+  # Creates all-encompassing Net instance named :Top.
+  # 
+  def set_up_Top_net
+    Net().new name: :Top # all-encompassing :Top net
+    # Hook new places to add themselves magically to the :Top net.
+    Place().new_instance_closure { |new_inst| net( :Top ) << new_inst }
+    # Hook new transitions to add themselves magically to the :Top net.
+    Transition().new_instance_closure { |new_inst| net( :Top ) << new_inst }    
+  end
+end # module YPetri::Workspace::PetriNetRelatedMethods

data/lib/y_petri/workspace/{instance_methods.rb → simulation_related_methods.rb}

@@ -1,21 +1,9 @@
 # -*- coding: utf-8 -*-
-
-module YPetri::Workspace::InstanceMethods
-  # Readers for @Place, @Transition, @Net instance variables, which should
-  # contain said classes, or their instance-specific subclasses.
-
-  # Place class or parametrized subclass.
-  # 
-  attr_reader :Place
-
-  # Transition class or parametrized subclass.
-  # 
-  attr_reader :Transition
-
-  # Net class or parametrized subclass.
-  # 
-  attr_reader :Net
-
+# Workspace instance methods related to simulation (initial marking
+# collections, clamp collections, inital marking collections, management
+# of simulations...)
+# 
+module YPetri::Workspace::SimulationRelatedMethods
   # Collections of clamps, initial marking vectors, and simulation settings.
   # 
   attr_reader :clamp_collections,
@@ -25,67 +13,18 @@ module YPetri::Workspace::InstanceMethods
   # Instance initialization.
   # 
   def initialize
-    set_up_Top_net # Sets up :Top net encompassing all places and transitions.
-
     @simulations = {} # { simulation => its settings }
     @clamp_collections = { Base: {} } # { collection name => clamp hash }
     @initial_marking_collections = { Base: {} } # { collection name => im hash }
     @simulation_settings_collections = # { collection name => ss hash }
       { Base: YPetri::DEFAULT_SIMULATION_SETTINGS.call }
+    super
   end
 
-  # Returns a place instance identified by the argument.
-  # 
-  def place which; Place().instance which end
-
-  # Returns a transition instance identified by the argument.
-  # 
-  def transition which; Transition().instance which end
-
-  # Returns a net instance identified by the argument.
-  # 
-  def net which; Net().instance which end
-
-  # Returns the name of a place identified by the argument.
-  # 
-  def p which; place( which ).name end
-
-  # Returns the name of a transition identified by the argument.
-  # 
-  def t which; transition( which ).name end
-
-  # Returns the name of a net identified by the argument.
-  # 
-  def n which; net( which ).name end
-
-  # Place instances.
-  # 
-  def places; Place().instances end
-
-  # Transition instances.
-  # 
-  def transitions; Transition().instances end
-
-  # Net instances.
-  # 
-  def nets; Net().instances end
-
   # Hash of simulation instances and their settings.
   # 
   def simulations; @simulations end
 
-  # Place names.
-  # 
-  def pp; places.map &:name end
-
-  # Transition names.
-  # 
-  def tt; transitions.map &:name end
-
-  # Net names.
-  # 
-  def nn; nets.map &:name end
-
   # Clamp collection names.
   # 
   def clamp_collection_names; @clamp_collections.keys end
@@ -239,16 +178,4 @@ module YPetri::Workspace::InstanceMethods
                                     .merge( initial_marking: im_hash,
                                             place_clamps: clamp_hash ) )
   end # def new_timed_simulation
-
-  private
-
-  # Creates all-encompassing Net instance named :Top.
-  # 
-  def set_up_Top_net
-    Net().new name: :Top # all-encompassing :Top net
-    # Hook new places to add themselves magically to the :Top net.
-    Place().new_instance_closure { |new_inst| net( :Top ) << new_inst }
-    # Hook new transitions to add themselves magically to the :Top net.
-    Transition().new_instance_closure { |new_inst| net( :Top ) << new_inst }    
-  end
-end # module YPetri::Workspace::InstanceMethods
+end # module YPetri::Workspace::SimulationRelatedMethods

data/lib/y_petri/workspace.rb

@@ -1,16 +1,16 @@
-#encoding: utf-8
-
-# Workspace holds places, transitions, nets and other assets needed for
-# simulation (settings, clamps, initial markings etc.). Workspace also
-# provides basic methods for their handling, but these are not too public.
-# YPetri interface is defined by YPetri::Manipulator.
+# Workspace holds places, transitions, nets and other assets needed to set up
+# and simulate Petri nets (settings, clamps, initial markings etc.). Workspace
+# provides basic, decent, vanilla methods to just do what is necessary. It is
+# up to YPetri::Manipulator to provide ergonomical DSL to the user.
 # 
 class YPetri::Workspace
   include NameMagic
 
-  require_relative 'workspace/instance_methods'
+  require_relative 'workspace/petri_net_related_methods'
   require_relative 'workspace/parametrized_subclassing'
+  require_relative 'workspace/simulation_related_methods'
 
-  include self::InstanceMethods
+  include self::PetriNetRelatedMethods
   prepend self::ParametrizedSubclassing
+  include self::SimulationRelatedMethods
 end