y_petri 2.1.3 → 2.1.6

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/y_petri/agent/petri_net_related.rb

@@ -78,15 +78,35 @@ module YPetri::Agent::PetriNetRelated
   # world. Rate closure has to be supplied as a block.
   # 
   def T( *ordered, **named, &block )
+    fail ArgumentError, "Timed transition constructor requires a block " +
+      "defining the rate function!" unless block
     world.Transition.new *ordered, **named.update( rate: block )
   end
 
+  # Timed stoichiometric transition constructor, that expects stoichiometry
+  # given directly as hash-collected arguments. Two special keys allowed are
+  # +:name+ (alias +:ɴ) and +:domain+. (Key +:codomain+ is not allowed.)
+  # 
+  def TS **stoichiometry, &block
+    args = { s: stoichiometry }
+    args.update name: stoichiometry.delete( :name ) if
+      stoichiometry.has? :name, syn!: :ɴn
+    args.update domain: stoichiometry.delete( :domain ) if
+      stoichiometry.has? :domain
+    T **args, &block
+  end
+
   # Assignment transition constructor: Creates a new assignment transition in
-  # the current world. Assignment closure has to be supplied as a block.
-  # 
-  def A( *ordered, **named, &block )
-    world.Transition.new *ordered,
-                         **named.update( assignment: true, action: block )
+  # the current world. Ordered arguments are collected as codomain. Domain key
+  # (+:domain) is optional. Assignment closure must be supplied in a block.
+  # 
+  def A( *codomain, **nn, &block )
+    fail ArgumentError, "Assignment transition constructor requires a block " +
+      "defining the assignment function!" unless block
+    world.Transition.new codomain: codomain,
+                         assignment: true,
+                         action: block,
+                         **nn
   end
 
   # Net constructor: Creates a new Net instance in the current world.

data/lib/y_petri/agent/selection.rb

@@ -1,12 +1,14 @@
-class YPetri::Agent::Selection
-  # TODO: This calls for refactor as Array subclass.
-  def initialize
-    clear
+class YPetri::Agent
+  class Selection
+    # TODO: This calls for refactor as Array subclass. No time right now...
+    def initialize
+      clear
+    end
+    def clear; @selection = [] end
+    def set *aa; @selection = aa end
+    def get; @selection end
+    def add arg; @selection << arg end
+    alias :<< :add
+    def subtract arg; @selection -= arg end
   end
-  def clear; @selection = [] end
-  def set *aa; @selection = aa end
-  def get; @selection end
-  def add arg; @selection << arg end
-  alias :<< :add
-  def subtract arg; @selection -= arg end
 end

data/lib/y_petri/agent/simulation_related.rb

@@ -191,7 +191,7 @@ module YPetri::Agent::SimulationRelated
   # collection).
   # 
   def set_step Δt
-    ssc.update step_size: Δt
+    ssc.update step: Δt
   end
   alias set_step_size set_step
 
@@ -212,7 +212,7 @@ module YPetri::Agent::SimulationRelated
   # settings collection).
   # 
   def set_sampling Δt
-    ssc.update sampling_period: Δt
+    ssc.update sampling: Δt
   end
 
   # Changes the simulation method of the current ssc (ssc = simulation
@@ -258,11 +258,8 @@ module YPetri::Agent::SimulationRelated
     # --> delta feature ids
     # --> flux feature ids
     # --> firing feature ids
-
     # take these features together
-
     # construct the labels and the time series for each
-
     # plot them
 
     return nil unless sim = world.simulations.values[-1] # sim@point
@@ -287,63 +284,22 @@ module YPetri::Agent::SimulationRelated
   # 
   def plot_state( place_ids=nil, except: [] )
     sim = simulation or return nil
-    feat = sim.pp( place_ids || sim.pp ) - sim.pp( Array except )
-    gnuplot sim.record.marking( feat ), time: sim.target_time,
-            title: "State plot", ylabel: "Marking"
+    rec = sim.recording
+    pp = sim.net.pp( place_ids.nil? ? net.pp : place_ids  ) -
+      sim.net.pp( except )
+    dataset = sim.recording.reduce_features( marking: pp )
+    dataset.plot
   end
   alias plot_marking plot_state
 
   # Plot the recorded flux (computed flux history at the sampling points).
   # 
-  def plot_flux( transition_ids=nil, **options )
-    sim = world.simulations.values[-1] or return nil # sim@point
-    tt = sim.TS_transitions( transition_ids ).sources
-    excluded = sim.transitions( Array options[:except] ).sources
-    tt -= excluded
-    flux = sim.recording.modify do |time, record|
-      [ time,
-        sim.at( time: time, marking: record ).TS_transitions( tt ).flux_vector ]
-    end
-    # Select a time series for each feature.
-    time_series = tt.map.with_index do |tr, i|
-      tr and flux.map { |time, flux| [ time, flux[i] ] }.transpose
-    end
-    # Time axis
-    time = sim.target_time
-    # Gnuplot call
-    gnuplot( time, tt.compact.names, time_series.compact,
-             title: "Flux plot", ylabel: "Flux [µMⁿ.s⁻¹]" )
-  end
-
-  private
-
-  # Gnuplots a recording. Target time or time range can be supplied as :time
-  # named argument.
-  # 
-  def gnuplot( dataset, time: nil, **nn )
-    event_vector = dataset.events
-    data_vectors = dataset.values.transpose
-    x_range = if time.is_a? Range then
-                "[#{time.begin}:#{time.end}]"
-              else
-                "[-0:#{SY::Time.magnitude( time ).amount rescue time}]"
-              end
-    labels = recording.features.labels
-
-    Gnuplot.open do |gp|
-      Gnuplot::Plot.new( gp ) do |plot|
-        plot.xrange x_range
-        plot.title nn[:title] || "Simulation plot"
-        plot.ylabel nn[:ylabel] || "Values"
-        plot.xlabel nn[:xlabel] || "Time [s]"
-
-        labels.zip( data_vectors ).each { |label, data_vector|
-          plot.data << Gnuplot::DataSet.new( [event_vector, data_vector] ) { |ds|
-            ds.with = "linespoints"
-            ds.title = lbl
-          }
-        }
-      end
-    end
+  def plot_flux( transition_ids=nil, except: [], **options )
+    sim = simulation or return nil
+    rec = sim.recording
+    tt = sim.net.tt( transition_ids.nil? ? net.tt : transition_ids ) -
+      sim.net.tt( except )
+    dataset = sim.recording.reduce_features( flux: tt )
+    dataset.plot( title: "Flux plot", ylabel: "Flux [µMⁿ.s⁻¹]" )
   end
 end # module YPetri::Agent::SimulationRelated

data/lib/y_petri/agent.rb

@@ -1,22 +1,20 @@
-#encoding: utf-8
+# encoding: utf-8
+
+require_relative 'agent/selection'
+require_relative 'agent/hash_key_pointer'
+require_relative 'agent/petri_net_related'
+require_relative 'agent/simulation_related'
 
 # Public command interface of YPetri.
 # 
-module YPetri
-  class Agent
-    attr_reader :world
-
-    def initialize
-      @world = YPetri::World.new
-      super
-    end
+class YPetri::Agent
+  ★ PetriNetRelated                  # ★ means include
+  ★ SimulationRelated
 
-    require_relative 'agent/selection'
-    require_relative 'agent/hash_key_pointer'
-    require_relative 'agent/petri_net_related'
-    require_relative 'agent/simulation_related'
+  attr_reader :world
 
-    include self::PetriNetRelated
-    include self::SimulationRelated
-  end # class Agent
-end # module YPetri
+  def initialize
+    @world = YPetri::World.new
+    super
+  end
+end # module YPetri::Agent

data/lib/y_petri/core/timed/euler.rb

@@ -2,19 +2,17 @@
 
 # Euler method.
 # 
-class YPetri::Core::Timed
-  module Euler
-    # Name of this method.
-    # 
-    def simulation_method
-      :euler
-    end
+module YPetri::Core::Timed::Euler
+  # Name of this method.
+  # 
+  def simulation_method
+    :euler
+  end
 
-    # Computes Δ for the period of Δt.
-    # 
-    def delta Δt
-      gradient * Δt
-    end
-    alias Δ delta
-  end # Euler
-end # YPetri::Core::Timed
+  # Computes Δ for the period of Δt.
+  # 
+  def delta Δt
+    gradient * Δt
+  end
+  alias Δ delta
+end # YPetri::Core::Timed::Euler

data/lib/y_petri/core/timed/pseudo_euler.rb

@@ -2,30 +2,28 @@
 
 # Euler method with timeless transitions firing after each step.
 # 
-class YPetri::Core::Timed
-  module PseudoEuler
-    include Euler
+module YPetri::Core::Timed::PseudoEuler
+  include YPetri::Core::Timed::Euler
 
-    # Name of this method.
-    # 
-    def simulation_method
-      :pseudo_euler
-    end
+  # Name of this method.
+  # 
+  def simulation_method
+    :pseudo_euler
+  end
 
-    # Computes Δ for the period of Δt.
-    # 
-    def delta Δt
-      super + delta_timeless
-    end
-    alias Δ delta
+  # Computes Δ for the period of Δt.
+  # 
+  def delta Δt
+    super + delta_timeless
+  end
+  alias Δ delta
 
-    # Makes a single step by Δt.
-    # 
-    def step! Δt=simulation.step
-      increment_marking_vector Δ( Δt )
-      assignment_transitions_all_fire!
-      simulation.increment_time! Δt
-      alert
-    end
-  end # PseudoEuler
-end # YPetri::Core::Timed
+  # Makes a single step by Δt.
+  # 
+  def step! Δt=simulation.step
+    increment_marking_vector Δ( Δt )
+    assignment_transitions_all_fire!
+    simulation.increment_time! Δt
+    alert
+  end
+end # YPetri::Core::Timed::PseudoEuler

data/lib/y_petri/core/timed/quasi_euler.rb

@@ -2,22 +2,20 @@
 
 # Euler method with timeless transitions firing every time tick.
 # 
-class YPetri::Core::Timed
-  module QuasiEuler
-    include Euler
+module YPetri::Core::Timed::QuasiEuler
+  include YPetri::Core::Timed::Euler
 
-    # Name of this method.
-    # 
-    def simulation_method
-      :quasi_euler
-    end
+  # Name of this method.
+  # 
+  def simulation_method
+    :quasi_euler
+  end
 
-    # Makes a single step by Δt.
-    # 
-    def step! Δt=simulation.step_size
-      fail NotImplementedError
-      # Now one would have to compare whichever comes first, time tick or the
-      # end of Δt, and then again and again, until Δt is fired...
-    end
-  end # QuasiEuler
-end # YPetri::Core::Timed
+  # Makes a single step by Δt.
+  # 
+  def step! Δt=simulation.step_size
+    fail NotImplementedError
+    # Now one would have to compare whichever comes first, time tick or the
+    # end of Δt, and then again and again, until Δt is fired...
+  end
+end # YPetri::Core::Timed::QuasiEuler

data/lib/y_petri/core/timed.rb

@@ -2,56 +2,54 @@
 
 # Timed simulation core.
 # 
-class YPetri::Core
-  class Timed < YPetri::Core
-    require_relative 'timed/euler.rb'
-    require_relative 'timed/pseudo_euler.rb' # timeless fire after each step
-    require_relative 'timed/quasi_euler.rb'  # timeless fire each time tick
+class YPetri::Core::Timed < YPetri::Core
+  require_relative 'timed/euler.rb'
+  require_relative 'timed/pseudo_euler.rb' # timeless fire after each step
+  require_relative 'timed/quasi_euler.rb'  # timeless fire each time tick
 
-    # Makes a single step by Δt.
-    # 
-    def step! Δt=simulation.step
-      increment_marking_vector Δ( Δt )
-      increment_time! Δt
-      note_state_change
-    end
+  # Makes a single step by Δt.
+  # 
+  def step! Δt=simulation.step
+    increment_marking_vector Δ( Δt )
+    increment_time! Δt
+    note_state_change
+  end
 
-    # Gradient for free places.
-    # 
-    def gradient
-      gradient_Ts + gradient_TS
-    end
-    alias ∇ gradient
+  # Gradient for free places.
+  # 
+  def gradient
+    gradient_Ts + gradient_TS
+  end
+  alias ∇ gradient
 
-    # Gradient contribution by Ts transitions.
-    # 
-    def gradient_Ts
-      simulation.Ts_gradient_closure.call
-    end
+  # Gradient contribution by Ts transitions.
+  # 
+  def gradient_Ts
+    simulation.Ts_gradient_closure.call
+  end
 
-    # Gradient contribution by TS transitions.
-    # 
-    def gradient_TS
-      ( simulation.TS_stoichiometry_matrix * flux_vector_TS )
-    end
+  # Gradient contribution by TS transitions.
+  # 
+  def gradient_TS
+    ( simulation.TS_stoichiometry_matrix * flux_vector_TS )
+  end
 
-    # Flux vector. The caller asserts that all the timed transitions are
-    # stoichiometric, or error.
-    # 
-    def flux_vector
-      msg = "#flux_vector method only applies to the timed simulations with " +
-        "no Ts transitions. Try #flux_vector_TS instead!"
-      fail msg unless Ts_transitions().empty?
-      simulation.TS_rate_closure.call
-    end
+  # Flux vector. The caller asserts that all the timed transitions are
+  # stoichiometric, or error.
+  # 
+  def flux_vector
+    msg = "#flux_vector method only applies to the timed simulations with " +
+      "no Ts transitions. Try #flux_vector_TS instead!"
+    fail msg unless Ts_transitions().empty?
+    simulation.TS_rate_closure.call
+  end
 
-    # Flux vector of TS transitions.
-    # 
-    def flux_vector_TS
-      simulation.TS_rate_closure.call
-    end
-  end # class Timed
-end # class YPetri::Core
+  # Flux vector of TS transitions.
+  # 
+  def flux_vector_TS
+    simulation.TS_rate_closure.call
+  end
+end # class YPetri::Core::Timed
 
 # In general, it is not required that all net elements are simulated with the
 # same method. Practically, ODE systems have many good simulation methods

data/lib/y_petri/core/timeless/pseudo_euler.rb

@@ -3,18 +3,16 @@
 # Implicit Euler for timeless nets. Simply, timeless transitions
 # fire simultaneously, after which A transitions (if any) fire.
 #
-class YPetri::Core::Timeless
-  module PseudoEuler
-    # Name of this method.
-    # 
-    def simulation_method
-      :pseudo_euler
-    end
+module YPetri::Core::Timeless::PseudoEuler
+  # Name of this method.
+  # 
+  def simulation_method
+    :pseudo_euler
+  end
 
-    def step!
-      increment_marking_vector Δ
-      assignment_transitions_all_fire!
-      alert
-    end
-  end # module PseudoEuler
-end # class YPetri::Core::Timeless
+  def step!
+    increment_marking_vector Δ
+    assignment_transitions_all_fire!
+    alert
+  end
+end # module YPetri::Core::Timeless::PseudoEuler

data/lib/y_petri/core/timeless.rb

@@ -2,11 +2,14 @@
 
 # Timeless simulation core.
 # 
-class YPetri::Core
-  class Timeless < YPetri::Core
-    require_relative 'timeless/pseudo_euler'
+class YPetri::Core::Timeless < YPetri::Core
+  require_relative 'timeless/pseudo_euler'
 
-    alias delta delta_timeless
-    alias Δ delta
-  end # class Timeless
-end # class YPetri::Core
+  def delta
+    delta_timeless
+  end
+
+  def Δ
+    delta
+  end
+end # class YPetri::Core::Timeless

data/lib/y_petri/core.rb

@@ -1,5 +1,8 @@
 # encoding: utf-8
 
+require_relative 'core/timed'
+require_relative 'core/timeless'
+
 class YPetri::Core
   DEFAULT_METHOD = :pseudo_euler
 
@@ -95,6 +98,3 @@ class YPetri::Core
     simulation.A_assignment_closure.call
   end
 end # class YPetri::Core
-
-require_relative 'core/timed'
-require_relative 'core/timeless'

data/lib/y_petri/dsl.rb

@@ -11,54 +11,54 @@ module YPetri
   delegate :world, to: :y_petri_agent
 
   # Petri net aspect.
-  delegate( :Place,
-            :Transition, :T, :A,
-            :Net,
-            :place, :transition, :pl, :tr,
-            :places, :transitions, :nets,
-            :pn, :tn, :nn,
-            :net_point,
-            :net_selection,
-            :net, :nnet,
-            :net_point_reset,
-            :net_point=,
-            to: :y_petri_agent )
+  delegate :Place,
+           :Transition, :T, :A,
+           :Net,
+           :place, :transition, :pl, :tr,
+           :places, :transitions, :nets,
+           :pn, :tn, :nn,
+           :net_point,
+           :net_selection,
+           :net, :nnet,
+           :net_point_reset,
+           :net_point=,
+           to: :y_petri_agent
 
   # Simulation aspect.
-  delegate( :simulation_point, :ssc_point, :cc_point, :imc_point,
-            :simulation_selection, :ssc_selection,
-            :cc_selection, :imc_selection,
-            :simulations,
-            :clamp_collections,
-            :initial_marking_collections,
-            :simulation_settings_collections,
-            :clamp_collection_names, :ncc,
-            :initial_marking_collection_names, :nimc,
-            :simulation_settings_collection_names, :nssc,
-            :set_clamp_collection, :set_cc,
-            :set_initial_marking_collection, :set_imc,
-            :set_simulation_settings_collection, :set_ssc,
-            :new_simulation,
-            :clamp_cc, :initial_marking_cc, :simulation_settings_cc,
-            :simulation_point_position,
-            :simulation,
-            :clamp_collection, :cc,
-            :initial_marking_collection, :imc,
-            :simulation_settings_collection, :ssc,
-            :clamp,
-            :initial_marking,
-            :set_step, :set_step_size,
-            :set_time, :set_target_time,
-            :set_sampling,
-            :set_simulation_method,
-            :new_timed_simulation,
-            :run!,
-            :print_recording,
-            :plot,
-            :plot_selected,
-#            :plot_state,
-            :plot_flux,
-            to: :y_petri_agent )
+  delegate :simulation_point, :ssc_point, :cc_point, :imc_point,
+           :simulation_selection, :ssc_selection,
+           :cc_selection, :imc_selection,
+           :simulations,
+           :clamp_collections,
+           :initial_marking_collections,
+           :simulation_settings_collections,
+           :clamp_collection_names, :ncc,
+           :initial_marking_collection_names, :nimc,
+           :simulation_settings_collection_names, :nssc,
+           :set_clamp_collection, :set_cc,
+           :set_initial_marking_collection, :set_imc,
+           :set_simulation_settings_collection, :set_ssc,
+           :new_simulation,
+           :clamp_cc, :initial_marking_cc, :simulation_settings_cc,
+           :simulation_point_position,
+           :simulation,
+           :clamp_collection, :cc,
+           :initial_marking_collection, :imc,
+           :simulation_settings_collection, :ssc,
+           :clamp,
+           :initial_marking,
+           :set_step, :set_step_size,
+           :set_time, :set_target_time,
+           :set_sampling,
+           :set_simulation_method,
+           :new_timed_simulation,
+           :run!,
+           :print_recording,
+           :plot,
+           :plot_selected,
+#          :plot_state,
+           :plot_flux,
+           to: :y_petri_agent
 
   def plot_state **nn
     simulation.recording.marking.plot **nn

data/lib/y_petri/fixed_assets.rb

@@ -4,4 +4,12 @@
 # 
 module YPetri
   GuardError = Class.new TypeError
+
+  Place = Class.new
+  Transition = Class.new
+  Net = Class.new
+  Simulation = Class.new
+  Core = Class.new
+  World = Class.new
+  Agent = Class.new
 end # module YPetri