y_petri 2.2.4 → 2.3.2

data/lib/y_petri/world/simulation_aspect.rb

@@ -0,0 +1,352 @@
+# encoding: utf-8
+
+# Workspace instance methods related to the Simulation aspect of YPetri
+# (stored marking collections, clamp collections, inital marking collections,
+# management of simulations...)
+# 
+module YPetri::World::SimulationAspect
+  # Collections of clamps, initial marking vectors, and simulation settings.
+  # 
+  attr_reader :clamp_collections,
+              :initial_marking_collections,
+              :simulation_settings_collections
+
+  # Instance initialization.
+  # 
+  def initialize
+    @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::Simulation::DEFAULT_SETTINGS.call
+                  .update YPetri::Simulation::Timed::DEFAULT_SETTINGS.call ) }
+    super
+  end
+
+  # Hash of simulation instances and their settings.
+  # 
+  def simulations
+    @simulations
+  end
+
+  # Clamp collection names.
+  # 
+  def clamp_collection_names
+    @clamp_collections.keys
+  end
+  alias ncc clamp_collection_names
+
+  # Initial marking collection names.
+  # 
+  def initial_marking_collection_names
+    @initial_marking_collections.keys
+  end
+  alias nimc initial_marking_collection_names
+
+  # Simulation settings collection names.
+  # 
+  def simulation_settings_collection_names
+    @simulation_settings_collections.keys
+  end
+  alias nssc simulation_settings_collection_names
+
+  # Clamp collection identified by the argument.
+  # 
+  def clamp_collection name=:Base
+    @clamp_collections[name]
+  end
+  alias cc clamp_collection
+
+  # Marking collection identified by the argument.
+  # 
+  def initial_marking_collection name=:Base
+    @initial_marking_collections[name]
+  end
+  alias imc initial_marking_collection
+
+  # Simulation settings collection specified by the argument.
+  # 
+  def simulation_settings_collection name=:Base
+    @simulation_settings_collections[name]
+  end
+  alias ssc simulation_settings_collection
+
+  # Creates a new clamp collection. If collection identifier is not given,
+  # resets :Base clamp collection to new values.
+  # 
+  def set_clamp_collection( name=:Base, clamp_hash )
+    @clamp_collections[name] = clamp_hash
+  end
+  alias set_cc set_clamp_collection
+
+  # Creates a new initial marking collection. If collection identifier is not
+  # given, resets :Base initial marking collection to new values.
+  # 
+  def set_initial_marking_collection( name=:Base, initial_marking_hash )
+    @initial_marking_collections[name] = initial_marking_hash
+  end
+  alias set_imc set_initial_marking_collection
+
+  # Creates a new simulation settings collection. If collection identifier is
+  # not given, resets :Base simulation settings collection to new values.
+  # 
+  def set_simulation_settings_collection( name=:Base, sim_set_hash )
+    @simulation_settings_collections[name] = sim_set_hash
+  end
+  alias set_ssc set_simulation_settings_collection
+
+  # Presents a simulation specified by the argument, which must be a hash with
+  # four items: :net, :clamp_collection, :inital_marking_collection and
+  # :simulation_settings_collection.
+  # 
+  def simulation settings={}
+    key = case settings
+          when ~:may_have then # it is a hash or equivalent
+            settings.may_have :net
+            settings.may_have :cc, syn!: :clamp_collection
+            settings.may_have :imc, syn!: :initial_marking_collection
+            settings.may_have :ssc, syn!: :simulation_settings_collection
+            { net:  net( settings[:net] || self.Net::Top ), # the key
+              cc:   settings[:cc]       || :Base,
+              imc:  settings[:imc]      || :Base,
+              ssc:  settings[:ssc]      || :Base }
+          else # use the unprocessed argument itself as the key
+            settings
+          end
+    @simulations[ key ]
+  end
+
+  # Makes a new timed simulation. Named arguments for this method are the same
+  # as for TimedSimulation#new, but in addition, :name can be supplied.
+  # 
+  # To create a simulation, simulation settings collection, initial marking
+  # collection, and clamp collection have to be specified. A <em>place clamp</em>,
+  # is a fixed value, at which the marking is held. Similarly, <em>initial
+  # marking</em> is the marking, which a free place receives at the beginning.
+  # Free places are those, that are not clamped. After initialization, marking
+  # of free places is allowed to change as the transition fire.
+  # 
+  # For example, having places :P1..:P5, clamped :P1, :P2 can be written as eg.:
+  # 
+  # * clamps = { P1: 4, P2: 5 }
+  #
+  # Places :P3, :P4, :P5 are <em>free</em>. Their initial marking has to be
+  # specified, which can be written as eg.:
+  #
+  # * initial_markings = { P3: 1, P4: 2, P5: 3 }
+  #
+  # As for simulation settings, their exact nature depends on the simulation
+  # method. For default Euler method, there are 3 important parameters:
+  #   - <em>step_size</em>,
+  #   - <em>sampling_period</em>,
+  #   - <em>target_time</em>
+  #   
+  # For example, default simulation settings are:
+  #
+  # * default_ss = { step_size: 0.1, sampling_period: 5, target_time: 60 }
+  # 
+  def new_simulation( net: Net()::Top, **nn )
+    net_inst = net( net )
+    nn.may_have :cc, syn!: :clamp_collection
+    nn.may_have :imc, syn!: :initial_marking_collection
+    nn.may_have :ssc, syn!: :simulation_settings_collection
+    cc_id = nn.delete( :cc ) || :Base
+    imc_id = nn.delete( :imc ) || :Base
+    ssc_id = nn.delete( :ssc ) || :Base
+    # Construct the simulation key:
+    key = if nn.has? :name, syn!: :ɴ then # explicit key (name)
+            nn[:name]
+          else                       # constructed key
+            {}.merge( net: net_inst,
+                       cc: cc_id,
+                       imc: imc_id,
+                       ssc: ssc_id )
+              .merge( nn )
+          end
+    # Let's clarify what we got so far.
+    sim_settings = ssc( ssc_id )
+    mc_hash = cc( cc_id )
+    im_hash = imc( imc_id )
+    # Create and return the simulation
+    sim = net_inst.simulation **sim_settings.merge( initial_marking: im_hash,
+                                                    marking_clamps: mc_hash
+                                                    ).merge( nn )
+    @simulations[ key ] = sim
+  end
+end # module YPetri::World::SimulationAspect
+# encoding: utf-8
+
+# Workspace instance methods related to the Simulation aspect of YPetri
+# (stored marking collections, clamp collections, inital marking collections,
+# management of simulations...)
+# 
+module YPetri::World::SimulationAspect
+  # Collections of clamps, initial marking vectors, and simulation settings.
+  # 
+  attr_reader :clamp_collections,
+              :initial_marking_collections,
+              :simulation_settings_collections
+
+  # Instance initialization.
+  # 
+  def initialize
+    @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::Simulation::DEFAULT_SETTINGS.call
+                  .update YPetri::Simulation::Timed::DEFAULT_SETTINGS.call ) }
+    super
+  end
+
+  # Hash of simulation instances and their settings.
+  # 
+  def simulations
+    @simulations
+  end
+
+  # Clamp collection names.
+  # 
+  def clamp_collection_names
+    @clamp_collections.keys
+  end
+  alias ncc clamp_collection_names
+
+  # Initial marking collection names.
+  # 
+  def initial_marking_collection_names
+    @initial_marking_collections.keys
+  end
+  alias nimc initial_marking_collection_names
+
+  # Simulation settings collection names.
+  # 
+  def simulation_settings_collection_names
+    @simulation_settings_collections.keys
+  end
+  alias nssc simulation_settings_collection_names
+
+  # Clamp collection identified by the argument.
+  # 
+  def clamp_collection name=:Base
+    @clamp_collections[name]
+  end
+  alias cc clamp_collection
+
+  # Marking collection identified by the argument.
+  # 
+  def initial_marking_collection name=:Base
+    @initial_marking_collections[name]
+  end
+  alias imc initial_marking_collection
+
+  # Simulation settings collection specified by the argument.
+  # 
+  def simulation_settings_collection name=:Base
+    @simulation_settings_collections[name]
+  end
+  alias ssc simulation_settings_collection
+
+  # Creates a new clamp collection. If collection identifier is not given,
+  # resets :Base clamp collection to new values.
+  # 
+  def set_clamp_collection( name=:Base, clamp_hash )
+    @clamp_collections[name] = clamp_hash
+  end
+  alias set_cc set_clamp_collection
+
+  # Creates a new initial marking collection. If collection identifier is not
+  # given, resets :Base initial marking collection to new values.
+  # 
+  def set_initial_marking_collection( name=:Base, initial_marking_hash )
+    @initial_marking_collections[name] = initial_marking_hash
+  end
+  alias set_imc set_initial_marking_collection
+
+  # Creates a new simulation settings collection. If collection identifier is
+  # not given, resets :Base simulation settings collection to new values.
+  # 
+  def set_simulation_settings_collection( name=:Base, sim_set_hash )
+    @simulation_settings_collections[name] = sim_set_hash
+  end
+  alias set_ssc set_simulation_settings_collection
+
+  # Presents a simulation specified by the argument, which must be a hash with
+  # four items: :net, :clamp_collection, :inital_marking_collection and
+  # :simulation_settings_collection.
+  # 
+  def simulation settings={}
+    key = case settings
+          when ~:may_have then # it is a hash or equivalent
+            settings.may_have :net
+            settings.may_have :cc, syn!: :clamp_collection
+            settings.may_have :imc, syn!: :initial_marking_collection
+            settings.may_have :ssc, syn!: :simulation_settings_collection
+            { net:  net( settings[:net] || self.Net::Top ), # the key
+              cc:   settings[:cc]       || :Base,
+              imc:  settings[:imc]      || :Base,
+              ssc:  settings[:ssc]      || :Base }
+          else # use the unprocessed argument itself as the key
+            settings
+          end
+    @simulations[ key ]
+  end
+
+  # Makes a new timed simulation. Named arguments for this method are the same
+  # as for TimedSimulation#new, but in addition, :name can be supplied.
+  # 
+  # To create a simulation, simulation settings collection, initial marking
+  # collection, and clamp collection have to be specified. A <em>place clamp</em>,
+  # is a fixed value, at which the marking is held. Similarly, <em>initial
+  # marking</em> is the marking, which a free place receives at the beginning.
+  # Free places are those, that are not clamped. After initialization, marking
+  # of free places is allowed to change as the transition fire.
+  # 
+  # For example, having places :P1..:P5, clamped :P1, :P2 can be written as eg.:
+  # 
+  # * clamps = { P1: 4, P2: 5 }
+  #
+  # Places :P3, :P4, :P5 are <em>free</em>. Their initial marking has to be
+  # specified, which can be written as eg.:
+  #
+  # * initial_markings = { P3: 1, P4: 2, P5: 3 }
+  #
+  # As for simulation settings, their exact nature depends on the simulation
+  # method. For default Euler method, there are 3 important parameters:
+  #   - <em>step_size</em>,
+  #   - <em>sampling_period</em>,
+  #   - <em>target_time</em>
+  #   
+  # For example, default simulation settings are:
+  #
+  # * default_ss = { step_size: 0.1, sampling_period: 5, target_time: 60 }
+  # 
+  def new_simulation( net: Net()::Top, **nn )
+    net_inst = net( net )
+    nn.may_have :cc, syn!: :clamp_collection
+    nn.may_have :imc, syn!: :initial_marking_collection
+    nn.may_have :ssc, syn!: :simulation_settings_collection
+    cc_id = nn.delete( :cc ) || :Base
+    imc_id = nn.delete( :imc ) || :Base
+    ssc_id = nn.delete( :ssc ) || :Base
+    # Construct the simulation key:
+    key = if nn.has? :name, syn!: :ɴ then # explicit key (name)
+            nn[:name]
+          else                       # constructed key
+            {}.merge( net: net_inst,
+                       cc: cc_id,
+                       imc: imc_id,
+                       ssc: ssc_id )
+              .merge( nn )
+          end
+    # Let's clarify what we got so far.
+    sim_settings = ssc( ssc_id )
+    mc_hash = cc( cc_id )
+    im_hash = imc( imc_id )
+    # Create and return the simulation
+    sim = net_inst.simulation **sim_settings.merge( initial_marking: im_hash,
+                                                    marking_clamps: mc_hash
+                                                    ).merge( nn )
+    @simulations[ key ] = sim
+  end
+end # module YPetri::World::SimulationAspect

data/lib/y_petri/world.rb

@@ -1,8 +1,8 @@
 # encoding: utf-8
 
 require_relative 'world/dependency'
-require_relative 'world/petri_net_related'
-require_relative 'world/simulation_related'
+require_relative 'world/petri_net_aspect'
+require_relative 'world/simulation_aspect'
 
 # As the name suggests, represents the world. Holds places, transitions, nets
 # and other assets needed to set up and simulate Petri nets (settings, clamps,
@@ -11,8 +11,8 @@ require_relative 'world/simulation_related'
 # 
 class YPetri::World
   ★ NameMagic                        # ★ means include
-  ★ PetriNetRelated
-  ★ SimulationRelated
+  ★ PetriNetAspect
+  ★ SimulationAspect
 
   def initialize
     # Parametrize the Place / Transition / Net classes.

data/lib/y_petri.rb

@@ -35,7 +35,7 @@ require_relative 'y_petri/core'
 require_relative 'y_petri/agent'
 require_relative 'y_petri/dsl'
 
-# YPetri represents Petri net (PN) formalims.
+# YPetri represents Petri net (PN) formalisms.
 #
 # A PN consists of places and transitions. There are also arcs, "arrows"
 # connecting places and transitions, but these are not considered first class

data/test/agent_test.rb

@@ -100,7 +100,8 @@ describe YPetri::Agent do
       rec.marking.plot
       rec.flux.plot
       rec.gradient.plot
-      rec.delta( Δt: 1 ).plot
+      rec.delta_timed( Δt: 1 ).plot
+      rec.delta_timeless( Δt: 1 ).plot
       @m.plot_marking
       @m.plot_flux
       @m.plot_gradient

data/test/examples/demonstrator.rb

@@ -1,5 +1,8 @@
 #encoding: utf-8
 
+# A working demonstration of the simulation functionality, but
+# the resulting curve looks weird (too straight), look into it.
+
 require 'y_petri'
 include YPetri
 
@@ -161,4 +164,4 @@ Transition name: :TMPK_DeoxyTMP_DeoxyTDP,
 
 # execution
 run!
-plot_recording
+recording.plot

data/test/examples/demonstrator_2.rb

@@ -1,5 +1,10 @@
 #encoding: utf-8
 
+# This file demonstrates execution with values of SY::Magnitude type
+# (ie. values with assigned physical units). It works, but the execution
+# is slow and the recording is not fully adapted to the use of physical
+# units yet.
+
 require 'y_petri'
 include YPetri
 require 'sy'

data/test/examples/demonstrator_4.rb

@@ -1,5 +1,7 @@
 #encoding: utf-8
 
+# Unfinished demonstration of TTP pathway simulation, search for FIXME.
+
 require 'y_petri'
 include YPetri
 require 'sy'
@@ -46,10 +48,11 @@ DeoxyUMP = Place m!: 2.70                # Traut1994pcp
 DeoxyUDP = Place m!: 0.5                 # Traut1994pcp
 DeoxyUTP = Place m!: 0.7                 # Traut1994pcp
 
-DeoxyThymidine = Place m!: 0.5           # Traut1994pcp
+Thymidine = Place m!: 0.5                # Traut1994pcp
 DeoxyTMP = Place m!: 0.0                 # in situ
 DeoxyTDP = Place m!: 2.4                 # Traut1994pcp
 DeoxyTTP = Place m!: 17.0                # Traut1994pcp
+DeoxyT23P = Place m!: 2.4 + 17.0
 
 # === Empirical places (in arbitrary units)
 
@@ -75,19 +78,17 @@ TK1tetra = Place m!: 0                   # TK1 in the tetramer form (phosphoryla
 
 # Assignment transition keeping TK1_di level based on total TK1 monomer
 Transition name: :TK1_di_ϝ,
-           assignment: true,
            domain: TK1,
            codomain: TK1di,
-           action: lambda { |monomer|    # solution of a quadratic equation for dimer / tetramer balance
+           assignment: lambda { |monomer|    # solution of a quadratic equation for dimer / tetramer balance
                      TK1_4mer_Kd / 4 * ( ( 1 + 4 / TK1_4mer_Kd * monomer ) ** 0.5 - 1 )
                    }
 
 # Assignment transition keeping TK1_tetra level based on total TK1 tetramer
 Transition name: :TK1_tetra_ϝ,
-           assignment: true,
            domain: [ TK1, TK1di ],
            codomain: TK1tetra,
-           action: lambda { |monomer, dimer| # based on equation monomer = dimer * 2 + tetramer * 4
+           assignment: lambda { |monomer, dimer| # based on equation monomer = dimer * 2 + tetramer * 4
              monomer / 4 - dimer / 2
 }
 

data/test/examples/example_2.rb

@@ -1,5 +1,7 @@
 #encoding: utf-8
 
+# A minimalistic demonstration of the simulation capability.
+
 require 'y_petri'
 include YPetri
 

data/test/examples/manual_examples.rb

@@ -8,7 +8,8 @@ require 'mathn'
 set_step 10
 set_target_time 600
 set_sampling 10
-set_simulation_method :Euler_with_timeless_transitions_firing_after_each_step
+# Euler with timeless transitions firing after each step:
+set_simulation_method :PseudoEuler
 
 A = Place m!: 1
 B = Place m!: 10
@@ -16,13 +17,12 @@ C = Place m!: 0
 
 Transition name: :B_disappearing,
            s: { B: -1 },
-           action: lambda { |m|  m >= 1 ? 1 : 0 }
+           action: -> m {  m >= 1 ? 1 : 0 }
 
 Transition name: :C_held_at_half_B,
-           assignment: true,
            domain: :B,
            codomain: :C,
-           action: lambda { |x| x / 2 }
+           assignment: -> x { x / 2 }
 
 run!
 plot_recording