y_petri 2.1.51 → 2.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: af87fbeae3c77dced19c699d8295b148452f5743
+  metadata.gz: 83dcb590fe26b6d6bb33cf3294d36f3ec2e55739
+  data.tar.gz: 406058cde1b0a815b77dc4feedd0da86cd0613e6
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data/lib/y_petri/net.rb

@@ -44,8 +44,8 @@ class YPetri::Net
                  with: { net: self } )
   end
 
-  # Includes a place in the net. Returns _true_ if successful, _false_ if the
-  # place is already included in the net.
+  # Includes a place in the receiver. Returns _true_ if successful, _false_ if
+  # the place is already included in the receiver net. 
   # 
   def include_place id
     pl = Place().instance( id )
@@ -53,9 +53,9 @@ class YPetri::Net
     true.tap { @places << pl }
   end
 
-  # Includes a transition in the net. Returns _true_ if successful, _false_ if
-  # the transition is already included in the net. The arcs of the transition
-  # being included may only connect to the places already in the net.
+  # Includes a transition in the receiver. Returns _true_ if successful, _false_
+  # if the transition is already included in the net. The arcs of the transition
+  # being included may only connect to the places already in the receiver net.
   # 
   def include_transition id
     tr = Transition().instance( id )
@@ -65,9 +65,9 @@ class YPetri::Net
     true.tap { @transitions << tr }
   end
 
-  # Excludes a place from the net. Returns _true_ if successful, _false_ if the
-  # place was not found in the net. A place may not be excluded from the net so
-  # long as any transitions in the net connect to it.
+  # Excludes a place from the receiver. Returns _true_ if successful, _false_
+  # if the place was not found in the receiver net. A place may not be excluded
+  # from the receiver so long as any transitions therein connect to it.
   # 
   def exclude_place id
     pl = Place().instance( id )
@@ -76,33 +76,75 @@ class YPetri::Net
     false.tap { return true if @places.delete( pl ) }
   end
 
-  # Excludes a transition from the net. Returns _true_ if successful, _false_ if
-  # the transition was not found in the net.
+  # Excludes a transition from the receiver. Returns _true_ if successful,
+  # _false_ if the transition was not found in the receiver net.
   # 
   def exclude_transition id
     tr = Transition().instance( id )
     false.tap { return true if @transitions.delete( tr ) }
   end
 
-  # Includes an element in the net.
+  # Includes another net in the receiver net. Returns _true_ if successful
+  # (ie. if there was any change to the receiver net), _false_ if the receiver
+  # net already includes the argument net.
+  # 
+  def include_net id
+    net = Net().instance( id )
+    p_rslt = net.pp.map { |p| include_place p }.reduce :|
+    t_rslt = net.tt.map { |t| include_transition t }.reduce :|
+    p_rslt || t_rslt
+  end
+  alias merge! include_net
+
+  # Excludes another net from the receiver net. Returns _true_ if successful
+  # (ie. if there was any change to the receiver net), _false_ if the receiver
+  # net contained no element of the argument net.
+  # 
+  def exclude_net id
+    net = Net().instance( id )
+    t_rslt = net.tt.map { |t| exclude_transition t }.reduce :|
+    p_rslt = net.pp.map { |p| exclude_place p }.reduce :|
+    p_rslt || t_rslt
+  end
+
+  # Includes an element (place or transition) in the net.
   # 
   def << element_id
     begin
-      element = self.class.place( element_id )
-      type = :place
+      type, element = :place, self.class.place( element_id )
     rescue NameError, TypeError
       begin
-        element = self.class.transition( element_id )
-        type = :transition
+        type, element = :transition, self.class.transition( element_id )
       rescue NameError, TypeError => err
         raise TypeError, "Current world contains no place or transition " +
           "identified by #{element_id}! (#{err})"
       end
     end
-    # Separated to minimize the code inside rescue clause:
-    if type == :place then include_place element
-    elsif type == :transition then include_transition element
-    else fail "Implementation error in YPetri::Net#<<!" end
+    case type # Factored out to minimize the code inside the rescue clause.
+    when :place then include_place( element )
+    when :transition then include_transition( element )
+    else fail "Implementation error!" end
+    return self # important to enable chaining, eg. foo_net << p1 << p2 << t1
+  end
+
+  # Creates a new net that contains all the places and transitions of both
+  # operands.
+  # 
+  def + other
+    self.class.send( :new ).tap do |net|
+      net.merge! self
+      net.merge! other
+    end
+  end
+
+  # Creates a new net that contains the places and transition of the receiver
+  # after excluding the second operand.
+  # 
+  def - other
+    self.class.send( :new ).tap do |net|
+      net.merge! self
+      net.exclude_net other
+    end
   end
 
   # Is the net _functional_?
@@ -133,10 +175,10 @@ class YPetri::Net
   # Returns a string briefly describing the net.
   # 
   def to_s
-    "#<Net: " +
-      ( name.nil? ? "%s" : "name: #{name}, %s" ) %
-      "#{pp.size rescue '∅'} places, #{tt.size rescue '∅'} transitions" +
-      ">"
+    form = "#<Net: %s>"
+    content = ( name.nil? ? "%s" : "name: #{name}, %s" ) %
+      "#{pp.size rescue '∅'} places, #{tt.size rescue '∅'} transitions"
+    form % content
   end
 
   # Inspect string of the instance.

data/lib/y_petri/version.rb

@@ -1,4 +1,4 @@
 module YPetri
-  VERSION = "2.1.51"
+  VERSION = "2.2.0"
   DEBUG = false
 end

data/test/acceptance/simulation_with_physical_units_test.rb

@@ -1,5 +1,5 @@
 #! /usr/bin/ruby
-# -*- coding: utf-8 -*-
+# encoding: utf-8
 
 gem 'minitest', '=4.7.4'
 require 'minitest/autorun'

data/test/acceptance/visualization_test.rb

@@ -16,7 +16,7 @@ describe "Graphviz visualization" do
     @m.Place name: :D, m!: 2.5
     @m.Transition name: :A_pump, s: { A: -1 }, rate: proc { 0.005 }
     @m.Transition name: :B_decay, s: { B: -1 }, rate: 0.05
-    @m.Transition name: :C_guard, assignment: true, codomain: :C, action: -> { 2 }
+    @m.Transition name: :C_guard, codomain: :C, assignment: -> { 2 }
   end
 
   it "should work" do

data/test/agent_test.rb

@@ -1,7 +1,7 @@
 #! /usr/bin/ruby
 # encoding: utf-8
 
-gem 'minitest', '=4.7.4'
+# gem 'minitest', '=4.7.4' # try uncommenting this line if problems appear
 require 'minitest/autorun'
 require_relative '../lib/y_petri'     # tested component itself
 # require 'y_petri'

data/test/net_test.rb

@@ -1,7 +1,7 @@
 #! /usr/bin/ruby
 # encoding: utf-8
 
-gem 'minitest', '=4.7.4'
+# gem 'minitest', '=4.7.4' # try uncommenting this line if problems appear
 require 'minitest/autorun'
 require_relative '../lib/y_petri'     # tested component itself
 # require 'y_petri'

data/test/place_test.rb

@@ -1,7 +1,7 @@
 #! /usr/bin/ruby
 # encoding: utf-8
 
-gem 'minitest', '=4.7.4'
+# gem 'minitest', '=4.7.4' # try uncommenting this line if problems appear
 require 'minitest/autorun'
 require_relative '../lib/y_petri'     # tested component itself
 # require 'y_petri'

data/test/simulation_test.rb

@@ -1,7 +1,7 @@
 #! /usr/bin/ruby
 # encoding: utf-8
 
-gem 'minitest', '=4.7.4'
+# gem 'minitest', '=4.7.4' # try uncommenting this line if problems appear
 require 'minitest/autorun'
 require_relative '../lib/y_petri'     # tested component itself
 # require 'y_petri'

data/test/transition_test.rb

@@ -1,7 +1,7 @@
 #! /usr/bin/ruby
 # encoding: utf-8
 
-gem 'minitest', '=4.7.4'
+# gem 'minitest', '=4.7.4' # try uncommenting this line if problems appear
 require 'minitest/autorun'
 require 'y_support/typing'
 

data/test/world_test.rb

@@ -1,7 +1,7 @@
 #! /usr/bin/ruby
 # encoding: utf-8
 
-gem 'minitest', '=4.7.4'
+# gem 'minitest', '=4.7.4' # try uncommenting this line if problems appear
 require 'minitest/autorun'
 require_relative '../lib/y_petri'     # tested component itself
 # require 'y_petri'

data/test/y_petri_test.rb

@@ -1,7 +1,7 @@
 #! /usr/bin/ruby
 # encoding: utf-8
 
-gem 'minitest', '=4.7.4'
+# gem 'minitest', '=4.7.4' # try uncommenting this line if problems appear
 require 'minitest/autorun'
 require_relative '../lib/y_petri' # tested component itself
 # require 'y_petri'

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: y_petri
 version: !ruby/object:Gem::Version
-  version: 2.1.51
+  version: 2.2.0
 platform: ruby
 authors:
 - boris
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-09-01 00:00:00.000000000 Z
+date: 2013-10-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: y_support
@@ -182,10 +182,8 @@ files:
 - test/examples/manual_examples.rb
 - test/net_test.rb
 - test/place_test.rb
-- test/sim_test
 - test/simulation_test.rb
 - test/transition_test.rb
-- test/ttp_pathway.rb
 - test/world_mock.rb
 - test/world_test.rb
 - test/y_petri_test.rb
@@ -230,10 +228,8 @@ test_files:
 - test/examples/manual_examples.rb
 - test/net_test.rb
 - test/place_test.rb
-- test/sim_test
 - test/simulation_test.rb
 - test/transition_test.rb
-- test/ttp_pathway.rb
 - test/world_mock.rb
 - test/world_test.rb
 - test/y_petri_test.rb

data/test/sim_test

@@ -1,565 +0,0 @@
-#! /usr/bin/ruby
-# -*- coding: utf-8 -*-
-
-require 'minitest/spec'
-require 'minitest/autorun'
-require_relative '../lib/y_petri'     # tested component itself
-# require 'y_petri'
-# require 'sy'
-require_relative 'workspace_mock'
-
-describe YPetri::Simulation::TransitionRepresentation do
-  before do
-    @pç, @tç, @nç = WORKSPACE_MOCK.()
-    # Set up places:
-    @p1 = @pç.nw "P1", 1
-    @p2 = @pç.nw "P2", 2
-    @p3 = @pç.nw "P3", 3
-    @p4 = @pç.nw "P4", 4
-    @p5 = @pç.nw "P5", 5
-    # Set up transitions:
-    @t1 = @tç.nw "T1", s: { @p1 => -1, @p2 => -1, @p4 => 1 },
-                       rate: 0.1
-    @t2 = @tç.nw "T2", s: { @p1 => -1, @p3 => 1 },
-                       rate: -> a { a * 0.5 }
-    @t3 = @tç.nw "T3", s: { @p1 => -1, @p2 => -1, @p4 => 1 },
-                        domain: @p3,
-                        rate: -> a { a * 0.5 }
-    @net = @nç.new << @p1 << @p2 << @p3 << @p4 << @p5
-    @net.include_transition! @t1
-    @net.include_transition! @t2
-    @net << @t3
-    @s = YPetri::Simulation.new net: @net,
-                                marking_clamps: { @p1 => 2.0, @p5 => 2.0 },
-                                initial_marking: { @p2 => @p2.default_marking,
-                                                   @p3 => @p3.default_marking,
-                                                   @p4 => @p4.default_marking }
-  end
-
-  it "exposes the net" do
-    @s.net.must_equal @net
-    @s.net.places.size.must_equal 5
-    @s.net.transitions.size.must_equal 3
-    assert @net.include? @t1
-    assert @s.net.include? @t1
-    assert @net.include? @t2
-    assert @s.net.include? @t2
-    assert @net.include? @t3
-    assert @s.net.include? @t3
-    @s.net.transitions.size.must_equal 3
-  end
-
-  it "exposes Petri net places" do
-    @s.places.map( &:source ).must_equal [ @p1, @p2, @p3, @p4, @p5 ]
-    @s.pn.must_equal [ :P1, :P2, :P3, :P4, :P5 ]
-  end
-
-  it "exposes Petri net transitions" do
-    @s.transitions.map( &:source ).must_equal [ @t1, @t2, @t3 ]
-    @s.tn.must_equal [ :T1, :T2, :T3 ]
-  end
-
-  it "exposes place clamps" do
-    @s.marking_clamps.values.must_equal [2, 2]
-    @s.n_clamped.must_equal [:P1, :P5]
-  end
-
-  it "presents free places" do
-    @s.free_places.map( &:source ).must_equal [ @p2, @p3, @p4 ]
-    @s.n_free.must_equal [ :P2, :P3, :P4 ]
-  end
-
-  it "presents clamped places" do
-    @s.n_clamped.must_equal [ :P1, :P5 ]
-    @s.clamped_places.map( &:source ).must_equal [ @p1, @p5 ]
-  end
-
-  it "exposes initial marking" do
-    ( @s.free_places.map( &:source ) >> @s.im( *@s.free_places ) )
-      .must_equal( { @p2 => 2, @p3 => 3, @p4 => 4 } )
-    ( @s.n_free >> @s.im( *@s.free_places ) )
-        .must_equal( { P2: 2, P3: 3, P4: 4 } )
-    @s.im.must_equal [ 2, 3, 4 ]
-    @s.im_vector.must_equal Matrix[[2], [3], [4]]
-    @s.im_vector.must_equal @s.iᴍ
-  end
-
-  it "exposes marking (simulation state)" do
-    @s.marking.must_equal [2, 3, 4] # (we're after reset)
-    @s.free_places( :m ).must_equal( { @p2 => 2, @p3 => 3, @p4 => 4 } )
-    @s.free_pp( :m ).must_equal( { P2: 2, P3: 3, P4: 4 } )
-    @s.ᴍ.must_equal Matrix[[2], [3], [4]]
-  end
-
-  it "separately exposes marking of clamped places" do
-    @s.m( *@s.clamped_places ).must_equal [ 2, 2 ]
-    @s.clamped_places( :m_clamped ).must_equal( { @p1 => 2, @p5 => 2 } )
-    @s.clamped_pp( :m_clamped ).must_equal( { P1: 2, P5: 2 } )
-    @s.ᴍ_clamped.must_equal Matrix[[2], [2]]
-  end
-
-  it "exposes marking of all places (with capitalized M)" do
-    @s.pn.must_equal [:P1, :P2, :P3, :P4, :P5]
-    @s.m.must_equal [ 2, 2, 3, 4, 2 ]
-    ( @s.places >> @s.m( *@s.places ) )
-      .must_equal( { @p1 => 2, @p2 => 2, @p3 => 3, @p4 => 4, @p5 => 2 } )
-    @s.marking_vector.must_equal Matrix[[2], [2], [3], [4], [2]]
-  end
-
-  it "has stoichiometry matrix for 3. tS transitions" do
-    @s.tS_stoichiometry_matrix.must_equal Matrix.empty( 3, 0 )
-    @s.tS_SM.must_equal Matrix.empty( 3, 0 )
-  end
-
-  it "has stoichiometry matrix for 6. TS transitions" do
-    @s.TS_SM.must_equal Matrix[[-1,  0, -1], [0, 1, 0], [1, 0, 1]]
-    @s.SM.must_equal @s.TS_SM
-  end
-
-  it "presents 1. TS transitions" do
-    assert_equal [@t1, @t2, @t3], @s.TS_transitions.map( &:source )
-    assert_equal( { @t1 => :T1, @t2 => :T2, @t3 => :T3 },
-                  @s.TS_transitions.map( &:source ) >> @s.n_TS )
-    assert_equal [:T1, :T2, :T3], @s.n_TS
-  end
-
-  it "presents 2. Ts transitions" do
-    assert_equal [], @s.Ts_transitions
-    assert_equal [], @s.n_Ts
-  end
-
-  it "presents 3. tS transitions" do
-    assert_equal [], @s.tS_transitions
-    assert_equal [], @s.n_tS
-  end
-
-  it "presents 4. ts transitions" do
-    assert_equal [], @s.ts_transitions
-    assert_equal [], @s.n_ts
-  end
-
-  it "presents A transitions" do
-    assert_equal [], @s.A_transitions
-    assert_equal [], @s.n_A
-  end
-
-  it "presents S transitions" do
-    assert_equal [@t1, @t2, @t3], @s.S_transitions.map( &:source )
-    assert_equal [:T1, :T2, :T3], @s.n_S
-  end
-
-  it "presents s transitions" do
-    assert_equal [], @s.s_transitions
-    assert_equal [], @s.n_s
-  end
-
-  it "1. handles TS transitions" do
-    @s.transitions.TS.rate_closures.size.must_equal 3
-    @s.transitions.TS.flux_vector.must_equal Matrix.column_vector( [ 0.4, 1.0, 1.5 ] )
-    @s.φ_for_SR.must_equal @s.flux_vector
-    @s.SR_tt( :φ_for_SR ).must_equal( { T1: 0.4, T2: 1.0, T3: 1.5 } )
-    @s.first_order_action_vector_for_SR( 1 )
-      .must_equal Matrix.column_vector [ 0.4, 1.0, 1.5 ]
-    @s.SR_tt( :first_order_action_for_SR, 1 ).must_equal( T1: 0.4, T2: 1.0, T3: 1.5 )
-    @s.Δ_SR( 1 ).must_equal Matrix[[-1.9], [1.0], [1.9]]
-    @s.free_pp( :Δ_SR, 1 ).must_equal( { P2: -1.9, P3: 1.0, P4: 1.9 } )
-  end
-
-  it "2. handles Ts transitions" do
-    assert_equal [], @s.transitions.Ts.gradient_closures
-    @s.transitions.Ts.delta( 1.0 ).must_equal Matrix.zero( @s.n_free.size, 1 )
-  end
-
-  it "3. handles tS transitions" do
-    @s.transitions.tS.firing_closures.must_equal []
-    @s.transitions.tS.firing_vector.must_equal Matrix.column_vector( [] )
-    @s.transitions.tS.delta.must_equal Matrix.zero( @s.n_free.size, 1 )
-  end
-
-  it "1. handles ts transitions" do
-    @s.transitions.ts.delta_closures.must_equal []
-  end
-
-  it "presents sparse stoichiometry vectors for its transitions" do
-    @s.transition( @t1 ).sparse_sv.must_equal Matrix.cv( [-1, 0, 1] )
-    @s.sparse_stoichiometry_vector( of: @t1 )
-      .must_equal Matrix.cv( [-1, -1, 0, 1, 0] )
-  end
-
-  it "presents correspondence matrices free, clamped => all places" do
-    @s.f2a.must_equal Matrix[[0, 0, 0], [1, 0, 0], [0, 1, 0],
-                                    [0, 0, 1], [0, 0, 0]]
-    @s.c2a.must_equal Matrix[[1, 0], [0, 0], [0, 0], [0, 0], [0, 1]]
-  end
-end
-
-describe ::YPetri::Simulation do
-  before do
-    @pç, @tç, @nç = WORKSPACE_MOCK.()
-    # Set up places:
-    @p1 = @pç.nw "P1", 1
-    @p2 = @pç.nw "P2", 2
-    @p3 = @pç.nw "P3", 3
-    @p4 = @pç.nw "P4", 4
-    @p5 = @pç.nw "P5", 5
-    # Set up transitions:
-    @t1 = @tç.nw "T1", s: { @p1 => -1, @p2 => -1, @p4 => 1 },
-                       rate: 0.1
-    @t2 = @tç.nw "T2", s: { @p1 => -1, @p3 => 1 },
-                       rate: -> a { a * 0.5 }
-    @t3 = @tç.new "T3", s: { @p1 => -1, @p2 => -1, @p4 => 1 },
-                        domain: @p3,
-                        rate: -> a { a * 0.5 }
-    @net = @nç.new << @p1 << @p2 << @p3 << @p4 << @p5
-    @net.include_transition! @t1
-    @net.include_transition! @t2
-    @net << @t3
-    @s = YPetri::Simulation.new net: @net,
-                                marking_clamps: { @p1 => 2.0, @p5 => 2.0 },
-                                initial_marking: { @p2 => @p2.default_marking,
-                                                   @p3 => @p3.default_marking,
-                                                   @p4 => @p4.default_marking }
-  end
-
-  it "exposes the net" do
-    @s.net.must_equal @net
-    @s.net.places.size.must_equal 5
-    @s.net.transitions.size.must_equal 3
-    assert @net.include? @t1
-    assert @s.net.include? @t1
-    assert @net.include? @t2
-    assert @s.net.include? @t2
-    assert @net.include? @t3
-    assert @s.net.include? @t3
-    @s.net.transitions.size.must_equal 3
-  end
-
-  it "exposes Petri net places" do
-    @s.places.map( &:source ).must_equal [ @p1, @p2, @p3, @p4, @p5 ]
-    @s.pn.must_equal [ :P1, :P2, :P3, :P4, :P5 ]
-  end
-
-  it "exposes Petri net transitions" do
-    @s.transitions.map( &:source ).must_equal [ @t1, @t2, @t3 ]
-    @s.tn.must_equal [ :T1, :T2, :T3 ]
-  end
-
-  it "exposes place clamps" do
-    @s.marking_clamps.values.must_equal [2, 2]
-    @s.n_clamped.must_equal [:P1, :P5]
-  end
-
-  it "presents free places" do
-    @s.free_places.map( &:source ).must_equal [ @p2, @p3, @p4 ]
-    @s.n_free.must_equal [ :P2, :P3, :P4 ]
-  end
-
-  it "presents clamped places" do
-    @s.n_clamped.must_equal [ :P1, :P5 ]
-    @s.clamped_places.map( &:source ).must_equal [ @p1, @p5 ]
-  end
-
-  it "exposes initial marking" do
-    ( @s.free_places.map( &:source ) >> @s.im( *@s.free_places ) )
-      .must_equal( { @p2 => 2, @p3 => 3, @p4 => 4 } )
-    ( @s.n_free >> @s.im( *@s.free_places ) )
-        .must_equal( { P2: 2, P3: 3, P4: 4 } )
-    @s.im.must_equal [ 2, 3, 4 ]
-    @s.im_vector.must_equal Matrix[[2], [3], [4]]
-    @s.im_vector.must_equal @s.iᴍ
-  end
-
-  it "exposes marking (simulation state)" do
-    @s.marking.must_equal [2, 3, 4] # (we're after reset)
-    @s.free_places( :m ).must_equal( { @p2 => 2, @p3 => 3, @p4 => 4 } )
-    @s.free_pp( :m ).must_equal( { P2: 2, P3: 3, P4: 4 } )
-    @s.ᴍ.must_equal Matrix[[2], [3], [4]]
-  end
-
-  it "separately exposes marking of clamped places" do
-    @s.m( *@s.clamped_places ).must_equal [ 2, 2 ]
-    @s.clamped_places( :m_clamped ).must_equal( { @p1 => 2, @p5 => 2 } )
-    @s.clamped_pp( :m_clamped ).must_equal( { P1: 2, P5: 2 } )
-    @s.ᴍ_clamped.must_equal Matrix[[2], [2]]
-  end
-
-  it "exposes marking of all places (with capitalized M)" do
-    @s.pn.must_equal [:P1, :P2, :P3, :P4, :P5]
-    @s.m.must_equal [ 2, 2, 3, 4, 2 ]
-    ( @s.places >> @s.m( *@s.places ) )
-      .must_equal( { @p1 => 2, @p2 => 2, @p3 => 3, @p4 => 4, @p5 => 2 } )
-    @s.marking_vector.must_equal Matrix[[2], [2], [3], [4], [2]]
-  end
-
-  it "has stoichiometry matrix for 3. tS transitions" do
-    @s.tS_stoichiometry_matrix.must_equal Matrix.empty( 3, 0 )
-    @s.tS_SM.must_equal Matrix.empty( 3, 0 )
-  end
-
-  it "has stoichiometry matrix for 6. TS transitions" do
-    @s.TS_SM.must_equal Matrix[[-1,  0, -1], [0, 1, 0], [1, 0, 1]]
-    @s.SM.must_equal @s.TS_SM
-  end
-
-  it "presents 1. TS transitions" do
-    assert_equal [@t1, @t2, @t3], @s.TS_transitions.map( &:source )
-    assert_equal( { @t1 => :T1, @t2 => :T2, @t3 => :T3 },
-                  @s.TS_transitions.map( &:source ) >> @s.n_TS )
-    assert_equal [:T1, :T2, :T3], @s.n_TS
-  end
-
-  it "presents 2. Ts transitions" do
-    assert_equal [], @s.Ts_transitions
-    assert_equal [], @s.n_Ts
-  end
-
-  it "presents 3. tS transitions" do
-    assert_equal [], @s.tS_transitions
-    assert_equal [], @s.n_tS
-  end
-
-  it "presents 4. ts transitions" do
-    assert_equal [], @s.ts_transitions
-    assert_equal [], @s.n_ts
-  end
-
-  it "presents A transitions" do
-    assert_equal [], @s.A_transitions
-    assert_equal [], @s.n_A
-  end
-
-  it "presents S transitions" do
-    assert_equal [@t1, @t2, @t3], @s.S_transitions.map( &:source )
-    assert_equal [:T1, :T2, :T3], @s.n_S
-  end
-
-  it "presents s transitions" do
-    assert_equal [], @s.s_transitions
-    assert_equal [], @s.n_s
-  end
-
-  it "1. handles TS transitions" do
-    @s.transitions.TS.rate_closures.size.must_equal 3
-    @s.transitions.TS.flux_vector.must_equal Matrix.column_vector( [ 0.4, 1.0, 1.5 ] )
-    @s.φ_for_SR.must_equal @s.flux_vector
-    @s.SR_tt( :φ_for_SR ).must_equal( { T1: 0.4, T2: 1.0, T3: 1.5 } )
-    @s.first_order_action_vector_for_SR( 1 )
-      .must_equal Matrix.column_vector [ 0.4, 1.0, 1.5 ]
-    @s.SR_tt( :first_order_action_for_SR, 1 ).must_equal( T1: 0.4, T2: 1.0, T3: 1.5 )
-    @s.Δ_SR( 1 ).must_equal Matrix[[-1.9], [1.0], [1.9]]
-    @s.free_pp( :Δ_SR, 1 ).must_equal( { P2: -1.9, P3: 1.0, P4: 1.9 } )
-  end
-
-  it "2. handles Ts transitions" do
-    assert_equal [], @s.transitions.Ts.gradient_closures
-    @s.transitions.Ts.delta( 1.0 ).must_equal Matrix.zero( @s.n_free.size, 1 )
-  end
-
-  it "3. handles tS transitions" do
-    @s.transitions.tS.firing_closures.must_equal []
-    @s.transitions.tS.firing_vector.must_equal Matrix.column_vector( [] )
-    @s.transitions.tS.delta.must_equal Matrix.zero( @s.n_free.size, 1 )
-  end
-
-  it "1. handles ts transitions" do
-    @s.transitions.ts.delta_closures.must_equal []
-  end
-
-  it "presents sparse stoichiometry vectors for its transitions" do
-    @s.transition( @t1 ).sparse_sv.must_equal Matrix.cv( [-1, 0, 1] )
-    @s.sparse_stoichiometry_vector( of: @t1 )
-      .must_equal Matrix.cv( [-1, -1, 0, 1, 0] )
-  end
-
-  it "presents correspondence matrices free, clamped => all places" do
-    @s.f2a.must_equal Matrix[[0, 0, 0], [1, 0, 0], [0, 1, 0],
-                                    [0, 0, 1], [0, 0, 0]]
-    @s.c2a.must_equal Matrix[[1, 0], [0, 0], [0, 0], [0, 0], [0, 1]]
-  end
-end
-
-
-describe ::YPetri::Simulation do
-  before do
-    @pç, @tç, @nç = WORKSPACE_MOCK.()
-    # Set up places:
-    @p1 = @pç.nw "P1", 1
-    @p2 = @pç.nw "P2", 2
-    @p3 = @pç.nw "P3", 3
-    @p4 = @pç.nw "P4", 4
-    @p5 = @pç.nw "P5", 5
-    # Set up transitions:
-    @t1 = @tç.nw "T1", s: { @p1 => -1, @p2 => -1, @p4 => 1 },
-                       rate: 0.1
-    @t2 = @tç.nw "T2", s: { @p1 => -1, @p3 => 1 },
-                       rate: -> a { a * 0.5 }
-    @t3 = @tç.new "T3", s: { @p1 => -1, @p2 => -1, @p4 => 1 },
-                        domain: @p3,
-                        rate: -> a { a * 0.5 }
-    @net = @nç.new << @p1 << @p2 << @p3 << @p4 << @p5
-    @net.include_transition! @t1
-    @net.include_transition! @t2
-    @net << @t3
-    @s = YPetri::Simulation.new net: @net,
-                                marking_clamps: { @p1 => 2.0, @p5 => 2.0 },
-                                initial_marking: { @p2 => @p2.default_marking,
-                                                   @p3 => @p3.default_marking,
-                                                   @p4 => @p4.default_marking }
-  end
-
-  it "exposes the net" do
-    @s.net.must_equal @net
-    @s.net.places.size.must_equal 5
-    @s.net.transitions.size.must_equal 3
-    assert @net.include? @t1
-    assert @s.net.include? @t1
-    assert @net.include? @t2
-    assert @s.net.include? @t2
-    assert @net.include? @t3
-    assert @s.net.include? @t3
-    @s.net.transitions.size.must_equal 3
-  end
-
-  it "exposes Petri net places" do
-    @s.places.map( &:source ).must_equal [ @p1, @p2, @p3, @p4, @p5 ]
-    @s.pn.must_equal [ :P1, :P2, :P3, :P4, :P5 ]
-  end
-
-  it "exposes Petri net transitions" do
-    @s.transitions.map( &:source ).must_equal [ @t1, @t2, @t3 ]
-    @s.tn.must_equal [ :T1, :T2, :T3 ]
-  end
-
-  it "exposes place clamps" do
-    @s.marking_clamps.values.must_equal [2, 2]
-    @s.n_clamped.must_equal [:P1, :P5]
-  end
-
-  it "presents free places" do
-    @s.free_places.map( &:source ).must_equal [ @p2, @p3, @p4 ]
-    @s.n_free.must_equal [ :P2, :P3, :P4 ]
-  end
-
-  it "presents clamped places" do
-    @s.n_clamped.must_equal [ :P1, :P5 ]
-    @s.clamped_places.map( &:source ).must_equal [ @p1, @p5 ]
-  end
-
-  it "exposes initial marking" do
-    ( @s.free_places.map( &:source ) >> @s.im( *@s.free_places ) )
-      .must_equal( { @p2 => 2, @p3 => 3, @p4 => 4 } )
-    ( @s.n_free >> @s.im( *@s.free_places ) )
-        .must_equal( { P2: 2, P3: 3, P4: 4 } )
-    @s.im.must_equal [ 2, 3, 4 ]
-    @s.im_vector.must_equal Matrix[[2], [3], [4]]
-    @s.im_vector.must_equal @s.iᴍ
-  end
-
-  it "exposes marking (simulation state)" do
-    @s.marking.must_equal [2, 3, 4] # (we're after reset)
-    @s.free_places( :m ).must_equal( { @p2 => 2, @p3 => 3, @p4 => 4 } )
-    @s.free_pp( :m ).must_equal( { P2: 2, P3: 3, P4: 4 } )
-    @s.ᴍ.must_equal Matrix[[2], [3], [4]]
-  end
-
-  it "separately exposes marking of clamped places" do
-    @s.m( *@s.clamped_places ).must_equal [ 2, 2 ]
-    @s.clamped_places( :m_clamped ).must_equal( { @p1 => 2, @p5 => 2 } )
-    @s.clamped_pp( :m_clamped ).must_equal( { P1: 2, P5: 2 } )
-    @s.ᴍ_clamped.must_equal Matrix[[2], [2]]
-  end
-
-  it "exposes marking of all places (with capitalized M)" do
-    @s.pn.must_equal [:P1, :P2, :P3, :P4, :P5]
-    @s.m.must_equal [ 2, 2, 3, 4, 2 ]
-    ( @s.places >> @s.m( *@s.places ) )
-      .must_equal( { @p1 => 2, @p2 => 2, @p3 => 3, @p4 => 4, @p5 => 2 } )
-    @s.marking_vector.must_equal Matrix[[2], [2], [3], [4], [2]]
-  end
-
-  it "has stoichiometry matrix for 3. tS transitions" do
-    @s.tS_stoichiometry_matrix.must_equal Matrix.empty( 3, 0 )
-    @s.tS_SM.must_equal Matrix.empty( 3, 0 )
-  end
-
-  it "has stoichiometry matrix for 6. TS transitions" do
-    @s.TS_SM.must_equal Matrix[[-1,  0, -1], [0, 1, 0], [1, 0, 1]]
-    @s.SM.must_equal @s.TS_SM
-  end
-
-  it "presents 1. TS transitions" do
-    assert_equal [@t1, @t2, @t3], @s.TS_transitions.map( &:source )
-    assert_equal( { @t1 => :T1, @t2 => :T2, @t3 => :T3 },
-                  @s.TS_transitions.map( &:source ) >> @s.n_TS )
-    assert_equal [:T1, :T2, :T3], @s.n_TS
-  end
-
-  it "presents 2. Ts transitions" do
-    assert_equal [], @s.Ts_transitions
-    assert_equal [], @s.n_Ts
-  end
-
-  it "presents 3. tS transitions" do
-    assert_equal [], @s.tS_transitions
-    assert_equal [], @s.n_tS
-  end
-
-  it "presents 4. ts transitions" do
-    assert_equal [], @s.ts_transitions
-    assert_equal [], @s.n_ts
-  end
-
-  it "presents A transitions" do
-    assert_equal [], @s.A_transitions
-    assert_equal [], @s.n_A
-  end
-
-  it "presents S transitions" do
-    assert_equal [@t1, @t2, @t3], @s.S_transitions.map( &:source )
-    assert_equal [:T1, :T2, :T3], @s.n_S
-  end
-
-  it "presents s transitions" do
-    assert_equal [], @s.s_transitions
-    assert_equal [], @s.n_s
-  end
-
-  it "1. handles TS transitions" do
-    @s.transitions.TS.rate_closures.size.must_equal 3
-    @s.transitions.TS.flux_vector.must_equal Matrix.column_vector( [ 0.4, 1.0, 1.5 ] )
-    @s.φ_for_SR.must_equal @s.flux_vector
-    @s.SR_tt( :φ_for_SR ).must_equal( { T1: 0.4, T2: 1.0, T3: 1.5 } )
-    @s.first_order_action_vector_for_SR( 1 )
-      .must_equal Matrix.column_vector [ 0.4, 1.0, 1.5 ]
-    @s.SR_tt( :first_order_action_for_SR, 1 ).must_equal( T1: 0.4, T2: 1.0, T3: 1.5 )
-    @s.Δ_SR( 1 ).must_equal Matrix[[-1.9], [1.0], [1.9]]
-    @s.free_pp( :Δ_SR, 1 ).must_equal( { P2: -1.9, P3: 1.0, P4: 1.9 } )
-  end
-
-  it "2. handles Ts transitions" do
-    assert_equal [], @s.transitions.Ts.gradient_closures
-    @s.transitions.Ts.delta( 1.0 ).must_equal Matrix.zero( @s.n_free.size, 1 )
-  end
-
-  it "3. handles tS transitions" do
-    @s.transitions.tS.firing_closures.must_equal []
-    @s.transitions.tS.firing_vector.must_equal Matrix.column_vector( [] )
-    @s.transitions.tS.delta.must_equal Matrix.zero( @s.n_free.size, 1 )
-  end
-
-  it "1. handles ts transitions" do
-    @s.transitions.ts.delta_closures.must_equal []
-  end
-
-  it "presents sparse stoichiometry vectors for its transitions" do
-    @s.transition( @t1 ).sparse_sv.must_equal Matrix.cv( [-1, 0, 1] )
-    @s.sparse_stoichiometry_vector( of: @t1 )
-      .must_equal Matrix.cv( [-1, -1, 0, 1, 0] )
-  end
-
-  it "presents correspondence matrices free, clamped => all places" do
-    @s.f2a.must_equal Matrix[[0, 0, 0], [1, 0, 0], [0, 1, 0],
-                                    [0, 0, 1], [0, 0, 0]]
-    @s.c2a.must_equal Matrix[[1, 0], [0, 0], [0, 0], [0, 0], [0, 1]]
-  end
-end

data/test/ttp_pathway.rb

@@ -1,233 +0,0 @@
-#! /usr/bin/ruby
-# coding: utf-8
-
-# ==============================================================================
-# 
-# Thymidine triphosphate pathway model.
-# 
-# Author: Boris Stitnicky
-# Affiliation:
-# ... etc etc same shit as in SBML
-# 
-# ==============================================================================
-
-# === Load the required libraries.
-require 'y_nelson' # This pathway model uses FPN domain model.
-require 'sy'       # This pathway model uses 'sy' metrology domain model.
-require 'mathn'    # Standard library 'mathn' is required.
-include YNelson    # pull in the DSL
-
-require "./ttp_pathway/version"             # version number
-require './ttp_pathway/michaelis_menten'    # basic function definitions
-require './ttp_pathway/general_assumptions' # general model assumptions
-
-# === Load the chosen cell cycle model.
-require "./ttp_pathway/simple_cell_cycle"
-
-# === Load the original version of the dTTP pathway based on the literature.
-require "./ttp_pathway/literature_model"
-
-# === Simulate it.
-set_step 1 # in seconds
-set_target_time 24.h.in :s
-set_sampling 5.min.in :s
-set_simulation_method :pseudo_euler
-sim = new_simulation guarded: false
-sim.guarded?
-sim.run! upto: 10
-sim.run! upto: 20
-sim.run! upto: 30
-sim.run! upto: 40
-# FIXME: Here it breaks if step is set to
-#     set_step 5 # seconds
-# it seems that the problem is actually caused by one of the closures
-# returning an incompatible result (imaginary number in this particular case),
-# which causes the whole marking vector become imaginary numbers and fail upon
-# comparison (#>) subsequently.
-#
-# The challenge here is to make it easy to debug the models. In execution, I am
-# against artificial constraints on place marking, and not just because it slows
-# things down, but mainly because such thing is not a part of the Petri net
-# business model as I understand it. But at debug time, I am for "type" checking
-# that identify the source of problem values. And that should be implemented in
-# simulation, in those several #create_*_closures at the end of the class. There
-# should be versions of these closures that check the values of the transition
-# functions as they are produced and pinpoint where the problem is coming from.
-#
-# Obviously, YNelson at its current shape has no problems simulating well-written
-# nets with good simulation settings
-#
-# I am not going to program this right now. I'll just look at the simulation
-# class, and that will be it for this week. Next programming session: Monday.
-sim.run! upto: 50
-sim.run! upto: 60
-sim.run! upto: 70
-sim.run! upto: 80
-sim.run! upto: 90
-sim.run! upto: 100
-sim.run! upto: 1000
-sim.run! upto: 10000
-sim.run!
-
-sim = new_timed_simulation( guarded: true )
-sim.run! upto: 1000
-sim.run! upto: 1000
-
-# It turns out that simply, the step was too big
-
-# === Load the acceptance tests for the dTTP pathway behavior.
-require_relative "ttp_pathway/acceptance_tests"
-
-# === Run those tests.
-test simulation
-
-# === Load the pathway updates according to human judgment.
-require_relative "ttp_pathway/model_correction"
-
-# === Rerun the simulation.
-run!
-
-# === Run those tests.
-test simulation
-
-# Now, having at our disposal a satisfactory dTTP pathway, we can simulate
-# its behavior throughout the cell cycle.
-
-# === Rerun the simulation.
-run!
-
-# === Visualization suggestions
-plot :all, except: Timer # marking of all the FPN places except Timer
-
-plot [ S_phase, A_phase, Cdc20A ] # cell-cycle places marking
-plot [ S_phase, A_phase, Cdc20A, TK1, TK1di, TK1tetra, TK1di_P, TMPK ] # TTP pathway concentrations
-plot [ S_phase, TK1, TK1di, TK1tetra, TK1di_P ] # TTP pathway enzyme concentrations
-plot [ S_phase, Thymidine, TMP, TDP, TTP, T23P ] # TTP patwhay concentrations simplified
-plot :flux, except: Clock # all flux except time flow
-plot :flux, except: [ Clock, T23P_flux_clamp, TMP_flux_clamp,
-                      Thymidine_flux_clamp ] # all except flux clamps
-plot :state, except: [ Timer, AMP, ADP, ATP, UTP, UDP, UMP, GMP, DeoxyATP,
-                       DeoxyADP, DeoxyAMP, DeoxyCytidine, DeoxyCMP, DeoxyCDP,
-                       DeoxyCTP, DeoxyGTP, DeoxyGMP, DeoxyUridine, DeoxyUMP,
-                       DeoxyUDP, DeoxyUTP, DeoxyT23P ] # cell cycle marking
-
-# Now let's look into the graph visualization.
-
-# Define function to display it with kioclient
-# 
-def showit( fɴ )
-  system "sleep 0.2; kioclient exec 'file:%s'" %
-    File.expand_path( '.', fɴ )
-end
-
-# Define enzyme places
-enzyme_places = {
-  TK1: "TK1",
-  TK1di: "TK1 dimer",
-  TK1di_P: "TK1 phosphorylated dimer",
-  TK1tetra: "TK1 tetramer",
-  TMPK: "TMPK"
-}
-
-# Define small molecule places
-small_molecule_places = {
-  Thymidine: "Thymidine",
-  TMP: "Thymidine monophosphate",
-  T23P: "Thymidine diphosphate / triphosphate pool",
-  TDP: "Thymidine diphosphate",
-  TTP: "Thymidine triphosphate"
-}
-
-# Define graphviz places
-def graphviz places
-  require 'graphviz'
-  γ = GraphViz.new :G, type: :digraph  # Create a new graph
-
-  # # set global node options
-  # γ.node[:color] = "#ddaa66"
-  # γ.node[:style] = "filled"
-  # γ.node[:shape] = "box"
-  # γ.node[:penwidth] = "1"
-  # γ.node[:fontname] = "Trebuchet MS"
-  # γ.node[:fontsize] = "8"
-  # γ.node[:fillcolor] = "#ffeecc"
-  # γ.node[:fontcolor] = "#775500"
-  # γ.node[:margin] = "0.0"
-
-  # # set global edge options
-  # γ.edge[:color] = "#999999"
-  # γ.edge[:weight] = "1"
-  # γ.edge[:fontsize] = "6"
-  # γ.edge[:fontcolor] = "#444444"
-  # γ.edge[:fontname] = "Verdana"
-  # γ.edge[:dir] = "forward"
-  # γ.edge[:arrowsize] = "0.5"
-
-  nodes = Hash[ places.map { |pɴ, label|         # make nodes
-                  [ pɴ, γ.add_nodes( label ) ]
-                } ]
-
-  places.each { |pɴ, label|                      # add edges
-    p = place pɴ
-    p.upstream_places.each { |up|
-      node = nodes[ pɴ ]
-      next unless places.map { |ɴ, _| ɴ }.include? up.name
-      next if up == p
-      upstream_node = nodes[ up.name ]
-      upstream_node << node
-    }
-  }
-
-  γ.output png: "enzymes.png"        # Generate output image
-  showit "enzymes.png"
-end
-
-[ enzyme_places, small_molecule_places ].each { |ꜧ|
-  ꜧ.define_singleton_method :+ do |o| merge o end }
-
-graphviz enzyme_places
-graphviz small_molecule_places
-graphviz enzyme_places + small_molecule_places # combining pathways
-
-net.visualize
-
-
-# ==============================================================================
-# 
-# 1. Please note that the script contained in this file does not constitute
-# programming in the sense of software development. It is simply scripted
-# user interaction with YPetri FPN simulator. This user interaction takes
-# place inside the interactive Ruby session (irb), or it can be saved and
-# run all at once as a script. The user has at her disposal the devices and
-# language constructs of full-fledged Ruby. The user is not sandboxed (the
-# problem of many GUI-based "applications"). In other words, the simulation
-# software does not wrap its host language. Rather, it extends Ruby, giving
-# its interactive session new, pathway-specific abilities. No constraints
-# are placed on how complicated or intelligent the user's use of the software
-# can be.
-#
-# 2. However, on this dTTP pathway model, it can be already noted, that there
-# would be certain actions, that the user will have to repeat in most of
-# her biological models usin YPetri. For example, Michaelis & Menten function
-# definitions are to be expected in many pathway models. More seriously, the
-# Petri net models of enzymes and signal proteins suffer exponential explosion
-# with number of eligible reactants, competitive inhibitors, and other
-# interacting molecules. In typical smaller pathway models, this explosion is
-# not deadly, because only few of these interacting molecules are considered.
-# But the amount of scripting the user is required to do would still be
-# reduced many times, if such enzymes and signal proteins can be expressed
-# declaratively, rather than by manual enumeration of their Petri net
-# transitions. All of this provides motivation towards developing even more
-# concise way of pathway encoding than that provided by plain FPN.
-#
-# 3. In the planned more concise pathway encoding (that would subsume the
-# functionality of the current standards such as SBML), there is one more
-# major concern – storing relations. I feel tempted to use Ted Nelson's zz
-# structure as an alternative to usual SQL and non-SQL relational databases.
-# The usability of zz structures in bioinformatics has already been noted.
-# However, I am aware of the advantage held by the existing database merely
-# by the virtue of its maturity. To account for the possibility, that my zz
-# domain model would become a bottleneck, I will leave the back door open on
-# the possibility of using existing database software later on.
-# 
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