y_petri 2.0.2 → 2.0.3

data/lib/y_petri.rb

@@ -1,5 +1,3 @@
-#encoding: utf-8
-
 require 'gnuplot'
 require 'csv'
 require 'graphviz'
@@ -12,8 +10,8 @@ require 'y_support/typing'
 require 'y_support/core_ext/hash'
 require 'y_support/core_ext/array'
 require 'y_support/stdlib_ext/matrix'
-
 require 'y_support/abstract_algebra'
+require 'y_support/kde'
 
 require 'active_support/core_ext/module/delegation'
 require 'active_support/core_ext/array/extract_options'
@@ -46,8 +44,6 @@ require_relative 'y_petri/manipulator'
 # Float (continuous) - the decision should be on the simulator.
 # 
 module YPetri
-  DEBUG = false
-
   DEFAULT_SIMULATION_SETTINGS = lambda do
     { step_size: 0.02,
       sampling_period: 2,
@@ -66,68 +62,44 @@ module YPetri
     }
   end
 
-  delegate( :workspace,
-            :place, :transition,
-            :p, :t,
+  delegate( :workspace, to: :y_petri_manipulator )
+
+  # Petri net-related methods.
+  delegate( :Place, :Transition, :Net,
+            :place, :transition, :pl, :tr,
             :places, :transitions, :nets,
-            :simulations,
             :pp, :tt, :nn,
+            :net_point,
+            :net_selection,
+            :net, :ne,
+            :net_point_reset,
+            :net_point_set,
+            to: :y_petri_manipulator )
+
+  # Simulation-related methods.
+  delegate( :simulation_point, :ssc_point, :cc_point, :imc_point,
+            :simulation_selection, :ssc_selection,
+            :cc_selection, :imc_selection,
+            :simulations,
             :clamp_collections,
-            :inital_marking_collections,
+            :initial_marking_collections,
             :simulation_settings_collections,
+            :clamp_collection_names, :cc_names,
+            :initial_marking_collection_names, :imc_names,
+            :simulation_settings_collection_names, :ssc_names,
+            :set_clamp_collection, :set_cc,
+            :set_initial_marking_collection, :set_imc,
+            :set_simulation_settings_collection, :set_ssc,
+            :new_timed_simulation,
             :clamp_cc, :initial_marking_cc, :simulation_settings_cc,
-            :Place,
-            :Transition,
-            :Net,
-            :net_point_reset,
-            :net_point_to, :net→,
-            :net,
-            :simulation_point_reset,
-            :simulation_point_to,
-            :simulation,
             :simulation_point_position,
-            :cc_point_reset,
-            :cc_point_to, :cc→,
+            :simulation,
             :clamp_collection, :cc,
-            :cc_point_position,
-            :imc_point_reset,
-            :imc_point_to, :imc→,
             :initial_marking_collection, :imc,
-            :imc_point_position,
-            :ssc_point_reset,
-            :ssc_point_to, :ssc→,
             :simulation_settings_collection, :ssc,
-            :ssc_point_position,
-            :net_selection,
-            :simulation_selection,
-            :ssc_selection,
-            :cc_selection,
-            :imc_selection,
-            :net_selection_clear,
-            :net_select!,
-            :net_select,
-            :net_unselect,
-            :simulation_selection_clear,
-            :simulation_select!,
-            :simulation_select,
-            :simulation_unselect,
-            :cc_selection_clear,
-            :cc_select!,
-            :cc_select,
-            :cc_unselect,
-            :imc_selection_clear,
-            :imc_select!,
-            :imc_select,
-            :imc_unselect,
-            :ssc_selection_clear,
-            :ssc_select!,
-            :ssc_select,
-            :ssc_unselect,
             :clamp,
-            :initial_marking, :im,
-            :set_step, :set_step_size,
-            :set_time, :set_target_time,
-            :set_sampling,
+            :initial_marking,
+            :set_step, :set_time, :set_sampling,
             :set_simulation_method,
             :new_timed_simulation,
             :run!,
@@ -136,6 +108,5 @@ module YPetri
             :plot_selected,
             :plot_state,
             :plot_flux,
-            :plot_all,
             to: :y_petri_manipulator )
 end

data/test/y_petri_test.rb

@@ -302,11 +302,11 @@ describe ::YPetri::Transition do
   describe "6. stoichiometric transitions with rate (SR transitions)" do
     before do
       # now this should give standard mass action by magic:
-      @SR1 = @ç.new s: { @p1 => -1, @p2 => -1, @p4 => 1 }, flux: 0.1
-      # while this has custom flux closure
-      @SR2 = @ç.new s: { @p1 => -1, @p3 => 1 }, flux: λ { |a| a * 0.5 }
+      @SR1 = @ç.new s: { @p1 => -1, @p2 => -1, @p4 => 1 }, rate: 0.1
+      # while this has custom closure
+      @SR2 = @ç.new s: { @p1 => -1, @p3 => 1 }, rate: λ { |a| a * 0.5 }
       # while this one even has domain specified:
-      @SR3 = @ç.new s: { @p1 => -1, @p2 => -1, @p4 => 1 }, upstream_arcs: @p3, flux: λ { |a| a * 0.5 }
+      @SR3 = @ç.new s: { @p1 => -1, @p2 => -1, @p4 => 1 }, upstream_arcs: @p3, rate: λ { |a| a * 0.5 }
     end
 
     it "should init and work" do
@@ -598,13 +598,14 @@ describe ::YPetri::Simulation do
     @p5 = @pç.new name: "P5", default_marking: 5
     @t1 = @tç.new name: "T1",
                   s: { @p1 => -1, @p2 => -1, @p4 => 1 },
-                  flux: 0.1
+                  rate: 0.1
     @t2 = @tç.new name: "T2",
                   s: { @p1 => -1, @p3 => 1 },
-                  flux: λ { |a| a * 0.5 }
+                  rate: λ { |a| a * 0.5 }
     @t3 = @tç.new name: "T3",
                   s: { @p1 => -1, @p2 => -1, @p4 => 1 },
-                  domain: @p3, flux: λ { |a| a * 0.5 }
+                  domain: @p3,
+                  rate: λ { |a| a * 0.5 }
     @net = @nç.new << @p1 << @p2 << @p3 << @p4 << @p5
     @net.include_transition! @t1
     @net.include_transition! @t2
@@ -818,7 +819,7 @@ describe ::YPetri::Simulation do
   it "5. handles sR transitions" do
     assert_equal [], @s.rate_closures_for_sR
     assert_equal [], @s.rate_closures_for_s
-    @s.gradient_for_sR.must_equal Matrix.zero( @s.free_pp.size, 1 )
+    # @s.gradient_for_sR.must_equal Matrix.zero( @s.free_pp.size, 1 )
     @s.Δ_Euler_for_sR( 1.0 ).must_equal Matrix.zero( @s.free_pp.size, 1 )
   end
 
@@ -934,7 +935,7 @@ describe ::YPetri::TimedSimulation do
     end
   end
 
-  describe "timed 'isomerization' with flux given as λ" do
+  describe "timed 'isomerization' with given as λ" do
     before do
       @t2 = ::YPetri::Transition.new s: { @a => -1, @c => 1 },
                                      rate_closure: λ { |a| a * 0.5 }
@@ -1020,9 +1021,9 @@ describe ::YPetri::Workspace do
   it "should present places, transitions, nets, simulations" do
     assert_kind_of ::YPetri::Net, @w.Net::Top
     assert_equal @pp[0], @w.place( "AA" )
-    assert_equal :AA, @w.p( @pp[0] )
+    assert_equal :AA, @w.pl( @pp[0] )
     assert_equal @tt[0], @w.transition( "AA_BB_assembly" )
-    assert_equal :AA_appearing, @w.t( @tt[1] )
+    assert_equal :AA_appearing, @w.tr( @tt[1] )
     assert_equal @pp, @w.places
     assert_equal @tt, @w.transitions
     assert_equal 1, @w.nets.size
@@ -1070,49 +1071,43 @@ describe ::YPetri::Manipulator do
   it "has net basic points" do
     # --- net point related assets ---
     @m.net_point_reset
-    @m.net_point_to @m.workspace.net( :Top )
+    @m.net_point_set @m.workspace.net( :Top )
     @m.net.must_equal @m.workspace.Net::Top
     # --- simulation point related assets ---
-    @m.simulation_point_reset
-    @m.simulation_point_to nil
+    @m.simulation_point.reset
     @m.simulation.must_equal nil
-    @m.simulation_point_position.must_equal nil
+    @m.simulation_point.key.must_equal nil
     # --- cc point related assets ---
-    @m.cc_point_reset
-    @m.cc_point_to :Base
+    @m.cc_point.reset
+    @m.cc_point.set :Base
     @m.cc.must_equal @m.workspace.clamp_collection
     @m.cc.wont_equal :Base
-    @m.cc_point_position.must_equal :Base
+    @m.cc_point.key.must_equal :Base
     # --- imc point related assets ---
-    @m.imc_point_reset
-    @m.imc_point_to :Base
+    @m.imc_point.reset
+    @m.imc_point.set :Base
     @m.imc.must_equal @m.workspace.initial_marking_collection
     @m.imc.wont_equal :Base
-    @m.imc_point_position.must_equal :Base
+    @m.imc_point.key.must_equal :Base
     # --- ssc point related assets ---
-    @m.ssc_point_reset
-    @m.ssc_point_to :Base
+    @m.ssc_point.reset
+    @m.ssc_point.set :Base
     @m.ssc.must_equal @m.workspace.simulation_settings_collection
     @m.ssc.wont_equal :Base
-    @m.ssc_point_position.must_equal :Base
+    @m.ssc_point.key.must_equal :Base
   end
 
   it "has basic selections" do
-    @m.net_selection_clear
-    @m.simulation_selection_clear
-    @m.cc_selection_clear
-    @m.imc_selection_clear
-    @m.ssc_selection_clear
-    @m.net_selection.must_equal []
-    @m.simulation_selection.must_equal []
-    @m.ssc_selection.must_equal []
-    @m.cc_selection.must_equal []
-    @m.imc_selection.must_equal []
-    [ :net, :simulation, :cc, :imc, :ssc ].each { |sym1|
-      [ :select!, :select, :unselect ].each { |sym2|
-        @m.must_respond_to "#{sym1}_#{sym2}"
-      }
-    }
+    @m.net_selection.clear
+    @m.simulation_selection.clear
+    @m.cc_selection.clear
+    @m.imc_selection.clear
+    @m.ssc_selection.clear
+    @m.net_selection.get.must_equal []
+    @m.simulation_selection.get.must_equal []
+    @m.ssc_selection.get.must_equal []
+    @m.cc_selection.get.must_equal []
+    @m.imc_selection.get.must_equal []
   end
 
   it "presents some methods from workspace" do
@@ -1198,7 +1193,7 @@ end
 #     @m.place( :B ).marking = 5
 #     @m.places.map( &:name ).must_equal [:A, :B, :C]
 #     @m.places.map( &:marking ).must_equal [2, 5, 7.77]
-#     @m.transition( :A2B ).connectivity.must_equal [ @m.place( :A ), @m.place( :B ) ]
+#     @m.transition( :A2B ).arcs.must_equal [ @m.place( :A ), @m.place( :B ) ]
 #     @m.transition( :A2B ).fire!
 #     @m.places.map( &:marking ).must_equal [1, 6, 7.77]
 #     @m.transition( :A2B ).fire!
@@ -1228,7 +1223,7 @@ end
 #     @m.net.must_be_kind_of ::YPetri::Net
 #     @m.run!
 #     @m.simulation.must_be_kind_of ::YPetri::TimedSimulation
-#     @m.plot_recording
+#     @m.plot_state
 #     sleep 3
 #   end
 # end
@@ -1369,7 +1364,7 @@ end
 
 #   it "should work" do
 #     @m.run!
-#     @m.plot_recording
+#     @m.plot_state
 #     sleep 3
 #   end
 # end
@@ -1514,7 +1509,7 @@ end
 #     # === Simulation execution
 #     @m.run!
 #     # === Plotting of the results
-#     @m.plot_recording
+#     @m.plot_state
 #     sleep 20
 #   end
 # end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: y_petri
 version: !ruby/object:Gem::Version
-  version: 2.0.2
+  version: 2.0.3
 platform: ruby
 authors:
 - boris
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-05-02 00:00:00.000000000 Z
+date: 2013-05-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: y_support
@@ -70,6 +70,10 @@ files:
 - lib/y_petri/demonstrator_3.rb
 - lib/y_petri/demonstrator_4.rb
 - lib/y_petri/manipulator.rb
+- lib/y_petri/manipulator/hash_key_pointer.rb
+- lib/y_petri/manipulator/petri_net_related_methods.rb
+- lib/y_petri/manipulator/selection.rb
+- lib/y_petri/manipulator/simulation_related_methods.rb
 - lib/y_petri/net.rb
 - lib/y_petri/place.rb
 - lib/y_petri/simulation.rb
@@ -77,10 +81,10 @@ files:
 - lib/y_petri/transition.rb
 - lib/y_petri/version.rb
 - lib/y_petri/workspace.rb
-- lib/y_petri/workspace/instance_methods.rb
 - lib/y_petri/workspace/parametrized_subclassing.rb
+- lib/y_petri/workspace/petri_net_related_methods.rb
+- lib/y_petri/workspace/simulation_related_methods.rb
 - test/simple_manual_examples.rb
-- test/y_petri_graph.png
 - test/y_petri_test.rb
 - y_petri.gemspec
 homepage: ''
@@ -102,11 +106,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.0
+rubygems_version: 2.0.3
 signing_key: 
 specification_version: 4
 summary: a Petri net domain model and simulator
 test_files:
 - test/simple_manual_examples.rb
-- test/y_petri_graph.png
 - test/y_petri_test.rb