y_petri 2.1.18 → 2.1.20

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data/README.md

@@ -1,26 +1,93 @@
 # YPetri
 
-y_petri is a Petri net domain model and simulator
+`YPetri` is a domain model and a simulator of _functional_ _Petri_ _nets_,
+a family of Petri nets, whose transitions have functions attached to them.
 
-## Installation
-
-Add this line to your application's Gemfile:
-
-    gem 'y_petri'
-
-And then execute:
-
-    $ bundle
+## Usage
 
-Or install it yourself as:
+`YPetri` provides a _domain_ _specific_ _language_ (DSL), that can be loaded by:
+```ruby
+  require 'y_petri'
+  include YPetri
+```
+Now, one can create places:
+```ruby
+  A = Place()
+  B = Place()
+  places.names # you can shorten this to #pn
+  #=> [:A, :B]
+  # Setting their marking:
+  A.marking = 2
+  B.marking = 5
+```
+And transitions:
+```ruby
+  A2B = Transition stoichiometry: { A: -1, B: 1 }
+  #=> #<Transition: A2B (tS) >
+  A2B.stoichiometry
+  #=> [-1, 1]
+  A2B.s
+  #=> {:A=>-1, :B=>1}
+  A2B.arcs.names
+  #=> [:A, :B]
+  A2B.timeless?
+  #=> true
+  A2B.enabled?
+  #=> true
+```
+Explanation of the keywords: _arcs_, _enabled_ are standard Petri net terms,
+_stoichiometry_ means arcs with the amount of tokens to add / take from the
+connected places when the transition fires, _timeless_ means that firing of
+the transition is not defined in time.
 
-    $ gem install y_petri
+We can now play the _token_ _game_:
+```ruby
+  places.map &:marking
+  #=> [2, 5]
+  A2B.fire!
+  places.map &:marking
+  #=> [1, 6]
+  A2B.fire!
+  places.map &:marking
+  #=> [0, 7]
+```
 
-## Usage
+## Advanced usage
 
-y_petri can be used either interactively (in irb with
-'include YPetri'), or from another program. YPetri::Manipulator
-provides the command interface.
+A Petri net is mostly used as a wiring diagram of some real-world system. Such
+Petri net can then be used to generate (implicitly or explicitly) a more specific
+simulation of that real-world system. This is represented by `YPetri::Simulation`
+class. If a Petri net with only _timed_ transitions is considered, it can then
+be used to generate (implicitly or explicitly) a system of ordinary differential
+equations (ODE). A Simulation class instance generated from such Petri net can
+then be used to eg. solve the initial value problem by numeric integration of the
+ODE system using one of the available numerical methods:
+```ruby
+  # Start a fresh irb session!
+  require 'y_petri'
+  include YPetri
+  A = Place default_marking: 0.5
+  B = Place default_marking: 0.5
+  A_pump = Transition s: { A: -1 }, rate: proc { 0.005 }
+  B_decay = Transition s: { B: -1 }, rate: 0.05
+  net
+  #=> #<Net: name: Top, 2pp, 2tt >
+  run!
+```
+Simulation can now be accessed through `simulation` DSL method:
+```ruby
+  simulation
+  #=> #<Simulation: time: 60, pp: 2, tt: 2, oid: -XXXXXXXXX>
+  simulation.settings
+  #=> {:method=>:pseudo_euler, :guarded=>false, :step=>0.1, :sampling=>5, :time=>0..60}
+  print_recording
+```
+If you have `gnuplot` gem installed properly, you can view plots:
+```ruby
+  plot_state
+  plot_flux
+```
+So much for the demo for now! Thanks for trying YPetri!
 
 ## Contributing
 

data/lib/y_petri/net/data_set.rb

@@ -252,4 +252,12 @@ class YPetri::Net::DataSet < Hash
   def inspect
     to_s
   end
+
+  # Pretty print the dataset.
+  # 
+  def print precision: 4, distance: precision + 4
+    features.labels.print_as_line precision: precision, distance: distance
+    puts '-' * features.size * distance
+    records.each.print_as_line precision: precision, distance: distance
+  end
 end # YPetri::Net::Dataset

data/lib/y_petri/simulation.rb

@@ -1,4 +1,4 @@
-#encoding: utf-8
+# encoding: utf-8
 
 require_relative 'simulation/matrix'
 require_relative 'simulation/dependency'

data/lib/y_petri/version.rb

@@ -1,4 +1,4 @@
 module YPetri
-  VERSION = "2.1.18"
+  VERSION = "2.1.20"
   DEBUG = false
 end

data/test/simulation_test.rb

@@ -119,7 +119,7 @@ describe YPetri::Simulation do
             @sim.ts_tt.first.domain.names.must_equal []
             @sim.timed?.must_equal false
             @sim.m.must_equal [1, 2]
-            @sim.pm.must_equal( { A: 1, B: 2 } )
+            @sim.p_m.must_equal( { A: 1, B: 2 } )
             @sim.recording.must_equal( { 0 => [1, 2]} )
             @sim.simulation_method.must_equal :pseudo_euler
             @sim.core.must_be_kind_of YPetri::Core
@@ -133,7 +133,7 @@ describe YPetri::Simulation do
             cl = @sim.send( :transitions ).ts.delta_closure
             cl.call.must_equal Matrix[ [1], [0] ]
             @sim.step!
-            @sim.pm.must_equal( { A: 2, B: 2 } ) # marking of A goes up by 1
+            @sim.p_m.must_equal( { A: 2, B: 2 } ) # marking of A goes up by 1
             @sim.recording.must_equal( { 0 => [1, 2], 1 => [2, 2] } )
           end
         end
@@ -277,7 +277,8 @@ describe "timeless simulation" do
       .must_equal [2.5, 4.5]
     -> { ds.interpolate( 1.5 ) }.must_raise TypeError
     ds.reconstruct( event: 2 )
-      .pm.must_equal( { U: 2.5, V: 4.5 } )
+      .p_m.must_equal( { U: 2.5, V: 4.5 } )
+    ds.reconstruct( event: 2 ).must_respond_to( :pm )
     ds.marking.slice( 2..4 ).series
       .must_equal [[2.5, 2.5, 2.5], [4.5, 5.5, 6.5]]
     ds.marking.slice( 2..4 )

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: y_petri
 version: !ruby/object:Gem::Version
-  version: 2.1.18
+  version: 2.1.20
 platform: ruby
 authors:
 - boris