added labelled petri/reaction net compatibility

docs/make.jl

@@ -67,6 +67,7 @@ makedocs(
       "examples/Ross-Macdonald.md"
     ],
     "Threshold Linear Networks" => "TLN.md",
+    "AlgebraicPetri Integration" => "AlgebraicPetri.md",
     "Library Reference" => "api.md"
   ]
 )

docs/src/AlgebraicPetri.md

@@ -0,0 +1,27 @@
+# AlgebraicPetri.jl Integration
+
+You can construct a [`ContinuousResourceSharer`](@ref) from an Open Petri Net for any kind of network supported by AlgebraicPetri.jl including:
+
+1. OpenPetriNet
+2. OpenLabelledPetriNet
+3. OpenLabelledReactionNet
+
+````@example AlgPetri
+using AlgebraicPetri
+using AlgebraicDynamics
+Brusselator = LabelledPetriNet([:A, :B, :D, :E, :X, :Y],
+  :t1 => (:A => (:X, :A)),
+  :t2 => ((:X, :X, :Y) => (:X, :X, :X)),
+  :t3 => ((:B, :X) => (:Y, :D, :B)),
+  :t4 => (:X => :E)
+)
+````
+
+You just call the constructor for ContinuousResourceSharer on an Open Petri Net. 
+The constructor knows where to use labels or integers for the state variables.
+It also knows to get parameters from the ReactionNet and enclose them into the dynamics.
+
+````@example AlgPetri
+open_bruss = Open([:A, :D], Brusselator, [:A, :B])
+rs = ContinuousResourceSharer{Float64}(open_bruss)
+````

ext/AlgebraicDynamicsAlgebraicPetriExt.jl

@@ -3,17 +3,36 @@ module AlgebraicDynamicsAlgebraicPetriExt
 using AlgebraicPetri
 using AlgebraicDynamics
 using Catlab
+using LabelledArrays
 import AlgebraicDynamics.UWDDynam: ContinuousResourceSharer
 
-function ContinuousResourceSharer{T}(pn::Union{OpenPetriNet, OpenLabelledPetriNet}) where T
-    nstates = nparts(apex(pn), :S)
-    portmap = vcat(map(legs(pn)) do f
-      f[:S](parts(dom(f), :S))
-    end...)
-    nports = length(portmap)
-    vf(u, p, t) = vectorfield(apex(pn))(zeros(nstates), u, p, t)
-
-    ContinuousResourceSharer{T}(nports, nstates, vf, portmap)
-  end
+export OpenNet
 
+"""    OpenNet=Union{OpenPetriNet,OpenLabelledPetriNet,OpenLabelledReactionNet}
+
+A type alias for any kind of open network from AlgebraicPetri.
+"""
+const OpenNet = Union{OpenPetriNet,OpenLabelledPetriNet,OpenLabelledReactionNet}
+
+# vecfields need to be initialized differently depending on type of net
+function dynamics(pn::OpenPetriNet,T::Type,ns::Int64)
+  vf(u, p, t) = vectorfield(apex(pn))(zeros(T,ns), u, p, t)
+end
+
+function dynamics(pn::OpenLabelledPetriNet,T::Type,ns::Int64)
+  vf(u, p, t) = vectorfield(apex(pn))(LVector(NamedTuple{tuple(snames(apex(pn))...)}(zeros(T,ns))), u, p, t)
+end
+
+function dynamics(pn::OpenLabelledReactionNet,T::Type,ns::Int64)
+  vf(u, p, t) = vectorfield(apex(pn))(LVector(NamedTuple{tuple(snames(apex(pn))...)}(zeros(T,ns))), u, rates(apex(pn)), t)
+end
+
+function ContinuousResourceSharer{T}(pn::OpenNet) where T
+  nstates = nparts(apex(pn), :S)
+  portmap = vcat(map(legs(pn)) do f
+    f[:S](parts(dom(f), :S))
+  end...)
+  nports = length(portmap)
+  ContinuousResourceSharer{T}(nports, nstates, dynamics(pn,T,nstates), portmap)
+end
 end

test/ext/AlgebraicPetri.jl

@@ -2,26 +2,48 @@ using AlgebraicDynamics
 using AlgebraicPetri
 using Catlab
 using Test
+using AlgebraicDynamics.UWDDynam
+using LabelledArrays
 
-@testset "AlgebraicPetri" begin 
-    birth_petri = Open(PetriNet(1, 1=>(1,1)));
-    rs = ContinuousResourceSharer{Float64}(birth_petri)
-    @test nstates(rs) == 1
-    @test nports(rs) == 1
-    @test portmap(rs) == [1]
-    u = [1.0]; p = [2.0];
-    @test eval_dynamics(rs, u, p, 0) == [2.0]
-
-    Brusselator= LabelledPetriNet([:A, :B, :D, :E, :X, :Y], 
-      :t1 => (:A => (:X, :A)),
-      :t2 => ((:X, :X, :Y) => (:X, :X, :X)),
-      :t3 => ((:B, :X) => (:Y, :D, :B)),
-      :t4 => (:X => :E)
-    )
-
-    open_bruss = Open([:A, :D], Brusselator, [:A, :B])
-    rs = ContinuousResourceSharer{Float64}(open_bruss)
-    @test nstates(rs) == 6
-    @test nports(rs) == 4
-    @test portmap(rs) == [1,3, 1,2]
-  end
+
+@testset "AlgebraicPetri" begin
+  birth_petri = Open(PetriNet(1, 1 => (1, 1)))
+  rs = ContinuousResourceSharer{Float64}(birth_petri)
+  @test nstates(rs) == 1
+  @test nports(rs) == 1
+  @test portmap(rs) == [1]
+  u = [1.0]
+  p = [2.0]
+  @test eval_dynamics(rs, u, p, 0) == [2.0]
+
+  labelled_birth_petri = Open(LabelledPetriNet([:foo], (:bar, (:foo => (:foo, :foo)))))
+  rs = ContinuousResourceSharer{Float64}(labelled_birth_petri)
+  @test nstates(rs) == 1
+  @test nports(rs) == 1
+  @test portmap(rs) == [1]
+  u = LVector(foo=1.0)
+  p = LVector(bar=2.0)
+  @test eval_dynamics(rs, u, p, 0) == [2.0]
+
+  labelled_birth_react = Open(LabelledReactionNet{Float64}{Float64}([:foo => 1.0], ((:bar => 2.0), (:foo => (:foo, :foo)))))
+  rs = ContinuousResourceSharer{Float64}(labelled_birth_react)
+  @test nstates(rs) == 1
+  @test nports(rs) == 1
+  @test portmap(rs) == [1]
+  u = LVector(NamedTuple(zip(snames(apex(labelled_birth_react)), Vector(subpart(apex(labelled_birth_react), :concentration)))))
+  p = LVector(bar=2.0)
+  @test eval_dynamics(rs, u, p, 0) == [2.0]
+
+  Brusselator = LabelledPetriNet([:A, :B, :D, :E, :X, :Y],
+    :t1 => (:A => (:X, :A)),
+    :t2 => ((:X, :X, :Y) => (:X, :X, :X)),
+    :t3 => ((:B, :X) => (:Y, :D, :B)),
+    :t4 => (:X => :E)
+  )
+
+  open_bruss = Open([:A, :D], Brusselator, [:A, :B])
+  rs = ContinuousResourceSharer{Float64}(open_bruss)
+  @test nstates(rs) == 6
+  @test nports(rs) == 4
+  @test portmap(rs) == [1, 3, 1, 2]
+end