ENH: add documentation for AlgebraicPetri

Integration

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 +1,19 @@
+# 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
+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)
+````

ext/AlgebraicDynamicsAlgebraicPetriExt.jl

@@ -6,25 +6,33 @@ using Catlab
 using LabelledArrays
 import AlgebraicDynamics.UWDDynam: ContinuousResourceSharer
 
+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 vf(pn::OpenPetriNet,T::Type,ns::Int64)
+function dynamics(pn::OpenPetriNet,T::Type,ns::Int64)
   vf(u, p, t) = vectorfield(apex(pn))(zeros(T,ns), u, p, t)
 end
 
-function vf(pn::OpenLabelledPetriNet,T::Type,ns::Int64)
+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 vf(pn::OpenLabelledReactionNet,T::Type,ns::Int64)
+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::Union{OpenPetriNet,OpenLabelledPetriNet,OpenLabelledReactionNet}) where T
+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, vf(pn,T,nstates), portmap)
+  ContinuousResourceSharer{T}(nports, nstates, dynamics(pn,T,nstates), portmap)
 end
 end