Updated to Petriv1 with stochastic differential equations (#10)

.gitignore

@@ -16,6 +16,7 @@ deps/src/
 # Build artifacts for creating documentation generated by the Documenter package
 docs/build/
 docs/site/
+docs/src/examples
 
 # File generated by Pkg, the package manager, based on a corresponding Project.toml
 # It records a fixed state of all packages used by the project. As such, it should not be

Project.toml

@@ -2,7 +2,7 @@ name = "AlgebraicPetri"
 uuid = "4f99eebe-17bf-4e98-b6a1-2c4f205a959b"
 license = "MIT"
 authors = ["Micah Halter <micah@mehalter.com>"]
-version = "0.2.0"
+version = "0.3.0"
 
 [deps]
 AutoHashEquals = "15f4f7f2-30c1-5605-9d31-71845cf9641f"
@@ -12,7 +12,7 @@ Petri = "4259d249-1051-49fa-8328-3f8ab9391c33"
 [compat]
 AutoHashEquals = "0.2.0"
 Catlab = "0.7.0"
-Petri = "0.4.0"
+Petri = "1.0.0"
 julia = "1.0"
 
 [extras]

docs/Project.toml

@@ -6,3 +6,4 @@ Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Petri = "4259d249-1051-49fa-8328-3f8ab9391c33"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"

examples/covid/Project.toml

@@ -4,3 +4,4 @@ Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Petri = "4259d249-1051-49fa-8328-3f8ab9391c33"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"

examples/covid/_generate_figs.jl

@@ -1,6 +1,7 @@
 # +
 include("epidemiology.jl")
 
+using OrdinaryDiffEq
 using Catlab.Graphics.Graphviz: run_graphviz
 
 # +
@@ -46,7 +47,7 @@ save_graph(Graph(p_sir), "sir_graph.svg")
 u0 = [10.0, 1, 0]
 p = [0.4, 0.4]
 # create and solve ODE problem
-prob = ODEProblem(vectorfields(p_sir),u0,(0.0,7.5),p)
+prob = ODEProblem(p_sir,u0,(0.0,7.5),p)
 sol = OrdinaryDiffEq.solve(prob,Tsit5())
 # visualize the solution
 splot(sol, "sir_soln.svg")
@@ -58,7 +59,7 @@ save_graph(Graph(p_seir), "seir_graph.svg")
 u0 = [10.0, 1, 0, 0]
 p = [0.9, 0.2, 0.5]
 # create and solve ODE problem
-prob = ODEProblem(vectorfields(p_seir),u0,(0.0,15.0),p)
+prob = ODEProblem(p_seir,u0,(0.0,15.0),p)
 sol = OrdinaryDiffEq.solve(prob,Tsit5())
 # visualize the solution
 splot(sol, "seir_soln.svg")
@@ -70,7 +71,7 @@ save_graph(Graph(p_seird), "seird_graph.svg")
 u0 = [10.0, 1, 0, 0, 0]
 p = [0.9, 0.2, 0.5, 0.1]
 # create and solve ODE problem
-prob = ODEProblem(vectorfields(p_seird),u0,(0.0,15.0),p)
+prob = ODEProblem(p_seird,u0,(0.0,15.0),p)
 sol = OrdinaryDiffEq.solve(prob,Tsit5())
 # visualize the solution
 splot(sol, "seird_soln.svg")
@@ -100,7 +101,7 @@ u0[2]  = 1
 # Define transition rates
 params = seirdparams(3, 5)
 # Generate and solve resulting ODE
-prob = ODEProblem(vectorfields(p_seird_3),u0,tspan,params)
+prob = ODEProblem(p_seird_3,u0,tspan,params)
 sol = OrdinaryDiffEq.solve(prob,Tsit5())
 splotchannels(sol, "seird")
 
@@ -109,7 +110,7 @@ function drawsol(f, a, b, p, dir)
     println("INFO: Processing $dir")
     dynparams = waveparams(f, a/sum(u0), b/sum(u0),p)
     mkpath(dir)
-    prob = ODEProblem(vectorfields(p_seird_3),u0,tspan, dynparams)
+    prob = ODEProblem(p_seird_3,u0,tspan, dynparams)
     sol = OrdinaryDiffEq.solve(prob,Tsit5(), saveat=1:1:tspan[2])
     splotchannels(sol, dir)
     savefig(plot(sol.t, f(a,b,p), ylim=(0,12), legend=false, linewidth=5), "$dir/transmissability.svg")

examples/covid/covid.jl

@@ -15,7 +15,6 @@ using Catlab.Programs
 using Catlab.CategoricalAlgebra.ShapeDiagrams
 using Catlab.WiringDiagrams
 using Catlab.Graphics
-using Catlab.Graphics.Graphviz: Graph
 
 import Catlab.Theories: id
 
@@ -95,8 +94,8 @@ params = seirdparams(3, 5);
 
 # Generate, solve, and visualize resulting ODE
 
-prob = ODEProblem(vectorfields(p_seird_3),u0,tspan,params);
-sol = OrdinaryDiffEq.solve(prob,Tsit5());
+prob = ODEProblem(p_seird_3,u0,tspan,params);
+sol = solve(prob,Tsit5());
 
 plot(sol)
 
@@ -126,7 +125,7 @@ a,b,p = 10, 1, 1/6
 
 dynparams = waveparams(asymptotic, a/sum(u0), b/sum(u0),p)
 
-prob = ODEProblem(vectorfields(p_seird_3),u0,tspan, dynparams)
-sol = OrdinaryDiffEq.solve(prob,Tsit5(), saveat=1:1:tspan[2])
+prob = ODEProblem(p_seird_3,u0,tspan, dynparams)
+sol = solve(prob,Tsit5(), saveat=1:1:tspan[2])
 
-plot(sol)
+plot(sol)

examples/covid/epidemiology.jl

@@ -5,13 +5,12 @@
 using AlgebraicPetri.Epidemiology
 
 using Petri
-using OrdinaryDiffEq
+using StochasticDiffEq
 using Plots
 
 using Catlab.Theories
 using Catlab.CategoricalAlgebra.ShapeDiagrams
 using Catlab.Graphics
-using Catlab.Graphics.Graphviz: Graph
 
 display_wd(ex) = to_graphviz(ex, orientation=LeftToRight, labels=true);
 
@@ -34,8 +33,8 @@ Graph(p_sir)
 u0 = [10.0, 1, 0];
 p = [0.4, 0.4];
 
-prob = ODEProblem(vectorfields(p_sir),u0,(0.0,7.5),p);
-sol = OrdinaryDiffEq.solve(prob,Tsit5());
+prob,cb = SDEProblem(p_sir,u0,(0.0,7.5),p);
+sol = solve(prob,SRA1(),callback=cb)
 
 plot(sol)
 
@@ -61,8 +60,8 @@ Graph(p_seir)
 u0 = [10.0, 1, 0, 0];
 p = [0.9, 0.2, 0.5];
 
-prob = ODEProblem(vectorfields(p_seir),u0,(0.0,15.0),p);
-sol = OrdinaryDiffEq.solve(prob,Tsit5());
+prob,cb = SDEProblem(p_seir,u0,(0.0,15.0),p);
+sol = solve(prob,SRA1(),callback=cb)
 
 plot(sol)
 
@@ -86,7 +85,7 @@ Graph(p_seird)
 u0 = [10.0, 1, 0, 0, 0];
 p = [0.9, 0.2, 0.5, 0.1];
 
-prob = ODEProblem(vectorfields(p_seird),u0,(0.0,15.0),p);
-sol = OrdinaryDiffEq.solve(prob,Tsit5());
+prob,cb = SDEProblem(p_seird,u0,(0.0,15.0),p);
+sol = solve(prob,SRA1(),callback=cb)
 
-plot(sol)
+plot(sol)

examples/predation/lotka-volterra.jl

@@ -14,7 +14,6 @@ using Catlab.Programs
 using Catlab.CategoricalAlgebra.ShapeDiagrams
 using Catlab.WiringDiagrams
 using Catlab.Graphics
-using Catlab.Graphics.Graphviz: Graph
 
 display_wd(ex) = to_graphviz(ex, orientation=LeftToRight, labels=true);
 
@@ -58,8 +57,8 @@ Graph(lotka_petri)
 
 u0 = [40, 2];
 p = [4.0, 1.0, 2.0];
-prob = ODEProblem(vectorfields(lotka_petri),u0,(0.0,8.0),p);
-sol = OrdinaryDiffEq.solve(prob,Tsit5(),abstol=1e-6);
+prob = ODEProblem(lotka_petri,u0,(0.0,8.0),p);
+sol = solve(prob,Tsit5(),abstol=1e-6);
 plot(sol)
 
 # There is also a second syntax that is easier to write for programmers
@@ -108,6 +107,6 @@ Graph(dual_lv_petri)
 
 u0 = [40, 2, 1];
 p = [4.0, 1.0, 2.0, 2.5, 1.5];
-prob = ODEProblem(vectorfields(dual_lv_petri),u0,(0.0,8.0),p);
-sol = OrdinaryDiffEq.solve(prob,Tsit5(),abstol=1e-6);
+prob = ODEProblem(dual_lv_petri,u0,(0.0,8.0),p);
+sol = solve(prob,Tsit5(),abstol=1e-6);
 plot(sol)

src/AlgebraicPetri.jl

@@ -104,8 +104,6 @@ function (::Type{PetriCospan})(l::AbstractVector, m::Petri.Model, r::AbstractVec
                        id(PetriFunctor), m)
 end
 
-NullPetri(n::Int) = Petri.Model(collect(1:n), Vector{Tuple{Dict{Int, Number}, Dict{Int, Number}}}())
-
 @instance BiproductCategory(PetriCospanOb, PetriCospan) begin
     dom(f::PetriCospan) = PetriCospanOb(dom(left(f)).n)
     codom(f::PetriCospan) = PetriCospanOb(dom(right(f)).n)
@@ -126,7 +124,7 @@ NullPetri(n::Int) = Petri.Model(collect(1:n), Vector{Tuple{Dict{Int, Number}, Di
     id(X::PetriCospanOb) = PetriCospan(
         Cospan(id(FinOrd(X.n)), id(FinOrd(X.n))),
         id(PetriFunctor),
-        NullPetri(X.n))
+        EmptyPetri(X.n))
 
     otimes(X::PetriCospanOb, Y::PetriCospanOb) = PetriCospanOb(X.n + Y.n)
 
@@ -153,28 +151,28 @@ NullPetri(n::Int) = Petri.Model(collect(1:n), Vector{Tuple{Dict{Int, Number}, Di
             Cospan(
                 id(FinOrd(Z.n)),
                 FinOrdFunction(vcat(X.n+1:Z.n, 1:X.n), Z.n, Z.n)
-            ), id(PetriFunctor), NullPetri(Z.n))
+            ), id(PetriFunctor), EmptyPetri(Z.n))
     end
 
     mcopy(X::PetriCospanOb) = PetriCospan(
         Cospan(
             id(FinOrd(X.n)),
             FinOrdFunction(vcat(1:X.n,1:X.n), 2*X.n, X.n)
-        ), id(PetriFunctor), NullPetri(X.n))
+        ), id(PetriFunctor), EmptyPetri(X.n))
 
     mmerge(X::PetriCospanOb) = PetriCospan(
         Cospan(
             FinOrdFunction(vcat(1:X.n,1:X.n), 2*X.n, X.n),
             id(FinOrd(X.n))
-        ), id(PetriFunctor), NullPetri(X.n))
+        ), id(PetriFunctor), EmptyPetri(X.n))
 
     create(X::PetriCospanOb) = PetriCospan(
         Cospan(FinOrdFunction(Int[], 0, X.n), id(FinOrd(X.n))),
-        id(PetriFunctor), NullPetri(X.n))
+        id(PetriFunctor), EmptyPetri(X.n))
 
     delete(X::PetriCospanOb) = PetriCospan(
         Cospan(id(FinOrd(X.n)), FinOrdFunction(Int[], 0, X.n)),
-        id(PetriFunctor), NullPetri(X.n))
+        id(PetriFunctor), EmptyPetri(X.n))
 
     pair(f::PetriCospan, g::PetriCospan) = compose(mcopy(dom(f)), otimes(f, g))
     copair(f::PetriCospan, g::PetriCospan) = compose(otimes(f, g), mmerge(codom(f)))