Merge pull request #47 from korsbo/function_overload

Function overload

Author: ChrisRackauckas

REQUIRE

@@ -1,5 +1,5 @@
 julia 0.6
-DiffEqJump 1.0.0
+DiffEqJump 4.2.0
 DiffEqBase 3.4.0
 Compat 0.17.0
 DataStructures 0.4.6

src/DiffEqBiological.jl

@@ -17,7 +17,7 @@ include("maketype.jl")
 include("problem.jl")
 
 export @reaction_network, @reaction_func
-export ODEProblem, SDEProblem, JumpProblem, SteadyStateProblem
+export SDEProblem, JumpProblem, SteadyStateProblem
 
 Reaction(args...) = error("""
  The old Reaction DSL is deprecated for a new

src/problem.jl

@@ -1,10 +1,6 @@
-### ODEProblem ###
-DiffEqBase.ODEProblem(rn::AbstractReactionNetwork, args...; kwargs...) =
-    ODEProblem(rn.f, args...; kwargs...)
-
 ### SDEProblem ###
-DiffEqBase.SDEProblem(rn::AbstractReactionNetwork, args...; kwargs...) =
-    SDEProblem(rn.f,rn.g, args...;noise_rate_prototype=rn.p_matrix, kwargs...)
+DiffEqBase.SDEProblem(rn::AbstractReactionNetwork, u0::Union{AbstractArray, Number}, args...; kwargs...) =
+    SDEProblem(rn, rn.g, u0, args...;noise_rate_prototype=rn.p_matrix, kwargs...)
 
 ### JumpProblem ###
 function DiffEqJump.JumpProblem(prob,aggregator::Direct,rn::AbstractReactionNetwork; kwargs...)

src/reaction_network.jl

@@ -110,6 +110,14 @@ function coordinate(name, ex::Expr, p, scale_noise)
     push!(exprs,typeex)
     push!(exprs,constructorex)
 
+    ## Overload the type so that it can act as a function.
+    overloadex = :(((f::$name))(du, u, p, t::Number) = f.f(du, u, p, t)) |> esc
+    push!(exprs,overloadex)
+
+    ## Add a method which allocates the `du` and returns it instead of being inplace
+    overloadex = :(((f::$name))(u,p,t::Number) = (du=similar(u); f(du,u,p,t); du)) |> esc
+    push!(exprs,overloadex)
+
     # export type constructor
     def_const_ex = :(($name)()) |> esc
     push!(exprs,def_const_ex)

test/REQUIRE

@@ -1,3 +1,3 @@
 OrdinaryDiffEq
 StochasticDiffEq
-SteadyStateDiffEq
+SteadyStateDiffEq 0.4.0

test/solver_test.jl

@@ -41,3 +41,5 @@ sol1 = solve(prob1,Tsit5())
 prob2 = ODEProblem(equi_model,[100.],(0.,200.))
 sol2 = solve(prob2,Tsit5())
 @test 1.5*sol1[end][1] < sol2[end][1]
+
+@test sol1.prob.f isa AbstractReactionNetwork