remove parametric types

Author: isaacsas

src/systems/reaction/reactionsystem.jl

@@ -69,12 +69,12 @@ function Reaction(rate, subs, prods, substoich, prodstoich;
       (isnothing(prodstoich)&&isnothing(substoich)) && error("Both substrate and product stochiometry inputs cannot be nothing.")
       if isnothing(subs)
         subs = Vector{Operation}()
-        isnothing(substoich) && error("If substrates are nothing, substrate stiocihometries have to be so too.")
+        !isnothing(substoich) && error("If substrates are nothing, substrate stiocihometries have to be so too.")
         substoich = typeof(prodstoich)()
     end
     if isnothing(prods)
         prods = Vector{Operation}()
-        isnothing(prodstoich) && error("If products are nothing, product stiocihometries have to be so too.")
+        !isnothing(prodstoich) && error("If products are nothing, product stiocihometries have to be so too.")
         prodstoich = typeof(substoich)()
     end
     ns = isnothing(netstoich) ? get_netstoich(subs, prods, substoich, prodstoich) : netstoich
@@ -120,15 +120,15 @@ Continuing from the example in the [`Reaction`](@ref) definition:
 rs = ReactionSystem(rxs, t, [A,B,C,D], k)
 ```
 """
-struct ReactionSystem{U,V,W,X} <: AbstractSystem
+struct ReactionSystem <: AbstractSystem
     """The reactions defining the system."""
-    eqs::Vector{Reaction{U,V}}
+    eqs::Vector{Reaction}
     """Independent variable (usually time)."""
-    iv::Variable{X}
+    iv::Variable
     """Dependent (state) variables representing amount of each species."""
-    states::Vector{Variable{W}}
+    states::Vector{Variable}
     """Parameter variables."""
-    ps::Vector{Variable{X}}
+    ps::Vector{Variable}
     """The name of the system"""
     name::Symbol
     """systems: The internal systems"""

test/reactionsystem.jl

@@ -84,9 +84,12 @@ G2 = sf.g(u,p,t)
 # test with JumpSystem
 js = convert(JumpSystem, rs)
 
-@test all(map(i -> typeof(js.eqs[i]) <: DiffEqJump.MassActionJump, [1]))
-@test all(map(i -> typeof(js.eqs[i]) <: DiffEqJump.ConstantRateJump, 2:5))
-@test all(map(i -> typeof(js.eqs[i]) <: DiffEqJump.VariableRateJump, 6:7))
+midxs = 1:14
+cidxs = 15:18
+vidxs = 19:20
+@test all(map(i -> typeof(js.eqs[i]) <: DiffEqJump.MassActionJump, midxs))
+@test all(map(i -> typeof(js.eqs[i]) <: DiffEqJump.ConstantRateJump, cidxs))
+@test all(map(i -> typeof(js.eqs[i]) <: DiffEqJump.VariableRateJump, vidxs))
 
 pars = rand(length(k)); u0 = rand(1:10,4); time = rand();
 jumps = Vector{Union{ConstantRateJump, MassActionJump, VariableRateJump}}(undef,length(rxs))
@@ -116,21 +119,21 @@ jumps[20] = VariableRateJump((u,p,t) -> p[20]*t*u[1]*binomial(u[2],2)*u[3], inte
 
 statetoid = Dict(convert(Variable,state) => i for (i,state) in enumerate(states(js)))
 parammap = map((x,y)->Pair(x(),y),parameters(js),pars)
-maj = MT.assemble_maj(js.eqs[1], statetoid, ModelingToolkit.substituter(first.(parammap), last.(parammap)),eltype(pars))
-for i = 1:14
-  @test abs(jumps[i].scaled_rates - maj.scaled_rates[i]) < 100*eps()
-  @test jumps[i].reactant_stoch == maj.reactant_stoch[i]
-  @test jumps[i].net_stoch == maj.net_stoch[i]
+for i in midxs
+  maj = MT.assemble_maj(js.eqs[i], statetoid, ModelingToolkit.substituter(parammap),eltype(pars))
+  @test abs(jumps[i].scaled_rates - maj.scaled_rates) < 100*eps()
+  @test jumps[i].reactant_stoch == maj.reactant_stoch
+  @test jumps[i].net_stoch == maj.net_stoch
 end
-for i = 15:18
-  crj = MT.assemble_crj(js, js.eqs[i-13], statetoid)
+for i in cidxs
+  crj = MT.assemble_crj(js, js.eqs[i], statetoid)
   @test isapprox(crj.rate(u0,p,time), jumps[i].rate(u0,p,time))
   fake_integrator1 = (u=zeros(4),p=p,t=0); fake_integrator2 = deepcopy(fake_integrator1);
   crj.affect!(fake_integrator1); jumps[i].affect!(fake_integrator2);
   @test fake_integrator1 == fake_integrator2
 end
-for i = 19:20
-  crj = MT.assemble_vrj(js, js.eqs[i-13], statetoid)
+for i in vidxs
+  crj = MT.assemble_vrj(js, js.eqs[i], statetoid)
   @test isapprox(crj.rate(u0,p,time), jumps[i].rate(u0,p,time))
   fake_integrator1 = (u=zeros(4),p=p,t=0.); fake_integrator2 = deepcopy(fake_integrator1);
   crj.affect!(fake_integrator1); jumps[i].affect!(fake_integrator2);