Fix broken Liouville transform test/documentation

Author: hersle

src/systems/diffeqs/basic_transformations.jl

@@ -14,26 +14,20 @@ the final value of `trJ` is the probability of ``u(t)``.
 Example:
 
 ```julia
-using ModelingToolkit, OrdinaryDiffEq, Test
+using ModelingToolkit, OrdinaryDiffEq
 
 @independent_variables t
 @parameters α β γ δ
 @variables x(t) y(t)
 D = Differential(t)
+eqs = [D(x) ~ α*x - β*x*y, D(y) ~ -δ*y + γ*x*y]
+@named sys = ODESystem(eqs, t)
 
-eqs = [D(x) ~ α*x - β*x*y,
-       D(y) ~ -δ*y + γ*x*y]
-
-sys = ODESystem(eqs)
 sys2 = liouville_transform(sys)
-@variables trJ
-
-u0 = [x => 1.0,
-      y => 1.0,
-      trJ => 1.0]
-
-prob = ODEProblem(complete(sys2),u0,tspan,p)
-sol = solve(prob,Tsit5())
+sys2 = complete(sys2)
+u0 = [x => 1.0, y => 1.0, sys2.trJ => 1.0]
+prob = ODEProblem(sys2, u0, tspan, p)
+sol = solve(prob, Tsit5())
 ```
 
 Where `sol[3,:]` is the evolution of `trJ` over time.
@@ -46,14 +40,14 @@ Optimal Transport Approach
 Abhishek Halder, Kooktae Lee, and Raktim Bhattacharya
 https://abhishekhalder.bitbucket.io/F16ACC2013Final.pdf
 """
-function liouville_transform(sys::AbstractODESystem)
+function liouville_transform(sys::AbstractODESystem; kwargs...)
     t = get_iv(sys)
     @variables trJ
     D = ModelingToolkit.Differential(t)
     neweq = D(trJ) ~ trJ * -tr(calculate_jacobian(sys))
     neweqs = [equations(sys); neweq]
     vars = [unknowns(sys); trJ]
-    ODESystem(neweqs, t, vars, parameters(sys), checks = false)
+    ODESystem(neweqs, t, vars, parameters(sys); checks = false, name = nameof(sys), kwargs...)
 end
 
 function change_independent_variable(sys::AbstractODESystem, iv, eq = nothing; verbose = false, kwargs...)

test/basic_transformations.jl

@@ -1,37 +1,29 @@
 using ModelingToolkit, OrdinaryDiffEq, Test
 
 @independent_variables t
-@parameters α β γ δ
-@variables x(t) y(t)
 D = Differential(t)
 
-eqs = [D(x) ~ α * x - β * x * y,
-    D(y) ~ -δ * y + γ * x * y]
+@testset "Liouville transform" begin
+    @parameters α β γ δ
+    @variables x(t) y(t)
+    eqs = [D(x) ~ α * x - β * x * y, D(y) ~ -δ * y + γ * x * y]
+    @named sys = ODESystem(eqs, t)
+    sys = complete(sys)
 
-sys = ODESystem(eqs)
+    u0 = [x => 1.0, y => 1.0]
+    p = [α => 1.5, β => 1.0, δ => 3.0, γ => 1.0]
+    tspan = (0.0, 10.0)
+    prob = ODEProblem(sys, u0, tspan, p)
+    sol = solve(prob, Tsit5())
 
-u0 = [x => 1.0,
-    y => 1.0]
+    sys2 = liouville_transform(sys)
+    sys2 = complete(sys2)
 
-p = [α => 1.5,
-    β => 1.0,
-    δ => 3.0,
-    γ => 1.0]
-
-tspan = (0.0, 10.0)
-prob = ODEProblem(sys, u0, tspan, p)
-sol = solve(prob, Tsit5())
-
-sys2 = liouville_transform(sys)
-@variables trJ
-
-u0 = [x => 1.0,
-    y => 1.0,
-    trJ => 1.0]
-
-prob = ODEProblem(sys2, u0, tspan, p, jac = true)
-sol = solve(prob, Tsit5())
-@test sol[end, end] ≈ 1.0742818931017244
+    u0 = [x => 1.0, y => 1.0, sys2.trJ => 1.0]
+    prob = ODEProblem(sys2, u0, tspan, p, jac = true)
+    sol = solve(prob, Tsit5())
+    @test sol[end, end] ≈ 1.0742818931017244
+end
 
 @testset "Change independent variable" begin
     @independent_variables t