Merge pull request #1050 from SciML/update_dae_tests

Fix DAE tests

Author: TorkelE

test/compositional_modelling/component_based_model_creation.jl

@@ -46,8 +46,8 @@ let
         sys₂.μ => (log(2) / 600), sys₃.α₀ => 5e-4, sys₃.α => 0.5, sys₃.K => 40.0,
         sys₃.n => 2, sys₃.δ => (log(2) / 120), sys₃.β => (20 * log(2) / 120),
         sys₃.μ => (log(2) / 600)]
-    u₀ = [sys₁.m => 0.0, sys₁.P => 20.0, sys₁.R => 0.0, sys₂.m => 0.0, sys₂.P => 0.0,
-        sys₂.R => 0.0, sys₃.m => 0.0, sys₃.P => 0.0, sys₃.R => 0.0]
+    u₀ = [sys₁.m => 0.0, sys₁.P => 20.0, sys₂.m => 0.0, sys₂.P => 0.0,
+        sys₃.m => 0.0, sys₃.P => 0.0]
     tspan = (0.0, 100000.0)
     oprob = ODEProblem(oderepressilator, u₀, tspan, pvals)
     sol = solve(oprob, Tsit5())
@@ -94,13 +94,15 @@ let
     @test all(isapprox.(sol(tvs, idxs = sys₁.P), sol2(tvs, idxs = 4), atol = 1e-4))
 
     # Test conversion to nonlinear system.
+    u₀_nl = [sys₁.m => 0.0, sys₁.P => 20.0, sys₁.R => 0.0, sys₂.m => 0.0, sys₂.P => 0.0,
+        sys₂.R => 0.0, sys₃.m => 0.0, sys₃.P => 0.0, sys₃.R => 0.0]
     @named nsys = NonlinearSystem(connections, [], [])
     @named ssrepressilator = ReactionSystem(t; systems = [nsys, sys₁, sys₂, sys₃])
     ssrepressilator = complete(ssrepressilator)
     @named nlrepressilator = convert(NonlinearSystem, ssrepressilator, include_zero_odes = false)
     sys2 = structural_simplify(nlrepressilator)
     @test length(equations(sys2)) <= 6
-    nlprob = NonlinearProblem(sys2, u₀, pvals)
+    nlprob = NonlinearProblem(sys2, u₀_nl, pvals)
     sol = solve(nlprob, NLSolveJL(), abstol = 1e-9)
     @test sol[sys₁.P] ≈ sol[sys₂.P] ≈ sol[sys₃.P]
     @test sol[sys₁.m] ≈ sol[sys₂.m] atol=1e-7
@@ -113,7 +115,7 @@ let
     @named nlrepressilator = convert(NonlinearSystem, fsys, include_zero_odes = false)
     sys2 = structural_simplify(nlrepressilator)
     @test length(equations(sys2)) <= 6
-    nlprob = NonlinearProblem(sys2, u₀, pvals)
+    nlprob = NonlinearProblem(sys2, u₀_nl, pvals)
     sol = solve(nlprob, NLSolveJL(), abstol = 1e-9)
     @test sol[sys₁.P] ≈ sol[sys₂.P] ≈ sol[sys₃.P]
     @test sol[sys₁.m] ≈ sol[sys₂.m] atol=1e-7
@@ -131,7 +133,7 @@ let
     @named nlrepressilator = convert(NonlinearSystem, repressilator2, include_zero_odes = false)
     sys2 = structural_simplify(nlrepressilator)
     @test length(equations(sys2)) <= 6
-    nlprob = NonlinearProblem(sys2, u₀, pvals)
+    nlprob = NonlinearProblem(sys2, u₀_nl, pvals)
     sol = solve(nlprob, NLSolveJL(), abstol = 1e-9)
     @test sol[sys₁.P] ≈ sol[sys₂.P] ≈ sol[sys₃.P]
     @test sol[sys₁.m] ≈ sol[sys₂.m] atol=1e-7
@@ -252,7 +254,7 @@ let
     @named nlrepressilator = convert(NonlinearSystem, repressilator2, include_zero_odes = false)
     sys2 = structural_simplify(nlrepressilator)
     @test length(equations(sys2)) <= 6
-    nlprob = NonlinearProblem(sys2, u₀, pvals)
+    nlprob = NonlinearProblem(sys2, u₀_nl, pvals)
     sol = solve(nlprob, NLSolveJL(), abstol = 1e-9)
     @test sol[sys₁.P] ≈ sol[sys₂.P] ≈ sol[sys₃.P]
     @test sol[sys₁.m] ≈ sol[sys₂.m] atol=1e-7

test/dsl/dsl_options.jl

@@ -784,7 +784,7 @@ let
     @test isequal(equations(rn)[4], 3Y + X  ~ S + X*d)
 
     # Checks that simulations has the correct output
-    u0 = Dict([S => 1 + rand(rng), X => 1 + rand(rng), Y => 1 + rand(rng)])
+    u0 = Dict([S => 1 + rand(rng)])
     ps = Dict([p => 1 + rand(rng), d => 1 + rand(rng), k => 1 + rand(rng)])
     oprob = ODEProblem(rn, u0, (0.0, 10000.0), ps; structural_simplify=true)
     sol = solve(oprob, Tsit5(); abstol=1e-9, reltol=1e-9)
@@ -895,7 +895,7 @@ let
     @test equations(rn)[3] isa Equation
 
     # Checks that simulations has the correct output
-    u0 = Dict([S => 1 + rand(rng), X => 1 + rand(rng), Y => 1 + rand(rng)])
+    u0 = Dict([S => 1 + rand(rng), Y => 1 + rand(rng)])
     ps = Dict([p => 1 + rand(rng), d => 1 + rand(rng), k => 1 + rand(rng)])
     oprob = ODEProblem(rn, u0, (0.0, 10000.0), ps; structural_simplify=true)
     sol = solve(oprob, Tsit5(); abstol=1e-9, reltol=1e-9)
@@ -1025,4 +1025,3 @@ let
     @parameters v n
     @test isequal(Catalyst.expand_registered_functions(equations(rn4)[1]), D(A) ~ v*(A^n))
 end
-

test/miscellaneous_tests/reactionsystem_serialisation.jl

@@ -513,6 +513,7 @@ let
         d, X --> 0, [misc = x -> 2x]
     end
     @test_throws Exception save_reactionsystem("test_serialisation.jl", rs)
+    rm("test_serialisation.jl")
 end
 
 # Test connection field.