Merge pull request #870 from SciML/remove_param_lists

Remove @paraemter lists in test_networks.jl

Author: TorkelE

test/test_networks.jl

@@ -10,22 +10,19 @@ reaction_networks_weird = Vector{ReactionSystem}(undef, 10)
 
 ### Standard reaction networks. ###
 reaction_networks_standard[1] = @reaction_network rns1 begin
-    @parameters p1 p2 p3 k1 k2 k3 k4 d1 d2 d3
     (p1, p2, p3), ∅ → (X1, X2, X3)
     (k1, k2), X2 ⟷ X1 + 2X3
     (k3, k4), X1 ⟷ X3
     (d1, d2, d3), (X1, X2, X3) → ∅
 end
 
 reaction_networks_standard[2] = @reaction_network rns2 begin
-    @parameters v1 K1 v2 K2 d
     mmr(X2, v1, K1), ∅ → X1
     mm(X1, v2, K2), ∅ → X2
     d, X1 + X2 → ∅
 end
 
 reaction_networks_standard[3] = @reaction_network rns3 begin
-    @parameters v1 K1 v2 K2 k1 k2 k3 k4 d
     mm(X2, v1, K1), ∅ → X1
     mm(X3, v2, K2), ∅ → X2
     (k1, k2), X1 ⟷ X3
@@ -34,7 +31,6 @@ reaction_networks_standard[3] = @reaction_network rns3 begin
 end
 
 reaction_networks_standard[4] = @reaction_network rns4 begin
-    @parameters v1 K1 v2 K2 v3 K3 v4 K4 d1 d2 d3 d4
     mmr(X4, v1, K1), ∅ → X1
     mmr(X1, v2, K2), ∅ → X2
     mmr(X2, v3, K3), ∅ → X3
@@ -43,7 +39,6 @@ reaction_networks_standard[4] = @reaction_network rns4 begin
 end
 
 reaction_networks_standard[5] = @reaction_network rns5 begin
-    @parameters p k1 k2 k3 k4 k5 k6 d
     p, ∅ → X1
     (k1, k2), X1 ⟷ X2
     (k3, k4), X2 ⟷ X3
@@ -52,7 +47,6 @@ reaction_networks_standard[5] = @reaction_network rns5 begin
 end
 
 reaction_networks_standard[6] = @reaction_network rns6 begin
-    @parameters p1 p2 k1 k2 k3 k4 k5 k6 d
     (p1, p2), ∅ → (X1, X2)
     (k1, k2), 2X1 ⟷ X3
     (k3, k4), X2 + X3 ⟷ 4X4
@@ -61,23 +55,20 @@ reaction_networks_standard[6] = @reaction_network rns6 begin
 end
 
 reaction_networks_standard[7] = @reaction_network rns7 begin
-    @parameters p1 p2 p3 k1 k2 k3 v1 K1 d1 d2 d3 d4 d5
     (p1, p2, p3), ∅ → (X1, X2, X3)
     (k1, k2), X1 + 2X2 ⟷ X4
     (mm(X3, v1, K1), k3), X4 ⟷ X5
     (d1, d2, d3, d4, d5), (X1, X2, X3, X4, X5) → ∅
 end
 
 reaction_networks_standard[8] = @reaction_network rns8 begin
-    @parameters p k1 k2 k3 d
     p, ∅ → 2X1
     k1, X1 → X2
     (k2, k3), X2 → X3
     d, X3 → ∅
 end
 
 reaction_networks_standard[9] = @reaction_network rns9 begin
-    @parameters p1 p2 p3 d1 d2 d3 k1 k2 k3 k4 k5 k6
     (p1, p2, p3), ∅ ⟶ (X1, X2, X3)
     (d1, d2, d3), (X1, X2, X3) ⟶ ∅
     (k1, k2), X1 + X2 ⟷ X3
@@ -86,7 +77,6 @@ reaction_networks_standard[9] = @reaction_network rns9 begin
 end
 
 reaction_networks_standard[10] = @reaction_network rns10 begin
-    @parameters p k1 k2 k3 k4 k5 k6 k7 k8 d
     p, ∅ ⟶ X1
     (k1, k2), X1 → X2
     (k3, k4), X2 → X3
@@ -98,37 +88,32 @@ end
 ### Network with Hill functions ###.
 
 reaction_networks_hill[1] = @reaction_network rnh1 begin
-    @parameters v1 v2 K1 K2 n1 n2 d1 d2
     hillr(X2, v1, K1, n1), ∅ → X1
     hillr(X1, v2, K2, n2), ∅ → X2
     (d1, d2), (X1, X2) → ∅
 end
 
 reaction_networks_hill[2] = @reaction_network rnh2 begin
-    @parameters v1 v2 v3 K1 K2 K3 n1 n2 n3 d1 d2 d3
     hillr(X3, v1, K1, n1), ∅ → X1
     hillr(X1, v2, K2, n2), ∅ → X2
     hillr(X2, v3, K3, n3), ∅ → X3
     (d1, d2, d3), (X1, X2, X3) → ∅
 end
 
 reaction_networks_hill[3] = @reaction_network rnh3 begin
-    @parameters v1 K1 n1 v2 K2 n2 d
     hillr(X2, v1, K1, n1), ∅ → X1
     hill(X1, v2, K2, n2), ∅ → X2
     d, X1 + X2 → ∅
 end
 
 reaction_networks_hill[4] = @reaction_network rnh4 begin
-    @parameters v1 K1 n1 v2 K2 n2 v3 K3 n3 d1 d2 d3
     hillr(X2, v1, K1, n1) * hillr(X3, v1, K1, n1), ∅ → X1
     hillr(X1, v2, K2, n2) * hillr(X3, v2, K2, n2), ∅ → X2
     hillr(X1, v3, K3, n3) * hillr(X2, v3, K3, n3), ∅ → X3
     (d1, d2, d3), (X1, X2, X3) ⟶ ∅
 end
 
 reaction_networks_hill[5] = @reaction_network rnh5 begin
-    @parameters v1 K1 n1 v2 K2 n2 v3 K3 n3 v4 K4 n4 v5 K5 n5 k1 k2 k3 k4 k5 k6 d1 d2 d3 d4 d5
     hillr(X2, v1, K1, n1) * hill(X4, v1, K1, n1), ∅ → X1
     hill(X5, v2, K2, n2), ∅ → X2
     hill(X3, v3, K3, n3), ∅ → X3
@@ -141,35 +126,30 @@ reaction_networks_hill[5] = @reaction_network rnh5 begin
 end
 
 reaction_networks_hill[6] = @reaction_network rnh6 begin
-    @parameters v K n d
     v / 10 + hill(X1, v, K, n), ∅ → X1
     d, X1 → ∅
 end
 
 reaction_networks_hill[7] = @reaction_network rnh7 begin
-    @parameters v K n k1 k2 k3 d
     v / 10 + hill(X1, v, K, n), ∅ → X1 + X2
     (k1, k2), X1 + X2 ↔ X3
     k3, X3 → X1
     d, (X1, X2, X3) → ∅
 end
 
 reaction_networks_hill[8] = @reaction_network rnh8 begin
-    @parameters v1 K1 n1 v2 K2 n2 v3 K3 n3 v4 K4 n4 d1 d2 d3
     hill(X2, v1, K1, n1), ∅ → X1
     hillr(X1, v2, K2, n2) * hill(X3, v3, K3, n3), ∅ → X2
     hill(X2, v4, K4, n4), ∅ → X3
     (d1, d2, d3), (X1, X2, X3) → ∅
 end
 
 reaction_networks_hill[9] = @reaction_network rnh9 begin
-    @parameters v1 K1 n1 v2 K2 n2 d
     hill(X1, v1, K1, n1) * hillr(X1, v2, K2, n2), ∅ → X1
     d, X1 → ∅
 end
 
 reaction_networks_hill[10] = @reaction_network rnh10 begin
-    @parameters v1 K1 n1 v2 K2 n2 k1 k2 k3 k4 k5 k6 d1 d2
     hill(X2, v1, K1, n1), ∅ → X1
     hillr(X4, v2, K2, n2), ∅ → X2
     (k1, k2), 2X1 + X2 ⟷ X3
@@ -181,69 +161,60 @@ end
 ### Reaction networks were some linear combination concentrations remain fixed (steady state values depends on initial conditions). ###
 
 reaction_networks_constraint[1] = @reaction_network rnc1 begin
-    @parameters k1 k2 k3 k4 k5 k6
     (k1, k2), X1 ↔ X2
     (k3, k4), X2 ↔ X3
     (k5, k6), X3 ↔ X1
 end
 reaction_network_constraints[1] = [1 1 1]
 
 reaction_networks_constraint[2] = @reaction_network rnc2 begin
-    @parameters k1 k2 k3 k4 k5 k6
     (k1, k2), X1 ↔ 2X1
     (k3, k4), X1 + X2 ↔ X3
     (k5, k6), X3 ↔ X2
 end
 reaction_network_constraints[2] = [0 1 1]
 
 reaction_networks_constraint[3] = @reaction_network rnc3 begin
-    @parameters k1 k2 k3 k4 p k5 d
     (k1, k2 * X5), X1 ↔ X2
     (k3 * X5, k4), X3 ↔ X4
     (p + k5 * X2 * X3, d), ∅ ↔ X5
 end
 reaction_network_constraints[3] = [0 0 1 1 0; 1 1 0 0 0]
 
 reaction_networks_constraint[4] = @reaction_network rnc4 begin
-    @parameters k1 k2 v K d
     (k1, k2), X1 + X2 ↔ X3
     (mm(X3, v, K), d), ∅ ↔ X4
 end
 reaction_network_constraints[4] = [0 1 1 0; -1 1 0 0]
 
 reaction_networks_constraint[5] = @reaction_network rnc5 begin
-    @parameters k1 k2 k3 k4 k5 k6
     (k1, k2), X1 ↔ 2X2
     (k3, k4), 2X2 ↔ 3X3
     (k5, k6), 3X3 ↔ 4X4
 end
 reaction_network_constraints[5] = [12 6 4 3]
 
 reaction_networks_constraint[6] = @reaction_network rnc6 begin
-    @parameters v1 K1 v2 K2 v3 K3
     mmr(X1, v1, K1), X1 → X2
     mmr(X2, v2, K2), X2 → X3
     mmr(X3, v3, K3), X3 → X1
 end
 reaction_network_constraints[6] = [1 1 1]
 
 reaction_networks_constraint[7] = @reaction_network rnc7 begin
-    @parameters k1 k2 k3 k4 v K d
     (k1, k2), X1 + X2 ↔ X3
     (mm(X3, v, K), d), ∅ ↔ X2
     (k3, k4), X2 ↔ X4
 end
 reaction_network_constraints[7] = [1 0 1 0]
 
 reaction_networks_constraint[8] = @reaction_network rnc8 begin
-    @parameters k1 k2 v1 K1 v2 K2
     (k1, k2), X1 + X2 ↔ X3
     (mm(X3, v1, K1), mm(X4, v2, K2)), X3 ↔ X4
 end
 reaction_network_constraints[8] = [-1 1 0 0; 0 1 1 1]
 
 reaction_networks_constraint[9] = @reaction_network rnc9 begin
-    @parameters k1 k2 k3 k4 k5 k6
     (k1, k2), X1 + X2 ↔ X3
     (k3, k4), X3 + X4 ↔ X5
     (k5, k6), X5 + X6 ↔ X7
@@ -252,7 +223,6 @@ reaction_network_constraints[9] = [1 0 1 0 1 0 1; -1 1 0 0 0 0 0; 0 0 0 1 1 0 1;
                                    0 0 0 0 0 1 1]
 
 reaction_networks_constraint[10] = @reaction_network rnc10 begin
-    @parameters kBw kDw kD kB1 kB2 kB3 kB4 kB5 kD1 kD2 kD3 kD4 kD5 kK1 kK2 kP kDeg v0 F K λW λV
     kDeg, (w, w2, w2v, v, w2v2, vP, σB, w2σB) ⟶ ∅
     kDeg, vPp ⟶ phos
     (kBw, kDw), 2w ⟷ w2
@@ -274,7 +244,6 @@ reaction_network_constraints[10] = [0 0 0 0 0 0 0 0 1 1]
 
 # Brusselator.
 reaction_networks_real[1] = @reaction_network rnr1 begin
-    @parameters A B
     A, ∅ → X
     1, 2X + Y → 3X
     B, X → Y
@@ -283,7 +252,6 @@ end
 
 # The B.subtilis σV Lysozyme stress response.
 reaction_networks_real[2] = @reaction_network rnr2 begin
-    @parameters v0 v K n kD kB kC deg S
     v0 + hill(σ, v, K, n), ∅ → (σ + A)
     deg, (σ, A, Aσ) → ∅
     (kB, kD), A + σ ↔ Aσ
@@ -292,7 +260,6 @@ end
 
 # A cell cycle model
 reaction_networks_real[3] = @reaction_network rnr3 begin
-    @parameters k1 k2p k2pp k3p k3pp A J3 k4 m J4
     k1, 0 --> Y
     k2p, Y --> 0
     k2pp * P, Y --> 0
@@ -304,7 +271,6 @@ end
 
 # A bistable switch
 reaction_networks_real[4] = @reaction_network rnr4 begin
-    @parameters d v1 K1 n1 v2 K2 n2
     d, (X, Y) → ∅
     hillr(Y, v1, K1, n1), ∅ → X
     hillr(X, v2, K2, n2), ∅ → Y
@@ -313,28 +279,24 @@ end
 ### Reaction networks that contain weird functions, stuff, and other oddities ###
 
 reaction_networks_weird[1] = @reaction_network rnw1 begin
-    @parameters p d
     exp(p), ∅ → X
     d * exp(X), X → ∅
 end
 
 reaction_networks_weird[2] = @reaction_network rnw2 begin
-    @parameters k1 k2 k3 k4
     k1, ∅ → X
     k2 * log(12 + X), X → Y
     k3 * log(3 + Y), Y → Z
     log(5, 6 + k4), Z → ∅
 end
 
 reaction_networks_weird[3] = @reaction_network rnw3 begin
-    @parameters d v1 K1 n1 v2 K2 n2
     d, (X, Y) → ∅
     hillr(hill(Y, v2, K2, n2), v1, K1, n1), ∅ → X
     hillr(hill(X, v1, K1, n1), v2, K2, n2), ∅ → Y
 end
 
 reaction_networks_weird[4] = @reaction_network rnw4 begin
-    @parameters p k1 k2 k3 k4 k5 k6 d
     p, ∅ → X1
     (k1, X2^X3), X1 ⟷ X2
     (X2 / X4, k4), X2 ⟷ X3
@@ -343,14 +305,12 @@ reaction_networks_weird[4] = @reaction_network rnw4 begin
 end
 
 reaction_networks_weird[5] = @reaction_network rnw5 begin
-    @parameters k1 k2 k3 k4 k5 k6
     (k1 * tanh(X1), k2), X1 ↔ 2X1
     (2 + sin(X1), 3 + sin(k3)), X1 + X2 ↔ X3
     (k5, 4 + cos(X3 + X1) + sin(X2)), X3 ↔ X2
 end
 
 reaction_networks_weird[6] = @reaction_network rnw6 begin
-    @parameters p d
     (p, d), ∅ ↔ X1
     (p, d), ∅ ↔ X1
     (p, d), ∅ ↔ X1
@@ -360,15 +320,13 @@ reaction_networks_weird[6] = @reaction_network rnw6 begin
 end
 
 reaction_networks_weird[7] = @reaction_network rnw7 begin
-    @parameters k1 k2 k3
     k1, X1 → X2
     0, X2 → X3
     k2, X3 → X4
     k3, X4 → X5
 end
 
 reaction_networks_weird[8] = @reaction_network rnw8 begin
-    @parameters k1 k2 k3 k4 k5 k6 k7 k8 k9
     k1 + X3, X1 → X2
     k2 * X4, X2 → X3
     k3 / (X5 + 0.01), X3 → X4
@@ -381,13 +339,11 @@ reaction_networks_weird[8] = @reaction_network rnw8 begin
 end
 
 reaction_networks_weird[9] = @reaction_network rnw9 begin
-    @parameters p v1 K1 n1 v2 K2 n2 v3 K3 n3 v4 K4 n4
     p, ∅ → X1
     hill(hill(hill(hill(X1, v1, K1, n1), v2, K2, n2), v3, K3, n3), v4, K4, n4), X1 → ∅
 end
 
 reaction_networks_weird[10] = @reaction_network rnw10 begin
-    @parameters d
     d, 5X1 → 4X1
 end