drop mutable network tests

Author: isaacsas

test/programmatic_model_creation/programmatic_model_expansion.jl

@@ -32,189 +32,3 @@ let
     @test length(get_unknowns(empty_network_1)) == 0
     @test length(ps) == 0
 end
-
-# Tests creating a network and adding reactions.
-let
-    unfinished_network = @reaction_network begin
-        @parameters k0 k1 k2 k3 k4
-        (k1, k2), X1 ↔ X2
-        (k3, k4), X3 ↔ X4
-    end
-    @add_reactions unfinished_network begin
-        @parameters k0 k3 k4 k5 k6
-        (k3, k4), X3 ↔ X4
-        (k5, k6), X5 ↔ X6
-    end
-    @add_reactions unfinished_network begin
-        @parameters k0 k5 k6 k7 k8
-        (k5, k6), X5 ↔ X6
-        (k7, k8), X7 ↔ X8
-    end
-    @test length(get_unknowns(unfinished_network)) == 8
-    @test length(get_ps(unfinished_network)) == 9
-end
-
-# Compares test network to identical network constructed via @add_reactions.
-# @add_reactions is getting deprecated though?
-let
-    identical_networks = Vector{Pair}()
-
-    step_by_step_network_1 = @reaction_network rns5 begin
-        @parameters p k1 k2 k3 k4
-        p, ∅ → X1
-        (k1, k2), X1 ⟷ X2
-        (k3, k4), X2 ⟷ X3
-    end
-    @add_reactions step_by_step_network_1 begin
-        @parameters k5 k6
-        (k5, k6), X3 ⟷ X4
-    end
-    @add_reactions step_by_step_network_1 begin
-        @parameters d
-        d, X4 → ∅
-    end
-    push!(identical_networks, reaction_networks_standard[5] => step_by_step_network_1)
-
-    step_by_step_network_2 = @reaction_network rns7 begin (p1, p2, p3), ∅ → (X1, X2, X3) end
-    @add_reactions step_by_step_network_2 begin
-        @parameters k1 k2 k3 v1 K1 d1 d2 d3 d4 d5
-        (k1, k2), X1 + 2X2 ⟷ X4
-        (mm(X3, v1, K1), k3), X4 ⟷ X5
-        (d1, d2, d3, d4, d5), (X1, X2, X3, X4, X5) → ∅
-    end
-    push!(identical_networks, reaction_networks_standard[7] => step_by_step_network_2)
-
-    step_by_step_network_3 = @reaction_network rns10 begin
-        @parameters p k1 k2 k3 k4
-        p, ∅ ⟶ X1
-        (k1, k2), X1 → X2
-    end
-    @add_reactions step_by_step_network_3 begin
-        @parameters p k1 k2 k3 k4 k5 k6
-        (k3, k4), X2 → X3
-        (k5, k6), X3 → X4
-    end
-    @add_reactions step_by_step_network_3 begin
-        @parameters p k1 k2 k3 k4 k5 k6 k7 k8 d
-        (k7, k8), X4 → X5
-        d, X5 ⟶ ∅
-    end
-    push!(identical_networks, reaction_networks_standard[10] => step_by_step_network_3)
-
-    step_by_step_network_4 = @reaction_network rnh7 begin
-        @parameters v K n k1 k2 k3 d
-        v / 10 + hill(X1, v, K, n),
-        ∅ → X1 + X2
-    end
-    @add_reactions step_by_step_network_4 begin
-        @parameters k1 k2
-        k1, X1 + X2 → X3
-        k2, X3 → X1 + X2
-    end
-    @add_reactions step_by_step_network_4 begin
-        @parameters k2 k3 d
-        k3, X3 → X1
-        d, (X1, X2, X3) → ∅
-    end
-    push!(identical_networks, reaction_networks_hill[7] => step_by_step_network_4)
-
-    step_by_step_network_5 = @reaction_network rnc1 begin
-        @parameters k1 k2 k3 k4 k5 k6
-        (k1, k2), X1 ↔ X2
-        (k3, k4), X2 ↔ X3
-    end
-    @add_reactions step_by_step_network_5 begin
-        @parameters k5
-        k5, X3 → X1
-    end
-    @add_reactions step_by_step_network_5 begin
-        @parameters k6
-        k6, X1 → X3
-    end
-    push!(identical_networks, reaction_networks_constraint[1] => step_by_step_network_5)
-
-    step_by_step_network_6 = @reaction_network rnc5 begin
-        @parameters k1 k2 k3 k4 k5 k6
-        (k1, k2), X1 ↔ 2X2
-    end
-    @add_reactions step_by_step_network_6 begin
-        @parameters k3 k4
-        (k3, k4), 2X2 ↔ 3X3
-    end
-    @add_reactions step_by_step_network_6 begin
-        @parameters k5 k6
-        (k5, k6), 3X3 ↔ 4X4
-    end
-    push!(identical_networks, reaction_networks_constraint[5] => step_by_step_network_6)
-
-    step_by_step_network_7 = @reaction_network rnr3 begin
-        @parameters k1 k2p k2pp k3p k3pp A J3 k4 m J4
-        k2p, Y → 0
-    end
-    @add_reactions step_by_step_network_7 begin
-    @parameters k3p k3pp A J3 k2pp
-        (k3p + k3pp * A) / (J3 + Po), Po → P
-        k2pp * P, Y → 0
-    end
-    @add_reactions step_by_step_network_7 begin
-        @parameters k1
-        k1, 0 → Y
-    end
-    @add_reactions step_by_step_network_7 begin
-        @parameters k4 m J4
-        (k4 * m) / (J4 + P), Y + P → Y + Po
-    end
-    push!(identical_networks, reaction_networks_real[3] => step_by_step_network_7)
-
-    @parameters k1
-    step_by_step_network_8 = @reaction_network rnw7
-    addparam!(step_by_step_network_8, k1)
-    @add_reactions step_by_step_network_8 begin
-        @parameters k1
-        k1, X1 → X2
-        0, X2 → X3
-    end
-    @add_reactions step_by_step_network_8 begin
-        @parameters k2 k3
-        k2, X3 → X4
-        k3, X4 → X5
-    end
-    push!(identical_networks, reaction_networks_weird[7] => step_by_step_network_8)
-
-    step_by_step_network_9 = @reaction_network rnw10
-    @add_reactions step_by_step_network_9 begin
-        @parameters d
-        d, 5X1 → 4X1
-    end
-    push!(identical_networks, reaction_networks_weird[10] => step_by_step_network_9)
-
-    function permute_ps(pvals, rn1, rn2)
-        ps1 = parameters(rn1)
-        ps2 = parameters(rn2)
-        pvals2 = similar(pvals)
-        for (i, p) in enumerate(ps2)
-            pidx = findfirst(isequal(p), ps1)
-            pvals2[i] = pvals[pidx]
-        end
-        pvals2
-    end
-
-    for networks in identical_networks
-        f1 = ODEFunction(complete(convert(ODESystem, networks[1])), jac = true)
-        f2 = ODEFunction(complete(convert(ODESystem, networks[2])), jac = true)
-        g1 = SDEFunction(complete(convert(SDESystem, networks[1])))
-        g2 = SDEFunction(complete(convert(SDESystem, networks[2])))
-        @test networks[1] == networks[2]
-        for factor in [1e-2, 1e-1, 1e0, 1e1]
-            u0 = factor * rand(rng, length(get_unknowns(networks[1])))
-            pp = factor * rand(rng, length(get_ps(networks[1])))
-
-            # needed because this code assumes an ordering of the parameters and species...
-            pp2 = permute_ps(pp, networks[1], networks[2])
-            t = rand(rng)
-            @test all(abs.(f1(u0, pp, t) .- f2(u0, pp2, t)) .< 1000 * eps())
-            @test all(abs.(f1.jac(u0, pp, t) .- f2.jac(u0, pp2, t)) .< 1000 * eps())
-            @test all(abs.(g1(u0, pp, t) .- g2(u0, pp2, t)) .< 1000 * eps())
-        end
-    end
-end