add tests

test/extensions/bifurcation_kit.jl

@@ -1,16 +1,84 @@
 ### Fetch Packages ###
 using Bifurcationkit, Catalyst, Test
 
+# Sets rnd number.
+using StableRNGs
+rng = StableRNG(12345)
+
 ### Run Tests ###
 
-# Brusselator, tests that a Hopf bifurcation is found.
+# Brusselator extended with conserved species.
+# Runs full computation, checks values corresponds to known values.
+# Checks that teh correct bifurcation point is found at the correct position.
+# Checks that bifurcation diagrams can be computed for systems with conservation laws.
+# Checks that bifurcation diagrams can be computed for systems with default values.
+# Checks that bifurcation diagrams can be computed for systems with non-constant rate.
 let 
+    # Create model
+    extended_brusselator = @reaction_network begin
+        @species W(t) = 2.0
+        @parameters k2 = 0.5
+        A, ∅ → X
+        1, 2X + Y → 3X
+        B, X → Y
+        1, X → ∅
+        (k1*Y, k2), V <--> W
+    end
+    @unpack A, B, k1
+    u0_guess = [:X => 1.0, :Y => 1.0, :V => 0.0, :W => 0.0]
+    p_start = [A => 1.0, B => 4.0, k1 => 0.1]
+
+    # Computes bifurcation diagram.
+    ifurcationProblem(extended_brusselator, u0_guess, p_start, :B; plot_var=:V, u0 = [:V => 1.0])
+    p_span = (0.1, 6.0)
+    opt_newton = NewtonPar(tol = 1e-9, max_iterations = 100)
+    opts_br = ContinuationPar(dsmin = 0.0001, dsmax = 0.001, ds = 0.0001,
+        max_steps = 200000, nev = 2, newton_options = opt_newton,
+        p_min = p_span[1], p_max = p_span[2],
+        detect_bifurcation = 3, n_inversion = 4, tol_bisection_eigenvalue = 1e-8, dsmin_bisection = 1e-9)
+    bif_dia = bifurcationdiagram(bprob, PALC(), 2, (args...) -> opts_br; bothside=true)
 
+    # Checks computed V values are correct (Formula: V = k2*(V0+W0)/(k1*Y+k2), where Y=2*B.)
+    B_vals = getfield.(bif_dia.γ.branch, :param)
+    V_vals = getfield.(bif_dia.γ.branch, :x)
+    @test all(V_vals .≈ 0.5*(1.0+2.0) ./ (0.1 .* 2*B_vals .+ 0.5))
+
+    # Checks that the bifurcation point is correct.
+    @test length(bif_dia.γ.specialpoint) == 3 # Includes start and end point.
+    hopf_bif_point = filter(sp -> sp.type == :hopf, bif_dia.γ.specialpoint)[1]
+    @test isapprox(hopf_bif_point.param, 1.5, atol=1e-5)
 end
 
-# Bistable switch with deflation, tests that bifurcation diagrams works while multistability exists for initial point.
+# Bistable switch.
+# Checks that the same bifurcation problem is created as for BifurcationKit.
+# Checks with Symbolics as bifurcation and plot vars.
 let 
+    # Creates BifurcationProblem via Catalyst.
+    bistable_switch = @reaction_network begin
+        0.1 + hill(X,v,K,n), 0 --> X
+        d, X --> 0
+    end
+    @unpack x, v, K, n, d = rn
+    u0_guess = [x => 1.0]
+    p_start = [v => 5.0, K => 2.5, n => 3, d => 1.0]
+    bprob = BifurcationProblem(bistable_switch, u0_guess, p_start, K; jac=false; plot_var=x)
+
+    # Creates BifurcationProblem via BifurcationKit.
+    function bistable_switch_BK(u, p)
+        X, = u
+        v, K, n, d = p
+        return [0.1 + v*(X^n)/(X^n + K^n) - d*X]
+    end
+    bprob_BK = BifurcationProblem(bistable_switch_BK, [1.0], [5.0, 2.5, 3, 1.0], (@lens _[1]); record_from_solution = (x, p) -> x[1])
 
+    # Check the same function have been generated.
+    bprob.u0 == bprob_BK.u0
+    bprob.params == bprob_BK.params
+    for repeat = 1:20
+        u0 = rand(rng, 1)
+        p = rand(rng, 4)
+        @test bprob_BK.VF.F(u0, p) == bprob.VF.F(u0, p)
+    end
 end
 
 # Three-state system, tests that bifurcation diagrams works for systems with conserved quantities.

test/test_networks.jl

@@ -178,7 +178,7 @@ reaction_networks_hill[10] = @reaction_network rnh10 begin
     (d1, d2), (X5, X6) → ∅
 end
 
-### Reaction networks were some linnear combination concentrations remain fixed (steady state values depends on initial conditions). ###
+### 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