init finish

Author: TorkelE

test/compositional_modelling/component_based_model_creation.jl

@@ -6,7 +6,7 @@
 using Catalyst, LinearAlgebra, OrdinaryDiffEq, SciMLNLSolve, Test
 using ModelingToolkit: nameof
 
-# Fetch test networks.
+# Sets the default `t` to use.
 t = default_t()
 
 

test/dsl/dsl_advanced_model_construction.jl

@@ -1,6 +1,6 @@
 #! format: off
 
-### Fetch Packages and Set Global Variables ###
+### Prepares Tests ###
 
 # Fetch packages.
 using Catalyst, ModelingToolkit
@@ -76,12 +76,12 @@ end
 
 ### Test Interpolation Within the DSL ###
 
-# Tests basic interpolation cases.
 
 # Declares parameters and species used across the test.
 @parameters α k k1 k2
 @species A(t) B(t) C(t) D(t)
 
+# Tests basic interpolation cases.
 let
     AA = A
     AAA = A^2 + B
@@ -101,7 +101,6 @@ let
     rn2 = ReactionSystem([Reaction(k, [AA,C], [D])], t; name=:rn)
     @test rn == rn2
 end
-
 let
     BB = B; A2 = A
     rn = @reaction_network rn begin
@@ -113,7 +112,6 @@ let
                         t; name=:rn)
     @test rn == rn2
 end
-
 let
     AA = A
     kk1 = k^2*A

test/dsl/dsl_basic_model_construction.jl

@@ -4,12 +4,14 @@
 using DiffEqBase, Catalyst, Random, Test
 using ModelingToolkit: operation, istree, get_unknowns, get_ps, get_eqs, get_systems,
                        get_iv, nameof
-t = default_t()
 
-# Sets rnd number.
+# Sets stable rng number.
 using StableRNGs
 rng = StableRNG(12345)
 
+# Sets the default `t` to use.
+t = default_t()
+
 # Fetch test networks and functions.
 include("../test_networks.jl")
 include("../test_functions.jl")
@@ -33,7 +35,7 @@ function all_reactants(eqs)
     return Set{Symbol}(unique(all_reactants))
 end
 
-# Gets all parameters (where every reaction rate is constant)
+# Gets all parameters (where every reaction rate is constant).
 function all_parameters(eqs)
     return Set(unique(map(eq -> opname(eq.rate), eqs)))
 end
@@ -371,7 +373,7 @@ let
     end
 end
 
-# Test that I works as a name.
+# Test that the `I` symbol works as a quantity name.
 let
     rn = @reaction_network begin
         k1, S + I --> 2I
@@ -382,7 +384,7 @@ let
     @test any(isequal(I), unknowns(rn))
 end
 
-# Tests backwards and double arrows.
+# Tests backwards and bi-directional arrows.
 let
     rn1 = @reaction_network arrowtest begin
         (a1, a2), C <--> 0
@@ -401,7 +403,7 @@ let
     @test rn1 == rn2
 end
 
-# Tests arrow variants in "@reaction" macro .
+# Tests arrow variants in `@reaction`` macro .
 let
     @test isequal((@reaction k, 0 --> X), (@reaction k, X <-- 0))
     @test isequal((@reaction k, 0 --> X), (@reaction k, X ⟻ 0))

test/dsl/dsl_options.jl

@@ -423,7 +423,7 @@ let
     end
 end
 
-### Test independent variable designation ###
+### Test Independent Variable Designations ###
 
 # Test ivs in DSL.
 let
@@ -651,7 +651,7 @@ let
     @test length(unknowns(rn2)) == 2
 end
 
-# Tests specific declaration of Observables as species/variables
+# Tests specific declaration of observables as species/variables.
 let
     rn = @reaction_network begin
         @species X(t)
@@ -742,7 +742,7 @@ let
 end
 
 
-### Test `@equations` for Coupled CRN/Equations Models ###
+### Test `@equations` Option for Coupled CRN/Equations Models ###
 
 # Checks creation of basic network.
 # Check indexing of output solution.

test/miscellaneous_tests/api.jl

@@ -300,119 +300,6 @@ let
     testnetwork(rn, B, Z, Δ, lcs, 0, subrn, lcd)
 end
 
-### Tests Reversibility ###
-
-# Test function.
-function testreversibility(rn, B, rev, weak_rev)
-    @test isreversible(rn) == rev
-    subrn = subnetworks(rn)
-    @test isweaklyreversible(rn, subrn) == weak_rev
-end
-
-# Tests reversibility for networks with known reversibility.
-let
-    rn = @reaction_network begin
-        (k2, k1), A1 <--> A2 + A3
-        k3, A2 + A3 --> A4
-        k4, A4 --> A5
-        (k6, k5), A5 <--> 2A6
-        k7, 2A6 --> A4
-        k8, A4 + A5 --> A7
-    end
-    rev = false
-    weak_rev = false
-    testreversibility(rn, reactioncomplexes(rn)[2], rev, weak_rev)
-end
-let
-    rn = @reaction_network begin
-        (k2, k1), A1 <--> A2 + A3
-        k3, A2 + A3 --> A4
-        k4, A4 --> A5
-        (k6, k5), A5 <--> 2A6
-        k7, A4 --> 2A6
-        (k9, k8), A4 + A5 <--> A7
-    end
-    rev = false
-    weak_rev = false
-    testreversibility(rn, reactioncomplexes(rn)[2], rev, weak_rev)
-end
-let
-    rn = @reaction_network begin
-        k1, A --> B
-        k2, A --> C
-    end
-    rev = false
-    weak_rev = false
-    testreversibility(rn, reactioncomplexes(rn)[2], rev, weak_rev)
-end
-let
-    rn = @reaction_network begin
-        k1, A --> B
-        k2, A --> C
-        k3, B + C --> 2A
-    end
-    rev = false
-    weak_rev = false
-    testreversibility(rn, reactioncomplexes(rn)[2], rev, weak_rev)
-end
-let
-    rn = @reaction_network begin
-        (k2, k1), A <--> 2B
-        (k4, k3), A + C --> D
-        k5, D --> B + E
-        k6, B + E --> A + C
-    end
-    rev = false
-    weak_rev = true
-    testreversibility(rn, reactioncomplexes(rn)[2], rev, weak_rev)
-end
-let
-    rn = @reaction_network begin
-        (k2, k1), A + E <--> AE
-        k3, AE --> B + E
-    end
-    rev = false
-    weak_rev = false
-    testreversibility(rn, reactioncomplexes(rn)[2], rev, weak_rev)
-end
-let
-    rn = @reaction_network begin
-        (k2, k1), A + E <--> AE
-        (k4, k3), AE <--> B + E
-    end
-    rev = true
-    weak_rev = true
-    testreversibility(rn, reactioncomplexes(rn)[2], rev, weak_rev)
-end
-let
-    rn = @reaction_network begin (k2, k1), A + B <--> 2A end
-    rev = true
-    weak_rev = true
-    testreversibility(rn, reactioncomplexes(rn)[2], rev, weak_rev)
-end
-let
-    rn = @reaction_network begin
-        k1, A + B --> 3A
-        k2, 3A --> 2A + C
-        k3, 2A + C --> 2B
-        k4, 2B --> A + B
-    end
-    rev = false
-    weak_rev = true
-    testreversibility(rn, reactioncomplexes(rn)[2], rev, weak_rev)
-end
-let
-    rn = @reaction_network begin
-        (k2, k1), A + E <--> AE
-        (k4, k3), AE <--> B + E
-        k5, B --> 0
-        k6, 0 --> A
-    end
-    rev = false
-    weak_rev = false
-    testreversibility(rn, reactioncomplexes(rn)[2], rev, weak_rev)
-end
-
 ### Other Tests ###
 
 let
@@ -504,76 +391,6 @@ let
     @test norm(sol.u - sol5.u) ≈ 0
 end
 
-# Test conservation law elimination.
-let
-    rn = @reaction_network begin
-        (k1, k2), A + B <--> C
-        (m1, m2), D <--> E
-        b12, F1 --> F2
-        b23, F2 --> F3
-        b31, F3 --> F1
-    end
-    osys = complete(convert(ODESystem, rn; remove_conserved = true))
-    @unpack A, B, C, D, E, F1, F2, F3, k1, k2, m1, m2, b12, b23, b31 = osys
-    u0 = [A => 10.0, B => 10.0, C => 0.0, D => 10.0, E => 0.0, F1 => 8.0, F2 => 0.0,
-        F3 => 0.0]
-    p = [k1 => 1.0, k2 => 0.1, m1 => 1.0, m2 => 2.0, b12 => 1.0, b23 => 2.0, b31 => 0.1]
-    tspan = (0.0, 20.0)
-    oprob = ODEProblem(osys, u0, tspan, p)
-    sol = solve(oprob, Tsit5(); abstol = 1e-10, reltol = 1e-10)
-    oprob2 = ODEProblem(rn, u0, tspan, p)
-    sol2 = solve(oprob2, Tsit5(); abstol = 1e-10, reltol = 1e-10)
-    oprob3 = ODEProblem(rn, u0, tspan, p; remove_conserved = true)
-    sol3 = solve(oprob3, Tsit5(); abstol = 1e-10, reltol = 1e-10)
-
-    tv = range(tspan[1], tspan[2], length = 101)
-    for s in species(rn)
-        @test isapprox(sol(tv, idxs = s), sol2(tv, idxs = s))
-        @test isapprox(sol2(tv, idxs = s), sol2(tv, idxs = s))
-    end
-
-    nsys = complete(convert(NonlinearSystem, rn; remove_conserved = true))
-    nprob = NonlinearProblem{true}(nsys, u0, p)
-    nsol = solve(nprob, NewtonRaphson(); abstol = 1e-10)
-    nprob2 = ODEProblem(rn, u0, (0.0, 100.0 * tspan[2]), p)
-    nsol2 = solve(nprob2, Tsit5(); abstol = 1e-10, reltol = 1e-10)
-    nprob3 = NonlinearProblem(rn, u0, p; remove_conserved = true)
-    nsol3 = solve(nprob3, NewtonRaphson(); abstol = 1e-10)
-    for s in species(rn)
-        @test isapprox(nsol[s], nsol2(tspan[2], idxs = s))
-        @test isapprox(nsol2(tspan[2], idxs = s), nsol3[s])
-    end
-
-    u0 = [A => 100.0, B => 20.0, C => 5.0, D => 10.0, E => 3.0, F1 => 8.0, F2 => 2.0,
-        F3 => 20.0]
-    ssys = complete(convert(SDESystem, rn; remove_conserved = true))
-    sprob = SDEProblem(ssys, u0, tspan, p)
-    sprob2 = SDEProblem(rn, u0, tspan, p)
-    sprob3 = SDEProblem(rn, u0, tspan, p; remove_conserved = true)
-    ists = ModelingToolkit.get_unknowns(ssys)
-    sts = ModelingToolkit.get_unknowns(rn)
-    istsidxs = findall(in(ists), sts)
-    u1 = copy(sprob.u0)
-    u2 = sprob2.u0
-    u3 = copy(sprob3.u0)
-    du1 = similar(u1)
-    du2 = similar(u2)
-    du3 = similar(u3)
-    g1 = zeros(length(u1), numreactions(rn))
-    g2 = zeros(length(u2), numreactions(rn))
-    g3 = zeros(length(u3), numreactions(rn))
-    sprob.f(du1, u1, sprob.p, 1.0)
-    sprob2.f(du2, u2, sprob2.p, 1.0)
-    sprob3.f(du3, u3, sprob3.p, 1.0)
-    @test isapprox(du1, du2[istsidxs])
-    @test isapprox(du2[istsidxs], du3)
-    sprob.g(g1, u1, sprob.p, 1.0)
-    sprob2.g(g2, u2, sprob2.p, 1.0)
-    sprob3.g(g3, u3, sprob3.p, 1.0)
-    @test isapprox(g1, g2[istsidxs, :])
-    @test isapprox(g2[istsidxs, :], g3)
-end
-
 # Tests non-integer stoichiometry.
 let
     function test_stoich(T, rn)

test/miscellaneous_tests/compound_macro.jl

@@ -214,7 +214,7 @@ let
     @test isequal(component_coefficients(A2), component_coefficients(B2))
 end
 
-###  Check @compounds Macro ###
+### Test @compounds Macro ###
 
 # Basic @compounds syntax.
 let 

test/miscellaneous_tests/reaction_balancing.jl

@@ -8,7 +8,7 @@ t = default_t()
 
 ### Basic Tests ###
 
-# Functionality tests (a).
+# Functionality tests (1).
 let
     @parameters k
     @species H(t) O(t)
@@ -33,7 +33,7 @@ let
     @test isequal(brxs, brxs_macro)
 end
 
-# Functionality tests (a).
+# Functionality tests (2).
 let
     @parameters k
     @species C(t) H(t) O(t)
@@ -58,7 +58,7 @@ let
 end
 
 
-### Test Across Various Reactions ###
+### Test Using Various Reactions ###
 
 # @reaction k, H2O --> H2O
 let