up

Author: vyudu

src/dsl.jl

@@ -921,12 +921,8 @@ end
 
 # Recursively escape functions in the right-hand-side of an equation written using user-defined functions. Special function calls like "hill(...)" are not expanded.
 function escape_equation_RHS!(eqexpr::Expr)
-    # lhs = recursive_escape_functions!(eqexpr.args[2])
-    # eqexpr.args[2] = lhs
-
     rhs = recursive_escape_functions!(eqexpr.args[3])
     eqexpr.args[3] = rhs
-
     eqexpr
 end
 

test/dsl/dsl_options.jl

@@ -153,77 +153,6 @@ let
     @test issetequal(parameters(rn5), @parameters k B X)
 end
 
-# Test whether user-defined functions are properly expanded in equations. 
-let
-    f(A, t) = 2*A*t
-
-    # Test user-defined function
-    rn = @reaction_network begin
-        @equations D(A) ~ f(A, t)
-    end
-    @test length(equations(rn)) == 1
-    @test equations(rn)[1] isa Equation
-    @species A(t)
-    @test isequal(equations(rn)[1], D(A) ~ 2*A*t)
-
-
-    hill_unregistered(A, v, K, n) = v*(A^n) / (A^n + K^n)
-    rn2 = @reaction_network begin
-        @parameters v K n
-        @equations D(A) ~ hill_unregistered(A, v, K, n)
-    end
-    @test length(equations(rn2)) == 1
-    @test equations(rn2)[1] isa Equation
-    @parameters v K n
-    @test isequal(equations(rn2)[1], D(A) ~ v*(A^n) / (A^n + K^n))
-
-    hill2(A, v, K, n) = v*(A^n) / (A^n + K^n)
-    @register_symbolic hill2(A, v, K, n)
-    # Test Catalyst function
-    rn2r = @reaction_network begin
-        @parameters v K n
-        @equations D(A) ~ hill2(A, v, K, n)
-    end
-    @test length(equations(rn2r)) == 1
-    @test equations(rn2r)[1] isa Equation
-    @parameters v K n
-    @test isequal(equations(rn2r)[1], D(A) ~ hill2(A, v, K, n))
-
-
-    rn3 = @reaction_network begin
-        @species Iapp(t)
-        @equations begin
-            D(A) ~ Iapp
-            Iapp ~ f(A,t)
-        end
-    end
-    @test length(equations(rn3)) == 2
-    @test equations(rn3)[1] isa Equation
-    @test equations(rn3)[2] isa Equation
-    @variables Iapp(t)
-    @test isequal(equations(rn3)[1], D(A) ~ Iapp)
-    @test isequal(equations(rn3)[2], Iapp ~ 2*A*t)
-
-    @species Iapp(t) A(t)
-    eq = [D(A) ~ Iapp, Iapp ~ f(A, t)]
-    @named rn3_sym = ReactionSystem(eq, t)
-    rn3_sym = complete(rn3_sym)
-    @test isequivalent(rn3, rn3_sym)
-    
-    
-
-
-    g(A, K, n) = A^n + K^n
-    rn4 = @reaction_network begin
-        @parameters v K n
-        @equations D(A) ~ hill(A, v, K, n)*g(A, K, n)
-    end
-    @test length(equations(rn4)) == 1
-    @test equations(rn4)[1] isa Equation
-    @parameters v n
-    @test isequal(Catalyst.expand_registered_functions(equations(rn4)[1]), D(A) ~ v*(A^n))
-end
-
 # Test inferring with stoichiometry symbols and interpolation.
 let
     @parameters k g h gg X y [isconstantspecies = true]
@@ -1024,3 +953,76 @@ let
     @unpack k1, A = rn3
     @test isequal(rl, k1*A^2)
 end
+
+# Test whether user-defined functions are properly expanded in equations. 
+let
+    f(A, t) = 2*A*t
+
+    # Test user-defined function
+    rn = @reaction_network begin
+        @equations D(A) ~ f(A, t)
+    end
+    @test length(equations(rn)) == 1
+    @test equations(rn)[1] isa Equation
+    @species A(t)
+    @test isequal(equations(rn)[1], D(A) ~ 2*A*t)
+
+
+    # Test whether expansion happens properly for unregistered/registered functions. 
+    hill_unregistered(A, v, K, n) = v*(A^n) / (A^n + K^n)
+    rn2 = @reaction_network begin
+        @parameters v K n
+        @equations D(A) ~ hill_unregistered(A, v, K, n)
+    end
+    @test length(equations(rn2)) == 1
+    @test equations(rn2)[1] isa Equation
+    @parameters v K n
+    @test isequal(equations(rn2)[1], D(A) ~ v*(A^n) / (A^n + K^n))
+
+    hill2(A, v, K, n) = v*(A^n) / (A^n + K^n)
+    @register_symbolic hill2(A, v, K, n)
+    # Registered symbolic function should not expand. 
+    rn2r = @reaction_network begin
+        @parameters v K n
+        @equations D(A) ~ hill2(A, v, K, n)
+    end
+    @test length(equations(rn2r)) == 1
+    @test equations(rn2r)[1] isa Equation
+    @parameters v K n
+    @test isequal(equations(rn2r)[1], D(A) ~ hill2(A, v, K, n))
+
+
+    rn3 = @reaction_network begin
+        @species Iapp(t)
+        @equations begin
+            D(A) ~ Iapp
+            Iapp ~ f(A,t)
+        end
+    end
+    @test length(equations(rn3)) == 2
+    @test equations(rn3)[1] isa Equation
+    @test equations(rn3)[2] isa Equation
+    @variables Iapp(t)
+    @test isequal(equations(rn3)[1], D(A) ~ Iapp)
+    @test isequal(equations(rn3)[2], Iapp ~ 2*A*t)
+
+    # Test whether the DSL and symbolic ways of creating the network generate the same system
+    @species Iapp(t) A(t)
+    eq = [D(A) ~ Iapp, Iapp ~ f(A, t)]
+    @named rn3_sym = ReactionSystem(eq, t)
+    rn3_sym = complete(rn3_sym)
+    @test isequivalent(rn3, rn3_sym)
+    
+    
+    # Test more complicated expression involving both registered function and a user-defined function. 
+    g(A, K, n) = A^n + K^n
+    rn4 = @reaction_network begin
+        @parameters v K n
+        @equations D(A) ~ hill(A, v, K, n)*g(A, K, n)
+    end
+    @test length(equations(rn4)) == 1
+    @test equations(rn4)[1] isa Equation
+    @parameters v n
+    @test isequal(Catalyst.expand_registered_functions(equations(rn4)[1]), D(A) ~ v*(A^n))
+end
+