Merge pull request #989 from SciML/more_t_isa_parameter

More t is now a parameter test

docs/src/model_creation/chemistry_related_functionality.md

@@ -103,7 +103,7 @@ In all of these cases, the left-hand side must be enclosed within `()`.
 While we generally do not need to specify independent variables for compound, if the components (together) have more than one independent variable, this *must be done*:
 ```@example chem1
 t = default_t()
-@variables s
+@parameters s
 @species N(s) O(t) 
 @compound NO2(t,s) ~ N + 2O
 ```

docs/unpublished/pdes.md

@@ -43,7 +43,7 @@ end
 We now define the reaction model
 ```julia
 t = default_t()
-@variables x y
+@parameters x y
 @species U(x,y,t) V(x,y,t) W(x,y,t)
 rxs = [Reaction(k[1], [U, W], [V, W]),
        Reaction(k[2], [V], [W], [2], [1]),

test/dsl/dsl_options.jl

@@ -436,7 +436,8 @@ let
     end
 
     @parameters k k2
-    @variables s x D(x) E(s) F(s,x)
+    @parameters s x
+    @variables D(x) E(s) F(s,x)
     @species A(s,x) B(s) C(x) C2(s,x)
     rx = Reaction(k*k2*D, [A, B], [C, C2], [E, 1], [F, 1])
     @named ivstest = ReactionSystem([rx], s; spatial_ivs = [x])

test/miscellaneous_tests/compound_macro.jl

@@ -103,7 +103,7 @@ end
 
 # Test using different independent variable combinations.
 let
-    @variables x y z
+    @parameters x y z
     @species C(t) H(x) N(x) O(t) P(t,x) S(x,y)
 
     # Checks that wrong (or absent) independent variable produces errors.

test/miscellaneous_tests/reactionsystem_serialisation.jl

@@ -213,7 +213,7 @@ end
 # Checks for system with non-default independent variable.
 let
     # Prepares parameters/variables/species with complicated dependencies.
-    @variables τ
+    @parameters τ
     @parameters begin
         b = 3.0
         c

test/reactionsystem_core/coupled_equation_crn_systems.jl

@@ -182,7 +182,8 @@ end
 # The system is mostly made up to be non-trivial, but reliably solvable.
 let
     @parameters p d a b c
-    @variables τ A(τ) B(τ) C(τ)
+    @parameters τ
+    @variables A(τ) B(τ) C(τ)
     @species X(τ)
     Δ = Differential(τ)
     eqs = [
@@ -265,7 +266,8 @@ end
 # Checks that non-default iv is inferred correctly from reactions/equations.
 let
     # Create coupled model.
-    @variables τ A(τ) B(τ)
+    @parameters τ
+    @variables A(τ) B(τ)
     @species X(τ) X2(τ)
     @parameters k1 k2 k b1 b2
     D = Differential(τ)
@@ -607,7 +609,8 @@ let
 
     # Declares the model in a messy fashion, and simulates it.
     osol_messy = let
-        @variables τ M(τ) H(τ)=h_max
+        @parameters τ
+        @variables M(τ) H(τ)=h_max
         @species S(τ) I(τ) R(τ)
         Δ = Differential(τ)
         eqs_messy = [
@@ -972,7 +975,8 @@ end
 # Checks that various erroneous coupled system declarations yield errors.
 let
     @parameters p1 p2
-    @variables τ  U1(τ) V1(t)
+    @parameters τ
+    @variables U1(τ) V1(t)
     @species R1(τ) R2(τ) S1(t) S2(t)
     E = Differential(τ)
 
@@ -989,7 +993,7 @@ let
     # Equation with variable using non-declared independent variable.
     @test_throws Exception ReactionSystem([
         Reaction(p1, [S1], [S2]),
-        U1 ~ S1 + p2
+        E(U1) ~ S1 + p2
     ], t; name = :rs)
 
     # Differential with respect to non-declared independent variable.

test/reactionsystem_core/custom_crn_functions.jl

@@ -141,7 +141,8 @@ end
 # Tests `Equation`s.
 # Tests using non-default independent variable.
 let
-    @variables T X(T) Y(T)
+    @parameters T
+    @variables X(T) Y(T)
     @parameters K V N 
 
     eq1 = 0 ~ mm(X, V, K)

test/reactionsystem_core/reactionsystem.jl

@@ -628,6 +628,30 @@ let
     @test_throws Exception convert(NonlinearSystem, nc)
 end
 
+# Checks that the same name cannot be used for two different of parameters/species/variables.
+let
+    # Stores a parameter, a species, and a variable (with identical names) in different variables.
+    x_p = let
+        only(@parameters x) 
+    end
+    x_sp = let
+        only(@species x(t)) 
+    end
+    x_v = let
+        only(@variables x(t)) 
+    end
+
+    # Checks that creating systems with different in combination produces errors.
+    # Currently broken on MTK, potentially fix in Catalyst once sorted out there (https://github.com/SciML/ModelingToolkit.jl/issues/2883).
+    @parameters d
+    @species X(t)
+    rx = Reaction(d, [X], [])
+    @test_broken false # (not sure how to mark a `@test_throws` as broken)
+    # @test_throws rs1 = ReactionSystem([rx], t, [X, x_sp,], [d, x_p]; name = :rs)
+    # @test_throws rs2 = ReactionSystem([rx], t, [X, X, x_v], [d, x_p]; name = :rs)
+    # @test_throws rs2 = ReactionSystem([rx], t, [X, x_sp, x_v], [d]; name = :rs)
+end
+
 ### Other Tests ###
 
 # Test for https://github.com/SciML/ModelingToolkit.jl/issues/436.

test/spatial_modelling/simulate_PDEs.jl

@@ -19,7 +19,7 @@ end
 let
     t = default_t()
     @parameters k[1:7] D[1:3] n0[1:3] A
-    @variables x y
+    @parameters x y
     @species U(x, y, t) V(x, y, t) W(x, y, t)
     rxs = [Reaction(k[1], [U, W], [V, W]),
         Reaction(k[2], [V], [W], [2], [1]),