up

Author: TorkelE

HISTORY.md

@@ -29,7 +29,7 @@ end
   @equations D(D(V)) ~ 1
 end
 ```
-Please note that this cannot be used at the same time as `D` is used to represent a species, variable, or parameter. 
+Please note that this cannot be used at the same time as `D` is used to represent a species, variable, or parameter (including is these are implicitly designated as such by e.g. appearing as a reaction reactant). 
 - Array symbolics support is more consistent with ModelingToolkit v9. Parameter
   arrays are no longer scalarized by Catalyst, while species and variables
   arrays still are (as in ModelingToolkit). As such, parameter arrays should now

src/dsl.jl

@@ -357,7 +357,7 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
     # Excludes any parameters already extracted (if they also was a variable).
     declared_syms = union(declared_syms, species_extracted)
     vars_extracted, add_default_diff, equations = read_equations_options(
-        options, declared_syms; requiredec)
+        options, declared_syms, parameters_extracted; requiredec)
     variables = vcat(variables_declared, vars_extracted)
     parameters_extracted = setdiff(parameters_extracted, vars_extracted)
 
@@ -705,7 +705,7 @@ end
 # `vars_extracted`: A vector with extracted variables (lhs in pure differential equations only).
 # `dtexpr`: If a differential equation is defined, the default derivative (D ~ Differential(t)) must be defined.
 # `equations`: a vector with the equations provided.
-function read_equations_options(options, syms_declared; requiredec = false)
+function read_equations_options(options, syms_declared, parameters_extracted; requiredec = false)
     # Prepares the equations. First, extracts equations from provided option (converting to block form if required).
     # Next, uses MTK's `parse_equations!` function to split input into a vector with the equations.
     eqs_input = haskey(options, :equations) ? options[:equations].args[3] : :(begin end)
@@ -725,8 +725,7 @@ function read_equations_options(options, syms_declared; requiredec = false)
         end
 
         # If the default differential (`D`) is used, record that it should be decalred later on.
-
-        if !in(eq, syms_declared) && find_D_call(eq)
+        if (:D ∉ union(syms_declared, parameters_extracted)) && find_D_call(eq)
             requiredec && throw(UndeclaredSymbolicError(
                 "Unrecognized symbol D was used as a differential in an equation: \"$eq\". Since the @require_declaration flag is set, all differentials in equations must be explicitly declared using the @differentials option."))
             add_default_diff = true

test/dsl/dsl_options.jl

@@ -614,11 +614,11 @@ let
         #@equations D(V) ~ 1 - V
         #d, X --> 0
     #end
-    @test_broken false # @test_throws Exception @eval @reaction_network begin
-        #@parameters D
-        #@equations D(V) ~ 1 - V
-        #d, X --> 0
-    #end
+    @test_throws Exception @eval @reaction_network begin
+        @parameters D
+        @equations D(V) ~ 1 - V
+        d, X --> 0
+    end
 
     # Symbol only occurring in events.
     @test_throws Exception @eval @reaction_network begin