Add @no_infer flag for turning off species/variable/parameter inferring

src/dsl.jl

@@ -71,7 +71,7 @@ const pure_rate_arrows = Set{Symbol}([:(=>), :(<=), :⇐, :⟽, :⇒, :⟾, :⇔
 # Declares the keys used for various options.
 const option_keys = (:species, :parameters, :variables, :ivs, :compounds, :observables,
     :default_noise_scaling, :differentials, :equations,
-    :continuous_events, :discrete_events, :combinatoric_ratelaws)
+    :continuous_events, :discrete_events, :combinatoric_ratelaws, :require_declaration)
 
 ### `@species` Macro ###
 
@@ -220,13 +220,14 @@ struct ReactionStruct
     products::Vector{ReactantStruct}
     rate::ExprValues
     metadata::Expr
+    rxexpr::Expr
 
     function ReactionStruct(sub_line::ExprValues, prod_line::ExprValues, rate::ExprValues,
-            metadata_line::ExprValues)
+            metadata_line::ExprValues, rx_line::Expr)
         sub = recursive_find_reactants!(sub_line, 1, Vector{ReactantStruct}(undef, 0))
         prod = recursive_find_reactants!(prod_line, 1, Vector{ReactantStruct}(undef, 0))
         metadata = extract_metadata(metadata_line)
-        new(sub, prod, rate, metadata)
+        new(sub, prod, rate, metadata, rx_line)
     end
 end
 
@@ -283,6 +284,17 @@ function extract_metadata(metadata_line::Expr)
     return metadata
 end
 
+
+
+struct UndeclaredSymbolicError <: Exception
+    msg::String
+end
+
+function Base.showerror(io::IO, err::UndeclaredSymbolicError) 
+    print(io, "UndeclaredSymbolicError: ")
+    print(io, err.msg)
+end
+
 ### DSL Internal Master Function ###
 
 # Function for creating a ReactionSystem structure (used by the @reaction_network macro).
@@ -308,6 +320,7 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
     compound_expr, compound_species = read_compound_options(options)
     continuous_events_expr = read_events_option(options, :continuous_events)
     discrete_events_expr = read_events_option(options, :discrete_events)
+    requiredec = haskey(options, :require_declaration)
 
     # Parses reactions, species, and parameters.
     reactions = get_reactions(reaction_lines)
@@ -317,7 +330,7 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
 
     # Reads equations. 
     vars_extracted, add_default_diff, equations = read_equations_options(
-        options, variables_declared)
+        options, variables_declared; requiredec)
     variables = vcat(variables_declared, vars_extracted)
 
     # Handle independent variables
@@ -341,13 +354,13 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
 
     # Reads observables.
     observed_vars, observed_eqs, obs_syms = read_observed_options(
-        options, [species_declared; variables], all_ivs)
+        options, [species_declared; variables], all_ivs; requiredec)
 
     # Collect species and parameters, including ones inferred from the reactions. 
     declared_syms = Set(Iterators.flatten((parameters_declared, species_declared,
         variables)))
     species_extracted, parameters_extracted = extract_species_and_parameters!(
-        reactions, declared_syms)
+        reactions, declared_syms; requiredec)
 
     species = vcat(species_declared, species_extracted)
     parameters = vcat(parameters_declared, parameters_extracted)
@@ -425,15 +438,15 @@ function get_reactions(exprs::Vector{Expr}, reactions = Vector{ReactionStruct}(u
                 error("Error: Must provide a tuple of reaction rates when declaring a bi-directional reaction.")
             end
             push_reactions!(reactions, reaction.args[2], reaction.args[3],
-                rate.args[1], metadata.args[1], arrow)
+                rate.args[1], metadata.args[1], arrow, line)
             push_reactions!(reactions, reaction.args[3], reaction.args[2],
-                rate.args[2], metadata.args[2], arrow)
+                rate.args[2], metadata.args[2], arrow, line)
         elseif in(arrow, fwd_arrows)
             push_reactions!(reactions, reaction.args[2], reaction.args[3],
-                rate, metadata, arrow)
+                rate, metadata, arrow, line)
         elseif in(arrow, bwd_arrows)
             push_reactions!(reactions, reaction.args[3], reaction.args[2],
-                rate, metadata, arrow)
+                rate, metadata, arrow, line)
         else
             throw("Malformed reaction, invalid arrow type used in: $(MacroTools.striplines(line))")
         end
@@ -467,7 +480,7 @@ end
 # Takes a reaction line and creates reaction(s) from it and pushes those to the reaction array.
 # Used to create multiple reactions from, for instance, `k, (X,Y) --> 0`.
 function push_reactions!(reactions::Vector{ReactionStruct}, sub_line::ExprValues,
-        prod_line::ExprValues, rate::ExprValues, metadata::ExprValues, arrow::Symbol)
+        prod_line::ExprValues, rate::ExprValues, metadata::ExprValues, arrow::Symbol, line::Expr)
     # The rates, substrates, products, and metadata may be in a tupple form (e.g. `k, (X,Y) --> 0`).
     # This finds the length of these tuples (or 1 if not in tuple forms). Errors if lengs inconsistent.
     lengs = (tup_leng(sub_line), tup_leng(prod_line), tup_leng(rate), tup_leng(metadata))
@@ -490,7 +503,7 @@ function push_reactions!(reactions::Vector{ReactionStruct}, sub_line::ExprValues
 
         push!(reactions,
             ReactionStruct(get_tup_arg(sub_line, i),
-                get_tup_arg(prod_line, i), get_tup_arg(rate, i), metadata_i))
+                get_tup_arg(prod_line, i), get_tup_arg(rate, i), metadata_i, line))
     end
 end
 
@@ -511,20 +524,26 @@ end
 
 # Function looping through all reactions, to find undeclared symbols (species or
 # parameters), and assign them to the right category.
-function extract_species_and_parameters!(reactions, excluded_syms)
+function extract_species_and_parameters!(reactions, excluded_syms; requiredec = false)
     species = OrderedSet{Union{Symbol, Expr}}()
     for reaction in reactions
         for reactant in Iterators.flatten((reaction.substrates, reaction.products))
             add_syms_from_expr!(species, reactant.reactant, excluded_syms)
+            (!isempty(species) && requiredec) && throw(UndeclaredSymbolicError(
+                                                                               "Unrecognized variables $(join(species, ", ")) detected in reaction expression: \"$(string(reaction.rxexpr))\". Since the flag @require_declaration is declared, all species must be explicitly declared with the @species macro."))
         end
     end
 
     foreach(s -> push!(excluded_syms, s), species)
     parameters = OrderedSet{Union{Symbol, Expr}}()
     for reaction in reactions
         add_syms_from_expr!(parameters, reaction.rate, excluded_syms)
+        (!isempty(parameters) && requiredec) && throw(UndeclaredSymbolicError(
+                                                                              "Unrecognized parameter $(join(parameters, ", ")) detected in rate expression: $(reaction.rate) for the following reaction expression: \"$(string(reaction.rxexpr))\". Since the flag @require_declaration is declared, all parameters must be explicitly declared with the @parameters macro."))
         for reactant in Iterators.flatten((reaction.substrates, reaction.products))
             add_syms_from_expr!(parameters, reactant.stoichiometry, excluded_syms)
+            (!isempty(parameters) && requiredec) && throw(UndeclaredSymbolicError(
+                                                                                  "Unrecognized parameters $(join(parameters, ", ")) detected in the stoichiometry for reactant $(reactant.reactant) in the following reaction expression: \"$(string(reaction.rxexpr))\". Since the flag @require_declaration is declared, all parameters must be explicitly declared with the @parameters macro."))
         end
     end
 
@@ -682,7 +701,7 @@ 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, variables_declared)
+function read_equations_options(options, variables_declared; 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)
@@ -711,9 +730,13 @@ function read_equations_options(options, variables_declared)
             diff_var = lhs.args[2]
             if in(diff_var, forbidden_symbols_error)
                 error("A forbidden symbol ($(diff_var)) was used as an variable in this differential equation: $eq")
+            elseif (!in(diff_var, variables_declared)) && requiredec
+                throw(UndeclaredSymbolicError(
+                                              "Unrecognized symbol $(diff_var) was used as a variable in an equation: \"$eq\". Since the @require_declaration flag is set, all variables in equations must be explicitly declared via @variables, @species, or @parameters."))
+            else
+                add_default_diff = true
+                in(diff_var, variables_declared) || push!(vars_extracted, diff_var)
             end
-            add_default_diff = true
-            in(diff_var, variables_declared) || push!(vars_extracted, diff_var)
         end
     end
 
@@ -752,7 +775,7 @@ function create_differential_expr(options, add_default_diff, used_syms, tiv)
 end
 
 # Reads the observables options. Outputs an expression ofr creating the observable variables, and a vector of observable equations.
-function read_observed_options(options, species_n_vars_declared, ivs_sorted)
+function read_observed_options(options, species_n_vars_declared, ivs_sorted; requiredec = false)
     if haskey(options, :observables)
         # Gets list of observable equations and prepares variable declaration expression.
         # (`options[:observables]` includes `@observables`, `.args[3]` removes this part)
@@ -763,6 +786,10 @@ function read_observed_options(options, species_n_vars_declared, ivs_sorted)
         for (idx, obs_eq) in enumerate(observed_eqs.args)
             # Extract the observable, checks errors, and continues the loop if the observable has been declared.
             obs_name, ivs, defaults, metadata = find_varinfo_in_declaration(obs_eq.args[2])
+            if (requiredec && !in(obs_name, species_n_vars_declared))
+                throw(UndeclaredSymbolicError(
+                                              "An undeclared variable ($obs_name) was declared as an observable in the following observable equation: \"$obs_eq\". Since the flag @require_declaration is set, all variables must be declared with the @species, @parameters, or @variables macros."))
+            end
             isempty(ivs) ||
                 error("An observable ($obs_name) was given independent variable(s). These should not be given, as they are inferred automatically.")
             isnothing(defaults) ||

test/dsl/dsl_options.jl

@@ -1022,3 +1022,73 @@ let
     @parameters v n
     @test isequal(Catalyst.expand_registered_functions(equations(rn4)[1]), D(A) ~ v*(A^n))
 end
+
+### test that @no_infer properly throws errors when undeclared variables are written
+
+import Catalyst: UndeclaredSymbolicError
+let
+    # Test error when species are inferred
+    @test_throws UndeclaredSymbolicError @macroexpand @reaction_network begin
+        @require_declaration
+        @parameters k 
+        k, A --> B
+    end
+    @test_nowarn @macroexpand @reaction_network begin
+        @require_declaration
+        @species A(t) B(t)
+        @parameters k
+        k, A --> B
+    end
+
+    # Test error when a parameter in rate is inferred
+    @test_throws UndeclaredSymbolicError @macroexpand @reaction_network begin
+        @require_declaration
+        @species A(t) B(t)
+        @parameters k
+        k*n, A --> B
+    end
+    @test_nowarn @macroexpand @reaction_network begin
+        @require_declaration
+        @parameters n k
+        @species A(t) B(t)
+        k*n, A --> B
+    end
+
+    # Test error when a parameter in stoichiometry is inferred
+    @test_throws UndeclaredSymbolicError @macroexpand @reaction_network begin
+        @require_declaration
+        @parameters k
+        @species A(t) B(t)
+        k, n*A --> B
+    end
+    @test_nowarn @macroexpand @reaction_network begin
+        @require_declaration
+        @parameters k n
+        @species A(t) B(t)
+        k, n*A --> B
+    end
+
+    # Test error when a variable in an equation is inferred
+    @test_throws UndeclaredSymbolicError @macroexpand @reaction_network begin
+        @require_declaration
+        @equations D(V) ~ V^2
+    end
+    @test_nowarn @macroexpand @reaction_network begin
+        @require_declaration
+        @variables V(t)
+        @equations D(V) ~ V^2
+    end
+
+    # Test error when a variable in an observable is inferred
+    @test_throws UndeclaredSymbolicError @macroexpand @reaction_network begin
+        @require_declaration
+        @variables X1(t)
+        @observables X2 ~ X1
+    end
+    @test_nowarn @macroexpand @reaction_network begin
+        @require_declaration
+        @variables X1(t) X2(t)
+        @observables X2 ~ X1
+    end
+end
+