Refactor "srcd/sl.jl" file

src/Catalyst.jl

@@ -40,6 +40,7 @@ import ModelingToolkit: check_variables,
 
 import Base: (==), hash, size, getindex, setindex, isless, Sort.defalg, length, show
 import MacroTools, Graphs
+using MacroTools: striplines
 import Graphs: DiGraph, SimpleGraph, SimpleDiGraph, vertices, edges, add_vertices!, nv, ne
 import DataStructures: OrderedDict, OrderedSet
 import Parameters: @with_kw_noshow

src/chemistry_functionality.jl

@@ -86,7 +86,7 @@ function make_compound(expr)
     # Cannot extract directly using e.g. "getfield.(composition, :reactant)" because then 
     # we get something like :([:C, :O]), rather than :([C, O]).
     composition = Catalyst.recursive_find_reactants!(expr.args[3], 1,
-        Vector{ReactantStruct}(undef, 0))
+        Vector{ReactantInternal}(undef, 0))
     components = :([])                                      # Becomes something like :([C, O]).                                         
     coefficients = :([])                                    # Becomes something like :([1, 2]). 
     for comp in composition

src/expression_utils.jl

@@ -2,15 +2,18 @@
 
 # Function that handles variable interpolation.
 function esc_dollars!(ex)
-    if ex isa Expr
-        if ex.head == :$
-            return esc(:($(ex.args[1])))
-        else
-            for i in 1:length(ex.args)
-                ex.args[i] = esc_dollars!(ex.args[i])
-            end
+    # If we do not have an expression: recursion has finished and we return the input.
+    (ex isa Expr) || (return ex)
+
+    # If we have encountered an interpolation, perform the appropriate modification, else recur. 
+    if ex.head == :$
+        return esc(:($(ex.args[1])))
+    else
+        for i in eachindex(ex.args)
+            ex.args[i] = esc_dollars!(ex.args[i])
         end
     end
+
     ex
 end
 
@@ -22,28 +25,23 @@ end
 ### Parameters/Species/Variables Symbols Correctness Checking ###
 
 # Throws an error when a forbidden symbol is used.
-function forbidden_symbol_check(v)
-    !isempty(intersect(forbidden_symbols_error, v)) &&
-        error("The following symbol(s) are used as species or parameters: " *
-              ((map(s -> "'" * string(s) * "', ",
-                  intersect(forbidden_symbols_error, v))...)) *
-              "this is not permitted.")
-    nothing
+function forbidden_symbol_check(sym)
+    isempty(intersect(forbidden_symbols_error, sym)) && return
+    used_forbidden_syms = intersect(forbidden_symbols_error, sym)
+    error("The following symbol(s) are used as species or parameters: $used_forbidden_syms, this is not permitted.")
 end
 
 # Throws an error when a forbidden variable is used (a forbidden symbol that is not `:t`).
-function forbidden_variable_check(v)
-    !isempty(intersect(forbidden_variables_error, v)) &&
-        error("The following symbol(s) are used as variables: " *
-              ((map(s -> "'" * string(s) * "', ",
-                  intersect(forbidden_variables_error, v))...)) *
-              "this is not permitted.")
+function forbidden_variable_check(sym)
+    isempty(intersect(forbidden_variables_error, sym)) && return
+    used_forbidden_syms = intersect(forbidden_variables_error, sym)
+    error("The following symbol(s) are used as variables: $used_forbidden_syms, this is not permitted.")
 end
 
+# Checks that no symbol was sued for multiple purposes.
 function unique_symbol_check(syms)
-    allunique(syms) ||
-        error("Reaction network independent variables, parameters, species, and variables must all have distinct names, but a duplicate has been detected. ")
-    nothing
+    allunique(syms) && return
+    error("Reaction network independent variables, parameters, species, and variables must all have distinct names, but a duplicate has been detected. ")
 end
 
 ### Catalyst-specific Expressions Manipulation ###

src/spatial_reaction_systems/spatial_reactions.jl

@@ -57,7 +57,7 @@ function make_transport_reaction(rateex, species)
     forbidden_symbol_check(union([species], parameters))
 
     # Creates expressions corresponding to actual code from the internal DSL representation.
-    sexprs = get_sexpr([species], Dict{Symbol, Expr}())
+    sexprs = get_usexpr([species], Dict{Symbol, Expr}())
     pexprs = get_pexpr(parameters, Dict{Symbol, Expr}())
     iv = :($(DEFAULT_IV_SYM) = default_t())
     trxexpr = :(TransportReaction($rateex, $species))

test/dsl/dsl_advanced_model_construction.jl

@@ -131,7 +131,7 @@ let
     end
     # Line number nodes aren't ignored so have to be manually removed
     Base.remove_linenums!(ex)
-    @test eval(Catalyst.make_reaction_system(ex)) isa ReactionSystem
+    @test eval(Catalyst.make_reaction_system(ex, QuoteNode(:name))) isa ReactionSystem
 end
 
 # Miscellaneous interpolation tests. Unsure what they do here (not related to DSL).
@@ -211,11 +211,11 @@ let
 end
 
 # Checks that repeated metadata throws errors.
-let
-    @test_throws LoadError @eval @reaction k, 0 --> X, [md1=1.0, md1=2.0]
-    @test_throws LoadError @eval @reaction_network begin
-        k, 0 --> X, [md1=1.0, md1=1.0]
-    end
+let 
+    @test_throws Exception @eval @reaction k, 0 --> X, [md1=1.0, md1=2.0] 
+    @test_throws Exception @eval @reaction_network begin
+        k, 0 --> X, [md1=1.0, md1=1.0] 
+    end 
 end
 
 # Tests for nested metadata.
@@ -267,6 +267,24 @@ let
     @test isequal(rn1,rn2)
 end
 
+# Tests that erroneous metadata declarations yields errors.
+let
+    # Malformed metadata/value separator.
+    @test_throws Exception @eval @reaction_network begin
+        d, X --> 0, [misc=>"Metadata should use `=`, not `=>`."]
+    end
+
+    # Malformed lhs
+    @test_throws Exception @eval @reaction_network begin
+        d, X --> 0, [misc,description=>"Metadata lhs should be a single symbol."]
+    end
+
+    # Malformed metadata separator.
+    @test_throws Exception @eval @reaction_network begin
+        d, X --> 0, [misc=>:misc; description="description"]
+    end
+end
+
 ### Other Tests ###
 
 # Test floating point stoichiometry work.
@@ -344,4 +362,4 @@ let
     rx = Reaction(k[1]*a+k[2], [X[1], X[2]], [Y, C], [1, V[1]], [V[2] * W, B])
     @named arrtest = ReactionSystem([rx], t)
     arrtest == rn
-end
+end

test/dsl/dsl_basic_model_construction.jl

@@ -55,6 +55,65 @@ end
 
 ## Run Tests ###
 
+# Tests the various network constructors. Test for `@network_component` and `@network_component`.
+# Tests for combinations of reactions/no reactions, no name/name/interpolated name.
+let
+    # Declare comparison networks programmatically.
+    @parameters d
+    @species X(t)
+    rx = Reaction(d, [X], [])
+
+    rs_empty = ReactionSystem([], t; name = :name)
+    rs = ReactionSystem([rx], t; name = :name)
+    rs_empty_comp = complete(rs_empty)
+    rs_comp = complete(rs)
+
+    # Declare empty networks.
+    name_sym = :name
+    rs_empty_1 = @network_component
+    rs_empty_2 = @network_component name
+    rs_empty_3 = @network_component $name_sym
+    rs_empty_comp_1 = @reaction_network
+    rs_empty_comp_2 = @reaction_network name
+    rs_empty_comp_3 = @reaction_network $name_sym
+
+    # Check that empty networks are correct.
+    isequivalent(rs_empty_1, rs_empty)
+    rs_empty_2 == rs_empty
+    rs_empty_3 == rs_empty
+    isequivalent(rs_empty_comp_1, rs_empty_comp)
+    rs_empty_comp_2 == rs_empty_comp
+    rs_empty_comp_3 == rs_empty_comp
+
+    # Declare non-empty networks.
+    rs_1 = @network_component begin
+        d, X --> 0
+    end
+    rs_2 = @network_component name begin
+        d, X --> 0
+    end
+    rs_3 = @network_component $name_sym begin
+        d, X --> 0
+    end
+    rs_comp_1 = @reaction_network begin
+        d, X --> 0
+    end
+    rs_comp_2 = @reaction_network name begin
+        d, X --> 0
+    end
+    rs_comp_3 = @reaction_network $name_sym begin
+        d, X --> 0
+    end
+
+    # Check that non-empty networks are correct.
+    isequivalent(rs_1, rs)
+    rs_2 == rs
+    rs_3 == rs
+    isequivalent(rs_empty_1, rs_empty)
+    rs_empty_2 == rs_empty
+    rs_empty_3 == rs_empty
+end
+
 # Test basic properties of networks.
 let
     basic_test(reaction_networks_standard[1], 10, [:X1, :X2, :X3],
@@ -404,7 +463,7 @@ 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))
@@ -437,6 +496,41 @@ let
     @test_throws LoadError @eval @reaction nothing, 0 --> B
     @test_throws LoadError @eval @reaction k, 0 --> im
     @test_throws LoadError @eval @reaction k, 0 --> nothing
+
+    # Checks that non-supported arrow type usage yields error.
+    @test_throws Exception @eval @reaction_network begin
+        d, X ⇻ 0
+    end
 end
 
+### Error Test ###
 
+# Erroneous `@reaction` usage.
+let
+    # Bi-directional reaction using the `@reaction` macro.
+    @test_throws Exception @eval @reaction (k1,k2), X1 <--> X2
+
+    # Bundles reactions.
+    @test_throws Exception @eval @reaction k, (X1,X2) --> 0
+end
+
+# Tests that malformed reactions yields errors.
+let
+    # Checks that malformed combinations of entries yields errors.
+    @test_throws Exception @eval @reaction_network begin
+        d, X --> 0, Y --> 0
+    end
+    @test_throws Exception @eval @reaction_network begin
+        d, X --> 0, [misc="Ok metadata"], [description="Metadata in (erroneously) extra []."]
+    end
+
+    # Checks that incorrect bundling yields error.
+    @test_throws Exception @eval @reaction_network begin
+        (k1,k2,k3), (X1,X2) --> 0
+    end
+
+    # Checks that incorrect stoichiometric expression yields an error.
+    @test_throws Exception @eval @reaction_network begin
+        k, X^Y --> XY
+    end
+end

test/dsl/dsl_options.jl

@@ -414,15 +414,44 @@ let
     spcs = (A, B1, B2, C)
     @test issetequal(unknowns(rn), sts)
     @test issetequal(species(rn), spcs)
+end
 
-    @test_throws ArgumentError begin
-        rn = @reaction_network begin
-            @variables K
-            k, K*A --> B
-        end
+# Tests errors in `@variables` declarations.
+let 
+    # Variable used as species in reaction.
+    @test_throws Exception @eval rn = @reaction_network begin
+        @variables K(t)
+        k, K + A --> B
+    end
+
+    # Tests error when disallowed name is used for variable.
+    @test_throws Exception @eval @reaction_network begin
+        @variables π(t)
+    end
+end
+
+
+# Tests that duplicate iv/parameter/species/variable names cannot be provided.
+let
+    @test_throws Exception @eval @reaction_network begin
+        @spatial_ivs X
+        @species X(t)
+    end
+    @test_throws Exception @eval @reaction_network begin
+        @parameters X
+        @species X(t)
+    end
+    @test_throws Exception @eval @reaction_network begin
+        @species X(t)
+        @variables X(t)
+    end
+    @test_throws Exception @eval @reaction_network begin
+        @parameters X
+        @variables X(t)
     end
 end
 
+
 ### Test Independent Variable Designations ###
 
 # Test ivs in DSL.
@@ -739,6 +768,14 @@ let
         @observables $X ~ X1 + X2
         (k1,k2), X1 <--> X2
     end
+
+    # Observable metadata provided twice.
+    @test_throws Exception @eval @reaction_network begin
+        @species X2 [description="Twice the amount of X"]
+        @observables (X2, [description="X times two."]) ~ 2X 
+        d, X --> 0
+    end
+
 end
 
 
@@ -916,8 +953,15 @@ let
         @equations X ~ p - S
         (P,D), 0 <--> S
     end
+
+    # Differential equation using a forbidden variable (in the DSL).
+    @test_throws Exception @eval @reaction_network begin
+        @equations D(π) ~ -1
+    end
 end
 
+### Other DSL Option Tests ###
+
 # test combinatoric_ratelaws DSL option
 let
     rn = @reaction_network begin
@@ -951,3 +995,11 @@ let
     @unpack k1, A = rn3
     @test isequal(rl, k1*A^2)
 end
+
+# Erroneous `@default_noise_scaling` declaration (other noise scaling tests are mostly in the SDE file).
+let
+    # Default noise scaling with multiple entries.
+    @test_throws Exception @eval @reaction_network begin
+        @default_noise_scaling η1 η2
+    end 
+end