improve option error handling, more tests

Author: TorkelE

src/dsl.jl

@@ -637,9 +637,8 @@ end
 # the `default_noise_scaling` reaction metadata, otherwise, returns an empty vector.
 function read_default_noise_scaling_option(options)
     if haskey(options, :default_noise_scaling)
-        if (length(options[:default_noise_scaling].args) != 3)
-            error("@default_noise_scaling should only have a single expression as its input, this appears not to be the case: \"$(options[:default_noise_scaling])\"")
-        end
+        (length(options[:default_noise_scaling].args) != 3) &&
+            error("@default_noise_scaling should only have a single expression as its input, this appears not to be the case: \"$(options[:default_noise_scaling])\"")        
         return :([:noise_scaling => $(options[:default_noise_scaling].args[3])])
     end
     return :([])
@@ -649,11 +648,14 @@ end
 # of the compound species, and also the expression that crates them.
 function read_compound_options(options)
     # If the compound option is used, retrieve a list of compound species and  the option line
-    # that creates them (used to declare them as compounds at the end).
+    # that creates them (used to declare them as compounds at the end). Due to some expression
+    # handling, in the case of a single compound we must change to the `@compound` macro.
     if haskey(options, :compounds)
         cmpexpr_init = options[:compounds]
+        cmpexpr_init.args[3] = option_block_form(get_block_option(cmpexpr_init))
         cmps_declared = [find_varinfo_in_declaration(arg.args[2])[1]
                             for arg in cmpexpr_init.args[3].args]
+        (length(cmps_declared) == 1) && (cmpexpr_init.args[1] = Symbol("@compound"))
     else  # If option is not used, return empty vectors and expressions.
         cmpexpr_init = :()
         cmps_declared = Union{Symbol, Expr}[]
@@ -667,7 +669,7 @@ function read_events_option(options, event_type::Symbol)
     if event_type ∉ [:continuous_events, :discrete_events]
         error("Trying to read an unsupported event type.")
     end
-    events_input = haskey(options, event_type) ? options[event_type].args[3] :
+    events_input = haskey(options, event_type) ? get_block_option(options[event_type]) :
                    striplines(:(begin end))
     events_input = option_block_form(events_input)
 
@@ -701,7 +703,7 @@ end
 function read_equations_options!(diffsexpr, options, syms_unavailable, tiv; 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)
+    eqs_input = haskey(options, :equations) ? get_block_option(options[:equations]) : :(begin end)
     eqs_input = option_block_form(eqs_input)
     equations = Expr[]
     ModelingToolkit.parse_equations!(Expr(:block), equations,
@@ -759,8 +761,8 @@ function read_differentials_option(options)
     # Creates the differential expression.
     # If differentials was provided as options, this is used as the initial expression.
     # If the default differential (D(...)) was used in equations, this is added to the expression.
-    diffsexpr = (haskey(options, :differentials) ? options[:differentials].args[3] :
-                striplines(:(begin end)))
+    diffsexpr = (haskey(options, :differentials) ? 
+        get_block_option(options[:differentials]) : striplines(:(begin end)))
     diffsexpr = option_block_form(diffsexpr)
 
     # Goes through all differentials, checking that they are correctly formatted. Adds their
@@ -794,7 +796,7 @@ function read_observed_options(options, all_ivs, us_declared, all_syms; required
     if haskey(options, :observables)
         # Gets list of observable equations and prepares variable declaration expression.
         # (`options[:observables]` includes `@observables`, `.args[3]` removes this part)
-        obs_eqs = make_obs_eqs(options[:observables].args[3])
+        obs_eqs = make_obs_eqs(get_block_option(options[:observables]))
         obsexpr = Expr(:block, :(@variables))
         obs_syms = :([])
 

src/expression_utils.jl

@@ -34,6 +34,16 @@ end
 
 ### Catalyst-specific Expressions Manipulation ###
 
+# Many option inputs can be on a form `@option input` or `@option begin ... end`. In both these
+# cases we want to retrieve the third argument in the option expression. Further more, we wish
+# to throw an error if there is more inputs (suggesting e.g. multiple inputs on a single line).
+# Note that there are only some options for which we wish to make this check.
+function get_block_option(expr)
+    (length(expr.args) > 3) &&
+        error("An option input ($expr) is misformatted. Potentially, it has multiple inputs on a single lines, and these should be split across multiple lines using a `begin ... end` block.")
+    return expr.args[3]
+end
+
 # Some options takes input on form that is either `@option ...` or `@option begin ... end`.
 # This transforms input of the latter form to the former (with only one line in the `begin ... end` block)
 function option_block_form(expr)

test/dsl/dsl_basic_model_construction.jl

@@ -471,8 +471,8 @@ let
     @test isequal((@reaction k, 0 --> X), (@reaction k, 0 ⥟ X))
 end
 
-# Test that symbols with special meanings, or that are forbidden, are handled properly.
-let
+# Test that symbols with special meanings are handled properly.
+let 
     test_network = @reaction_network begin t * k, X --> ∅ end
     @test length(species(test_network)) == 1
     @test length(parameters(test_network)) == 1
@@ -491,11 +491,39 @@ let
     @test length(species(test_network)) == 1
     @test length(parameters(test_network)) == 0
     @test reactions(test_network)[1].rate == ℯ
+end
 
-    @test_throws LoadError @eval @reaction im, 0 --> B
-    @test_throws LoadError @eval @reaction nothing, 0 --> B
-    @test_throws LoadError @eval @reaction k, 0 --> im
-    @test_throws LoadError @eval @reaction k, 0 --> nothing
+# Check that forbidden symbols correctly generates errors.
+let
+    # @reaction macro, symbols that cannot be in the rate.
+    @test_throws Exception @eval @reaction im, 0 --> X
+    @test_throws Exception @eval @reaction nothing, 0 --> X
+    @test_throws Exception @eval @reaction Γ, 0 --> X
+    @test_throws Exception @eval @reaction ∅, 0 --> X
+    
+    # @reaction macro, symbols that cannot be a reactant.
+    @test_throws Exception @eval @reaction 1, 0 --> im
+    @test_throws Exception @eval @reaction 1, 0 --> nothing
+    @test_throws Exception @eval @reaction 1, 0 --> Γ
+    @test_throws Exception @eval @reaction 1, 0 --> ℯ
+    @test_throws Exception @eval @reaction 1, 0 --> pi
+    @test_throws Exception @eval @reaction 1, 0 --> π
+    @test_throws Exception @eval @reaction 1, 0 --> t
+    
+    # @reaction_network macro, symbols that cannot be in the rate.
+    @test_throws Exception @eval @reaction_network begin im, 0 --> X end
+    @test_throws Exception @eval @reaction_network begin nothing, 0 --> X end
+    @test_throws Exception @eval @reaction_network begin Γ, 0 --> X end
+    @test_throws Exception @eval @reaction_network begin ∅, 0 --> X end
+    
+    # @reaction_network macro, symbols that cannot be a reactant.
+    @test_throws Exception @eval @reaction_network begin 1, 0 --> im end
+    @test_throws Exception @eval @reaction_network begin 1, 0 --> nothing end
+    @test_throws Exception @eval @reaction_network begin 1, 0 --> Γ end
+    @test_throws Exception @eval @reaction_network begin 1, 0 --> ℯ end
+    @test_throws Exception @eval @reaction_network begin 1, 0 --> pi end
+    @test_throws Exception @eval @reaction_network begin 1, 0 --> π end
+    @test_throws Exception @eval @reaction_network begin 1, 0 --> t end
 
     # Checks that non-supported arrow type usage yields error.
     @test_throws Exception @eval @reaction_network begin

test/dsl/dsl_options.jl

@@ -1144,12 +1144,112 @@ end
 
 ### Other DSL Option Tests ###
 
+# Test that various options can be provided in block and single line form.
+# Also checks that the single line form takes maximally one argument.
+let
+    # The `@equations` option.
+    rn11 = @reaction_network rn1 begin
+        @equations D(V) ~ 1 - V
+    end
+    rn12 = @reaction_network rn1 begin
+        @equations begin
+            D(V) ~ 1 - V
+        end
+    end
+    @test isequal(rn11, rn12)
+    @test_throws Exception @eval @reaction_network begin
+        @equations D(V) ~ 1 - V D(W) ~ 1 - W
+    end
+
+    # The `@observables` option.
+    rn21 = @reaction_network rn1 begin
+        @species X(t)
+        @observables X2 ~ 2X
+    end
+    rn22 = @reaction_network rn1 begin
+        @species X(t)
+        @observables begin
+            X2 ~ 2X
+        end
+    end
+    @test isequal(rn21, rn22)
+    @test_throws Exception @eval @reaction_network begin
+        @species X(t)
+        @observables X2 ~ 2X X3 ~ 3X
+    end
+
+    # The `@compounds` option.
+    rn31 = @reaction_network rn1 begin
+        @species X(t)
+        @compounds X2 ~ 2X
+    end
+    rn32 = @reaction_network rn1 begin
+        @species X(t)
+        @compounds begin
+            X2 ~ 2X
+        end
+    end
+    @test isequal(rn31, rn32)
+    @test_throws Exception @eval @reaction_network begin
+        @species X(t)
+        @compounds X2 ~ 2X X3 ~ 3X
+    end
+
+    # The `@differentials` option.
+    rn41 = @reaction_network rn1 begin
+        @differentials D = Differential(t)
+    end
+    rn42 = @reaction_network rn1 begin
+        @differentials begin
+            D = Differential(t)
+        end
+    end
+    @test isequal(rn41, rn42)
+    @test_throws Exception @eval @reaction_network begin
+        @differentials D = Differential(t) Δ = Differential(t)
+    end
+
+    # The `@continuous_events` option.
+    rn51 = @reaction_network rn1 begin
+        @species X(t)
+        @continuous_events [X ~ 3.0] => [X ~ X - 1]
+    end
+    rn52 = @reaction_network rn1 begin
+        @species X(t)
+        @continuous_events begin
+            [X ~ 3.0] => [X ~ X - 1]
+        end
+    end
+    @test isequal(rn51, rn52)
+    @test_throws Exception @eval @reaction_network begin
+        @species X(t)
+        @continuous_events [X ~ 3.0] => [X ~ X - 1] [X ~ 1.0] => [X ~ X + 1]
+    end
+
+    # The `@discrete_events` option.
+    rn61 = @reaction_network rn1 begin
+        @species X(t)
+        @discrete_events [X > 3.0] => [X ~ X - 1]
+    end
+    rn62 = @reaction_network rn1 begin
+        @species X(t)
+        @discrete_events begin
+            [X > 3.0] => [X ~ X - 1]
+        end
+    end
+    @test isequal(rn61, rn62)
+    @test_throws Exception @eval @reaction_network begin
+        @species X(t)
+        @discrete_events [X > 3.0] => [X ~ X - 1] [X < 1.0] => [X ~ X + 1]
+    end
+end
+
 # test combinatoric_ratelaws DSL option
 let
     rn = @reaction_network begin
         @combinatoric_ratelaws false
         (k1,k2), 2A <--> B
-        end
+    end
     combinatoric_ratelaw = Catalyst.get_combinatoric_ratelaws(rn)
     @test combinatoric_ratelaw == false
     rl = oderatelaw(reactions(rn)[1]; combinatoric_ratelaw)
@@ -1159,7 +1259,7 @@ let
     rn2 = @reaction_network begin
         @combinatoric_ratelaws true
         (k1,k2), 2A <--> B
-        end
+    end
     combinatoric_ratelaw = Catalyst.get_combinatoric_ratelaws(rn2)
     @test combinatoric_ratelaw == true
     rl = oderatelaw(reactions(rn2)[1]; combinatoric_ratelaw)
@@ -1170,7 +1270,7 @@ let
     rn3 = @reaction_network begin
         @combinatoric_ratelaws $crl
         (k1,k2), 2A <--> B
-        end
+    end
     combinatoric_ratelaw = Catalyst.get_combinatoric_ratelaws(rn3)
     @test combinatoric_ratelaw == crl
     rl = oderatelaw(reactions(rn3)[1]; combinatoric_ratelaw)
@@ -1256,10 +1356,10 @@ let
     end
 end
 
-### test that @no_infer properly throws errors when undeclared variables are written ###
-
-import Catalyst: UndeclaredSymbolicError
+# test that @require_declaration properly throws errors when undeclared variables are written.
 let
+    import Catalyst: UndeclaredSymbolicError
+
     # Test error when species are inferred
     @test_throws UndeclaredSymbolicError @macroexpand @reaction_network begin
         @require_declaration