add additional tests, use argumenterror where appropriate

Author: TorkelE

src/spatial_reaction_systems/lattice_jump_systems.jl

@@ -30,7 +30,7 @@ function JumpProcesses.JumpProblem(lrs::LatticeReactionSystem, dprob, aggregator
                                    combinatoric_ratelaws = get_combinatoric_ratelaws(reactionsystem(lrs)), kwargs...)
     # Error checks.
     if !isnothing(dprob.f.sys)
-        error("Unexpected `DiscreteProblem` passed into `JumpProblem`. Was a `LatticeReactionSystem` used as input to the initial `DiscreteProblem`?")
+        throw(ArgumentError("Unexpected `DiscreteProblem` passed into `JumpProblem`. Was a `LatticeReactionSystem` used as input to the initial `DiscreteProblem`?"))
     end
 
     # Computes hopping constants and mass action jumps (requires some internal juggling).

src/spatial_reaction_systems/lattice_reaction_systems.jl

@@ -51,19 +51,22 @@ struct LatticeReactionSystem{Q,R,S,T} <: MT.AbstractTimeDependentSystem
                                    num_verts::Int64, num_edges::Int64, edge_iterator::T) where {Q,R,S,T}
         # Error checks.
         if !(R <: AbstractSpatialReaction)
-            error("The second argument must be a vector of AbstractSpatialReaction subtypes.") 
+            throw(ArgumentError("The second argument must be a vector of AbstractSpatialReaction subtypes."))
+        end
+        if !iscomplete(rs)
+            throw(ArgumentError("A non-complete `ReactionSystem` was used as input, this is not permitted."))
         end
         if !isempty(MT.get_systems(rs))
-            error("A non-flattened (hierarchical) `ReactionSystem` was used as input. `LatticeReactionSystem`s can only be based on non-hierarchical `ReactionSystem`s.")
+            throw(ArgumentError("A non-flattened (hierarchical) `ReactionSystem` was used as input. `LatticeReactionSystem`s can only be based on non-hierarchical `ReactionSystem`s."))
         end
         if length(species(rs)) != length(unknowns(rs))
-            error("The `ReactionSystem` used as input contain variable unknowns (in addition to species unknowns). This is not permitted (the input `ReactionSystem` must contain species unknowns only).")
+            throw(ArgumentError("The `ReactionSystem` used as input contain variable unknowns (in addition to species unknowns). This is not permitted (the input `ReactionSystem` must contain species unknowns only)."))
         end
         if length(reactions(rs)) != length(equations(rs))
-            error("The `ReactionSystem` used as input contain equations (in addition to reactions). This is not permitted.")
+            throw(ArgumentError("The `ReactionSystem` used as input contain equations (in addition to reactions). This is not permitted."))
         end
         if !isempty(MT.continuous_events(rs)) || !isempty(MT.discrete_events(rs))
-            @warn "The `ReactionSystem` used as input to `LatticeReactionSystem contain events. These will be ignored in any simulations based on the created `LatticeReactionSystem`."
+            throw(ArgumentError("The `ReactionSystem` used as input to `LatticeReactionSystem contain events. These will be ignored in any simulations based on the created `LatticeReactionSystem`."))
         end
         if !isempty(observed(rs))
             @warn "The `ReactionSystem` used as input to `LatticeReactionSystem contain observables. It will not be possible to access these from the created `LatticeReactionSystem`."
@@ -295,7 +298,7 @@ E.g. for a lattice `CartesianGrid(4,6)`, `(4,6)` is returned.
 grid_size(lrs::LatticeReactionSystem) = grid_size(lattice(lrs))
 grid_size(lattice::CartesianGridRej{N,T}) where {N,T} = lattice.dims
 grid_size(lattice::Array{Bool, N}) where {N} = size(lattice)
-grid_size(lattice::Graph) = error("Grid size is only defined for LatticeReactionSystems with grid-based lattices (not graph-based).")
+grid_size(lattice::Graphs.AbstractGraph) = throw(ArgumentError("Grid size is only defined for LatticeReactionSystems with grid-based lattices (not graph-based)."))
 
 """
     grid_dims(lrs::LatticeReactionSystem)
@@ -305,7 +308,7 @@ The output is either `1`, `2`, or `3`.
 """
 grid_dims(lrs::LatticeReactionSystem) = grid_dims(lattice(lrs))
 grid_dims(lattice::GridLattice{N,T}) where {N,T} = return N
-grid_dims(lattice::Graph) = error("Grid dimensions is only defined for LatticeReactionSystems with grid-based lattices (not graph-based).")
+grid_dims(lattice::Graphs.AbstractGraph) = throw(ArgumentError("Grid dimensions is only defined for LatticeReactionSystems with grid-based lattices (not graph-based)."))
 
 """
     get_lattice_graph(lrs::LatticeReactionSystem)
@@ -333,7 +336,6 @@ reactions(lrs::LatticeReactionSystem) = reactions(reactionsystem(lrs))
 MT.nameof(lrs::LatticeReactionSystem) = MT.nameof(reactionsystem(lrs))
 MT.get_iv(lrs::LatticeReactionSystem) = MT.get_iv(reactionsystem(lrs))
 MT.equations(lrs::LatticeReactionSystem) = MT.equations(reactionsystem(lrs))
-MT.equations(lrs::LatticeReactionSystem) = MT.equations(reactionsystem(lrs))
 MT.unknowns(lrs::LatticeReactionSystem) = MT.unknowns(reactionsystem(lrs))
 MT.get_metadata(lrs::LatticeReactionSystem) = MT.get_metadata(reactionsystem(lrs))
 

src/spatial_reaction_systems/spatial_ODE_systems.jl

@@ -208,7 +208,7 @@ function build_odefunction(lrs::LatticeReactionSystem, vert_ps::Vector{Pair{R,Ve
                            remove_conserved, checks) where {R,S,T}
     # Error check.
     if remove_conserved 
-        error("Removal of conserved quantities is currently not supported for `LatticeReactionSystem`s")
+        throw(ArgumentError("Removal of conserved quantities is currently not supported for `LatticeReactionSystem`s"))
     end
 
     # Prepares the inputs to the `LatticeTransportODEFunction` functor. 

src/spatial_reaction_systems/spatial_reactions.jl

@@ -165,5 +165,5 @@ function find_parameters_in_rate!(parameters, rateex::ExprValues)
             find_parameters_in_rate!(parameters, rateex.args[i])
         end
     end
-    nothing
+    return nothing
 end

src/spatial_reaction_systems/utility.jl

@@ -55,10 +55,10 @@ end
 function lattice_process_input(input::Dict{<:Any, T}, syms::Vector) where {T}
     # Error checks
     if !isempty(setdiff(keys(input), syms))
-        error("You have provided values for the following unrecognised parameters/initial conditions: $(setdiff(keys(input), syms)).")
+        throw(ArgumentError("You have provided values for the following unrecognised parameters/initial conditions: $(setdiff(keys(input), syms))."))
     end
     if !isempty(setdiff(syms, keys(input)))
-        error("You have not provided values for the following parameters/initial conditions: $(setdiff(syms, keys(input))).")
+        throw(ArgumentError("You have not provided values for the following parameters/initial conditions: $(setdiff(syms, keys(input)))."))
     end
 
     return [sym => input[sym] for sym in syms]
@@ -67,7 +67,7 @@ function lattice_process_input(input, syms::Vector)
     if ((input isa Vector) || (input isa Tuple)) && all(entry isa Pair for entry in input)
         return lattice_process_input(Dict(input), syms)
     end
-    error("Input parameters/initial conditions have the wrong format ($(typeof(input))). These should either be a Dictionary, or a Tuple or a Vector (where each entry is a Pair taking a parameter/species to its value).")
+    throw(ArgumentError("Input parameters/initial conditions have the wrong format ($(typeof(input))). These should either be a Dictionary, or a Tuple or a Vector (where each entry is a Pair taking a parameter/species to its value)."))
 end
 
 # Splits parameters into vertex and edge parameters.
@@ -100,7 +100,7 @@ function vertex_value_form(values, lrs::LatticeReactionSystem, sym::BasicSymboli
         # For the case where the i'th value of the vector corresponds to the value in the i'th vertex.
         # This is the only (non-uniform) case possible for graph grids.
         if (length(values) != num_verts(lrs)) 
-            error("You have provided ($(length(values))) values for $sym. This is not equal to the number of vertices ($(num_verts(lrs))).")
+            throw(ArgumentError("You have provided ($(length(values))) values for $sym. This is not equal to the number of vertices ($(num_verts(lrs)))."))
         end
         return values
     end
@@ -113,10 +113,10 @@ end
 function vertex_value_form(values::AbstractArray, num_verts::Int64, lattice::CartesianGridRej{N,T}, 
                            sym::BasicSymbolic) where {N,T}
     if size(values) != lattice.dims
-        error("The values for $sym did not have the same format as the lattice. Expected a $(lattice.dims) array, got one of size $(size(values))")
+        throw(ArgumentError("The values for $sym did not have the same format as the lattice. Expected a $(lattice.dims) array, got one of size $(size(values))"))
     end
     if (length(values) != num_verts) 
-        error("You have provided ($(length(values))) values for $sym. This is not equal to the number of vertices ($(num_verts)).")
+        throw(ArgumentError("You have provided ($(length(values))) values for $sym. This is not equal to the number of vertices ($(num_verts))."))
     end
     return [values[flat_idx] for flat_idx in 1:num_verts]
 end
@@ -125,7 +125,7 @@ end
 function vertex_value_form(values::AbstractArray, num_verts::Int64, lattice::Array{Bool,T}, 
                            sym::BasicSymbolic) where {T}
     if size(values) != size(lattice)
-        error("The values for $sym did not have the same format as the lattice. Expected a $(size(lattice)) array, got one of size $(size(values))")
+        throw(ArgumentError("The values for $sym did not have the same format as the lattice. Expected a $(size(lattice)) array, got one of size $(size(values))"))
     end
 
     # Pre-declares a vector with the values in each vertex (return_values).
@@ -139,7 +139,7 @@ function vertex_value_form(values::AbstractArray, num_verts::Int64, lattice::Arr
 
     # Checks that the correct number of values was provided, and returns the values.
     if (length(return_values) != num_verts) 
-        error("You have provided ($(length(return_values))) values for $sym. This is not equal to the number of vertices ($(num_verts)).")
+        throw(ArgumentError("You have provided ($(length(return_values))) values for $sym. This is not equal to the number of vertices ($(num_verts))."))
     end
     return return_values
 end
@@ -158,10 +158,10 @@ function edge_value_form(values, lrs::LatticeReactionSystem, sym)
 
     # Error checks.
     if nnz(values) != num_edges(lrs)
-        error("You have provided ($(nnz(values))) values for $sym. This is not equal to the number of edges ($(num_edges(lrs))).")
+        throw(ArgumentError("You have provided ($(nnz(values))) values for $sym. This is not equal to the number of edges ($(num_edges(lrs)))."))
     end
     if !all(Base.isstored(values, e[1], e[2]) for e in edge_iterator(lrs))
-        error("Values was not provided for some edges for edge parameter $sym.")
+        throw(ArgumentError("Values was not provided for some edges for edge parameter $sym."))
     end
 
     # Unlike initial conditions/vertex parameters, (unless uniform) edge parameters' values  are 
@@ -296,7 +296,7 @@ function compute_edge_value(exp, lrs::LatticeReactionSystem, edge_ps)
     # Finds the symbols in the expression. Checks that all correspond to edge parameters.
     relevant_syms = Symbolics.get_variables(exp)
     if !all(any(isequal(sym, p) for p in edge_parameters(lrs)) for sym in relevant_syms)
-        error("An non-edge parameter was encountered in expressions: $exp. Here, only edge parameters are expected.")
+        throw(ArgumentError("An non-edge parameter was encountered in expressions: $exp. Here, only edge parameters are expected."))
     end
 
     # Creates a Function tha computes the expressions value for a parameter set.
@@ -320,7 +320,7 @@ function compute_vertex_value(exp, lrs::LatticeReactionSystem; u = [], ps = [])
     # Finds the symbols in the expression. Checks that all correspond to unknowns or vertex parameters.
     relevant_syms = Symbolics.get_variables(exp)
     if any(any(isequal(sym) in edge_parameters(lrs)) for sym in relevant_syms)
-        error("An edge parameter was encountered in expressions: $exp. Here, only vertex-based components are expected.")
+        throw(ArgumentError("An edge parameter was encountered in expressions: $exp. Here, only vertex-based components are expected."))
     end
 
     # Creates a Function that computes the expressions value for a parameter set.

test/spatial_modelling/lattice_reaction_systems.jl

@@ -9,6 +9,27 @@ include("../spatial_test_networks.jl")
 # Pre declares a grid.
 grids = [very_small_2d_cartesian_grid, very_small_2d_masked_grid, very_small_2d_graph_grid]
 
+### Test Spatial Reactions ###
+
+# Test creation of TransportReaction with non-parameters in rate.
+# Tests that it works even when rate is highly nested.
+let 
+    @variables t
+    @species X(t) Y(t)
+    @parameters D1 D2 D3
+    @test_throws ErrorException TransportReaction(D1 + D2*(D3 + Y), X)
+    @test_throws ErrorException TransportReaction(Y, X)
+end
+
+# Checks that the `hash` functions works for `TransportReaction`s.
+let
+    tr1 = @transport_reaction D1 X
+    tr2 = @transport_reaction D1 X
+    tr3 = @transport_reaction D2 X
+    hash(tr1, 0x0000000000000001) == hash(tr2, 0x0000000000000001)
+    hash(tr2, 0x0000000000000001) != hash(tr3, 0x0000000000000001)
+end
+
 ### Tests LatticeReactionSystem Getters Correctness ###
 
 # Test case 1.
@@ -127,6 +148,37 @@ let
     end
 end
 
+# Tests using various more obscure types of getters.
+let
+    # Create LatticeReactionsSystems.
+    t = default_t()
+    @parameters p d kB kD
+    @species X(t) X2(t)
+    rxs = [
+        Reaction(p, [], [X])
+        Reaction(d, [X], [])
+        Reaction(kB, [X], [X2], [2], [1])
+        Reaction(kD, [X2], [X], [1], [2])
+    ]
+    @named rs = ReactionSystem(rxs, t; metadata = "Metadata string")
+    rs = complete(rs)
+    tr = @transport_reaction D X2
+    lrs = LatticeReactionSystem(rs, [tr], small_2d_cartesian_grid)
+
+    # Generic ones (simply forwards call to the non-spatial system).
+    @test isequal(reactions(lrs), rxs)
+    @test isequal(nameof(lrs), :rs)
+    @test isequal(ModelingToolkit.get_iv(lrs), t)
+    @test isequal(equations(lrs), rxs)
+    @test isequal(unknowns(lrs), [X, X2])
+    @test isequal(ModelingToolkit.get_metadata(lrs), "Metadata string")
+    @test isequal(ModelingToolkit.get_eqs(lrs), rxs)
+    @test isequal(ModelingToolkit.get_unknowns(lrs), [X, X2])
+    @test isequal(ModelingToolkit.get_ps(lrs), [p, d, kB, kD])
+    @test isequal(ModelingToolkit.get_systems(lrs), [])
+    @test isequal(independent_variables(lrs), [t])
+end
+
 ### Tests Spatial Reactions Getters Correctness ###
 
 # Test case 1.
@@ -233,16 +285,6 @@ end
 
 ### Tests Error generation ###
 
-# Test creation of TransportReaction with non-parameters in rate.
-# Tests that it works even when rate is highly nested.
-let 
-    @variables t
-    @species X(t) Y(t)
-    @parameters D1 D2 D3
-    @test_throws ErrorException TransportReaction(D1 + D2*(D3 + Y), X)
-    @test_throws ErrorException TransportReaction(Y, X)
-end
-
 # Network where diffusion species is not declared in non-spatial network.
 let 
     rs = @reaction_network begin
@@ -297,6 +339,59 @@ let
     end
 end
 
+# Tests various networks with non-permitted content.
+    let
+    tr = @transport_reaction D X
+
+    # Variable unknowns.
+    rs1 = @reaction_network begin
+        @variables V(t)
+        (p,d), 0 <--> X
+    end
+    @test_throws ArgumentError LatticeReactionSystem(rs1, [tr], short_path)
+
+    # Non-reaction equations.
+    rs2 = @reaction_network begin
+        @equations D(V) ~ X - V
+        (p,d), 0 <--> X
+    end
+    @test_throws ArgumentError LatticeReactionSystem(rs2, [tr], short_path)
+
+    # Events.
+    rs3 = @reaction_network begin
+        @discrete_events [1.0] => [p ~ p + 1]
+        (p,d), 0 <--> X
+    end
+    @test_throws ArgumentError LatticeReactionSystem(rs3, [tr], short_path)
+
+    # Observables (only generates a warning).
+    rs4 = @reaction_network begin
+        @observables X2 ~ 2X
+        (p,d), 0 <--> X
+    end
+    @test_logs (:warn, r"The `ReactionSystem` used as input to `LatticeReactionSystem contain observables. It *") match_mode=:any LatticeReactionSystem(rs4, [tr], short_path)
+end
+
+# Tests for hierarchical input system.
+let
+    t = default_t()
+    @parameters d
+    @species X(t)
+    rxs = [Reaction(d, [X], [])]
+    @named rs1 = ReactionSystem(rxs, t)
+    @named rs2 = ReactionSystem(rxs, t; systems = [rs1])
+    rs2 = complete(rs2)
+    @test_throws ArgumentError LatticeReactionSystem(rs2, [tr], short_path)
+end
+
+# Tests for non-complete input `ReactionSystem`.
+let
+    tr = @transport_reaction D X
+    rs = @network_component begin
+        (p,d), 0 <--> X
+    end
+    @test_throws ArgumentError LatticeReactionSystem(rs1, [tr], short_path)
+end
 
 ### Tests Grid Vertex and Edge Number Computation ###
 

test/spatial_modelling/lattice_reaction_systems_ODEs.jl

@@ -547,7 +547,7 @@ let
     @test all(isequal.(ss_1, ss_2))
 end
 
-### ODEProblem & Integrator Interfacing ### 
+### ODEProblem & Integrator Interfacing ###
 
 # Checks that basic interfacing with ODEProblem parameters (getting and setting) works.
 let
@@ -788,4 +788,41 @@ let
             end
         end
     end
+end
+
+
+### Error Tests ###
+
+# Checks that attempting to remove conserved quantities yields an error.
+let
+    lrs = LatticeReactionSystem(binding_system, binding_srs, very_small_2d_masked_grid)
+    @test_throws ArgumentError ODEProblem(lrs, binding_u0, (0.0, 10.0), binding_p; remove_conserved = true)
+end
+
+# Checks that various erroneous inputs to `ODEProblem` yields errors.
+let
+    # Create `LatticeReactionSystem`.
+    @parameters d1 d2 D [edgeparameter=true]
+    @species X1(t) X2(t)
+    rxs = [Reaction(d1, [X1], [])]
+    @named rs = ReactionSystem(rxs, t)
+    rs = complete(rs)
+    lrs = LatticeReactionSystem(rs, [TransportReaction(D, X1)], CartesianGrid((4,)))
+
+    # Attempts to create `ODEProblem` using various faulty inputs.
+    u0 = [X1 => 1.0]
+    tspan = (0.0, 1.0)
+    ps = [d1 => 1.0, D => 0.1]
+    @test_throws ArgumentError ODEProblem(lrs, [1.0], tspan, ps)
+    @test_throws ArgumentError ODEProblem(lrs, u0, tspan, [1.0, 0.1])
+    @test_throws ArgumentError ODEProblem(lrs, [X1 => 1.0, X2 => 2.0], tspan, ps)
+    @test_throws ArgumentError ODEProblem(lrs, u0, tspan, [d1 => 1.0, d2 => 0.2, D => 0.1])
+    @test_throws ArgumentError ODEProblem(lrs, [X1 => [1.0, 2.0, 3.0]], tspan, ps)
+    @test_throws ArgumentError ODEProblem(lrs, u0, tspan, [d1 => [1.0, 2.0, 3.0], D => 0.1])
+    @test_throws ArgumentError ODEProblem(lrs, [X1 => [1.0 2.0; 3.0 4.0]], tspan, ps)
+    @test_throws ArgumentError ODEProblem(lrs, u0, tspan, [d1 => [1.0 2.0; 3.0 4.0], D => 0.1])
+    bad_D_vals_1 = sparse([0.0 1.0 0.0 1.0; 1.0 0.0 1.0 0.0; 0.0 1.0 0.0 1.0; 1.0 0.0 1.0 0.0])
+    @test_throws ArgumentError ODEProblem(lrs, u0, tspan, [d1 => 1.0, D => bad_D_vals_1])
+    bad_D_vals_2 = sparse([0.0 0.0 0.0 1.0; 1.0 0.0 1.0 0.0; 0.0 1.0 0.0 1.0; 1.0 0.0 0.0 0.0])
+    @test_throws ArgumentError ODEProblem(lrs, u0, tspan, [d1 => 1.0, D => bad_D_vals_2])
 end

test/spatial_modelling/lattice_reaction_systems_jumps.jl

@@ -203,4 +203,14 @@ let
 end
 
 
-### JumpProblem & Integrator Interfacing ### 
+### JumpProblem & Integrator Interfacing ### 
+
+
+### Other Tests ###
+
+# Checks that providing a non-spatial `DiscreteProblem` to a `JumpProblem` gives an error.
+let
+    lrs = LatticeReactionSystem(binding_system, binding_srs, very_small_2d_masked_grid)
+    dprob = DiscreteProblem(binding_system, binding_u0, (0.0, 10.0), binding_p[1:2])
+    @test_throws ArgumentError JumpProblem(lrs, dprob, NSM())
+end