revert lattice reaction system changes

Author: TorkelE

src/spatial_reaction_systems/lattice_reaction_systems.jl

@@ -25,17 +25,17 @@ struct LatticeReactionSystem{S,T} # <: MT.AbstractTimeDependentSystem
     All parameters related to the lattice reaction system
     (both with spatial and non-spatial effects).
     """
-    parameters::Vector{Any}
+    parameters::Vector{BasicSymbolic{Real}}
     """
     Parameters which values are tied to vertexes (adjacencies), 
     e.g. (possibly) have an unique value at each vertex of the system.
     """
-    vertex_parameters::Vector{Any}
+    vertex_parameters::Vector{BasicSymbolic{Real}}
     """
     Parameters which values are tied to edges (adjacencies), 
     e.g. (possibly) have an unique value at each edge of the system.
     """
-    edge_parameters::Vector{Any}
+    edge_parameters::Vector{BasicSymbolic{Real}}
 
     function LatticeReactionSystem(rs::ReactionSystem{S}, spatial_reactions::Vector{T},
                                    lattice::DiGraph; init_digraph = true) where {S, T}
@@ -52,7 +52,7 @@ struct LatticeReactionSystem{S,T} # <: MT.AbstractTimeDependentSystem
         num_species = length(unique([species(rs); spat_species]))
         rs_edge_parameters = filter(isedgeparameter, parameters(rs))
         if isempty(spatial_reactions)
-            srs_edge_parameters = Vector{Any}[]
+            srs_edge_parameters = Vector{BasicSymbolic{Real}}[]
         else
             srs_edge_parameters = setdiff(reduce(vcat, [parameters(sr) for sr in spatial_reactions]), parameters(rs))
         end

test/runtests.jl

@@ -4,6 +4,23 @@ using SafeTestsets
 ### Run the tests ###
 @time begin
 
+    ### Tests the properties of ReactionSystems. ###
+    @time @safetestset "Reactions" begin include("reactionsystem_structure/reactions.jl") end
+    @time @safetestset "ReactionSystem" begin include("reactionsystem_structure/reactionsystem.jl") end
+    @time @safetestset "Higher Order Reactions" begin include("reactionsystem_structure/higher_order_reactions.jl") end
+
+    ### Tests model creation via the @reaction_network DSL. ###
+    @time @safetestset "Basic DSL" begin include("dsl/dsl_basics.jl") end
+    @time @safetestset "DSL Model Construction" begin include("dsl/dsl_model_construction.jl") end
+    @time @safetestset "Custom CRN Functions" begin include("dsl/custom_functions.jl") end
+    @time @safetestset "DSL Options" begin include("dsl/dsl_options.jl") end
+
+    ### Non-DSL model creation and modification. ###
+    @time @safetestset "ReactionSystem Components Based Creation" begin include("programmatic_model_creation/component_based_model_creation.jl") end
+    @time @safetestset "Programmatic Model Expansion" begin include("programmatic_model_creation/programmatic_model_expansion.jl") end
+
+    # Runs various miscellaneous tests.
+    @time @safetestset "API" begin include("miscellaneous_tests/api.jl") end
     @time @safetestset "Symbolic Stoichiometry" begin include("miscellaneous_tests/symbolic_stoichiometry.jl") end
     @time @safetestset "NonlinearProblems and Steady State Solving" begin include("miscellaneous_tests/nonlinear_solve.jl") end
     @time @safetestset "Events" begin include("miscellaneous_tests/events.jl") end
@@ -25,8 +42,7 @@ using SafeTestsets
     ### Tests Spatial Network Simulations. ###
     @time @safetestset "PDE Systems Simulations" begin include("spatial_reaction_systems/simulate_PDEs.jl") end
     @time @safetestset "Lattice Reaction Systems" begin include("spatial_reaction_systems/lattice_reaction_systems.jl") end
-    # Requires internal rework due to permitting non-default parameter types. However, rework have already been carried out in a separate branch.
-    # @time @safetestset "ODE Lattice Systems Simulations" begin include("spatial_reaction_systems/lattice_reaction_systems_ODEs.jl") end
+    @time @safetestset "ODE Lattice Systems Simulations" begin include("spatial_reaction_systems/lattice_reaction_systems_ODEs.jl") end
 
     ### Tests network visualization. ###
     @time @safetestset "Latexify" begin include("visualization/latexify.jl") end

test/spatial_reaction_systems/lattice_reaction_systems.jl

@@ -275,10 +275,12 @@ let
     @test_throws ErrorException LatticeReactionSystem(rs, [tr], grid)
 end
 
+
 ### Test Designation of Parameter Types ###
+# Currently not supported. Won't be until the LatticeReactionSystem internal update is merged.
 
 # Checks that parameter types designated in the non-spatial `ReactionSystem` is handled correctly.
-let
+@test_broken let
     # Declares LatticeReactionSystem with designated parameter types.
     rs = @reaction_network begin
         @parameters begin
@@ -326,7 +328,7 @@ end
 
 # Checks that programmatically declared parameters (with types) can be used in `TransportReaction`s.
 # Checks that LatticeReactionSystem with non-default parameter types can be simulated.
-let
+@test_broken let
     rs = @reaction_network begin
         @parameters p::Float32
         (p,d), 0 <--> X
@@ -354,11 +356,12 @@ end
 
 # Tests that LatticeReactionSystem cannot be generated where transport reactions depend on parameters
 # that have a type designated in the non-spatial `ReactionSystem`.
-let
-    rs = @reaction_network begin
-        @parameters D::Int64
-        (p,d), 0 <--> X
-    end
-    tr = @transport_reaction D X 
-    @test_throws Exception LatticeReactionSystem(rs, tr, grid)
-end
+@test_broken false
+# let
+#     rs = @reaction_network begin
+#         @parameters D::Int64
+#         (p,d), 0 <--> X
+#     end
+#     tr = @transport_reaction D X 
+#     @test_throws Exception LatticeReactionSystem(rs, tr, grid)
+# end