round 3

Author: TorkelE

src/dsl.jl

@@ -476,7 +476,7 @@ function push_reactions!(reactions::Vector{ReactionStruct}, sub_line::ExprValues
             error("Some reaction metadata fields where repeated: $(metadata_entries)")
         end
 
-        push!(reactions,ReactionStruct(get_tup_arg(sub_line, i),
+        push!(reactions, ReactionStruct(get_tup_arg(sub_line, i),
             get_tup_arg(prod_line, i), get_tup_arg(rate, i), metadata_i))
     end
 end

src/spatial_reaction_systems/spatial_ODE_systems.jl

@@ -171,8 +171,8 @@ function build_odefunction(lrs::LatticeReactionSystem, vert_ps::Vector{Vector{T}
             set_nonzero = true)
         if sparse
             f = LatticeTransportODEf(ofunc_sparse, vert_ps, transport_rates, edge_ps, lrs)
-            jac_vals = build_jac_prototype(ofunc_sparse.jac_prototype, transport_rates, lrs;
-                set_nonzero = true)
+            jac_vals = build_jac_prototype( ofunc_sparse.jac_prototype, transport_rates,
+                lrs; set_nonzero = true)
             J = LatticeTransportODEjac(ofunc_dense, vert_ps, lrs, jac_vals, edge_ps, true)
             jac_prototype = jac_vals
         else
@@ -184,8 +184,8 @@ function build_odefunction(lrs::LatticeReactionSystem, vert_ps::Vector{Vector{T}
         if sparse
             ofunc_sparse = ODEFunction(osys; jac = false, sparse = true)
             f = LatticeTransportODEf(ofunc_sparse, vert_ps, transport_rates, edge_ps, lrs)
-            jac_prototype = build_jac_prototype(ofunc_sparse.jac_prototype, transport_rates,
-                lrs; set_nonzero = false)
+            jac_prototype = build_jac_prototype(ofunc_sparse.jac_prototype, 
+                transport_rates, lrs; set_nonzero = false)
         else
             ofunc_dense = ODEFunction(osys; jac = false, sparse = false)
             f = LatticeTransportODEf(ofunc_dense, vert_ps, transport_rates, edge_ps, lrs)

src/spatial_reaction_systems/spatial_reactions.jl

@@ -96,7 +96,7 @@ function check_spatial_reaction_validity(rs::ReactionSystem, tr::TransportReacti
     if any(isequal(tr.species, s) && !isequivalent(tr.species, s) for s in species(rs))
         error("A transport reaction used a species, $(tr.species), with metadata not matching its lattice reaction system. Please fetch this species from the reaction system and used in transport reaction creation.")
     end
-    if any(isequal(rs_p, tr_p) && !isequivalent(rs_p, tr_p) for rs_p in parameters(rs), 
+    if any(isequal(rs_p, tr_p) && !isequivalent(rs_p, tr_p) for rs_p in parameters(rs),
             tr_p in Symbolics.get_variables(tr.rate))
         error("A transport reaction used a parameter with metadata not matching its lattice reaction system. Please fetch this parameter from the reaction system and used in transport reaction creation.")
     end

src/spatial_reaction_systems/utility.jl

@@ -268,7 +268,7 @@ end
 # This is stored in location_types.
 function get_component_value(values::Vector{<:Vector}, component_idx::Int64,
         location_idx::Int64, location_types::Vector{Bool})
-    return get_component_value(values[component_idx], location_idx, 
+    return get_component_value(values[component_idx], location_idx,
         location_types[component_idx])
 end
 # For a components value (which is a vector of either length 1 or some other length), retrieves its value.