round 4

Author: TorkelE

src/chemistry_functionality.jl

@@ -105,8 +105,9 @@ function make_compound(expr)
     isempty(ivs) && (species_expr = insert_independent_variable(species_expr, :(..)))
 
     # Expression which when evaluated gives a vector with all the ivs of the components.
-    ivs_get_expr = :(unique(reduce(vcat, [arguments(ModelingToolkit.unwrap(comp))
-        for comp in $components])))
+    ivs_get_expr = :(unique(reduce(
+        vcat, [arguments(ModelingToolkit.unwrap(comp))
+               for comp in $components])))
 
     # Creates the found expressions that will create the compound species.
     # The `Expr(:escape, :(...))` is required so that the expressions are evaluated in 

src/dsl.jl

@@ -476,8 +476,9 @@ 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),
-            get_tup_arg(prod_line, i), get_tup_arg(rate, i), metadata_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
 
@@ -773,8 +774,9 @@ function read_observed_options(options, species_n_vars_declared, ivs_sorted)
                 # then we get something like :([:X1, :X2]), rather than :([X1, X2]).
                 dep_var_expr = :(filter(!MT.isparameter,
                     Symbolics.get_variables($(obs_eq.args[3]))))
-                ivs_get_expr = :(unique(reduce(vcat, [arguments(MT.unwrap(dep))
-                    for dep in $dep_var_expr])))
+                ivs_get_expr = :(unique(reduce(
+                    vcat, [arguments(MT.unwrap(dep))
+                           for dep in $dep_var_expr])))
                 ivs_get_expr_sorted = :(sort($(ivs_get_expr);
                     by = iv -> findfirst(MT.getname(iv) == ivs for ivs in $ivs_sorted)))
                 push!(observed_vars.args,

src/spatial_reaction_systems/spatial_ODE_systems.jl

@@ -171,7 +171,7 @@ 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,
+            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
@@ -184,7 +184,7 @@ 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, 
+            jac_prototype = build_jac_prototype(ofunc_sparse.jac_prototype,
                 transport_rates, lrs; set_nonzero = false)
         else
             ofunc_dense = ODEFunction(osys; jac = false, sparse = false)

src/spatial_reaction_systems/spatial_reactions.jl

@@ -96,8 +96,8 @@ 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),
-            tr_p in Symbolics.get_variables(tr.rate))
+    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