reduce more lines.

Author: TorkelE

src/spatial_reaction_systems/spatial_ODE_systems.jl

@@ -1,6 +1,6 @@
 ### Spatial ODE Functor Structures ###
 
-# Functor structure containing the information for the forcing function of a spatial ODE with spatial movement on a lattice.
+# Functor with information for the forcing function of a spatial ODE with spatial movement on a lattice.
 struct LatticeTransportODEf{Q,R,S,T}
     """The ODEFunction of the (non-spatial) reaction system which generated this function."""
     ofunc::Q
@@ -65,7 +65,7 @@ struct LatticeTransportODEf{Q,R,S,T}
     end
 end
 
-# Functor structure containing the information for the forcing function of a spatial ODE with spatial movement on a lattice.
+# Functor with information for the Jacobian function of a spatial ODE with spatial movement on a lattice.
 struct LatticeTransportODEjac{Q,R,S,T}
     """The ODEFunction of the (non-spatial) reaction system which generated this function."""
     ofunc::Q
@@ -123,7 +123,7 @@ function DiffEqBase.ODEProblem(lrs::LatticeReactionSystem, u0_in, tspan,
     end
 
     # Converts potential symmaps to varmaps
-    # Parameter conversion complicated since the vertex and edge parameters may be given in a tuple, or in a common vector.
+    # Vertex and edge parameters may be given in a tuple, or in a common vector, making parameter case complicated.
     u0_in = symmap_to_varmap(lrs, u0_in)
     p_in = (p_in isa Tuple{<:Any,<:Any}) ? 
             (symmap_to_varmap(lrs, p_in[1]),symmap_to_varmap(lrs, p_in[2])) :

src/spatial_reaction_systems/spatial_reactions.jl

@@ -95,7 +95,8 @@ 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) && !equivalent_metadata(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) && !equivalent_metadata(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

@@ -95,7 +95,9 @@ end
 # If the input is given in a map form, the vector needs sorting and the first value removed. 
 # The creates a Vector{Vector{Value}} or Vector{value} form, which is then again sent to lattice_process_input for reprocessing.
 function lattice_process_input(input::Vector{<:Pair}, syms::Vector{BasicSymbolic{Real}}, args...)
-    isempty(setdiff(first.(input), syms)) || error("Some input symbols are not recognised: $(setdiff(first.(input), syms)).")
+    if !isempty(setdiff(first.(input), syms)) 
+        error("Some input symbols are not recognised: $(setdiff(first.(input), syms)).")
+    end
     sorted_input = sort(input; by = p -> findfirst(isequal(p[1]), syms))
     return lattice_process_input(last.(sorted_input), syms, args...)
 end
@@ -148,7 +150,7 @@ function duplicate_trans_params!(edge_ps::Vector{Vector{Float64}}, lrs::LatticeR
 
         # A vector where we will put the edge parameters new values. 
         # Has the correct length (the number of directed edges in the lattice).
-        new_vals = Vector{Float64}(undef,lrs.num_edges)     
+        new_vals = Vector{Float64}(undef, lrs.num_edges)     
         # As we loop through the edges of the di-graph, this keeps track of each edge's index in the original graph. 
         original_edge_count = 0                             
         for edge in edges(lrs.lattice)                      # For each edge.
@@ -219,9 +221,11 @@ end
 
 # Creates a map, taking each species (with transportation) to its transportation rate.
 # The species is represented by its index (in species(lrs). 
-# If the rate is uniform across all edges, the vector will be length 1 (with this value), else there will be a separate value for each edge.
+# If the rate is uniform across all edges, the vector will be length 1 (with this value),
+# else there will be a separate value for each edge.
 # Pair{Int64, Vector{T}}[] is required in case vector is empty (otherwise it becomes Any[], causing type error later).
-function make_sidxs_to_transrate_map(vert_ps::Vector{Vector{Float64}}, edge_ps::Vector{Vector{T}}, lrs::LatticeReactionSystem) where T
+function make_sidxs_to_transrate_map(vert_ps::Vector{Vector{Float64}}, edge_ps::Vector{Vector{T}}, 
+                                                                lrs::LatticeReactionSystem) where T
     transport_rates_speciesmap = compute_all_transport_rates(vert_ps, edge_ps, lrs)
     return Pair{Int64, Vector{T}}[
         speciesmap(lrs.rs)[spat_rates[1]] => spat_rates[2] for spat_rates in transport_rates_speciesmap