updates

Author: TorkelE

src/expression_utils.jl

@@ -93,6 +93,16 @@ function is_escaped_expr(expr)
     return (expr isa Expr) && (expr.head == :escape) && (length(expr.args) == 1)
 end
 
+
+### Generic Expression Handling ###
+
+# Convert an expression with equal signs (e.g. :(a=1.0, b=2.0)) to one with pairs (e.g. :(a=>1.0, b=>2.0))
+function expr_equal_vector_to_pairs(expr_vec)
+    pair_vector = :([])
+    foreach(arg -> push!(pair_vector.args, arg.args[1] => arg.args[2]), expr_vec.args) 
+    return pair_vector
+end
+
 ### Old Stuff ###
 
 #This will be called whenever a function stored in funcdict is called.

src/reaction_network.jl

@@ -364,9 +364,10 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
     default_reaction_metadata = :([])
     compound_expr, compound_species = read_compound_options(options)
     check_default_noise_scaling!(default_reaction_metadata, options)
+    default_reaction_metadata = expr_equal_vector_to_pairs(default_reaction_metadata)
 
     # Parses reactions, species, and parameters.
-    reactions = get_reactions(reaction_lines; default_reaction_metadata)
+    reactions = get_reactions(reaction_lines)
     species_declared = [extract_syms(options, :species); compound_species]
     parameters_declared = extract_syms(options, :parameters)
     variables = extract_syms(options, :variables)
@@ -424,9 +425,12 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
         $observed_vars
         $comps
 
-        Catalyst.make_ReactionSystem_internal($rxexprs, $tiv, setdiff(union($spssym, $varssym, $compssym), $obs_syms),
-                                              $pssym; name = $name, spatial_ivs = $sivs,
-                                              observed = $observed_eqs)
+        Catalyst.remake_ReactionSystem_internal(
+            Catalyst.make_ReactionSystem_internal(
+                $rxexprs, $tiv, setdiff(union($spssym, $varssym, $compssym), $obs_syms),
+                $pssym; name = $name, spatial_ivs = $sivs, observed = $observed_eqs);
+            default_reaction_metadata = $default_reaction_metadata
+        )
     end
 end
 
@@ -593,8 +597,7 @@ function get_reaction(line)
 end
 
 # Generates a vector containing a number of reaction structures, each containing the information about one reaction.
-function get_reactions(exprs::Vector{Expr}, reactions = Vector{ReactionStruct}(undef, 0); 
-                       default_reaction_metadata = :([]))
+function get_reactions(exprs::Vector{Expr}, reactions = Vector{ReactionStruct}(undef, 0))
     for line in exprs
         # Reads core reaction information.
         arrow, rate, reaction, metadata = read_reaction_line(line)
@@ -604,16 +607,12 @@ function get_reactions(exprs::Vector{Expr}, reactions = Vector{ReactionStruct}(u
             if typeof(rate) != Expr || rate.head != :tuple
                 error("Error: Must provide a tuple of reaction rates when declaring a bi-directional reaction.")
             end
-            push_reactions!(reactions, reaction.args[2], reaction.args[3], rate.args[1], metadata.args[1], arrow; 
-                            default_reaction_metadata)
-            push_reactions!(reactions, reaction.args[3], reaction.args[2], rate.args[2], metadata.args[2], arrow; 
-                            default_reaction_metadata)
+            push_reactions!(reactions, reaction.args[2], reaction.args[3], rate.args[1], metadata.args[1], arrow)
+            push_reactions!(reactions, reaction.args[3], reaction.args[2], rate.args[2], metadata.args[2], arrow)
         elseif in(arrow, fwd_arrows)
-            push_reactions!(reactions, reaction.args[2], reaction.args[3], rate, metadata, arrow; 
-                            default_reaction_metadata)
+            push_reactions!(reactions, reaction.args[2], reaction.args[3], rate, metadata, arrow)
         elseif in(arrow, bwd_arrows)
-            push_reactions!(reactions, reaction.args[3], reaction.args[2], rate, metadata, arrow; 
-                            default_reaction_metadata)
+            push_reactions!(reactions, reaction.args[3], reaction.args[2], rate, metadata, arrow)
         else
             throw("Malformed reaction, invalid arrow type used in: $(MacroTools.striplines(line))")
         end
@@ -646,7 +645,7 @@ end
 # Used to create multiple reactions from, for instance, `k, (X,Y) --> 0`.
 # Handles metadata, e.g. `1.0, Z --> 0, [noise_scaling=η]`.
 function push_reactions!(reactions::Vector{ReactionStruct}, sub_line::ExprValues, prod_line::ExprValues, 
-                         rate::ExprValues, metadata::ExprValues, arrow::Symbol; default_reaction_metadata::Expr)  
+                         rate::ExprValues, metadata::ExprValues, arrow::Symbol)  
     # The rates, substrates, products, and metadata may be in a tupple form (e.g. `k, (X,Y) --> 0`).
     # This finds the length of these tuples (or 1 if not in tuple forms). Errors if lengs inconsistent.
     lengs = (tup_leng(sub_line), tup_leng(prod_line), tup_leng(rate), tup_leng(metadata))
@@ -658,7 +657,6 @@ function push_reactions!(reactions::Vector{ReactionStruct}, sub_line::ExprValues
     for i in 1:maximum(lengs)                       
         # If the `only_use_rate` metadata was not provided, this has to be infered from the arrow used.
         metadata_i = get_tup_arg(metadata, i)
-        merge_metadata!(metadata_i, default_reaction_metadata)
         if all([arg.args[1] != :only_use_rate for arg in metadata_i.args])
             push!(metadata_i.args, :(only_use_rate = $(in(arrow, pure_rate_arrows))))
         end
@@ -673,16 +671,6 @@ function push_reactions!(reactions::Vector{ReactionStruct}, sub_line::ExprValues
     end
 end
 
-# Merge the metadata encoded by a reaction with the default metadata (for all reactions) given by the system.
-# If a metadata value is present in both vectors, uses the non-default value.
-function merge_metadata!(metadata, default_reaction_metadata)
-    for entry in default_reaction_metadata.args
-        if !in(entry.args[1], arg.args[1] for arg in metadata.args)
-            push!(metadata.args, entry)
-        end
-    end
-end
-
 function processmult(op, mult, stoich)
     if (mult isa Number) && (stoich isa Number)
         op(mult, stoich)

src/reactionsystem.jl

@@ -756,6 +756,39 @@ function ReactionSystem(iv; kwargs...)
     ReactionSystem(Reaction[], iv, [], []; kwargs...)
 end
 
+
+"""
+    remake_ReactionSystem_internal(rs::ReactionSystem; 
+        default_reaction_metadata::Vector{Pair{Symbol, T}} = Vector{Pair{Symbol, Any}}()) where {T}
+
+Takes a reaction systems and reameks it, returning a modified reaction system. Modifications depend
+on which arguments are provided.
+
+Arguments:
+- `rs::ReactionSystem`: The `ReactionSystem` which you wish to make a remade version of.
+- `default_reaction_metadata::Vector{Pair{Symbol, T}}`: A vector with default `Reaction` metadata values.
+    Each metadata in each `Reaction` of the updated `ReactionSystem` will have teh value desiganted in
+    `default_reaction_metadata` (however, `Reaction`s that already have that metadata designated will not
+    have their value updated).
+"""
+#function remake_ReactionSystem_internal(rs::ReactionSystem;  default_reaction_metadata::Vector{Pair{Symbol, T}} = Vector{Pair{Symbol, Any}}()) where {T}
+function remake_ReactionSystem_internal(rs; default_reaction_metadata = default_reaction_metadata)
+    # Updates the metadata for all reactions (reactions are ignored).
+    updated_reactions = [set_default_metadata(rx, default_reaction_metadata) for rx in reactions(rs)]
+    rs = @set rs.rxs = updated_reactions  
+    return rs
+end
+
+# For a `Reaction`, adds missing default metadata values. Equations are passed back unmodified.
+function set_default_metadata(rx, default_metadata)
+    missing_metadata = filter(md -> !in(md[1], entry[1] for entry in rx.metadata), default_metadata)
+    updated_metadata = vcat(rx.metadata, missing_metadata)
+    updated_metadata = convert(Vector{Pair{Symbol, Any}}, updated_metadata)
+    return @set rx.metadata = updated_metadata
+end
+
+
+
 """
     isspatial(rn::ReactionSystem)