add command line args for different chemical species numbers

run_evolution.jl

@@ -3,6 +3,23 @@ Pkg.activate(".")
 using ReactionNetworkEvolution
 using ArgParse
 
+
+
+function parse_initial_concentrations(initial_concentrations::String)
+    # Strip whitespace
+    initial_concentrations = filter(x -> !isspace(x), initial_concentrations)
+    # Strip brackets
+    initial_concentrations = initial_concentrations[2:end-1]
+    # Separate by commas 
+    initial_concentrations = split(initial_concentrations, ",")
+    new_array = Vector{Float64}()
+    for num in initial_concentrations
+        push!(new_array, parse(Float64, num))
+    end
+    return new_array
+end
+
+
 s = ArgParseSettings()
 
 @add_arg_table s begin
@@ -12,6 +29,12 @@ s = ArgParseSettings()
     "--ntrials"
         arg_type = Int
         default = -1
+    "--nspecies"
+        arg_type = Int
+        default = 3
+    "--initial_concentrations"
+        arg_type = String
+        default = "[1., 5., 9.]"
     "--population_size"
         arg_type = Int
         default = -1
@@ -31,8 +54,12 @@ end
 
 parsed_args = parse_args(ARGS, s)
 
+parsed_args["initial_concentrations"] = parse_initial_concentrations(parsed_args["initial_concentrations"])
+
 ReactionNetworkEvolution.run_evolution(ngenerations=parsed_args["ngenerations"],
               ntrials=parsed_args["ntrials"],
+              nspecies=parsed_args["nspecies"],
+              initial_concentrations = parsed_args["initial_concentrations"],
               population_size=parsed_args["population_size"],
               pathtosettings=parsed_args["pathtosettings"],
               outputpath=parsed_args["outputpath"],

settings.json

@@ -5,7 +5,8 @@
 "percent_rateconstant_change": 20,			
 "p_new_rateconstant": 0.15,				
 "population_size": 100,						
-"ngenerations": 800,					
+"ngenerations": 800,
+"nspecies": 3,					
 "nreactions": 5,					
 "max_offspring_portion": 0.1,				
 "writeout_threshold": 0.05,				
@@ -30,5 +31,5 @@
 "same_fitness_crossover": false,			
 "same_fitness_percent_range": 5,		
 "process_output_oscillators": false,
-"objective_data_path": "",			
+"objective_data_path": "DEFAULT",			
 "note": ""}						

src/ReactionNetworkEvolution.jl

@@ -72,6 +72,8 @@ end
 function run_evolution(;
     ngenerations::Int64=-1,
     ntrials::Int64=-1,
+    nspecies::Int64=3,
+    initial_concentrations::Vector{Float64}=[1., 5., 9.],
     population_size::Int64=-1,
     pathtosettings::String="",
     outputpath::String="",
@@ -109,7 +111,7 @@ function run_evolution(;
         pathtosettings = "DEFAULT"
     end
 
-    settings, objectivefunction = read_usersettings(pathtosettings, ngenerations=ngenerations, population_size=population_size, seed=seed, note=note)
+    settings, objectivefunction = read_usersettings(pathtosettings, ngenerations=ngenerations, nspecies=nspecies, initial_concentrations=initial_concentrations, population_size=population_size, seed=seed, note=note)
 
     println("Beginning $ntrials trials with $(settings.ngenerations) generations each")
 

src/settings.jl

@@ -35,6 +35,7 @@ struct Settings
     p_new_rateconstant::Float64 # Probability of picking new rate constant during mutation vs slight change
     population_size::Int
     ngenerations::Int
+    nspecies::Int
     nreactions::Int
     max_offspring_portion::Float64 # The maximum portion of offspring a single species can have
     writeout_threshold::Float64 # Networks with this fitness or better will be saved
@@ -111,6 +112,7 @@ function read_usersettings(settings_dict::Dict{String, Any})
         "p_new_rateconstant" => 0.15,
         "population_size" => 100,
         "ngenerations" => 800,
+        "nspecies" => 3,
         "nreactions" => 5,
         "max_offspring_portion" => 0.1,
         "writeout_threshold" => 0.05,
@@ -161,6 +163,7 @@ function read_usersettings(settings_dict::Dict{String, Any})
                 settings["p_new_rateconstant"],
                 settings["population_size"],
                 settings["ngenerations"],
+                settings["nspecies"],
                 settings["nreactions"],
                 settings["max_offspring_portion"],
                 settings["writeout_threshold"],
@@ -195,7 +198,7 @@ function read_usersettings(settings_dict::Dict{String, Any})
 end
 
 
-function read_usersettings(path::String; ngenerations::Int64=-1, population_size::Int64=-1, seed::Int64=-1, note::String="")
+function read_usersettings(path::String; ngenerations::Int64=-1, nspecies::Int64=3, initial_concentrations::Vector{Float64}=[1., 5., 9.], population_size::Int64=-1, seed::Int64=-1, note::String="")
     settings = Dict(
         "portion_elite" => 0.1,
         "reaction_probabilities" => [.1, .4, .4, .1],
@@ -205,6 +208,7 @@ function read_usersettings(path::String; ngenerations::Int64=-1, population_size
         "p_new_rateconstant" => 0.15,
         "population_size" => 100,
         "ngenerations" => 800,
+        "nspecies" => 3,
         "nreactions" => 5,
         "max_offspring_portion" => 0.1,
         "writeout_threshold" => 0.05,
@@ -300,6 +304,19 @@ function read_usersettings(path::String; ngenerations::Int64=-1, population_size
     # Set the random seed
     Random.seed!(Int64(seed))
 
+    # Check if nspecies is supplied and update it if not default value
+    # Check if the number of species names match the number of species, if not, generate them
+    if nspecies != 3
+        settings["nspecies"] = 3
+        if length(settings["chemical_species_names"]) != nspecies
+            settings["chemical_species_names"] = generate_chemical_species_names(nspecies)
+        end
+        settings["initial_concentrations"] = initial_concentrations
+        if length(settings["initial_concentrations"]) != nspecies
+            error("number of initial conditions does not match number of chemical species")
+        end
+    end
+
     # Check if the user has supplied a note
     if note != ""
         settings["note"] = note
@@ -339,6 +356,7 @@ function read_usersettings(path::String; ngenerations::Int64=-1, population_size
                    settings["p_new_rateconstant"],
                    population_size,
                    ngenerations,
+                   settings["nspecies"],
                    settings["nreactions"],
                    settings["max_offspring_portion"],
                    settings["writeout_threshold"],
@@ -379,3 +397,11 @@ function writeout_settings(settings::Settings, filename::String)
         write(f, stringsettings)
     end
 end
+
+function generate_chemical_species_names(nspecies::Int64)
+    chemical_species_names = Vector{String}()
+    for i in 1:nspecies
+        push!(chemical_species_names, "S$i")
+    end
+    return chemical_species_names
+end