Merge pull request #2 from maxreiss123/develop

Develop

Author: maxreiss123

Project.toml

@@ -1,6 +1,6 @@
 name = "JGep"
 uuid = "2f0a5bb0-5f4f-4f7f-b515-93a1e67611af"
-authors = ["Max <reissmann28@gmail.com>"]
+authors = ["Max Reissmann <reissmannm@student.unimelb.edu.au>"]
 version = "0.1.0"
 
 [deps]

test/Entity_test.jl

@@ -0,0 +1,159 @@
+include("../src/Entities.jl")
+
+using .GepEntities
+using DynamicExpressions
+using Test
+using OrderedCollections
+using Random
+operators =  OperatorEnum(; binary_operators=[+, -, *, /], unary_operators=[sqrt])
+
+# Helper function to create test toolbox
+function create_test_toolbox()
+    
+
+    symbols = OrderedDict{Int8,Int8}(
+        1 => 2,  # Addition (+)
+        2 => 2,  # Multiplication (*)
+        3 => 1,  # SQRT
+        4 => 0,  # Variable x
+        5 => 0   # Constant 1.0
+    )
+    
+    callbacks = Dict{Int8,Function}(
+        1 => +,
+        2 => *,
+        3 => sqrt
+    )
+    
+    nodes = OrderedDict{Int8,Any}(
+        4 => Node{Float64}(feature=1),
+        5 => 1.0
+    )
+    
+    gep_probs = Dict{String,AbstractFloat}(
+        "mutation_prob" => 0.2,
+        "mutation_rate" => 0.1,
+        "inversion_prob" => 0.1,
+        "one_point_cross_over_prob" => 0.3,
+        "two_point_cross_over_prob" => 0.3,
+        "dominant_fusion_prob" => 0.2,
+        "rezessiv_fusion_prob" => 0.2,
+        "fusion_prob" => 0.2,
+        "fusion_rate" => 0.1,
+        "rezessiv_fusion_rate" => 0.1
+    )
+    
+    return Toolbox(2, 3, symbols, Int8[1], callbacks, nodes, gep_probs)
+end
+
+@testset "SymbolicEntities Tests" begin
+    @testset "Basic Setup" begin
+        toolbox = create_test_toolbox()
+        
+        @test toolbox.gene_count == 2
+        @test toolbox.head_len == 3
+        @test length(toolbox.headsyms) == 2  # + and *
+        @test length(toolbox.unary_syms) == 1  # square
+        @test length(toolbox.tailsyms) == 2  # x and 1.0
+    end
+
+    @testset "Chromosome Creation" begin
+        toolbox = create_test_toolbox()
+        Random.seed!(42)  # For reproducibility
+        chromosome = generate_chromosome(toolbox)
+        
+        @test chromosome isa Chromosome
+        @test length(chromosome.genes) == (toolbox.gene_count - 1 + 
+            toolbox.gene_count * (2 * toolbox.head_len + 1))
+        @test chromosome.compiled == true
+        @test chromosome.dimension_homogene == false
+        @test isnan(chromosome.fitness)
+    end
+
+    @testset "Function Compilation" begin
+        toolbox = create_test_toolbox()
+        Random.seed!(42)
+        chromosome = generate_chromosome(toolbox)
+        compile_expression!(chromosome, force_compile=true)
+        
+        @test chromosome.compiled == true
+        @test chromosome.compiled_function !== nothing
+        
+        # Test function evaluation
+        if !isnothing(chromosome.compiled_function)
+            result = chromosome.compiled_function([1.0], operators)
+            @test typeof(result[1]) <: Real
+        end
+    end
+
+    @testset "Genetic Operators" begin
+        toolbox = create_test_toolbox()
+        Random.seed!(42)
+        chromosome1 = generate_chromosome(toolbox)
+        chromosome2 = generate_chromosome(toolbox)
+        
+        genes1_original = copy(chromosome1.genes)
+        genes2_original = copy(chromosome2.genes)
+        
+        @testset "One Point Crossover" begin
+            c1, c2 = replicate(chromosome1, chromosome2, toolbox)
+            gene_one_point_cross_over!(c1, c2)
+            @test c1.genes != genes1_original || c2.genes != genes2_original
+        end
+        
+        @testset "Mutation" begin
+            c1 = Chromosome(copy(genes1_original), toolbox)
+            gene_mutation!(c1, 1.0)  # Force mutation
+            @test c1.genes != genes1_original
+        end
+        
+        @testset "Gene Fusion" begin
+            c1, c2 = replicate(chromosome1, chromosome2, toolbox)
+            gene_fussion!(c1, c2, 1.0)  # Force fusion
+            @test c1.genes != genes1_original || c2.genes != genes2_original
+        end
+        
+        @testset "Inversion" begin
+            pos_11 = toolbox.gene_count
+            pos_12 = toolbox.gene_count+toolbox.head_len-1
+            pos_21 = pos_12 + toolbox.head_len+2
+            pos_22 = pos_21 + toolbox.head_len-1
+            
+            c1 = Chromosome(copy(genes1_original), toolbox)
+
+
+            initial_head = copy(c1.genes[pos_11:pos_12])
+            initial_head2 = copy(c1.genes[pos_21:pos_22])
+
+            @show initial_head
+            @show initial_head2
+
+            gene_inversion!(c1)
+            @test c1.genes[toolbox.gene_count+1:toolbox.head_len+toolbox.gene_count] != initial_head || initial_head2 != c1.genes[9:11]
+        end
+    end
+    
+    @testset "Population Generation" begin
+        toolbox = create_test_toolbox()
+        population_size = 10
+        population = generate_population(population_size, toolbox)
+        
+        @test length(population) == population_size
+        @test all(x -> x isa Chromosome, population)
+        @test length(unique([p.genes for p in population])) == population_size
+    end
+
+    @testset "History Recording" begin
+        toolbox = create_test_toolbox()
+        population_size = 10
+        population = generate_population(population_size, toolbox)
+        
+        for (i, chromo) in enumerate(population)
+            set_fitness!(chromo, Float64(i))
+            @test fitness(chromo) == Float64(i)
+        end
+        
+        sorted_pop = sort(population, by=fitness)
+        @test issorted([fitness(c) for c in sorted_pop])
+    end
+end

test/Main_min_with_csv.jl

@@ -84,7 +84,7 @@ gene_count = 3
 head_len = 4
 
 best=runGep(epochs, pop_size, gene_count, head_len, utilized_syms,operators, callbacks, nodes, x_data',y_data, connection_syms, gep_params;
-
+loss_fun_str="mse", opt_method_const=:cg, hof=1)
 
 #Show the result of the optimization
 @show ("Fitness: (loss-fun): ", best[1].fitness)