From 994bdb164cde891a526748fb0502cdcc16a0c5a5 Mon Sep 17 00:00:00 2001
From: danielwilczak101 <44122838+danielwilczak101@users.noreply.github.com>
Date: Wed, 23 Sep 2020 21:58:48 -0400
Subject: [PATCH 1/4] Fixed all jacks code

---
 src/EasyGA.py                                 |  4 +-
 .../chromosome_structure/chromosome.py        | 35 +++++++++------
 src/initialization/gene_structure/gene.py     | 15 +++----
 .../population_structure/population.py        | 45 ++++++++++++++++---
 .../population_structure/test_population.py   | 14 ------
 src/initialization/random_initialization.py   | 31 +++++++------
 src/run_testing.py                            |  1 +
 7 files changed, 87 insertions(+), 58 deletions(-)

diff --git a/src/EasyGA.py b/src/EasyGA.py
index c5fb804..2a3c25c 100644
--- a/src/EasyGA.py
+++ b/src/EasyGA.py
@@ -25,7 +25,7 @@ class GA:
         # Defualt EastGA implimentation structure
         self.gene_function_impl = random_gene
         # Set the GA Configuration
-        self.initialization_impl = random_initialization()
+        self.initialization_impl = random_initialization
         #self.mutation_impl = PerGeneMutation(Mutation_rate)
         #self.selection_impl = TournamentSelection()
         #self.crossover_impl = FastSinglePointCrossover()
@@ -35,7 +35,7 @@ class GA:
 
     def initialize(self):
         # Create the first population
-        self.population = self.initialization_impl.initialize(
+        self.population = self.initialization_impl(
         self.population_size,
         self.chromosome_length,
         self.gene_function_impl)
diff --git a/src/initialization/chromosome_structure/chromosome.py b/src/initialization/chromosome_structure/chromosome.py
index 0f20b3e..02fe0b4 100644
--- a/src/initialization/chromosome_structure/chromosome.py
+++ b/src/initialization/chromosome_structure/chromosome.py
@@ -1,22 +1,31 @@
 class chromosome:
     # fitness = Empty, genes = [gene,gene,gene,etc]
-    def __init__(self):
+    def __init__(self, genes = []):
+        self.genes = genes
         self.fitness = None
-        self.genes = []
 
-    def add_gene(self,gene):
-        self.genes.append(gene)
+    def add_gene(self, gene, index = -1):
+        if index == -1:
+            index = len(self.genes) - 1
+        self.genes.insert(index, gene)
+
+    def remove_gene(self, index):
+        del self.genes[index]
+
+    def get_genes(self):
+        return self.genes
 
     def get_fitness(self):
         return self.fitness
 
-    def get_chromosome(self):
-        return self.genes
+    def set_gene(self, gene, index):
+        self.genes[index] = gene
 
-    def print_chromosome(self):
-        for i in range(len(self.genes)):
-            # Print the gene one by one.
-            if(i == len(self.genes) - 1):
-                print(f"[{self.genes[i].get_value()}]")
-            else:
-                print(f"[{self.genes[i].get_value()}],", end = '')
+    def set_genes(self, genes):
+        self.genes = genes
+
+    def set_fitness(self, fitness):
+        self.fitness = fitness
+
+    def __repr__(self):
+        return f"chromosome({self.genes.__repr__()})"
diff --git a/src/initialization/gene_structure/gene.py b/src/initialization/gene_structure/gene.py
index a956c9c..e309237 100644
--- a/src/initialization/gene_structure/gene.py
+++ b/src/initialization/gene_structure/gene.py
@@ -4,22 +4,21 @@ def check_gene(value):
     return value
 
 class gene:
-    # fitness = Empty, value = Define by gene function
     def __init__(self, value):
         self.fitness = None
         self.value = check_gene(value)
 
-    def set_fitness(self,fitness):
-        self.fitness = fitness
-
     def get_fitness(self):
         return self.fitness
 
     def get_value(self):
         return self.value
 
-    def print_value(self):
-        print(self.value)
+    def set_fitness(self, fitness):
+        self.fitness = fitness
 
-    def print_fitness(self):
-        print(self.fitness)
+    def set_value(self):
+        self.value = value
+
+    def __repr__(self):
+        return f"Gene({self.value} - Fitness{self.fitness})"
diff --git a/src/initialization/population_structure/population.py b/src/initialization/population_structure/population.py
index dc3068e..643a6a2 100644
--- a/src/initialization/population_structure/population.py
+++ b/src/initialization/population_structure/population.py
@@ -1,8 +1,43 @@
 class population:
     # population = [chromosome,chromosome,etc]
-    def __init__(self):
+    def __init__(self, chromosomes = []):
+        self.chromosomes = chromosomes
         self.fitness = None
-        self.chromosomes = []
-        
-    def add_chromosome(self,chromosome):
-        self.chromosomes.append(chromosome)
+
+    def get_closet_fitness(self,value):
+        # Get the chomosome that has the closets fitness to the value defined
+        pass
+
+    def add_chromosome(self, chromosome, index = -1):
+        if index == -1:
+            index = len(self.chromosomes) - 1
+        self.chromosomes.insert(index, chromosome)
+
+    def remove_chromosome(self, index):
+        del self.chromosomes[index]
+
+    def get_all_chromosomes(self):
+        return chromosomes
+
+    def get_fitness(self):
+        return self.fitness
+
+    def set_all_chromosomes(self, chromosomes):
+        self.chromosomes = chromosomes
+
+    def set_chromosome(self, chromosomes, index):
+        self.chromosome[index] = chromosome
+
+    def set_fitness(self, fitness):
+        self.fitness = fitness
+
+    def __repr__(self):
+        return f"population({self.chromosomes.__repr__()})"
+
+    def generate_first_chromosomes(self, chromosome_count, chromosome_length, gene_lower_bound, gene_upper_bound):
+        #Creating the chromosomes with Genes of random size
+        for x in range(chromosome_count):
+            chromosome = Chromosome(chromosome_length)
+            for y in range(chromosome_length):
+                chromosome.gene_set[y] = Gene(random.randint(gene_lower_bound[y], gene_upper_bound[y]))
+            self.chromosome_set.append(chromosome)
diff --git a/src/initialization/population_structure/test_population.py b/src/initialization/population_structure/test_population.py
index b187bb7..e69de29 100644
--- a/src/initialization/population_structure/test_population.py
+++ b/src/initialization/population_structure/test_population.py
@@ -1,14 +0,0 @@
-from population import population
-from chromosome import chromosome
-from gene import gene
-
-population = population()
-# Fill the population with chromosomes
-for i in range(population_size):
-    chromosome = chromosome()
-    #Fill the Chromosome with genes
-    for j in range(chromosome_length):
-        gene = gene(gene_function)
-        chromosome.add_gene(gene)
-
-    population.add_chromosome(chromosome)
diff --git a/src/initialization/random_initialization.py b/src/initialization/random_initialization.py
index 40da542..aeb78d5 100644
--- a/src/initialization/random_initialization.py
+++ b/src/initialization/random_initialization.py
@@ -3,19 +3,18 @@ from .population_structure.population import population as create_population
 from .chromosome_structure.chromosome import chromosome as create_chromosome
 from .gene_structure.gene import gene as create_gene
 
-class random_initialization:
-    def initialize(self,chromosome_length,population_size,gene_function):
-        # I dont understand why python needs this in its scope but it does.
-        global population
-        global chromosome
-        global gene
-        # Create the population object
-        population = create_population()
-        # Fill the population with chromosomes
-        for i in range(population_size):
-            chromosome = create_chromosome()
-            #Fill the Chromosome with genes
-            for j in range(chromosome_length):
-                chromosome.add_gene(create_gene(gene_function()))
-            population.add_chromosome(chromosome)
-        return population
+def random_initialization(chromosome_length,population_size,gene_function):
+    # I dont understand why python needs this in its scope but it does.
+    global population
+    global chromosome
+    global gene
+    # Create the population object
+    population = create_population()
+    # Fill the population with chromosomes
+    for i in range(population_size):
+        chromosome = create_chromosome()
+        #Fill the Chromosome with genes
+        for j in range(chromosome_length):
+            chromosome.add_gene(create_gene(gene_function()))
+        population.add_chromosome(chromosome)
+    return population
diff --git a/src/run_testing.py b/src/run_testing.py
index 7d9db70..63107b6 100644
--- a/src/run_testing.py
+++ b/src/run_testing.py
@@ -11,6 +11,7 @@ new_chromosome = ga.make_chromosome()
 # Makes a Population to store chromosomes in
 new_population = ga.make_population()
 
+# Creating population
 ga.initialize()
 
 print(ga.population)

From 9c5092525aa9029e3af5515185e8379a8fca8b69 Mon Sep 17 00:00:00 2001
From: danielwilczak101 <44122838+danielwilczak101@users.noreply.github.com>
Date: Wed, 23 Sep 2020 22:12:42 -0400
Subject: [PATCH 2/4] Fixed file and everything

---
 src/EasyGA.py                                                 | 2 +-
 .../{gene_creation => gene_function}/gene_random.py           | 0
 src/initialization/random_initialization.py                   | 4 ----
 3 files changed, 1 insertion(+), 5 deletions(-)
 rename src/initialization/{gene_creation => gene_function}/gene_random.py (100%)

diff --git a/src/EasyGA.py b/src/EasyGA.py
index 2a3c25c..6967527 100644
--- a/src/EasyGA.py
+++ b/src/EasyGA.py
@@ -4,7 +4,7 @@ from initialization.chromosome_structure.chromosome import chromosome as create_
 from initialization.gene_structure.gene import gene as create_gene
 
 # Import functions for defaults
-from initialization.gene_creation.gene_random import random_gene
+from initialization.gene_function.gene_random import random_gene
 # Import functionality defaults
 from initialization.random_initialization import random_initialization
 
diff --git a/src/initialization/gene_creation/gene_random.py b/src/initialization/gene_function/gene_random.py
similarity index 100%
rename from src/initialization/gene_creation/gene_random.py
rename to src/initialization/gene_function/gene_random.py
diff --git a/src/initialization/random_initialization.py b/src/initialization/random_initialization.py
index aeb78d5..cdef3ef 100644
--- a/src/initialization/random_initialization.py
+++ b/src/initialization/random_initialization.py
@@ -4,10 +4,6 @@ from .chromosome_structure.chromosome import chromosome as create_chromosome
 from .gene_structure.gene import gene as create_gene
 
 def random_initialization(chromosome_length,population_size,gene_function):
-    # I dont understand why python needs this in its scope but it does.
-    global population
-    global chromosome
-    global gene
     # Create the population object
     population = create_population()
     # Fill the population with chromosomes

From c4ead43d6d185e457a4e14a2ea5ba57b44c53788 Mon Sep 17 00:00:00 2001
From: Daniel Wilczak <danielwilczak101@gmail.com>
Date: Thu, 24 Sep 2020 15:02:58 -0400
Subject: [PATCH 3/4] Updated genes,chromosme,population prints

---
 src/initialization/chromosome_structure/chromosome.py |  5 ++++-
 src/initialization/gene_structure/gene.py             |  2 +-
 src/initialization/population_structure/population.py | 10 +++++++++-
 src/run_testing.py                                    |  7 +++----
 4 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/src/initialization/chromosome_structure/chromosome.py b/src/initialization/chromosome_structure/chromosome.py
index 02fe0b4..1880f54 100644
--- a/src/initialization/chromosome_structure/chromosome.py
+++ b/src/initialization/chromosome_structure/chromosome.py
@@ -28,4 +28,7 @@ class chromosome:
         self.fitness = fitness
 
     def __repr__(self):
-        return f"chromosome({self.genes.__repr__()})"
+        output_str = ''
+        for gene in self.genes:
+            output_str += gene.__repr__()
+        return output_str
diff --git a/src/initialization/gene_structure/gene.py b/src/initialization/gene_structure/gene.py
index e309237..ea3b547 100644
--- a/src/initialization/gene_structure/gene.py
+++ b/src/initialization/gene_structure/gene.py
@@ -21,4 +21,4 @@ class gene:
         self.value = value
 
     def __repr__(self):
-        return f"Gene({self.value} - Fitness{self.fitness})"
+        return f'[{self.value}]'
diff --git a/src/initialization/population_structure/population.py b/src/initialization/population_structure/population.py
index 643a6a2..fd80c28 100644
--- a/src/initialization/population_structure/population.py
+++ b/src/initialization/population_structure/population.py
@@ -32,7 +32,15 @@ class population:
         self.fitness = fitness
 
     def __repr__(self):
-        return f"population({self.chromosomes.__repr__()})"
+        pass
+
+    def print_all(self):
+        # Ex .Current population
+        #     Chromosome 1 - [gene][gene][gene][.etc] /  Chromosome fitness - #
+        print("Current population:")
+        for index in range(len(self.chromosomes)):
+            print(f'Chromosome - {index} {self.chromosomes[index]}', end = "")
+            print(f' / Fitness = {self.chromosomes[index].fitness}')
 
     def generate_first_chromosomes(self, chromosome_count, chromosome_length, gene_lower_bound, gene_upper_bound):
         #Creating the chromosomes with Genes of random size
diff --git a/src/run_testing.py b/src/run_testing.py
index 63107b6..1d5b785 100644
--- a/src/run_testing.py
+++ b/src/run_testing.py
@@ -14,7 +14,6 @@ new_population = ga.make_population()
 # Creating population
 ga.initialize()
 
-print(ga.population)
-
-for chromosome in ga.population.chromosomes:
-    print(chromosome.genes[0].__dict__)
+ga.population.print_all()
+print("")
+print(ga.population.chromosomes[0].__repr__())

From 45638ad4eb295cb95918b78b3447ecf3fedc5532 Mon Sep 17 00:00:00 2001
From: SimpleArt <71458112+SimpleArt@users.noreply.github.com>
Date: Thu, 24 Sep 2020 18:13:44 -0400
Subject: [PATCH 4/4] Fixed data structures

Fixed constructors with default arguments as well as the adders with default arguments.
---
 .../chromosome_structure/chromosome.py               | 12 ++++++++----
 .../population_structure/population.py               | 12 ++++++++----
 2 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/src/initialization/chromosome_structure/chromosome.py b/src/initialization/chromosome_structure/chromosome.py
index 1880f54..fecc278 100644
--- a/src/initialization/chromosome_structure/chromosome.py
+++ b/src/initialization/chromosome_structure/chromosome.py
@@ -1,12 +1,16 @@
 class chromosome:
-    # fitness = Empty, genes = [gene,gene,gene,etc]
-    def __init__(self, genes = []):
-        self.genes = genes
+    
+    # fitness = Empty; genes = [gene, gene, gene, etc.]
+    def __init__(self, genes = None):
+        if genes is None:
+            self.genes = []
+        else:
+            self.genes = genes
         self.fitness = None
 
     def add_gene(self, gene, index = -1):
         if index == -1:
-            index = len(self.genes) - 1
+            index = len(self.genes)
         self.genes.insert(index, gene)
 
     def remove_gene(self, index):
diff --git a/src/initialization/population_structure/population.py b/src/initialization/population_structure/population.py
index fd80c28..7973218 100644
--- a/src/initialization/population_structure/population.py
+++ b/src/initialization/population_structure/population.py
@@ -1,7 +1,11 @@
 class population:
-    # population = [chromosome,chromosome,etc]
-    def __init__(self, chromosomes = []):
-        self.chromosomes = chromosomes
+    
+    # fitness = Empty; population = [chromosome, chromosome, etc.]
+    def __init__(self, chromosomes = None):
+        if chromosomes is None:
+          self.chromosomes = []
+        else:
+          self.chromosomes = chromosomes
         self.fitness = None
 
     def get_closet_fitness(self,value):
@@ -10,7 +14,7 @@ class population:
 
     def add_chromosome(self, chromosome, index = -1):
         if index == -1:
-            index = len(self.chromosomes) - 1
+            index = len(self.chromosomes)
         self.chromosomes.insert(index, chromosome)
 
     def remove_chromosome(self, index):