{"action":"created","comment":{"url":"https://api.github.com/repos/youngpadawans/geneticexplorer/pulls/comments/67774333","id":67774333,"diff_hunk":"@@ -1,354 +1,265 @@\n-__author__ = 'theep_000'\n+\n+__author__ = \"Paul Comeau\"\n+__credits__ = [\"Paul Comeau\", \"Kaixin Cui\"]\n+__maintainer__ = \"Paul Comeau\"\n+__email__ = \"comeaupaul98@gmail.com\"\n+__status__ = \"Development\"\n \n import random\n import operator\n from collections import Counter\n-import sys\n-import argparse\n+from sys import argv\n+from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter\n+\n+\n+POSS_INGREDIENTS = [\"tomato sauce\", \"pesto\", \"mozzarella\", \"alfredo sauce\", \"pasta shells\", \"chile sauce\", \"pasta bowties\",\n+                    \"parmesan\", \"meatballs\", \"pasta tubes\", \"shredded chicken\", \"basil\", \"spinach\", \"chives\", \"shrimp\",\n+                    \"mushroom\", \"macaroni\", \"feta cheese\", \"noodles\", \"sausage\", \"olives\"]\n+\n+class Gene:\n+    \"\"\"formatting for the object of a single ingredient\n+    \"\"\"\n+\n+    __ingredient = \"\"\n+\n+    ingredient_score = {\"tomato sauce\": 7, \"pesto\": 5, \"mozzarella\": 5, \"alfredo sauce\": 10, \"pasta shells\": 7, \"chile sauce\": 5,\n+                  \"pasta bowties\": 5, \"parmesan\": 10, \"meatballs\": 8, \"pasta tubes\": 10, \"shredded chicken\": 10, \"basil\": 7,\n+                  \"spinach\": 10, \"chives\": 2, \"shrimp\": 2, \"mushroom\": 2, \"macaroni\": 5, \"feta cheese\": 2, \"noodles\": 7,\n+                  \"sausage\": 7, \"olives\": 0}\n+\n+    def __init__(self, ingredient):\n+        \"\"\"creates object from single ingredient\n+        \"\"\"\n \n-mutate_chance = 90\n-base_pop = 100\n-generation_max = 100\n+        self.__ingredient = ingredient\n \n-poss_ingredients = [\"tomato sauce\",\"pesto\",\"mozzarella\",\"alfredo sauce\", \"pasta shells\",\"chile sauce\", \"pasta bowties\", \"parmesan\",\"meatballs\",\"pasta tubes\",\"shredded chicken\",\"basil\", \"spinach\",\"chives\",\"shrimp\",\"mushroom\",\"macaroni\",\"feta cheese\",\"noodles\",\"sausage\",\"olives\"]\n \n-class pasta:\n-    #format and functions of the pasta chromosome\n+class PastaDish:\n+    \"\"\"format and functions of the pasta chromosome\n+    \"\"\"\n \n     __gene_1 = \"\"\n     __gene_2 = \"\"\n     __gene_3 = \"\"\n     __gene_4 = \"\"\n-    fitvalue = 0\n+    fit_value = 0\n \n-    def __init__ (self, gene_1, gene_2, gene_3, gene_4):\n-        #creates object from 4 genes\n+    def __init__(self, gene_1, gene_2, gene_3, gene_4):\n+        \"\"\"creates object from 4 genes\n+        \"\"\"\n \n         self.__gene_1 = gene_1\n         self.__gene_2 = gene_2\n         self.__gene_3 = gene_3\n         self.__gene_4 = gene_4\n \n-    def list_ing(self):\n-        #gives a list of the genes\n+    def listIng(self):\n+        \"\"\"gives a list of the genes\n+        \"\"\"\n+\n         return [self.__gene_1, self.__gene_2, self.__gene_3, self.__gene_4]\n \n-    def set_fitvalue(self):\n-        # Use to set fit value for each ingredient.\n+    def setFitValue(self):\n+        \"\"\"sets the fitness value of a chromosome\n+        \"\"\"\n+\n         fit_val = 0\n-        if self.__gene_1 == \"tomato_sauce\":\n-            fit_val += 7\n-        if self.__gene_2 == \"tomato_sauce\":\n-            fit_val += 7\n-        if self.__gene_3 == \"tomato_sauce\":\n-            fit_val += 7\n-        if self.__gene_4 == \"tomato_sauce\":\n-            fit_val += 7\n-        if self.__gene_1 == \"pesto\":\n-            fit_val += 5\n-        if self.__gene_2 == \"pesto\":\n-            fit_val += 5\n-        if self.__gene_3 == \"pesto\":\n-            fit_val += 5\n-        if self.__gene_4 == \"pesto\":\n-            fit_val += 5\n-        if self.__gene_1 == \"mozzarella\":\n-            fit_val += 5\n-        if self.__gene_2 == \"mozzarella\":\n-            fit_val += 5\n-        if self.__gene_3 == \"mozzarella\":\n-            fit_val += 5\n-        if self.__gene_4 == \"mozzarella\":\n-            fit_val += 5\n-        if self.__gene_1 == \"alfredo sauce\":\n-            fit_val += 10\n-        if self.__gene_2 == \"alfredo sauce\":\n-            fit_val += 10\n-        if self.__gene_3 == \"alfredo sauce\":\n-            fit_val += 10\n-        if self.__gene_4 == \"alfredo sauce\":\n-            fit_val += 10\n-        if self.__gene_1 == \"pasta shells\":\n-            fit_val += 7\n-        if self.__gene_2 == \"pasta shells\":\n-            fit_val += 7\n-        if self.__gene_3 == \"pasta shells\":\n-            fit_val += 7\n-        if self.__gene_4 == \"pasta shells\":\n-            fit_val += 7\n-        if self.__gene_1 == \"chile sauce\":\n-            fit_val += 5\n-        if self.__gene_2 == \"chile sauce\":\n-            fit_val += 5\n-        if self.__gene_3 == \"chile sauce\":\n-            fit_val += 5\n-        if self.__gene_4 == \"chile sauce\":\n-            fit_val += 5\n-        if self.__gene_1 == \"pasta bowties\":\n-            fit_val += 5\n-        if self.__gene_2 == \"pasta bowties\":\n-            fit_val += 5\n-        if self.__gene_3 == \"pasta bowties\":\n-            fit_val += 5\n-        if self.__gene_4 == \"pasta bowties\":\n-            fit_val += 5\n-        if self.__gene_1 == \"parmesan\":\n-            fit_val += 10\n-        if self.__gene_2 == \"parmesan\":\n-            fit_val += 10\n-        if self.__gene_3 == \"parmesan\":\n-            fit_val += 10\n-        if self.__gene_4 == \"parmesan\":\n-            fit_val += 10\n-        if self.__gene_1 == \"meatballs\":\n-            fit_val += 8\n-        if self.__gene_2 == \"meatballs\":\n-            fit_val += 8\n-        if self.__gene_3 == \"meatballs\":\n-            fit_val += 8\n-        if self.__gene_4 == \"meatballs\":\n-            fit_val += 8\n-        if self.__gene_1 == \"pasta tubes\":\n-            fit_val += 10\n-        if self.__gene_2 == \"pasta tubes\":\n-            fit_val += 10\n-        if self.__gene_3 == \"pasta tubes\":\n-            fit_val += 10\n-        if self.__gene_4 == \"pasta tubes\":\n-            fit_val += 10\n-        if self.__gene_1 == \"shredded chicken\":\n-            fit_val += 10\n-        if self.__gene_2 == \"shredded chicken\":\n-            fit_val += 10\n-        if self.__gene_3 == \"shredded chicken\":\n-            fit_val += 10\n-        if self.__gene_4 == \"shredded chicken\":\n-            fit_val += 10\n-        if self.__gene_1 == \"basil\":\n-            fit_val += 7\n-        if self.__gene_2 == \"basil\":\n-            fit_val += 7\n-        if self.__gene_3 == \"basil\":\n-            fit_val += 7\n-        if self.__gene_4 == \"basil\":\n-            fit_val += 7\n-        if self.__gene_1 == \"spinach\":\n-            fit_val += 10\n-        if self.__gene_2 == \"spinach\":\n-            fit_val += 10\n-        if self.__gene_3 == \"spinach\":\n-            fit_val += 10\n-        if self.__gene_4 == \"spinach\":\n-            fit_val += 10\n-        if self.__gene_1 == \"chives\":\n-            fit_val += 2\n-        if self.__gene_2 == \"chives\":\n-            fit_val += 2\n-        if self.__gene_3 == \"chives\":\n-            fit_val += 2\n-        if self.__gene_4 == \"chives\":\n-            fit_val += 2\n-        if self.__gene_1 == \"shrimp\":\n-            fit_val += 2\n-        if self.__gene_2 == \"shrimp\":\n-            fit_val += 2\n-        if self.__gene_3 == \"shrimp\":\n-            fit_val += 2\n-        if self.__gene_4 == \"shrimp\":\n-            fit_val += 2\n-        if self.__gene_1 == \"mushroom\":\n-            fit_val += 2\n-        if self.__gene_2 == \"mushroom\":\n-            fit_val += 2\n-        if self.__gene_3 == \"mushroom\":\n-            fit_val += 2\n-        if self.__gene_4 == \"mushroom\":\n-            fit_val += 2\n-        if self.__gene_1 == \"macaroni\":\n-            fit_val += 5\n-        if self.__gene_2 == \"macaroni\":\n-            fit_val += 5\n-        if self.__gene_3 == \"macaroni\":\n-            fit_val += 5\n-        if self.__gene_4 == \"macaroni\":\n-            fit_val += 5\n-        if self.__gene_1 == \"feta cheese\":\n-            fit_val += 2\n-        if self.__gene_2 == \"feta cheese\":\n-            fit_val += 2\n-        if self.__gene_3 == \"feta cheese\":\n-            fit_val += 2\n-        if self.__gene_4 == \"feta cheese\":\n-            fit_val += 2\n-        if self.__gene_1 == \"olives\":\n-            fit_val += 0\n-        if self.__gene_2 == \"olives\":\n-            fit_val += 0\n-        if self.__gene_3 == \"olives\":\n-            fit_val += 0\n-        if self.__gene_4 == \"olives\":\n-            fit_val += 0\n-        if self.__gene_1 == \"noodles\":\n-            fit_val += 7\n-        if self.__gene_2 == \"noodles\":\n-            fit_val += 7\n-        if self.__gene_3 == \"noodles\":\n-            fit_val += 7\n-        if self.__gene_4 == \"noodles\":\n-            fit_val += 7\n-        if self.__gene_1 == \"sausage\":\n-            fit_val += 7\n-        if self.__gene_2 == \"sausage\":\n-            fit_val += 7\n-        if self.__gene_3 == \"sausage\":\n-            fit_val += 7\n-        if self.__gene_4 == \"sausage\":\n-            fit_val += 7\n+        fit_val += Gene.ingredient_score[self.__gene_1]\n+        fit_val += Gene.ingredient_score[self.__gene_2]\n+        fit_val += Gene.ingredient_score[self.__gene_3]\n+        fit_val += Gene.ingredient_score[self.__gene_4]\n         self.fitvalue = fit_val\n \n-    def get_fitvalue(self):\n-        #gives the set fitvalue\n-        return self.fitvalue\n-\n-class Chrom_Population:\n-\n-    __chrom_list = []\n-    __chrom_fitdict = {}\n-    __prob_dict = {}\n+class ChromPopulation:\n+    \"\"\"format and fuctions of a population of chromosomes\n+    \"\"\"\n+    __chroms = []\n+    __chrom_fit = {}\n+    __probabilities = {}\n \n     def __init__(self, chrom_list):\n-        Chrom_Population.__chrom_list = chrom_list\n+        \"\"\"the given list defines the chomosome population\n+        \"\"\"\n+\n+        self.__chroms = chrom_list\n \n     def cull(self):\n-        #remove 10% of self\n-        count_rem = (len(self.__chrom_list)/10)\n-        execution =reversed(Counter(self.__chrom_fitdict).most_common()[-count_rem:])\n+        \"\"\"remove 10% of self\n+        \"\"\"\n+\n+        count_rem = (len(self.__chroms)/10)\n+        execution = reversed(Counter(self.__chrom_fit).most_common()[-count_rem:])\n         for object in execution:\n-            del self.__chrom_fitdict[object[0]]\n+            del self.__chrom_fit[object[0]]\n         pass\n \n-    def probability_parent(self):\n-        #creates a dictionary containing the probability of being selected as a parent\n-        self.__prob_dict = {}\n+    def probabilityParent(self):\n+        \"\"\"creates a dictionary containing the probability of being selected as a parent\n+        \"\"\"\n+\n+        self.__probabilities = {}\n         total = 0\n         prev_chance = 0\n-        fit_copy1 = self.__chrom_fitdict\n-        fit_copy2 = self.__chrom_fitdict\n+        fit_copy1 = self.__chrom_fit\n+        fit_copy2 = self.__chrom_fit\n         for chrom in fit_copy1:\n-            total += self.__chrom_fitdict[chrom]\n+            total += self.__chrom_fit[chrom]\n         for chrom in fit_copy2:\n             selection_chance = float(fit_copy2[chrom])/float(total) + prev_chance\n-            self.__prob_dict[chrom] = selection_chance\n+            self.__probabilities[chrom] = selection_chance\n             prev_chance = selection_chance\n         pass\n \n-    def parent_select(self):\n-        #selects parents based on probability dict\n-        parentchance_1 = random.random()\n-        parentchance_2 = random.random()\n-        prob_dic1 = self.__prob_dict\n-        prob_dic2 = self.__prob_dict\n+    def parentSelect(self):\n+        \"\"\"selects parents based on probability dict\n+        \"\"\"\n+        parent_chance_1 = random.random()\n+        parent_chance_2 = random.random()\n+        prob_dic1 = self.__probabilities\n+        prob_dic2 = self.__probabilities\n         def_check = 0\n         for chrom in prob_dic1:\n-            if prob_dic1[chrom] >= parentchance_1:\n+            if prob_dic1[chrom] >= parent_chance_1:\n                 parent_1 = chrom\n                 def_check = 1\n             if def_check == 1:\n                 break\n         def_check = 0\n         prev_parent = None\n         for chrom in prob_dic2:\n-            if prob_dic2[chrom] >= parentchance_2:\n+            if prob_dic2[chrom] >= parent_chance_2:\n                 parent_2 = chrom\n-                #if parent_2 == parent_1:\n-                    #if prev_parent != None:\n-                        #parent_2 = prev_parent\n-                    #if prev_parent == None:\n-                        #parent_2 = next(chrom)\n+                if parent_2 == parent_1:\n+                    if prev_parent == None:\n+                        pass\n+                    else:\n+                        parent_2 = prev_parent\n                 def_check = 1\n             if def_check == 1:\n                 break\n             prev_parent = chrom\n         parent_tuple = (parent_1, parent_2)\n         return parent_tuple\n \n-    def dict_producer(self):\n-        for chrom in self.__chrom_list:\n-            chrom.set_fitvalue()\n-            self.__chrom_fitdict[chrom] = chrom.get_fitvalue()\n+    def fitnessProducer(self):\n+        \"\"\"creates a dictionary containing pasta types and their fitness value\n+        \"\"\"\n+\n+        for chrom in self.__chroms:\n+            chrom.setFitValue()\n+            self.__chrom_fit[chrom] = chrom.fitvalue\n         pass\n \n-    def breed_et_mutate(self, couple_tuple):\n-        #mutates children after bred from two chromosomes\n+    def breedEtMutate(self, couple_tuple, mutate_chance):\n+        \"\"\"mutates children after bred from two chromosomes\n+        \"\"\"\n         pasta1 = couple_tuple[0]\n         pasta2 = couple_tuple[1]\n-        ingredients_1 = pasta1.list_ing()\n-        ingredients_2 = pasta2.list_ing()\n+        ingredients_1 = pasta1.listIng()\n+        ingredients_2 = pasta2.listIng()\n         ingredients_3 = []\n         mutated_child = []\n-        for num in range(0,1):\n+        for num in range(0, 1):\n             random_layout = random.randint(1, 6)\n             if random_layout == 1:","path":"PastaGA.py","position":391,"original_position":391,"commit_id":"e934f038afc34ae29506650dca909788e0267cca","original_commit_id":"e934f038afc34ae29506650dca909788e0267cca","user":{"login":"alicon","id":4838093,"avatar_url":"https://avatars.githubusercontent.com/u/4838093?v=3","gravatar_id":"","url":"https://api.github.com/users/alicon","html_url":"https://github.com/alicon","followers_url":"https://api.github.com/users/alicon/followers","following_url":"https://api.github.com/users/alicon/following{/other_user}","gists_url":"https://api.github.com/users/alicon/gists{/gist_id}","starred_url":"https://api.github.com/users/alicon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alicon/subscriptions","organizations_url":"https://api.github.com/users/alicon/orgs","repos_url":"https://api.github.com/users/alicon/repos","events_url":"https://api.github.com/users/alicon/events{/privacy}","received_events_url":"https://api.github.com/users/alicon/received_events","type":"User","site_admin":false},"body":"See if you can think of accomplishing the same thing here, without all the explicit calls. One thing to consider, would be  iterating through the list of genes/ingredient, and flip a coin which will have you decide which parent you will select from. 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