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# Derek M. Tishler
# nx plot example deap individual
# For post: https://groups.google.com/g/deap-users/c/nZFZpm5OPZA

import matplotlib.pyplot as plt
import networkx as nx
from networkx.drawing.nx_agraph import graphviz_layout

## May need is resuming session
#from deap import creator

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import sklearn.decomposition
import sklearn.ensemble
import sklearn.linear_model
import sklearn.preprocessing
import sklearn.svm
from sklearn.datasets import load_breast_cancer
from sklearn.model_selection import train_test_split

from baikal import Input, Model, make_step
from baikal.plot import plot_model

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import array
import random

import numpy

from deap import algorithms
from deap import base
from deap import creator
from deap import tools

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# Based on https://raw.githubusercontent.com/DEAP/deap/master/examples/ga/onemax_mp.py
# Using onemax(ignore the problem sorta) to show how to work with only normalized individuals
# Can Uses numpy individuals but no multiproc: https://deap.readthedocs.io/en/master/examples/ga_onemax_numpy.html

# Derek M Tishler, Dec 2020

import multiprocessing
import random
import sys

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# Derek Tishler

# Deap Hypervolume comparison for varying population size and number of objectives, 
# testing for use with high dimensional NSGA III with many objectives (over 8).)

# Discussion here, also required fitness_values.txt with 212x14 array of fitness values per ind in pop:
# https://groups.google.com/g/deap-users/c/XLfLa3at6pw

import numpy as np

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# Example of creating an individual with multiple 'parts'

# Derek M Tishler, Oct 2020

'''
Evolve a complex structure/individual, such as encoded hyperparamters of a mlp classifier
    individual_example = [encoded_solver__int, learning_rate__float, hidden_units__list]
example of a 10 layer network using adam solver with learning rate ~0.007:
    [0, 0.006592, [13, 89, 21, 100, 96, 100, 16, 67, 45, 88]]
'''

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# Example of using selTournamentDCD requiring assignCrowdingDist

# Based on deap/examples/ga/onemax_numpy.py
# https://github.com/DEAP/deap/blob/master/examples/ga/onemax_numpy.py

# Discussion:
# https://groups.google.com/forum/#!topic/deap-users/uU382eztuts

import random

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# Derek Tishler, answering a question from Deap Discussions:
# For Ning's question: https://groups.google.com/forum/#!topic/deap-users/W8wacFPyj9Y

# Based on symbreg example: https://github.com/DEAP/deap/blob/master/examples/gp/symbreg.py
# eaSimpleWithElitism from: https://github.com/PacktPublishing/Hands-On-Genetic-Algorithms-with-Python/blob/master/Chapter04/elitism.py


import operator
import math

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# Derek Tishler
# Aug 3 2020
# Based On:
# https://github.com/DEAP/deap/blob/master/examples/ga/onemax_short.py
# V2

import array
import random

import numpy as np

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#    This file is part of DEAP.
#
#    DEAP is free software: you can redistribute it and/or modify
#    it under the terms of the GNU Lesser General Public License as
#    published by the Free Software Foundation, either version 3 of
#    the License, or (at your option) any later version.
#
#    DEAP is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the