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Now with full Python 3.6 support!

tf2
Kai Staats 2019-06-08 22:27:44 -07:00 committed by GitHub
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Karoo_GP_User_Guide.pdf
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RELEASE_NOTES.txt
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@ -1,3 +1,16 @@
2019 06/08
Finally! Full Python 3.6 support!!!
And with this update, a substantial number of improvements and modifications. Most are related to the user interface
and associated menu. Namely, the (pause) menu is no longer built upon nested loops, therefore the user does not find
him or herself unable to conduct a clean exit. The code that supports the text-based queries is reduced in its
complexity, and in many cases made more brief. Some re-coloring of the interface text keeps like items in like
color schemes. Simple, and does not improve performance, but looks better, overall.
"Per my prior note (below), I do appreciate your patience and support, and do look forward to your feedback." --kai
2019 05/18 2019 05/18
"My apology to the users of Karoo GP for the incredible gap between the most recent and this update. My research and "My apology to the users of Karoo GP for the incredible gap between the most recent and this update. My research and

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karoo_gp.py
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@ -1,7 +1,7 @@
# Karoo GP (desktop + server combined) # Karoo GP (desktop + server combined)
# Use Genetic Programming for Classification and Symbolic Regression # Use Genetic Programming for Classification and Symbolic Regression
# by Kai Staats, MSc; see LICENSE.md # by Kai Staats, MSc with TensorFlow support provided by Iurii Milovanov; see LICENSE.md
# version 2.1 final for Python 2.7 # version 2.3 for Python 3.6
''' '''
A word to the newbie, expert, and brave-- A word to the newbie, expert, and brave--
@ -22,22 +22,22 @@ If you include the path to an external dataset, it will auto-load at launch:
If you include one or more additional arguments, they will override the default values, as follows: If you include one or more additional arguments, they will override the default values, as follows:
-ker [r,c,m] fitness function: (r)egression, (c)lassification, or (m)atching -ker [r,c,m] fitness function: (r)egression, (c)lassification, or (m)atching
-typ [f,g,r] Tree type: (f)ull, (g)row, or (r)amped half/half -typ [f,g,r] Tree type: (f)ull, (g)row, or (r)amped half/half
-bas [3...10] maximum Tree depth for initial population -bas [3...10] maximum Tree depth for initial population
-max [3...10] maximum Tree depth for entire run -max [3...10] maximum Tree depth for entire run
-min [3 to 2^(bas +1) - 1] minimum number of nodes -min [3 to 2^(bas +1) - 1] minimum number of nodes
-pop [10...1000] number of trees in each generational population -pop [10...1000] number of trees in each generational population
-gen [1...100] number of generations -gen [1...100] number of generations
-tor [7 per 100] number of trees selected for tournament -tor [7 per 100] number of trees selected for tournament
-evr [0.0...1.0] decimal percent of pop generated through Reproduction -evr [0.0...1.0] decimal percent of pop generated through Reproduction
-evp [0.0...1.0] decimal percent of pop generated through Point Mutation -evp [0.0...1.0] decimal percent of pop generated through Point Mutation
-evb [0.0...1.0] decimal percent of pop generated through Branch Mutation -evb [0.0...1.0] decimal percent of pop generated through Branch Mutation
-evc [0.0...1.0] decimal percent of pop generated through Crossover -evc [0.0...1.0] decimal percent of pop generated through Crossover
If you include any of the above flags, then you *must* also include a flag to load an external dataset. If you include any of the above flags, then you *must* also include a flag to load an external dataset.
-fil [path]/[to]/[data].csv an external dataset -fil [path]/[to]/[data].csv an external dataset
An example is given, as follows: An example is given, as follows:
@ -52,50 +52,50 @@ import argparse
import karoo_gp_base_class; gp = karoo_gp_base_class.Base_GP() import karoo_gp_base_class; gp = karoo_gp_base_class.Base_GP()
os.system('clear') os.system('clear')
print '\n\033[36m\033[1m' print ('\n\033[36m\033[1m')
print '\t ** ** ****** ***** ****** ****** ****** ******' print ('\t ** ** ****** ***** ****** ****** ****** ******')
print '\t ** ** ** ** ** ** ** ** ** ** ** ** **' print ('\t ** ** ** ** ** ** ** ** ** ** ** ** **')
print '\t ** ** ** ** ** ** ** ** ** ** ** ** **' print ('\t ** ** ** ** ** ** ** ** ** ** ** ** **')
print '\t **** ******** ****** ** ** ** ** ** *** *******' print ('\t **** ******** ****** ** ** ** ** ** *** *******')
print '\t ** ** ** ** ** ** ** ** ** ** ** ** **' print ('\t ** ** ** ** ** ** ** ** ** ** ** ** **')
print '\t ** ** ** ** ** ** ** ** ** ** ** ** **' print ('\t ** ** ** ** ** ** ** ** ** ** ** ** **')
print '\t ** ** ** ** ** ** ** ** ** ** ** ** **' print ('\t ** ** ** ** ** ** ** ** ** ** ** ** **')
print '\t ** ** ** ** ** ** ****** ****** ****** **' print ('\t ** ** ** ** ** ** ****** ****** ****** **')
print '\033[0;0m' print ('\033[0;0m')
print '\t\033[36m Genetic Programming in Python - by Kai Staats, version 2.1\033[0;0m' print ('\t\033[36m Genetic Programming in Python with TensorFlow - by Kai Staats, version 2.3\033[0;0m')
print '' print ('')
#++++++++++++++++++++++++++++++++++++++++++ #++++++++++++++++++++++++++++++++++++++++++
# User Interface for Configuation | # User Interface for Configuation |
#++++++++++++++++++++++++++++++++++++++++++ #++++++++++++++++++++++++++++++++++++++++++
if len(sys.argv) < 3: # either no command line argument (1) or a filename (2) is provided if len(sys.argv) < 3: # either no command line argument, or only a filename is provided
while True: while True:
try: try:
query = raw_input('\t Select (c)lassification, (r)egression, (m)atching, or (p)lay (default m): ') query = input('\t Select (c)lassification, (r)egression, (m)atching, or (p)lay (default m): ')
if query not in ['c','r','m','p','']: raise ValueError() if query in ['c','r','m','p','']: kernel = query or 'm'; break
else: kernel = query or 'm'; break else: raise ValueError()
except ValueError: print '\t\033[32m Select from the options given. Try again ...\n\033[0;0m' except ValueError: print ('\t\033[32m Select from the options given. Try again ...\n\033[0;0m')
except KeyboardInterrupt: sys.exit() except KeyboardInterrupt: sys.exit()
if kernel == 'p': # play mode if kernel == 'p': # play mode
while True: while True:
try: try:
query = raw_input('\t Select (f)ull or (g)row (default g): ') query = input('\t Select (f)ull or (g)row (default g): ')
if query not in ['f','g','']: raise ValueError() if query in ['f','g','']: tree_type = query or 'f'; break
else: tree_type = query or 'f'; break else: raise ValueError()
except ValueError: print '\t\033[32m Select from the options given. Try again ...\n\033[0;0m' except ValueError: print ('\t\033[32m Select from the options given. Try again ...\n\033[0;0m')
except KeyboardInterrupt: sys.exit() except KeyboardInterrupt: sys.exit()
while True: while True:
try: try:
query = raw_input('\t Enter the depth of the Tree (default 1): ') query = input('\t Enter the depth of the Tree (default 1): ')
if query not in str(range(1,11)) or query == '0': raise ValueError() if query == '': tree_depth_base = 1; break
elif query == '': tree_depth_base = 1; break elif int(query) in list(range(1,11)): tree_depth_base = int(query); break
else: tree_depth_base = int(query); break else: raise ValueError()
except ValueError: print '\t\033[32m Enter a number from 1 including 10. Try again ...\n\033[0;0m' except ValueError: print ('\t\033[32m Enter a number from 1 including 10. Try again ...\n\033[0;0m')
except KeyboardInterrupt: sys.exit() except KeyboardInterrupt: sys.exit()
tree_depth_max = tree_depth_base tree_depth_max = tree_depth_base
@ -110,56 +110,57 @@ if len(sys.argv) < 3: # either no command line argument (1) or a filename (2) is
while True: while True:
try: try:
query = raw_input('\t Select (f)ull, (g)row, or (r)amped 50/50 method (default r): ') query = input('\t Select (f)ull, (g)row, or (r)amped 50/50 method (default r): ')
if query not in ['f','g','r','']: raise ValueError() if query in ['f','g','r','']: tree_type = query or 'r'; break
else: tree_type = query or 'r'; break else: raise ValueError()
except ValueError: print '\t\033[32m Select from the options given. Try again ...\n\033[0;0m' except ValueError: print ('\t\033[32m Select from the options given. Try again ...\n\033[0;0m')
except KeyboardInterrupt: sys.exit() except KeyboardInterrupt: sys.exit()
while True: while True:
try: try:
query = raw_input('\t Enter depth of the \033[3minitial\033[0;0m population of Trees (default 3): ') query = input('\t Enter depth of the \033[3minitial\033[0;0m population of Trees (default 3): ')
if query not in str(range(1,11)) or query == '0': raise ValueError() if query == '': tree_depth_base = 3; break
elif query == '': tree_depth_base = 3; break elif int(query) in list(range(1,11)): tree_depth_base = int(query); break
else: tree_depth_base = int(query); break else: raise ValueError()
except ValueError: print '\t\033[32m Enter a number from 1 including 10. Try again ...\n\033[0;0m' except ValueError: print ('\t\033[32m Enter a number from 1 including 10. Try again ...\n\033[0;0m')
except KeyboardInterrupt: sys.exit() except KeyboardInterrupt: sys.exit()
while True: while True:
try: try:
query = raw_input('\t Enter maximum Tree depth (default %s): ' %str(tree_depth_base)) query = input('\t Enter maximum Tree depth (default %s): ' %str(tree_depth_base))
if query not in str(range(tree_depth_base,11)) or query == '0': raise ValueError() if query == '': tree_depth_max = tree_depth_base; break
elif query == '': tree_depth_max = tree_depth_base; break elif int(query) in list(range(tree_depth_base,11)): tree_depth_max = int(query); break
else: tree_depth_max = int(query); break else: raise ValueError()
except ValueError: print '\t\033[32m Enter a number > or = the initial Tree depth. Try again ...\n\033[0;0m' except ValueError: print ('\t\033[32m Enter a number from %s including 10. Try again ...\n\033[0;0m' %str(tree_depth_base))
except KeyboardInterrupt: sys.exit() except KeyboardInterrupt: sys.exit()
max_nodes = 2**(tree_depth_base+1)-1 # calc the max number of nodes for the given depth max_nodes = 2**(tree_depth_base+1)-1 # calc the max number of nodes for the given depth
while True: while True:
try: try:
query = raw_input('\t Enter minimum number of nodes for any given Tree (default 3; max %s): ' %str(max_nodes)) query = input('\t Enter minimum number of nodes for any given Tree (default 3; max %s): ' %str(max_nodes))
if query not in str(range(3,max_nodes + 1)) or query == '0' or query == '1' or query == '2': raise ValueError() if query == '': tree_depth_min = 3; break
elif query == '': tree_depth_min = 3; break elif int(query) in list(range(3,max_nodes + 1)): tree_depth_min = int(query); break
else: tree_depth_min = int(query); break else: raise ValueError()
except ValueError: print '\t\033[32m Enter a number from 3 including %s. Try again ...\n\033[0;0m' %str(max_nodes) except ValueError: print ('\t\033[32m Enter a number from 3 including %s. Try again ...\n\033[0;0m' %str(max_nodes))
except KeyboardInterrupt: sys.exit() except KeyboardInterrupt: sys.exit()
#while True: #while True:
#try: #try:
#swim = raw_input('\t Select (p)artial or (f)ull operator inclusion (default p): ') #query = input('\t Select (p)artial or (f)ull operator inclusion (default p): ')
#if swim not in ['p','f','']: raise ValueError() #if query == '': swim = 'p'; break
#swim = swim or 'p'; break #elif query in ['p','f']: swim = query; break
#except ValueError: print '\t\033[32m Select from the options given. Try again ...\n\033[0;0m' #else: raise ValueError()
#except ValueError: print ('\t\033[32m Select from the options given. Try again ...\n\033[0;0m')
#except KeyboardInterrupt: sys.exit() #except KeyboardInterrupt: sys.exit()
while True: while True:
try: try:
query = raw_input('\t Enter number of Trees in each population (default 100): ') query = input('\t Enter number of Trees in each population (default 100): ')
if query not in str(range(1,1001)) or query == '0': raise ValueError() if query == '': tree_pop_max = 100; break
elif query == '': tree_pop_max = 100; break elif int(query) in list(range(1,1001)): tree_pop_max = int(query); break
else: tree_pop_max = int(query); break else: raise ValueError()
except ValueError: print '\t\033[32m Enter a number from 1 including 1000. Try again ...\n\033[0;0m' except ValueError: print ('\t\033[32m Enter a number from 1 including 1000. Try again ...\n\033[0;0m')
except KeyboardInterrupt: sys.exit() except KeyboardInterrupt: sys.exit()
# calculate the tournament size # calculate the tournament size
@ -169,20 +170,20 @@ if len(sys.argv) < 3: # either no command line argument (1) or a filename (2) is
while True: while True:
try: try:
query = raw_input('\t Enter max number of generations (default 10): ') query = input('\t Enter max number of generations (default 10): ')
if query not in str(range(1,101)) or query == '0': raise ValueError() if query == '': gen_max = 10; break
elif query == '': gen_max = 10; break elif int(query) in list(range(1,101)): gen_max = int(query); break
gen_max = int(query); break else: raise ValueError()
except ValueError: print '\t\033[32m Enter a number from 1 including 100. Try again ...\n\033[0;0m' except ValueError: print ('\t\033[32m Enter a number from 1 including 100. Try again ...\n\033[0;0m')
except KeyboardInterrupt: sys.exit() except KeyboardInterrupt: sys.exit()
if gen_max > 1: if gen_max > 1:
while True: while True:
try: try:
query = raw_input('\t Display (i)nteractive, (g)eneration, (m)iminal, (s)ilent, or (d)e(b)ug (default m): ') query = input('\t Display (i)nteractive, (g)eneration, (m)iminal, (s)ilent, or (d)e(b)ug (default m): ')
if query not in ['i','g','m','s','db','']: raise ValueError() if query in ['i','g','m','s','db','']: display = query or 'm'; break
display = query or 'm'; break else: raise ValueError()
except ValueError: print '\t\033[32m Select from the options given. Try again ...\n\033[0;0m' except ValueError: print ('\t\033[32m Select from the options given. Try again ...\n\033[0;0m')
except KeyboardInterrupt: sys.exit() except KeyboardInterrupt: sys.exit()
else: display = 's' # display mode is not used, but a value must be passed else: display = 's' # display mode is not used, but a value must be passed
@ -203,7 +204,7 @@ if len(sys.argv) < 3: # either no command line argument (1) or a filename (2) is
# Command Line for Configuation | # Command Line for Configuation |
#++++++++++++++++++++++++++++++++++++++++++ #++++++++++++++++++++++++++++++++++++++++++
else: # two or more command line arguments provided else: # 2 or more command line arguments are provided
ap = argparse.ArgumentParser(description = 'Karoo GP Server') ap = argparse.ArgumentParser(description = 'Karoo GP Server')
ap.add_argument('-ker', action = 'store', dest = 'kernel', default = 'c', help = '[c,r,m] fitness function: (r)egression, (c)lassification, or (m)atching') ap.add_argument('-ker', action = 'store', dest = 'kernel', default = 'c', help = '[c,r,m] fitness function: (r)egression, (c)lassification, or (m)atching')
@ -249,9 +250,4 @@ else: # two or more command line arguments provided
gp.fx_karoo_gp(kernel, tree_type, tree_depth_base, tree_depth_max, tree_depth_min, tree_pop_max, gen_max, tourn_size, filename, evolve_repro, evolve_point, evolve_branch, evolve_cross, display, precision, swim, mode) gp.fx_karoo_gp(kernel, tree_type, tree_depth_base, tree_depth_max, tree_depth_min, tree_pop_max, gen_max, tourn_size, filename, evolve_repro, evolve_point, evolve_branch, evolve_cross, display, precision, swim, mode)
print '\n\033[3m "It is not the strongest of the species that survive, nor the most intelligent,\033[0;0m'
print '\033[3m but the one most responsive to change."\033[0;0m --Charles Darwin\n'
print '\033[3m Congrats!\033[0;0m Your Karoo GP run is complete.\n'
sys.exit()