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minor fix to support bash scripting

pull/13/head
kstaats 2018-05-10 09:09:21 -07:00
parent f2bb9b445e
commit 2ca722875f
2 changed files with 26 additions and 16 deletions
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6
RELEASE_NOTES.txt
View File

@ -1,3 +1,9 @@
2018 05/10
Returned full_path = os.path.realpath(__file__) (approx. line 342) to support bash scripting of automated runs. This
remains commented, but can be readily re-activated (remember to comment the next line down).
2018 04/22
1) Completed the isolation of the user interface from the base_class such that all mid-run parameter configurations and

36
modules/karoo_gp_base_class.py
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@ -2,7 +2,7 @@
# Define the methods and global variables used by Karoo GP
# by Kai Staats, MSc; see LICENSE.md
# Thanks to Emmanuel Dufourq and Arun Kumar for support during 2014-15 devel; TensorFlow support provided by Iurii Milovanov
# version 2.1
# version 2.1.1
'''
A NOTE TO THE NEWBIE, EXPERT, AND BRAVE
@ -302,7 +302,7 @@ class Base_GP(object):
print '\t\033[36m Tree', self.population_b[tree_id][0][1], 'yields (sym):\033[1m', self.algo_sym, '\033[0;0m'
elif menu_dict['input_a'] == 'load': # load population_s to replace population_a
self.fx_data_recover(self.filename['s']) # NEED TO replace 'r' with a user defined filename
self.fx_data_recover(self.filename['s']) # NEED TO replace 's' with a user defined filename
elif menu_dict['input_a'] == 'write': # write the evolving population_b to disk
self.fx_data_tree_write(self.population_b, 'b')
@ -339,6 +339,7 @@ class Base_GP(object):
'''
### 1) load the associated data set, operators, operands, fitness type, and coefficients ###
# full_path = os.path.realpath(__file__); cwd = os.path.dirname(full_path) # for user Marco Cavaglia
cwd = os.getcwd()
data_dict = {'c':cwd + '/files/data_CLASSIFY.csv', 'r':cwd + '/files/data_REGRESS.csv', 'm':cwd + '/files/data_MATCH.csv', 'p':cwd + '/files/data_PLAY.csv'}
@ -434,7 +435,8 @@ class Base_GP(object):
n = 0 # track row count
for row in target:
print 'row', row
n = n + 1
if n == 1: pass # skip first empty row
@ -498,7 +500,7 @@ class Base_GP(object):
'''
Save population_* to disk.
Called by: fx_karoo_gp, fx_karoo_gen_add, fx_eval_generation
Called by: fx_karoo_gp, fx_eval_generation
Arguments required: population, key
'''
@ -1069,10 +1071,10 @@ class Base_GP(object):
def fx_eval_generation(self):
'''
This method invokes the evaluation of an entire generation of Trees, as engaged by karoo_gp.py and fx_karoo_gen_add
function of this library. It automatically evaluates population_b before invoking the copy of _b to _a.
This method invokes the evaluation of an entire generation of Trees. It automatically evaluates population_b
before invoking the copy of _b to _a.
Called by: fx_karoo_gp, fx_karoo_gen_add
Called by: fx_karoo_gp
Arguments required: none
'''
@ -1552,7 +1554,7 @@ class Base_GP(object):
This method is automatically invoked with every Tournament Selection ('fx_fitness_tournament').
Called by: fx_karoo_gp, fx_karoo_gen_add
Called by: fx_karoo_gp
Arguments required: none
'''
@ -1685,7 +1687,7 @@ class Base_GP(object):
generation. This is analogous to a member of the prior generation directly entering the gene pool of the
subsequent (younger) generation.
Called by: fx_karoo_gp, fx_karoo_gen_add
Called by: fx_karoo_gp
Arguments required: none
'''
@ -1711,7 +1713,7 @@ class Base_GP(object):
functions (operators) and terminal nodes as terminals (variables). The size and shape of the Tree will remain
identical.
Called by: fx_karoo_gp, fx_karoo_gen_add
Called by: fx_karoo_gp
Arguments required: none
'''
@ -1739,7 +1741,7 @@ class Base_GP(object):
Ramped Half/Half, the size and shape of the Tree may grow smaller or larger, but it may not exceed
tree_depth_max as defined by the user.
Called by: fx_karoo_gp, fx_karoo_gen_add
Called by: fx_karoo_gp
Arguments required: none
'''
@ -1782,7 +1784,7 @@ class Base_GP(object):
For those who like to watch, select 'db' (debug mode) at the launch of Karoo GP or at any (pause).
Called by: fx_karoo_gp, fx_karoo_gen_add
Called by: fx_karoo_gp
Arguments required: none
'''
@ -2076,7 +2078,9 @@ class Base_GP(object):
Arguments required: tree, branch
'''
### insert branch_top from 'gp.tree' into 'tree' ### *_branch_top_copy merged with *_body_copy 2018 04/12
# *_branch_top_copy merged with *_body_copy 2018 04/12
### 1) insert branch_top from 'gp.tree' into 'tree' ###
branch_top = int(branch[0])
@ -2095,7 +2099,7 @@ class Base_GP(object):
print '\n\033[36m This is the Tree after a new node is inserted:\033[0;0m\n', tree; self.fx_karoo_pause()
### insert branch_body from 'gp.tree' into 'tree' ### *_branch_top_copy merged with *_body_copy 2018 04/12
### 2) insert branch_body from 'gp.tree' into 'tree' ###
node_count = 2 # set node count for 'gp.tree' to 2 as the new root has already replaced 'branch_top' (above)
@ -2268,7 +2272,7 @@ class Base_GP(object):
def fx_evolve_child_insert(self, tree, node, c_buffer):
'''
Insert child nodes.
Insert child node into the copy of a parent Tree.
Called by: fx_evolve_branch_insert
@ -2457,7 +2461,7 @@ class Base_GP(object):
Simply copying a list of arrays generates a pointer to the original list. Therefore we must append each array
to a new, empty array and then build a list of those new arrays.
Called by: fx_karoo_gp, fx_karoo_gen_add
Called by: fx_karoo_gp
Arguments required: pop_a, title
'''