def test_add_child_connected(self):
tp = Node(label="TP")
dp = Node(label="DP")
tp.add_child(dp)
tp2 = Node(label="TP")
with self.assertRaises(AssertionError):
tp2.add_child(dp)
def test_to_dict_simple(self):
tp = Node(label="TP")
dp = Node(label="DP")
tbar = Node(label="T<bar/>")
tp.add_child(dp)
tp.add_child(tbar)
self.assertEqual(tp.to_dict(), TestNode.SIMPLE_TREE_DICT)
def grow_tree(records, attributes, default = ''): if stopping_condition(records, attributes): label = classify(records) if label is None: label = default return Node(label = label) else: i, condition = find_best_split(records, attributes) default = classify(records) attributes[-1], attributes[i] = attributes[i], attributes[-1] name, v, values = attributes.pop() if v != False: root = Node(label = name + '<=' + str(v), test = condition) values = [True, False] else: root = Node(label = name, test = condition) for value in values: new_records = filter(lambda r: condition(r) == value, records) child = grow_tree(new_records, attributes, default) root.add_branch(value) root.add_child(child) attributes.append( (name, v, values) ) attributes[-1], attributes[i] = attributes[i], attributes[-1] return root
def test_add_child(self):
tp = Node()
dp = Node()
tp.label = "TP"
dp.label = "DP"
tp.add_child(dp)
self.assertIn(dp, tp.children)
self.assertEqual(dp.parent, tp)
def test_add_parent(self):
dp = Node(label="DP")
d = Node(label="D", value="the")
dp.add_child(d)
n = Node(label="N", value="cactus")
dp.add_child(n)
np = Node(label="NP")
n.add_parent(np)
self.assertIn(np, dp.children)
self.assertEqual(np, n.parent)
self.assertNotIn(n, dp.children)
def build_game_tree(self, depth, board, is_max, number):
cpy = copy.deepcopy(board)
r = Node(cpy, is_max, None)
if depth == 0 :
return r
el_moves = self.get_eligible_for_board(cpy, number)
for move in el_moves:
new_board, free_move = self.board._dummy_move_stones(number, move, cpy)
r_num = number if free_move else self.flip_number(number)
ci = self.build_game_tree(depth-1, new_board, (is_max if free_move else not is_max), r_num)
ci.set_move(move)
r.add_child(ci)
return r
class TestNodeMethods(unittest.TestCase):
def setUp(self):
# create test objects
self.n = Node('node1')
self.n2 = Node('node2', '2')
self.n3 = Node('node3', '3')
self.n4 = Node('node4', '4')
self.n5 = Node('node5', '5')
self.n6 = Node('node6', '6')
self.n7 = Node('node7', '7')
def tearDown(self):
# set objects to none or delete stuff
self.n = None
self.n2 = None
def test_get_id_where_no_id(self):
self.assertEqual(self.n.get_id(), None)
def test_get_id_and_title_n_n2(self):
self.assertEqual(self.n.get_title(), 'node1')
self.assertEqual(self.n2.get_title(), 'node2')
self.assertEqual(self.n2.get_id(), '2')
def test_string_repr(self):
self.assertEqual(self.n.__str__(), 'node1')
self.assertEqual(self.n2.__str__(), 'node2')
def test_adding_2_children(self):
self.n.add_child(self.n2)
self.n.add_child(self.n3)
children = Set()
children.add(self.n2)
children.add(self.n3)
self.assertEqual(self.n.get_children(), children)
def test_parent_id(self):
n = Node(id='6', parent_id='1')
self.assertEqual(n.get_parent_id(), '1')
def test_set_and_get_parent_id(self):
n = Node(id='1')
n.set_parent_id(0)
id = n.get_parent_id()
self.assertEqual(0, id)
class TestNode(unittest.TestCase):
def setUp(self) -> None:
self.node1 = Node('node1')
self.node2 = Node('node2')
self.node1.add_child(self.node2)
def test_add_child(self):
self.assertEqual(self.node2.parent, self.node1)
self.assertIn(self.node2, self.node1.children)
def test_id(self):
self.assertEqual(self.node1.id, 'node1')
self.assertEqual(self.node2.id, 'node1.node2')
def test_get(self):
node2 = self.node1.get('node2')
self.assertEqual(self.node2, node2)
def test_delete(self):
dp = Node(label="DP")
d = Node(label="D", value="the")
dp.add_child(d)
np = Node(label="NP")
dp.add_child(np)
n = Node(label="N", value="cactus")
np.add_child(n)
np.delete()
self.assertNotIn(np, dp.children)
self.assertNotIn(n, dp.children)
n = Node('taste',5)
p = Node('var',6)
q = Node('var',7)
r = Node('var',8)
s = Node('name',9)
myTree.add_node(n,myTree.get_root())
print("Traversing the tree after adding 1 node")
myTree.print_tree(myTree.get_root(),0)
myTree.add_node(p,myTree.search_node(myTree.get_root(),n.feature,n.value))
print("Traversing the tree after adding 2 nodes")
myTree.print_tree(myTree.get_root(),0)
myTree.add_node(q,myTree.search_node(myTree.get_root(),n.feature,n.value))
myTree.add_node(r,myTree.search_node(myTree.get_root(),q.feature,q.value))
print("Traversing the tree after adding 4 nodes")
myTree.print_tree(myTree.get_root(),0)
myTree.add_node(s,myTree.search_node(myTree.get_root(),r.feature,r.value))
"""
n.add_child(p)
n.add_child(q)
n.add_child(r)
r.add_child(s)
"""
print("Traversing the tree after adding 5 nodes")
myTree.print_tree(myTree.root,0)
def simulate_one_tree(n, pop_size):
""" Simulates trees according to the Kingman coalescent model.
inputs: number of available_nodes, n; effective population size, pop_size
output: coalescent tree with n available_nodes.
"""
from itertools import combinations
from random import choice
# each pair of lineages coalesces at rate 1/pop_size
# given k lineages, total rate of coalescence is combination(k, 2)/pop_size
k = n # setting lineages to n
t = 0
# Initialising node labels, heights to zero, and matrix
node_count = n
available_nodes = [Node(str(i)) for i in range(n)]
for node in available_nodes:
node.set_height(0)
# matrix = {available_nodes[i]: {available_nodes[j]: matrix[i][j] for j in range(n)} for i in range(n)}
while k > 1:
# updating time, t
rate = ncr(k, 2)/pop_size
# print(rate)
t_k = np.random.exponential(1/rate)
t = t + t_k
# new node m, with height t, and random children from available_nodes and popping them
m = Node(str(node_count))
node_count += 1
m.set_height(t)
# Gets the combinations of 2 different nodes and their indices (pairs) from the available_nodes
# Then setting into a list
pairs = combinations(enumerate(available_nodes), 2)
pairs = [(i[0], i[1]) for i in pairs]
# At this point each node in a pair is a tuple -> (available_nodes index, node object)
# Selecting a random pair (by index) and setting as children of m
# Note: index [0] is the index from available nodes | [1] is the node object
pairs_index = choice(range(len(pairs)))
left_child = pairs[pairs_index][0]
right_child = pairs[pairs_index][1]
m.add_child(left_child[1])
m.add_child(right_child[1])
# Removing added children from list of available_nodes
# Popping right child first to maintain index integrity of available_nodes
index_to_pop = right_child[0]
available_nodes.pop(index_to_pop)
index_to_pop = left_child[0]
available_nodes.pop(index_to_pop)
# adding m to set of available_nodes
available_nodes.append(m)
# one less lineage
k -= 1
# ----- End of While Loop -----
root_node = m
return Tree(root_node)
from tree import Node
Bob = Node("Bob")
Marni = Node("Marni")
Declan = Node("Declan")
Bob.add_child(Marni)
Bob.add_child(Declan)
Declan.parent = Bob
Declan.parent = Marni
print('Bob\'s children: ', Bob.children)
print('Marni\'s parent: ', Marni.parent)
print('Marni\'s children: ', Marni.children)
print('Declan\'s parent: ', Declan.parent)
print('Declan\'s children: ', Declan.children)
def test_Node_add_child_2():
_node = Node(1)
_node.add_child(2)
_node.add_child(3)
assert _node.children[1].data == 3
def test_Node_add_child_1():
_node = Node(1)
_node.add_child(2)
assert _node.children[0].data == 2
def action_reconstruct(current, **kwargs):
if current.visited:
return False, current
current.visited = True
handle_exits = kwargs.get('handle_exits', True)
if current.S[current.I.names['p']] == 1:
return False, current
"""
:type current: class Node
"""
from tree import Node
if not current.parent: # maybe Init process
return False, current
# 2 1 1
if current.S[current.I.names['g']] == current.parent.S[current.parent.I.names['g']] and \
current.S[current.I.names['s']] == current.parent.S[current.parent.I.names['s']]:
current.I.act = 'fork' + '(' + str(
current.S[current.I.names['pp']]) + ')'
if 'check_fds' in kwargs:
pass
# 2 2 2
# setsid
elif current.S[current.I.names['p']] == current.S[
current.I.names['g']] == current.S[current.I.names['s']]:
new_state = Node(data=(None, default_inh, None, [
current.S[current.I.names['p']],
current.parent.S[current.parent.I.names['g']],
current.parent.S[current.parent.I.names['s']],
current.S[current.I.names['pp']], current.S[4], current.S[5],
current.S[6], current.S[7]
]),
parent=current.parent,
visited=True)
current.parent.add_child(new_state)
current.parent.delete_child(index=current.index)
new_state.parent = current.parent
current.parent = new_state
new_state.I.act = 'fork' + '(' + str(
new_state.S[new_state.I.names['pp']]) + ')'
current.I.act = 'setsid()'
new_state.add_child(current)
# 1 2 1
# setsid(self)
if current.S[current.I.names['p']] == current.S[current.I.names['g']] and \
current.S[current.I.names['g']] != current.S[current.I.names['s']]:
new_state = Node(data=(None, default_inh, None, [
current.S[current.I.names['p']],
current.parent.S[current.parent.I.names['g']],
current.parent.S[current.parent.I.names['s']],
current.S[current.I.names['pp']], current.S[4], current.S[5],
current.S[6], current.S[7]
]),
parent=current.parent)
current.parent.add_child(new_state)
current.parent.delete_child(index=current.index)
current.parent = new_state
new_state.I.act = 'fork' + '(' + str(
new_state.S[new_state.I.names['pp']]) + ')'
current.I.act = 'setpgid' + '(self:' + str(
new_state.S[new_state.I.names['p']]) + ')'
new_state.add_child(current)
# check cs:
# correct_session_picker
# pass this elif or not - think after sleep :)
elif handle_exits and current.parent.S[current.parent.I.names['p']] == 1:
res = False
current.parent.delete_child(current.index)
# see the tree in previous articles
res, target = current.parent.dfs(
action=action_check_attr_eq,
name='g',
val=current.S[current.I.names['g']]) # if Ex group
if res:
res, target = current.parent.dfs(
action=action_check_attr_eq,
name='s',
val=current.S[current.I.names['s']])
if res:
node = Node(
data=(
None,
default_inh,
'fork(' + str(target.S[target.I.names['p']]) +
'),exit()',
[
current.S[current.I.names['p']], # refill this
current.S[current.I.names['g']],
current.S[current.I.names['s']],
target.S[target.I.names['p']],
current.S[4],
current.S[5],
current.S[6],
current.S[7]
]),
parent=target,
visited=True)
target.add_child(node)
current.parent.delete_child(current.index)
node.add_child(current)
#current.parent = node
current.S[current.I.names['pp']] = current.parent.S[
current.parent.I.names['p']]
current.I.act = 'fork' + '(' + str(
current.parent.S[current.I.names['pp']]) + ')'
else:
print('parsing error')
import sys
sys.exit(-1)
else:
res, target = current.parent.dfs(
action=action_check_attr_eq,
name='s',
val=current.S[current.I.names['s']]) # if Ex session
if res:
node_par = Node(
data=(
None,
default_inh,
'fork(' + str(target.S[target.I.names['p']]) + ')',
[
current.S[current.I.names['g']], # refill this
current.S[target.I.names['g']],
current.S[target.I.names['s']],
target.S[target.I.names['p']],
current.S[4],
current.S[5],
current.S[6],
current.S[7]
]),
parent=current.parent,
visited=True)
node_ch = Node(
data=(
None,
default_inh,
'setpgid(' + str(current.S[current.I.names['g']]) +
'),exit()',
[
current.S[current.I.names['g']], # refill this
current.S[current.I.names['g']],
current.S[target.I.names['s']],
target.S[node_par.I.names['p']],
current.S[4],
current.S[5],
current.S[6],
current.S[7]
]),
parent=node_par,
visited=True)
node_par.add_child(node_ch)
target.add_child(node_par)
current.parent.delete_child(current.index)
node_ch.add_child(current)
current.S[current.I.names['pp']] = current.parent.S[
current.parent.I.names['p']]
else:
node_par = Node(
data=(
None,
default_inh,
'fork(' +
str(current.parent.S[current.parent.I.names['p']]) +
')',
[
current.S[current.I.names['s']], # refill this
current.parent.S[current.parent.I.names['g']],
current.parent.S[current.parent.I.names['s']],
current.parent.S[current.parent.I.names['p']],
current.S[4],
current.S[5],
current.S[6],
current.S[7]
]),
parent=current.parent,
visited=True)
node_ch = Node(data=(None, default_inh, 'setsid(), exit()', [
current.S[current.I.names['s']],
current.S[current.I.names['s']],
current.S[current.I.names['s']],
node_par.S[node_par.I.names['p']], current.S[4],
current.S[5], current.S[6], current.S[7]
]),
parent=node_par,
visited=True)
node_br = Node(
data=(None, default_inh,
'fork(' + str(node_ch.S[node_ch.I.names['p']]) + ')',
[
current.S[current.I.names['g']],
current.S[current.I.names['s']],
current.S[current.I.names['s']],
node_ch.S[node_ch.I.names['p']], current.S[4],
current.S[5], current.S[6], current.S[7]
]),
parent=node_ch,
visited=True)
node_br2 = Node(
data=(None, default_inh, 'setpgid(self,' +
str(current.S[current.I.names['g']]) + '), exit()', [
current.S[current.I.names['g']],
current.S[current.I.names['g']],
current.S[current.I.names['s']],
node_br.S[node_br.I.names['p']], current.S[4],
current.S[5], current.S[6], current.S[7]
]),
parent=node_br,
visited=True)
node_par.add_child(node_ch)
current.parent.add_child(node_par)
current.parent.delete_child(current.index)
node_ch.add_child(node_br)
node_br.add_child(node_br2)
node_br2.add_child(current)
current.S[current.I.names['pp']] = node_ch.S[
node_ch.I.names['p']]
else:
res = False
if current.parent.I.act == 'setsid()':
# triple - see article - up of current's parent is reconstructed, which parent is target value
res, _ = current.parent.parent.parent.upbranch(
action=action_check_attr_eq,
name='p',
val=current.S[current.I.names['s']])
elif 'setpgid' in current.parent.I.act:
res, _ = current.parent.parent.parent.upbranch(
action=action_check_attr_eq,
name='p',
val=current.S[current.I.names['s']])
if res:
# current.parent.children = current.parent.delete_child(current.index)
current.parent.delete_child(
current.index
) # redundancy - needs dynamic refilling of children list!
current.parent = current.parent.parent
current.parent.add_child(current)
# look for group if not id is not suitable
if current.S[current.I.names['g']] != current.parent.S[
current.parent.I.names['g']]: ##loc_group(noself)
print('starting upbranch')
resg, root = current.upbranch(
action=action_check_attr_eq,
name='p',
val=current.S[current.I.names['s']])
print('upbranch is ok')
if resg:
print('resg')
r, _ = root.dfs(action=action_check_attr_eq,
name='p',
name2='g',
val=current.S[current.I.names['g']])
if r:
print('recons')
new_state = Node(data=(None, default_inh, None, [
current.S[current.I.names['p']],
current.parent.S[current.parent.I.names['g']],
current.parent.S[current.parent.I.names['s']],
current.S[current.I.names['pp']], current.S[4],
current.S[5], current.S[6], current.S[7]
]),
parent=current.parent)
current.parent.add_child(new_state)
current.parent.delete_child(index=current.index)
current.parent = new_state
new_state.I.act = 'fork' + '(' + str(
new_state.S[new_state.I.names['pp']]) + ')'
current.I.act = 'setpgid' + '(' + str(
new_state.S[new_state.I.names['p']]) + ';' + str(
current.S[current.I.names['g']]) + ')'
new_state.add_child(current)
else:
print('forku')
current.I.act = 'fork' + ' (' + str(
current.S[current.I.names['pp']]) + ')'
return False, current