307 lines
11 KiB
Python
307 lines
11 KiB
Python
import pytest
|
|
from itertools import chain, combinations, product
|
|
|
|
import networkx as nx
|
|
|
|
tree_all_pairs_lca = nx.tree_all_pairs_lowest_common_ancestor
|
|
all_pairs_lca = nx.all_pairs_lowest_common_ancestor
|
|
|
|
|
|
def get_pair(dictionary, n1, n2):
|
|
if (n1, n2) in dictionary:
|
|
return dictionary[n1, n2]
|
|
else:
|
|
return dictionary[n2, n1]
|
|
|
|
|
|
class TestTreeLCA(object):
|
|
@classmethod
|
|
def setup_class(cls):
|
|
cls.DG = nx.DiGraph()
|
|
edges = [(0, 1), (0, 2), (1, 3), (1, 4), (2, 5), (2, 6)]
|
|
cls.DG.add_edges_from(edges)
|
|
cls.ans = dict(tree_all_pairs_lca(cls.DG, 0))
|
|
gold = dict([((n, n), n) for n in cls.DG])
|
|
gold.update(dict(((0, i), 0) for i in range(1, 7)))
|
|
gold.update({(1, 2): 0,
|
|
(1, 3): 1,
|
|
(1, 4): 1,
|
|
(1, 5): 0,
|
|
(1, 6): 0,
|
|
(2, 3): 0,
|
|
(2, 4): 0,
|
|
(2, 5): 2,
|
|
(2, 6): 2,
|
|
(3, 4): 1,
|
|
(3, 5): 0,
|
|
(3, 6): 0,
|
|
(4, 5): 0,
|
|
(4, 6): 0,
|
|
(5, 6): 2})
|
|
|
|
cls.gold = gold
|
|
|
|
@staticmethod
|
|
def assert_has_same_pairs(d1, d2):
|
|
for (a, b) in ((min(pair), max(pair)) for pair in chain(d1, d2)):
|
|
assert get_pair(d1, a, b) == get_pair(d2, a, b)
|
|
|
|
def test_tree_all_pairs_lowest_common_ancestor1(self):
|
|
"""Specifying the root is optional."""
|
|
assert dict(tree_all_pairs_lca(self.DG)) == self.ans
|
|
|
|
def test_tree_all_pairs_lowest_common_ancestor2(self):
|
|
"""Specifying only some pairs gives only those pairs."""
|
|
test_pairs = [(0, 1), (0, 1), (1, 0)]
|
|
ans = dict(tree_all_pairs_lca(self.DG, 0, test_pairs))
|
|
assert (0, 1) in ans and (1, 0) in ans
|
|
assert len(ans) == 2
|
|
|
|
def test_tree_all_pairs_lowest_common_ancestor3(self):
|
|
"""Specifying no pairs same as specifying all."""
|
|
all_pairs = chain(combinations(self.DG, 2),
|
|
((node, node) for node in self.DG))
|
|
|
|
ans = dict(tree_all_pairs_lca(self.DG, 0, all_pairs))
|
|
self.assert_has_same_pairs(ans, self.ans)
|
|
|
|
def test_tree_all_pairs_lowest_common_ancestor4(self):
|
|
"""Gives the right answer."""
|
|
ans = dict(tree_all_pairs_lca(self.DG))
|
|
self.assert_has_same_pairs(self.gold, ans)
|
|
|
|
def test_tree_all_pairs_lowest_common_ancestor5(self):
|
|
"""Handles invalid input correctly."""
|
|
empty_digraph = tree_all_pairs_lca(nx.DiGraph())
|
|
pytest.raises(nx.NetworkXPointlessConcept, list, empty_digraph)
|
|
|
|
bad_pairs_digraph = tree_all_pairs_lca(self.DG, pairs=[(-1, -2)])
|
|
pytest.raises(nx.NodeNotFound, list, bad_pairs_digraph)
|
|
|
|
def test_tree_all_pairs_lowest_common_ancestor6(self):
|
|
"""Works on subtrees."""
|
|
ans = dict(tree_all_pairs_lca(self.DG, 1))
|
|
gold = dict((pair, lca) for (pair, lca) in self.gold.items()
|
|
if all(n in (1, 3, 4) for n in pair))
|
|
self.assert_has_same_pairs(gold, ans)
|
|
|
|
def test_tree_all_pairs_lowest_common_ancestor7(self):
|
|
"""Works on disconnected nodes."""
|
|
G = nx.DiGraph()
|
|
G.add_node(1)
|
|
assert {(1, 1): 1} == dict(tree_all_pairs_lca(G))
|
|
|
|
G.add_node(0)
|
|
assert {(1, 1): 1} == dict(tree_all_pairs_lca(G, 1))
|
|
assert {(0, 0): 0} == dict(tree_all_pairs_lca(G, 0))
|
|
|
|
pytest.raises(nx.NetworkXError, list, tree_all_pairs_lca(G))
|
|
|
|
def test_tree_all_pairs_lowest_common_ancestor8(self):
|
|
"""Raises right errors if not a tree."""
|
|
# Cycle
|
|
G = nx.DiGraph([(1, 2), (2, 1)])
|
|
pytest.raises(nx.NetworkXError, list, tree_all_pairs_lca(G))
|
|
# DAG
|
|
G = nx.DiGraph([(0, 2), (1, 2)])
|
|
pytest.raises(nx.NetworkXError, list, tree_all_pairs_lca(G))
|
|
|
|
def test_tree_all_pairs_lowest_common_ancestor9(self):
|
|
"""Test that pairs works correctly as a generator."""
|
|
pairs = iter([(0, 1), (0, 1), (1, 0)])
|
|
some_pairs = dict(tree_all_pairs_lca(self.DG, 0, pairs))
|
|
assert (0, 1) in some_pairs and (1, 0) in some_pairs
|
|
assert len(some_pairs) == 2
|
|
|
|
def test_tree_all_pairs_lowest_common_ancestor10(self):
|
|
"""Test that pairs not in the graph raises error."""
|
|
lca = tree_all_pairs_lca(self.DG, 0, [(-1, -1)])
|
|
pytest.raises(nx.NodeNotFound, list, lca)
|
|
|
|
def test_tree_all_pairs_lowest_common_ancestor11(self):
|
|
"""Test that None as a node in the graph raises an error."""
|
|
G = nx.DiGraph([(None, 3)])
|
|
pytest.raises(nx.NetworkXError, list, tree_all_pairs_lca(G))
|
|
pytest.raises(nx.NodeNotFound, list,
|
|
tree_all_pairs_lca(self.DG, pairs=G.edges()))
|
|
|
|
def test_tree_all_pairs_lowest_common_ancestor12(self):
|
|
"""Test that tree routine bails on DAGs."""
|
|
G = nx.DiGraph([(3, 4), (5, 4)])
|
|
pytest.raises(nx.NetworkXError, list, tree_all_pairs_lca(G))
|
|
|
|
def test_not_implemented_for(self):
|
|
NNI = nx.NetworkXNotImplemented
|
|
G = nx.Graph([(0, 1)])
|
|
pytest.raises(NNI, tree_all_pairs_lca, G)
|
|
pytest.raises(NNI, all_pairs_lca, G)
|
|
pytest.raises(NNI, nx.lowest_common_ancestor, G, 0, 1)
|
|
G = nx.MultiGraph([(0, 1)])
|
|
pytest.raises(NNI, tree_all_pairs_lca, G)
|
|
pytest.raises(NNI, all_pairs_lca, G)
|
|
pytest.raises(NNI, nx.lowest_common_ancestor, G, 0, 1)
|
|
G = nx.MultiDiGraph([(0, 1)])
|
|
pytest.raises(NNI, tree_all_pairs_lca, G)
|
|
pytest.raises(NNI, all_pairs_lca, G)
|
|
pytest.raises(NNI, nx.lowest_common_ancestor, G, 0, 1)
|
|
|
|
def test_tree_all_pairs_lowest_common_ancestor13(self):
|
|
"""Test that it works on non-empty trees with no LCAs."""
|
|
G = nx.DiGraph()
|
|
G.add_node(3)
|
|
ans = list(tree_all_pairs_lca(G))
|
|
assert ans == [((3, 3), 3)]
|
|
|
|
|
|
class TestDAGLCA:
|
|
@classmethod
|
|
def setup_class(cls):
|
|
cls.DG = nx.DiGraph()
|
|
nx.add_path(cls.DG, (0, 1, 2, 3))
|
|
nx.add_path(cls.DG, (0, 4, 3))
|
|
nx.add_path(cls.DG, (0, 5, 6, 8, 3))
|
|
nx.add_path(cls.DG, (5, 7, 8))
|
|
cls.DG.add_edge(6, 2)
|
|
cls.DG.add_edge(7, 2)
|
|
|
|
cls.root_distance = nx.shortest_path_length(cls.DG, source=0)
|
|
|
|
cls.gold = {(1, 1): 1,
|
|
(1, 2): 1,
|
|
(1, 3): 1,
|
|
(1, 4): 0,
|
|
(1, 5): 0,
|
|
(1, 6): 0,
|
|
(1, 7): 0,
|
|
(1, 8): 0,
|
|
(2, 2): 2,
|
|
(2, 3): 2,
|
|
(2, 4): 0,
|
|
(2, 5): 5,
|
|
(2, 6): 6,
|
|
(2, 7): 7,
|
|
(2, 8): 7,
|
|
(3, 3): 8,
|
|
(3, 4): 4,
|
|
(3, 5): 5,
|
|
(3, 6): 6,
|
|
(3, 7): 7,
|
|
(3, 8): 8,
|
|
(4, 4): 4,
|
|
(4, 5): 0,
|
|
(4, 6): 0,
|
|
(4, 7): 0,
|
|
(4, 8): 0,
|
|
(5, 5): 5,
|
|
(5, 6): 5,
|
|
(5, 7): 5,
|
|
(5, 8): 5,
|
|
(6, 6): 6,
|
|
(6, 7): 5,
|
|
(6, 8): 6,
|
|
(7, 7): 7,
|
|
(7, 8): 7,
|
|
(8, 8): 8}
|
|
cls.gold.update(((0, n), 0) for n in cls.DG)
|
|
|
|
def assert_lca_dicts_same(self, d1, d2, G=None):
|
|
"""Checks if d1 and d2 contain the same pairs and
|
|
have a node at the same distance from root for each.
|
|
If G is None use self.DG."""
|
|
if G is None:
|
|
G = self.DG
|
|
root_distance = self.root_distance
|
|
else:
|
|
roots = [n for n, deg in G.in_degree if deg == 0]
|
|
assert(len(roots) == 1)
|
|
root_distance = nx.shortest_path_length(G, source=roots[0])
|
|
|
|
for a, b in ((min(pair), max(pair)) for pair in chain(d1, d2)):
|
|
assert (root_distance[get_pair(d1, a, b)] ==
|
|
root_distance[get_pair(d2, a, b)])
|
|
|
|
def test_all_pairs_lowest_common_ancestor1(self):
|
|
"""Produces the correct results."""
|
|
self.assert_lca_dicts_same(dict(all_pairs_lca(self.DG)), self.gold)
|
|
|
|
def test_all_pairs_lowest_common_ancestor2(self):
|
|
"""Produces the correct results when all pairs given."""
|
|
all_pairs = list(product(self.DG.nodes(), self.DG.nodes()))
|
|
ans = all_pairs_lca(self.DG, pairs=all_pairs)
|
|
self.assert_lca_dicts_same(dict(ans), self.gold)
|
|
|
|
def test_all_pairs_lowest_common_ancestor3(self):
|
|
"""Produces the correct results when all pairs given as a generator."""
|
|
all_pairs = product(self.DG.nodes(), self.DG.nodes())
|
|
ans = all_pairs_lca(self.DG, pairs=all_pairs)
|
|
self.assert_lca_dicts_same(dict(ans), self.gold)
|
|
|
|
def test_all_pairs_lowest_common_ancestor4(self):
|
|
"""Graph with two roots."""
|
|
G = self.DG.copy()
|
|
G.add_edge(9, 10)
|
|
G.add_edge(9, 4)
|
|
gold = self.gold.copy()
|
|
gold[9, 9] = 9
|
|
gold[9, 10] = 9
|
|
gold[9, 4] = 9
|
|
gold[9, 3] = 9
|
|
gold[10, 4] = 9
|
|
gold[10, 3] = 9
|
|
gold[10, 10] = 10
|
|
|
|
testing = dict(all_pairs_lca(G))
|
|
|
|
G.add_edge(-1, 9)
|
|
G.add_edge(-1, 0)
|
|
self.assert_lca_dicts_same(testing, gold, G)
|
|
|
|
def test_all_pairs_lowest_common_ancestor5(self):
|
|
"""Test that pairs not in the graph raises error."""
|
|
pytest.raises(nx.NodeNotFound, all_pairs_lca, self.DG, [(-1, -1)])
|
|
|
|
def test_all_pairs_lowest_common_ancestor6(self):
|
|
"""Test that pairs with no LCA specified emits nothing."""
|
|
G = self.DG.copy()
|
|
G.add_node(-1)
|
|
gen = all_pairs_lca(G, [(-1, -1), (-1, 0)])
|
|
assert dict(gen) == {(-1, -1): -1}
|
|
|
|
def test_all_pairs_lowest_common_ancestor7(self):
|
|
"""Test that LCA on null graph bails."""
|
|
pytest.raises(nx.NetworkXPointlessConcept,
|
|
all_pairs_lca,
|
|
nx.DiGraph())
|
|
|
|
def test_all_pairs_lowest_common_ancestor8(self):
|
|
"""Test that LCA on non-dags bails."""
|
|
pytest.raises(nx.NetworkXError, all_pairs_lca,
|
|
nx.DiGraph([(3, 4), (4, 3)]))
|
|
|
|
def test_all_pairs_lowest_common_ancestor9(self):
|
|
"""Test that it works on non-empty graphs with no LCAs."""
|
|
G = nx.DiGraph()
|
|
G.add_node(3)
|
|
ans = list(all_pairs_lca(G))
|
|
assert ans == [((3, 3), 3)]
|
|
|
|
def test_all_pairs_lowest_common_ancestor10(self):
|
|
"""Test that it bails on None as a node."""
|
|
G = nx.DiGraph([(None, 3)])
|
|
pytest.raises(nx.NetworkXError, all_pairs_lca, G)
|
|
pytest.raises(nx.NodeNotFound, all_pairs_lca,
|
|
self.DG, pairs=G.edges())
|
|
|
|
def test_lowest_common_ancestor1(self):
|
|
"""Test that the one-pair function works on default."""
|
|
G = nx.DiGraph([(0, 1), (2, 1)])
|
|
sentinel = object()
|
|
assert (nx.lowest_common_ancestor(G, 0, 2, default=sentinel) is
|
|
sentinel)
|
|
|
|
def test_lowest_common_ancestor2(self):
|
|
"""Test that the one-pair function works on identity."""
|
|
G = nx.DiGraph()
|
|
G.add_node(3)
|
|
assert nx.lowest_common_ancestor(G, 3, 3) == 3
|