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test_util.py
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import unittest
import os
import logging
import numpy as np
import numpy.testing
from pycgtool.util import tuple_equivalent, extend_graph_chain, stat_moments, transpose_and_sample
from pycgtool.util import dir_up, backup_file, sliding, r_squared, dist_with_pbc
from pycgtool.util import SimpleEnum, FixedFormatUnpacker
class UtilTest(unittest.TestCase):
def test_tuple_equivalent(self):
t1 = (0, 1, 2)
t2 = (0, 1, 2)
self.assertTrue(tuple_equivalent(t1, t2))
t2 = (2, 1, 0)
self.assertTrue(tuple_equivalent(t1, t2))
t2 = (2, 1, 3)
self.assertFalse(tuple_equivalent(t1, t2))
def test_dist_with_pbc(self):
pos_a = np.array([1., 1., 1.])
pos_b = np.array([9., 9., 9.])
numpy.testing.assert_equal(np.array([8., 8., 8.]),
dist_with_pbc(pos_a, pos_b, np.array([0., 0., 0.])))
numpy.testing.assert_equal(np.array([8., 8., 8.]),
dist_with_pbc(pos_a, pos_b, np.array([20., 20., 20.])))
numpy.testing.assert_equal(np.array([-2., -2., -2.]),
dist_with_pbc(pos_a, pos_b, np.array([10., 10., 10.])))
def test_triplets_from_pairs(self):
pairs = [(0, 1), (1, 2), (2, 3)]
result = [(0, 1, 2), (1, 2, 3)]
self.assertEqual(result, sorted(extend_graph_chain(pairs, pairs)))
pairs = [(0, 1), (1, 2), (2, 3), (3, 0)]
result = [(0, 1, 2), (1, 0, 3), (1, 2, 3), (2, 3, 0)]
self.assertEqual(result, sorted(extend_graph_chain(pairs, pairs)))
def test_triplets_from_pairs_multires(self):
pairs = [("a", "b"), ("b", "c"), ("c", "d"), ("d", "+a")]
result = [("a", "b", "c"), ("b", "c", "d"), ("c", "d", "+a"), ("d", "+a", "+b")]
self.assertEqual(result, sorted(extend_graph_chain(pairs, pairs)))
def test_quadruplets_from_pairs(self):
pairs = [(0, 1), (1, 2), (2, 3)]
result = [(0, 1, 2, 3)]
triplets = extend_graph_chain(pairs, pairs)
self.assertEqual(result, sorted(extend_graph_chain(triplets, pairs)))
pairs = [(0, 1), (1, 2), (2, 3), (3, 0)]
triplets = extend_graph_chain(pairs, pairs)
result = [(0, 1, 2, 3), (1, 0, 3, 2), (1, 2, 3, 0), (2, 1, 0, 3)]
self.assertEqual(result, sorted(extend_graph_chain(triplets, pairs)))
def test_stat_moments(self):
t1 = [3, 3, 3, 3, 3]
t2 = [1, 2, 3, 4, 5]
np.testing.assert_allclose(np.array([3, 0]), stat_moments(t1))
np.testing.assert_allclose(np.array([3, 2]), stat_moments(t2))
def test_dir_up(self):
path = os.path.realpath(__file__)
self.assertEqual(path, dir_up(path, 0))
self.assertEqual(os.path.dirname(path), dir_up(path))
self.assertEqual(os.path.dirname(os.path.dirname(path)), dir_up(path, 2))
def test_backup_file(self):
try:
os.remove("testfile")
os.remove("#testfile.1#")
os.remove("#testfile.2#")
except OSError:
pass
logging.disable(logging.WARNING)
open("testfile", "a").close()
self.assertEqual("#testfile.1#", backup_file("testfile"))
open("testfile", "a").close()
self.assertTrue(os.path.exists("#testfile.1#"))
self.assertEqual("#testfile.2#", backup_file("testfile"))
open("testfile", "a").close()
self.assertTrue(os.path.exists("#testfile.2#"))
logging.disable(logging.NOTSET)
os.remove("testfile")
os.remove("#testfile.1#")
os.remove("#testfile.2#")
def test_sliding(self):
l = [0, 1, 2, 3, 4]
res = [(None, 0, 1), (0, 1, 2), (1, 2, 3), (2, 3, 4), (3, 4, None)]
for res, pair in zip(res, sliding(l)):
self.assertEqual(res, pair)
def test_r_squared(self):
ref = [i for i in range(5)]
fit = ref
self.assertEqual(1, r_squared(ref, fit))
fit = [2 for _ in range(5)]
self.assertEqual(0, r_squared(ref, fit))
fit = [i for i in range(1, 6)]
self.assertEqual(0.5, r_squared(ref, fit))
def test_transpose_and_sample_no_sample(self):
l = [(1, 2), (3, 4), (5, 6)]
l_t = [(1, 3, 5), (2, 4, 6)]
self.assertEqual(l_t, transpose_and_sample(l, None))
def test_transpose_and_sample(self):
l = [(1, 2), (3, 4), (5, 6)]
l_t = [(1, 3, 5), (2, 4, 6)]
l_t_test = transpose_and_sample(l, n=1)
self.assertEqual(1, len(l_t_test))
self.assertIn(l_t_test[0], l_t)
def test_simple_enum(self):
enum = SimpleEnum.enum("enum", ["one", "two", "three"])
self.assertTrue(enum.one == enum.one)
self.assertTrue(enum.one.compare_value(enum.one))
self.assertFalse(enum.two == enum.three)
self.assertFalse(enum.two.compare_value(enum.three))
with self.assertRaises(AttributeError):
_ = enum.four
with self.assertRaises(AttributeError):
enum.one = 2
enum2 = SimpleEnum.enum("enum2", ["one", "two", "three"])
with self.assertRaises(TypeError):
assert enum2.one == enum.one
self.assertTrue("one" in enum)
self.assertFalse("four" in enum)
def test_simple_enum_values(self):
enum = SimpleEnum.enum_from_dict("enum", {"one": 111,
"two": 111,
"three": 333})
self.assertTrue(enum.one == enum.one)
self.assertTrue(enum.one.compare_value(enum.one))
self.assertFalse(enum.one == enum.two)
self.assertTrue(enum.one.compare_value(enum.two))
self.assertFalse(enum.two == enum.three)
self.assertFalse(enum.two.compare_value(enum.three))
with self.assertRaises(AttributeError):
_ = enum.four
with self.assertRaises(AttributeError):
enum.one = 2
enum2 = SimpleEnum.enum("enum2", ["one", "two", "three"])
with self.assertRaises(TypeError):
assert enum2.one == enum.one
self.assertTrue("one" in enum)
self.assertEqual(111, enum.one.value)
self.assertFalse("four" in enum)
def test_fixed_format_unpacker_c(self):
unpacker = FixedFormatUnpacker("%-4d%5s%4.1f")
toks = unpacker.unpack("1234hello12.3")
self.assertEqual(3, len(toks))
self.assertEqual(1234, toks[0])
self.assertEqual("hello", toks[1])
self.assertAlmostEqual(12.3, toks[2])
def test_fixed_format_unpacker_fortran(self):
unpacker = FixedFormatUnpacker("I4,A5,F4.1",
FixedFormatUnpacker.FormatStyle.Fortran)
toks = unpacker.unpack("1234hello12.3")
self.assertEqual(3, len(toks))
self.assertEqual(1234, toks[0])
self.assertEqual("hello", toks[1])
self.assertAlmostEqual(12.3, toks[2])
def test_fixed_format_unpacker_fortran_space(self):
unpacker = FixedFormatUnpacker("I4,X3,A5,X2,F4.1",
FixedFormatUnpacker.FormatStyle.Fortran)
toks = unpacker.unpack("1234 x hello x12.3")
self.assertEqual(3, len(toks))
self.assertEqual(1234, toks[0])
self.assertEqual("hello", toks[1])
self.assertAlmostEqual(12.3, toks[2])
def test_fixed_format_unpacker_fortran_repeat(self):
unpacker = FixedFormatUnpacker("2I2,X3,A5,2X,F4.1",
FixedFormatUnpacker.FormatStyle.Fortran)
toks = unpacker.unpack("1234 x hello x12.3")
self.assertEqual(4, len(toks))
self.assertEqual(12, toks[0])
self.assertEqual(34, toks[1])
self.assertEqual("hello", toks[2])
self.assertAlmostEqual(12.3, toks[3])
if __name__ == '__main__':
unittest.main()