def test_repr_string():
# Just make sure the Unicode handling doesn't raise any exceptions.
print(approx(1.0))
print(approx([1.0, 2.0, 3.0]))
print(approx(inf))
print(approx(1.0, rel=nan))
print(approx(1.0, rel=inf))
def test_repr_string():
# Just make sure the Unicode handling doesn't raise any exceptions.
print(approx(1.0))
print(approx([1.0, 2.0, 3.0]))
print(approx(inf))
print(approx(1.0, rel=nan))
print(approx(1.0, rel=inf))
def test_decimal():
within_1e6 = [
(Decimal('1.000001'), Decimal('1.0')),
(Decimal('-1.000001'), Decimal('-1.0')),
]
for a, x in within_1e6:
assert a == approx(x, rel=Decimal('5e-6'), abs=0)
assert a != approx(x, rel=Decimal('5e-7'), abs=0)
def test_fraction():
within_1e6 = [
(1 + Fraction(1, 1000000), Fraction(1)),
(-1 - Fraction(-1, 1000000), Fraction(-1)),
]
for a, x in within_1e6:
assert a == approx(x, rel=5e-6, abs=0)
assert a != approx(x, rel=5e-7, abs=0)
def test_load_mass_spectra():
csv_path = "sample_data/mass_spectrum.csv"
ms = mass_and_me.load_mass_spectra([csv_path])[0]
assert ms.Mass[0] == approx(396.009089)
assert ms.Intensity[0] == approx(0)
assert ms.Mass[12] == approx(400.015755)
assert ms.Intensity[12] == approx(49.810793)
def test_int():
within_1e6 = [
(1000001, 1000000),
(-1000001, -1000000),
]
for a, x in within_1e6:
assert a == approx(x, rel=5e-6, abs=0)
assert a != approx(x, rel=5e-7, abs=0)
def test_load_mass_spectra():
csv_path = 'sample_data/mass_spectrum.csv'
ms = mass_and_me.load_mass_spectra([csv_path])[0]
assert ms.Mass[0] == approx(396.009089)
assert ms.Intensity[0] == approx(0)
assert ms.Mass[12] == approx(400.015755)
assert ms.Intensity[12] == approx(49.810793)
def test_decimal():
within_1e6 = [
(Decimal('1.000001'), Decimal('1.0')),
(Decimal('-1.000001'), Decimal('-1.0')),
]
for a, x in within_1e6:
assert a == approx(x, rel=Decimal('5e-6'), abs=0)
assert a != approx(x, rel=Decimal('5e-7'), abs=0)
def test_int():
within_1e6 = [
(1000001, 1000000),
(-1000001, -1000000),
]
for a, x in within_1e6:
assert a == approx(x, rel=5e-6, abs=0)
assert a != approx(x, rel=5e-7, abs=0)
def test_fraction():
within_1e6 = [
(1 + Fraction(1, 1000000), Fraction(1)),
(-1 - Fraction(-1, 1000000), Fraction(-1)),
]
for a, x in within_1e6:
assert a == approx(x, rel=5e-6, abs=0)
assert a != approx(x, rel=5e-7, abs=0)
def test_relative_tolerance():
within_1e8_rel = [
(1e8 + 1e0, 1e8),
(1e0 + 1e-8, 1e0),
(1e-8 + 1e-16, 1e-8),
]
for a, x in within_1e8_rel:
assert a == approx(x, rel=5e-8, abs=0.0)
assert a != approx(x, rel=5e-9, abs=0.0)
def test_absolute_tolerance():
within_1e8_abs = [
(1e8 + 9e-9, 1e8),
(1e0 + 9e-9, 1e0),
(1e-8 + 9e-9, 1e-8),
]
for a, x in within_1e8_abs:
assert a == approx(x, rel=0, abs=5e-8)
assert a != approx(x, rel=0, abs=5e-9)
def test_absolute_tolerance():
within_1e8_abs = [
(1e8 + 9e-9, 1e8),
(1e0 + 9e-9, 1e0),
(1e-8 + 9e-9, 1e-8),
]
for a, x in within_1e8_abs:
assert a == approx(x, rel=0, abs=5e-8)
assert a != approx(x, rel=0, abs=5e-9)
def test_relative_tolerance():
within_1e8_rel = [
(1e8 + 1e0, 1e8),
(1e0 + 1e-8, 1e0),
(1e-8 + 1e-16, 1e-8),
]
for a, x in within_1e8_rel:
assert a == approx(x, rel=5e-8, abs=0.0)
assert a != approx(x, rel=5e-9, abs=0.0)
def test_complex():
within_1e6 = [
( 1.000001 + 1.0j, 1.0 + 1.0j),
(1.0 + 1.000001j, 1.0 + 1.0j),
(-1.000001 + 1.0j, -1.0 + 1.0j),
(1.0 - 1.000001j, 1.0 - 1.0j),
]
for a, x in within_1e6:
assert a == approx(x, rel=5e-6, abs=0)
assert a != approx(x, rel=5e-7, abs=0)
def test_complex():
within_1e6 = [
(1.000001 + 1.0j, 1.0 + 1.0j),
(1.0 + 1.000001j, 1.0 + 1.0j),
(-1.000001 + 1.0j, -1.0 + 1.0j),
(1.0 - 1.000001j, 1.0 - 1.0j),
]
for a, x in within_1e6:
assert a == approx(x, rel=5e-6, abs=0)
assert a != approx(x, rel=5e-7, abs=0)
def test_log_transformation():
experiments, well = dummy_data({
'FSC-A': [100, 200, 300, 400, 500, 600],
'FITC-A': [1, 10, 100, 1000, 10000, 100000],
})
log_transformation = fcmcmp.LogTransformation()
log_transformation.channels = ['FITC-A']
log_transformation(experiments)
assert well.data['FSC-A'].tolist() == approx([100, 200, 300, 400, 500, 600])
assert well.data['FITC-A'].tolist() == approx([0, 1, 2, 3, 4, 5])
def test_inf_tolerance():
# Everything should be equal if the tolerance is infinite.
large_diffs = [
(1, 1000),
(1e-50, 1e50),
(-1.0, -1e300),
(0.0, 10),
]
for a, x in large_diffs:
assert a != approx(x, rel=0.0, abs=0.0)
assert a == approx(x, rel=inf, abs=0.0)
assert a == approx(x, rel=0.0, abs=inf)
assert a == approx(x, rel=inf, abs=inf)
def test_log_transformation():
experiments, well = dummy_data({
'FSC-A': [100, 200, 300, 400, 500, 600],
'FITC-A': [1, 10, 100, 1000, 10000, 100000],
})
log_transformation = fcmcmp.LogTransformation()
log_transformation.channels = ['FITC-A']
log_transformation(experiments)
assert well.data['FSC-A'].tolist() == approx(
[100, 200, 300, 400, 500, 600])
assert well.data['FITC-A'].tolist() == approx([0, 1, 2, 3, 4, 5])
def test_inf_tolerance():
# Everything should be equal if the tolerance is infinite.
large_diffs = [
(1, 1000),
(1e-50, 1e50),
(-1.0, -1e300),
(0.0, 10),
]
for a, x in large_diffs:
assert a != approx(x, rel=0.0, abs=0.0)
assert a == approx(x, rel=inf, abs=0.0)
assert a == approx(x, rel=0.0, abs=inf)
assert a == approx(x, rel=inf, abs=inf)
def test_expecting_zero():
examples = [
(ne, 1e-6, 0.0),
(ne, -1e-6, 0.0),
(eq, 1e-12, 0.0),
(eq, -1e-12, 0.0),
(ne, 2e-12, 0.0),
(ne, -2e-12, 0.0),
(ne, inf, 0.0),
(ne, nan, 0.0),
]
for op, a, x in examples:
assert op(a, approx(x, rel=0.0, abs=1e-12))
assert op(a, approx(x, rel=1e-6, abs=1e-12))
def test_expecting_zero():
examples = [
(ne, 1e-6, 0.0),
(ne, -1e-6, 0.0),
(eq, 1e-12, 0.0),
(eq, -1e-12, 0.0),
(ne, 2e-12, 0.0),
(ne, -2e-12, 0.0),
(ne, inf, 0.0),
(ne, nan, 0.0),
]
for op, a, x in examples:
assert op(a, approx(x, rel=0.0, abs=1e-12))
assert op(a, approx(x, rel=1e-6, abs=1e-12))
def test_opposite_sign():
examples = [
(eq, 1e-100, -1e-100),
(ne, 1e100, -1e100),
]
for op, a, x in examples:
assert op(a, approx(x))
def test_opposite_sign():
examples = [
(eq, 1e-100, -1e-100),
(ne, 1e100, -1e100),
]
for op, a, x in examples:
assert op(a, approx(x))
def test_expecting_nan():
examples = [
(nan, nan),
(-nan, -nan),
(nan, -nan),
(0.0, nan),
(inf, nan),
]
for a, x in examples:
# If there is a relative tolerance and the expected value is NaN,
# the actual tolerance is a NaN, which should be an error.
with pytest.raises(ValueError):
a != approx(x, rel=inf)
# You can make comparisons against NaN by not specifying a relative
# tolerance, so only an absolute tolerance is calculated.
assert a != approx(x, abs=inf)
def test_expecting_sequence():
within_1e8 = [
(1e8 + 1e0, 1e8),
(1e0 + 1e-8, 1e0),
(1e-8 + 1e-16, 1e-8),
]
actual, expected = zip(*within_1e8)
assert actual == approx(expected, rel=5e-8, abs=0.0)
def test_expecting_nan():
examples = [
(nan, nan),
(-nan, -nan),
(nan, -nan),
(0.0, nan),
(inf, nan),
]
for a, x in examples:
# If there is a relative tolerance and the expected value is NaN,
# the actual tolerance is a NaN, which should be an error.
with pytest.raises(ValueError):
a != approx(x, rel=inf)
# You can make comparisons against NaN by not specifying a relative
# tolerance, so only an absolute tolerance is calculated.
assert a != approx(x, abs=inf)
def test_expecting_sequence():
within_1e8 = [
(1e8 + 1e0, 1e8),
(1e0 + 1e-8, 1e0),
(1e-8 + 1e-16, 1e-8),
]
actual, expected = zip(*within_1e8)
assert actual == approx(expected, rel=5e-8, abs=0.0)
def test_nan_tolerance():
illegal_kwargs = [
dict(rel=nan),
dict(abs=nan),
dict(rel=nan, abs=nan),
]
for kwargs in illegal_kwargs:
with pytest.raises(ValueError):
1.1 == approx(1, **kwargs)
def test_nan_tolerance():
illegal_kwargs = [
dict(rel=nan),
dict(abs=nan),
dict(rel=nan, abs=nan),
]
for kwargs in illegal_kwargs:
with pytest.raises(ValueError):
1.1 == approx(1, **kwargs)
def test_expecting_inf():
examples = [
(eq, inf, inf),
(eq, -inf, -inf),
(ne, inf, -inf),
(ne, 0.0, inf),
(ne, nan, inf),
]
for op, a, x in examples:
assert op(a, approx(x))
def test_expecting_inf():
examples = [
(eq, inf, inf),
(eq, -inf, -inf),
(ne, inf, -inf),
(ne, 0.0, inf),
(ne, nan, inf),
]
for op, a, x in examples:
assert op(a, approx(x))
def test_inf_tolerance_expecting_zero():
# If the relative tolerance is zero but the expected value is infinite,
# the actual tolerance is a NaN, which should be an error.
illegal_kwargs = [
dict(rel=inf, abs=0.0),
dict(rel=inf, abs=inf),
]
for kwargs in illegal_kwargs:
with pytest.raises(ValueError):
1 == approx(0, **kwargs)
def test_inf_tolerance_expecting_zero():
# If the relative tolerance is zero but the expected value is infinite,
# the actual tolerance is a NaN, which should be an error.
illegal_kwargs = [
dict(rel=inf, abs=0.0),
dict(rel=inf, abs=inf),
]
for kwargs in illegal_kwargs:
with pytest.raises(ValueError):
1 == approx(0, **kwargs)
def test_negative_tolerance():
# Negative tolerances are not allowed.
illegal_kwargs = [
dict(rel=-1e100),
dict(abs=-1e100),
dict(rel=1e100, abs=-1e100),
dict(rel=-1e100, abs=1e100),
dict(rel=-1e100, abs=-1e100),
]
for kwargs in illegal_kwargs:
with pytest.raises(ValueError):
1.1 == approx(1, **kwargs)
def test_negative_tolerance():
# Negative tolerances are not allowed.
illegal_kwargs = [
dict(rel=-1e100),
dict(abs=-1e100),
dict(rel=1e100, abs=-1e100),
dict(rel=-1e100, abs=1e100),
dict(rel=-1e100, abs=-1e100),
]
for kwargs in illegal_kwargs:
with pytest.raises(ValueError):
1.1 == approx(1, **kwargs)
def test_exactly_equal():
examples = [
(2.0, 2.0),
(0.1e200, 0.1e200),
(1.123e-300, 1.123e-300),
(12345, 12345.0),
(0.0, -0.0),
(345678, 345678),
(Decimal('1.0001'), Decimal('1.0001')),
(Fraction(1, 3), Fraction(-1, -3)),
]
for a, x in examples:
assert a == approx(x)
def test_exactly_equal():
examples = [
(2.0, 2.0),
(0.1e200, 0.1e200),
(1.123e-300, 1.123e-300),
(12345, 12345.0),
(0.0, -0.0),
(345678, 345678),
(Decimal('1.0001'), Decimal('1.0001')),
(Fraction(1, 3), Fraction(-1, -3)),
]
for a, x in examples:
assert a == approx(x)
def test_zero_tolerance():
within_1e10 = [
(1.1e-100, 1e-100),
(-1.1e-100, -1e-100),
]
for a, x in within_1e10:
assert x == approx(x, rel=0.0, abs=0.0)
assert a != approx(x, rel=0.0, abs=0.0)
assert a == approx(x, rel=0.0, abs=5e-101)
assert a != approx(x, rel=0.0, abs=5e-102)
assert a == approx(x, rel=5e-1, abs=0.0)
assert a != approx(x, rel=5e-2, abs=0.0)
def test_zero_tolerance():
within_1e10 = [
(1.1e-100, 1e-100),
(-1.1e-100, -1e-100),
]
for a, x in within_1e10:
assert x == approx(x, rel=0.0, abs=0.0)
assert a != approx(x, rel=0.0, abs=0.0)
assert a == approx(x, rel=0.0, abs=5e-101)
assert a != approx(x, rel=0.0, abs=5e-102)
assert a == approx(x, rel=5e-1, abs=0.0)
assert a != approx(x, rel=5e-2, abs=0.0)
def test_default_tolerances():
# This tests the defaults as they are currently set. If you change the
# defaults, this test will fail but you should feel free to change it.
# None of the other tests (except the doctests) should be affected by
# the choice of defaults.
examples = [
# Relative tolerance used.
(eq, 1e100 + 1e94, 1e100),
(ne, 1e100 + 2e94, 1e100),
(eq, 1e0 + 1e-6, 1e0),
(ne, 1e0 + 2e-6, 1e0),
# Absolute tolerance used.
(eq, 1e-100, + 1e-106),
(eq, 1e-100, + 2e-106),
(eq, 1e-100, 0),
]
for op, a, x in examples:
assert op(a, approx(x))
def test_default_tolerances():
# This tests the defaults as they are currently set. If you change the
# defaults, this test will fail but you should feel free to change it.
# None of the other tests (except the doctests) should be affected by
# the choice of defaults.
examples = [
# Relative tolerance used.
(eq, 1e100 + 1e94, 1e100),
(ne, 1e100 + 2e94, 1e100),
(eq, 1e0 + 1e-6, 1e0),
(ne, 1e0 + 2e-6, 1e0),
# Absolute tolerance used.
(eq, 1e-100, +1e-106),
(eq, 1e-100, +2e-106),
(eq, 1e-100, 0),
]
for op, a, x in examples:
assert op(a, approx(x))
def test_expecting_sequence_wrong_len():
assert [1, 2] != approx([1])
assert [1, 2] != approx([1,2,3])
def test_operator_overloading():
assert 1 == approx(1, rel=1e-6, abs=1e-12)
assert not (1 != approx(1, rel=1e-6, abs=1e-12))
assert 10 != approx(1, rel=1e-6, abs=1e-12)
assert not (10 == approx(1, rel=1e-6, abs=1e-12))
def test_operator_overloading():
assert 1 == approx(1, rel=1e-6, abs=1e-12)
assert not (1 != approx(1, rel=1e-6, abs=1e-12))
assert 10 != approx(1, rel=1e-6, abs=1e-12)
assert not (10 == approx(1, rel=1e-6, abs=1e-12))
def test_reasonable_defaults():
# Whatever the defaults are, they should work for numbers close to 1
# than have a small amount of floating-point error.
assert 0.1 + 0.2 == approx(0.3)
def test_expecting_sequence_wrong_len():
assert [1, 2] != approx([1])
assert [1, 2] != approx([1, 2, 3])
def test_reasonable_defaults():
# Whatever the defaults are, they should work for numbers close to 1
# than have a small amount of floating-point error.
assert 0.1 + 0.2 == approx(0.3)
def test_custom_tolerances():
assert 1e8 + 1e0 == approx(1e8, rel=5e-8, abs=5e0)
assert 1e8 + 1e0 == approx(1e8, rel=5e-9, abs=5e0)
assert 1e8 + 1e0 == approx(1e8, rel=5e-8, abs=5e-1)
assert 1e8 + 1e0 != approx(1e8, rel=5e-9, abs=5e-1)
assert 1e0 + 1e-8 == approx(1e0, rel=5e-8, abs=5e-8)
assert 1e0 + 1e-8 == approx(1e0, rel=5e-9, abs=5e-8)
assert 1e0 + 1e-8 == approx(1e0, rel=5e-8, abs=5e-9)
assert 1e0 + 1e-8 != approx(1e0, rel=5e-9, abs=5e-9)
assert 1e-8 + 1e-16 == approx(1e-8, rel=5e-8, abs=5e-16)
assert 1e-8 + 1e-16 == approx(1e-8, rel=5e-9, abs=5e-16)
assert 1e-8 + 1e-16 == approx(1e-8, rel=5e-8, abs=5e-17)
assert 1e-8 + 1e-16 != approx(1e-8, rel=5e-9, abs=5e-17)
def test_custom_tolerances():
assert 1e8 + 1e0 == approx(1e8, rel=5e-8, abs=5e0)
assert 1e8 + 1e0 == approx(1e8, rel=5e-9, abs=5e0)
assert 1e8 + 1e0 == approx(1e8, rel=5e-8, abs=5e-1)
assert 1e8 + 1e0 != approx(1e8, rel=5e-9, abs=5e-1)
assert 1e0 + 1e-8 == approx(1e0, rel=5e-8, abs=5e-8)
assert 1e0 + 1e-8 == approx(1e0, rel=5e-9, abs=5e-8)
assert 1e0 + 1e-8 == approx(1e0, rel=5e-8, abs=5e-9)
assert 1e0 + 1e-8 != approx(1e0, rel=5e-9, abs=5e-9)
assert 1e-8 + 1e-16 == approx(1e-8, rel=5e-8, abs=5e-16)
assert 1e-8 + 1e-16 == approx(1e-8, rel=5e-9, abs=5e-16)
assert 1e-8 + 1e-16 == approx(1e-8, rel=5e-8, abs=5e-17)
assert 1e-8 + 1e-16 != approx(1e-8, rel=5e-9, abs=5e-17)
