def test_invalid_rt_has_none_ri(invalid_rt_data, indexed_data):
method = Kovats()
expected = [None, None, None, 741.5254237288136]
actual = method.compute(invalid_rt_data, indexed_data)
numpy.testing.assert_array_equal(actual, expected)
def test_exception_query_none(indexed_data):
method = Kovats()
with pytest.raises(AssertionError) as exception:
method.compute(None, indexed_data)
message = exception.value.args[0]
assert exception.typename == "AssertionError"
assert message == "Query data is 'None'."
def test_exception_reference_none(non_indexed_data):
method = Kovats()
with pytest.raises(AssertionError) as exception:
method.compute(non_indexed_data, None)
message = exception.value.args[0]
assert exception.typename == "AssertionError"
assert message == "Reference data is 'None'."
def test_compute_ri_basic_case(non_indexed_data, indexed_data):
method = Kovats()
expected = [
741.525424, 760.169492, 769.491525, 932.420091, 965.296804, 986.757991,
1078.823529, 1157.142857
]
actual = method.compute(non_indexed_data, indexed_data)
numpy.testing.assert_array_almost_equal(actual, expected)
def __call__(self, parser, namespace, values, option_string=None):
"""Function to be called on action invocation
Args:
parser (argparse.ArgumentParser): Passed implicitly.
namespace ([type]): Passed implicitly.
values (str): Method name indicating which method to use.
option_string (str, optional): Unused. Defaults to None.
"""
if values not in ['kovats', 'cubicspline']:
raise AssertionError(
"Method must be one of ['cubicspline', 'kovats'].")
if values == "kovats":
method = Kovats()
elif values == "cubicspline":
method = CubicSpline()
setattr(namespace, self.dest, method)
def load_method(method):
if method == 'kovats':
return Kovats()
if method == 'cubicspline':
return CubicSpline()
return None
import pytest
from RIAssigner.compute import ComputationMethod, CubicSpline, Kovats
@pytest.mark.parametrize('this, other, expected', [
[CubicSpline(), CubicSpline(), True],
[Kovats(), Kovats(), True],
[CubicSpline(), Kovats(), False],
[Kovats(), object(), False],
[CubicSpline(), object(), False],
])
def test_equal(this, other, expected):
actual = (this == other)
assert actual == expected
def test_abc():
with pytest.raises(TypeError) as exception:
method = ComputationMethod()
message = exception.value.args[0]
assert exception.typename == "TypeError"
assert str(message).startswith(
"Can't instantiate abstract class ComputationMethod with abstract method"
)
def test_construct():
compute = Kovats()
assert compute is not None
def test_ref_queries(reference_alkanes, queries):
method = Kovats()
data, expected = queries
actual = method.compute(data, reference_alkanes)
numpy.testing.assert_array_almost_equal(actual, expected)