def test_analysis_class_decorator():
# Issue #1511
# analysis_class should not raise
# a DeprecationWarning
u = mda.Universe(PSF, DCD)
def distance(a, b):
return np.linalg.norm((a.centroid() - b.centroid()))
Distances = base.analysis_class(distance)
with no_deprecated_call():
d = Distances(u.atoms[:10], u.atoms[10:20]).run()
def test_analysis_class():
ana_class = base.analysis_class(simple_function)
assert issubclass(ana_class, base.AnalysisBase)
assert issubclass(ana_class, base.AnalysisFromFunction)
u = mda.Universe(PSF, DCD)
step = 2
ana = ana_class(u.atoms).run(step=step)
results = []
for ts in u.trajectory[::step]:
results.append(simple_function(u.atoms))
results = np.asarray(results)
assert_equal(results, ana.results)
with pytest.raises(ValueError):
ana_class(2)
def test_analysis_class_decorator():
# Issue #1511
# analysis_class should not raise
# a DeprecationWarning
# PR 3194 - only one specific DeprecationWarning should be raised
u = mda.Universe(PSF, DCD)
def distance(a, b):
return np.linalg.norm((a.centroid() - b.centroid()))
Distances = base.analysis_class(distance)
# temporarily switch from no_deprecated_call to a standard warn capture
# revert in version 2.0
# with no_deprecated_call():
with pytest.warns(DeprecationWarning) as record:
d = Distances(u.atoms[:10], u.atoms[10:20]).run()
assert len(record) == 1
msg = ("The structure of the `results` array will change in MDAnalysis "
"version 2.0.")
assert str(record[0].message) == msg