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changed comparisons of scalars to use pytest.approx function #4090

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changed comparisons of scalars to use pytest.approx function and comp…
yickysan Mar 24, 2023
9c11631
made changes to the functions that failed the tests
yickysan Mar 25, 2023
4086def
changed argument from relative tolerance to absolute tolerance in num…
yickysan Mar 25, 2023
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93 changes: 53 additions & 40 deletions testsuite/MDAnalysisTests/analysis/test_align.py
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Original file line number Diff line number Diff line change
Expand Up @@ -166,7 +166,7 @@ def test_subselection_alignto(self, universe, reference, subselection, expectati

with expectation:
rmsd = align.alignto(universe, reference, subselection=subselection)
assert_almost_equal(rmsd[1], 0.0, decimal=9)
assert rmsd[1] == pytest.approx(0.0, rel=1e-09)

def test_no_atom_masses(self, universe):
#if no masses are present
Expand Down Expand Up @@ -198,25 +198,29 @@ def test_rmsd(self, universe, reference):
first_frame = bb.positions
universe.trajectory[-1]
last_frame = bb.positions
assert_almost_equal(rms.rmsd(first_frame, first_frame), 0.0, 5,
err_msg="error: rmsd(X,X) should be 0")

# pytest.approx function is used here because the output of rmsd() is a scalar
# all comparisons of scalars have been changed from using the function assert_almost_equal to pytest.approx function
assert rms.rmsd(first_frame, first_frame) == pytest.approx(0.0), "error: rmsd(X,X) should be 0"

# rmsd(A,B) = rmsd(B,A) should be exact but spurious failures in the
# 9th decimal have been observed (see Issue 57 comment #1) so we relax
# the test to 6 decimals.
# by default pytest.approx has a relaive tolerance of 1e-06
rmsd = rms.rmsd(first_frame, last_frame, superposition=True)
assert_almost_equal(
rms.rmsd(last_frame, first_frame, superposition=True), rmsd, 6,
err_msg="error: rmsd() is not symmetric")
assert_almost_equal(rmsd, 6.820321761927005, 5,
err_msg="RMSD calculation between 1st and last AdK frame gave wrong answer")

assert rms.rmsd(last_frame, first_frame, superposition=True) == pytest.approx(rmsd), "error: rmsd() is not symmetric"

assert rmsd == pytest.approx(6.820321761927005, rel=1e-05), "RMSD calculation between 1st and last AdK frame gave wrong answer"

# test masses as weights
last_atoms_weight = universe.atoms.masses
A = universe.trajectory[0]
B = reference.trajectory[-1]
rmsd = align.alignto(universe, reference, weights='mass')
rmsd_sup_weight = rms.rmsd(A, B, weights=last_atoms_weight, center=True,
superposition=True)
assert_almost_equal(rmsd[1], rmsd_sup_weight, 6)
assert rmsd[1] == pytest.approx(rmsd_sup_weight), "Not equal to tolerance rel=1e-06"

def test_rmsd_custom_mass_weights(self, universe, reference):
last_atoms_weight = universe.atoms.masses
Expand All @@ -226,15 +230,15 @@ def test_rmsd_custom_mass_weights(self, universe, reference):
weights=reference.atoms.masses)
rmsd_sup_weight = rms.rmsd(A, B, weights=last_atoms_weight, center=True,
superposition=True)
assert_almost_equal(rmsd[1], rmsd_sup_weight, 6)
assert rmsd[1] == pytest.approx(rmsd_sup_weight, abs=1e-06), "Not equal to tolerance rel=1e-06"

def test_rmsd_custom_weights(self, universe, reference):
weights = np.zeros(universe.atoms.n_atoms)
ca = universe.select_atoms('name CA')
weights[ca.indices] = 1
rmsd = align.alignto(universe, reference, select='name CA')
rmsd_weights = align.alignto(universe, reference, weights=weights)
assert_almost_equal(rmsd[1], rmsd_weights[1], 6)
assert rmsd[1] == pytest.approx(rmsd_weights[1], abs=1e-06), "Not equal to tolerance rel=1e-06"

def test_AlignTraj_outfile_default(self, universe, reference, tmpdir):
with tmpdir.as_cwd():
Expand Down Expand Up @@ -284,8 +288,9 @@ def test_AlignTraj(self, universe, reference, tmpdir):
x = align.AlignTraj(universe, reference, filename=outfile).run()
fitted = mda.Universe(PSF, outfile)

assert_almost_equal(x.results.rmsd[0], 6.9290, decimal=3)
assert_almost_equal(x.results.rmsd[-1], 5.2797e-07, decimal=3)

assert x.results.rmsd[0] == pytest.approx(6.9290, abs=1e-03), "Not equal to tolerance rel=1e-03"
assert x.results.rmsd[-1] == pytest.approx(5.2797e-07, abs=1e-03), "Not equal to tolerance rel=1e-03"

# RMSD against the reference frame
# calculated on Mac OS X x86 with MDA 0.7.2 r689
Expand All @@ -298,8 +303,10 @@ def test_AlignTraj_weighted(self, universe, reference, tmpdir):
x = align.AlignTraj(universe, reference,
filename=outfile, weights='mass').run()
fitted = mda.Universe(PSF, outfile)
assert_almost_equal(x.results.rmsd[0], 0, decimal=3)
assert_almost_equal(x.results.rmsd[-1], 6.9033, decimal=3)

assert x.results.rmsd[0] == pytest.approx(0, abs=1e-03), "Not equal to tolerance rel=1e-03"
assert x.results.rmsd[-1] == pytest.approx(6.9033, abs=1e-03), "Not equal to tolerance rel=1e-03"


self._assert_rmsd(reference, fitted, 0, 0.0,
weights=universe.atoms.masses)
Expand All @@ -318,16 +325,19 @@ def test_AlignTraj_custom_weights(self, universe, reference, tmpdir):
x_weights = align.AlignTraj(universe, reference,
filename=outfile, weights=weights).run()

assert_array_almost_equal(x.results.rmsd, x_weights.results.rmsd)
# changed fucnion from assert_array_almost_equal to assert_allclose
assert_allclose(x.results.rmsd, x_weights.results.rmsd)

def test_AlignTraj_custom_mass_weights(self, universe, reference, tmpdir):
outfile = str(tmpdir.join('align_test.dcd'))
x = align.AlignTraj(universe, reference,
filename=outfile,
weights=reference.atoms.masses).run()
fitted = mda.Universe(PSF, outfile)
assert_almost_equal(x.results.rmsd[0], 0, decimal=3)
assert_almost_equal(x.results.rmsd[-1], 6.9033, decimal=3)

assert x.results.rmsd[0] == pytest.approx(0, abs=1e-03), "Not equal to tolerance rel=1e-03"
assert x.results.rmsd[-1] == pytest.approx(6.9033, abs=1e-03), "Not equal to tolerance rel=1e-03"


self._assert_rmsd(reference, fitted, 0, 0.0,
weights=universe.atoms.masses)
Expand All @@ -347,8 +357,9 @@ def test_AlignTraj_in_memory(self, universe, reference, tmpdir):
x = align.AlignTraj(universe, reference, filename=outfile,
in_memory=True).run()
assert x.filename is None
assert_almost_equal(x.results.rmsd[0], 6.9290, decimal=3)
assert_almost_equal(x.results.rmsd[-1], 5.2797e-07, decimal=3)
assert x.results.rmsd[0] == pytest.approx(6.9290, abs=1e-03), "Not equal to tolerance rel=1e-03"
assert x.results.rmsd[-1] == pytest.approx(5.2797e-07, abs=1e-03), "Not equal to tolerance rel=1e-03"


# check in memory trajectory
self._assert_rmsd(reference, universe, 0, 6.929083044751061)
Expand All @@ -358,7 +369,7 @@ def _assert_rmsd(self, reference, fitted, frame, desired, weights=None):
fitted.trajectory[frame]
rmsd = rms.rmsd(reference.atoms.positions, fitted.atoms.positions,
superposition=True)
assert_almost_equal(rmsd, desired, decimal=5,
assert_allclose(rmsd, desired, atol=1e-5,
err_msg="frame {0:d} of fit does not have "
"expected RMSD".format(frame))

Expand Down Expand Up @@ -393,8 +404,9 @@ def test_alignto_partial_universe(self, universe, reference):
segB_free.translate(segB_bound.centroid() - segB_free.centroid())

align.alignto(u_free, u_bound, select=selection)
assert_array_almost_equal(segB_bound.positions, segB_free.positions,
decimal=3)
# changed function from assert_array_almost_equal to assert_allclose
assert_allclose(segB_bound.positions, segB_free.positions,
rtol=1e-03)


def _get_aligned_average_positions(ref_files, ref, select="all", **kwargs):
Expand Down Expand Up @@ -437,31 +449,31 @@ def test_average_structure_deprecated_attrs(self, universe, reference):
def test_average_structure(self, universe, reference):
ref, rmsd = _get_aligned_average_positions(self.ref_files, reference)
avg = align.AverageStructure(universe, reference).run()
assert_almost_equal(avg.results.universe.atoms.positions, ref,
decimal=4)
assert_almost_equal(avg.results.rmsd, rmsd)
assert_allclose(avg.results.universe.atoms.positions, ref,
atol=1e-04)
assert avg.results.rmsd == pytest.approx(rmsd)

def test_average_structure_mass_weighted(self, universe, reference):
ref, rmsd = _get_aligned_average_positions(self.ref_files, reference, weights='mass')
avg = align.AverageStructure(universe, reference, weights='mass').run()
assert_almost_equal(avg.results.universe.atoms.positions, ref,
decimal=4)
assert_almost_equal(avg.results.rmsd, rmsd)
assert_allclose(avg.results.universe.atoms.positions, ref,
atol=1e-04)
assert avg.results.rmsd == pytest.approx(rmsd)

def test_average_structure_select(self, universe, reference):
select = 'protein and name CA and resid 3-5'
ref, rmsd = _get_aligned_average_positions(self.ref_files, reference, select=select)
avg = align.AverageStructure(universe, reference, select=select).run()
assert_almost_equal(avg.results.universe.atoms.positions, ref,
decimal=4)
assert_almost_equal(avg.results.rmsd, rmsd)
assert_allclose(avg.results.universe.atoms.positions, ref,
atol=1e-04)
assert avg.results.rmsd == pytest.approx(rmsd)

def test_average_structure_no_ref(self, universe):
ref, rmsd = _get_aligned_average_positions(self.ref_files, universe)
avg = align.AverageStructure(universe).run()
assert_almost_equal(avg.results.universe.atoms.positions, ref,
decimal=4)
assert_almost_equal(avg.results.rmsd, rmsd)
assert_allclose(avg.results.universe.atoms.positions, ref,
atol=1e-04)
assert avg.results.rmsd == pytest.approx(rmsd)

def test_average_structure_no_msf(self, universe):
avg = align.AverageStructure(universe).run()
Expand All @@ -484,15 +496,16 @@ def test_average_structure_ref_frame(self, universe):
universe.trajectory[0]
ref, rmsd = _get_aligned_average_positions(self.ref_files, u)
avg = align.AverageStructure(universe, ref_frame=ref_frame).run()
assert_almost_equal(avg.results.universe.atoms.positions, ref,
decimal=4)
assert_almost_equal(avg.results.rmsd, rmsd)

assert_allclose(avg.results.universe.atoms.positions, ref,
atol=1e-04)
assert avg.results.rmsd == pytest.approx(rmsd)

def test_average_structure_in_memory(self, universe):
avg = align.AverageStructure(universe, in_memory=True).run()
reference_coordinates = universe.trajectory.timeseries().mean(axis=1)
assert_almost_equal(avg.results.universe.atoms.positions,
reference_coordinates, decimal=4)
assert_allclose(avg.results.universe.atoms.positions,
reference_coordinates, rtol=1e-04)
assert avg.filename is None


Expand Down