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Replaced numpy.testing.assert_almost_equal to numpy.testing.assert_allclose #4438

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merged 20 commits into from
Feb 24, 2024
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Replaced numpy.testing.assert_almost_equal to numpy.testing.assert_allclose #4438

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cb0391c
replaced assert_almost_equal() with assert_allclose() for more consi…
aditya292002 Jan 24, 2024
911c808
added the deleted statements
aditya292002 Jan 24, 2024
a90f4b5
made the changes as pointed by maintainer
aditya292002 Jan 25, 2024
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Merge branch 'MDAnalysis:develop' into develop
aditya292002 Jan 25, 2024
4353a09
Corrected error with occured in last commit
aditya292002 Jan 25, 2024
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changed test_base, bat, contracts, dihedrals, encore under testsuite/…
aditya292002 Jan 25, 2024
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corrected the error happened in last commit
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imported assert_allclose in the files
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corrected all the errors
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removed test_gnm.cpython-310-pytest-7.4.4.pyc.1853 bytecode file
aditya292002 Feb 2, 2024
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made all the changes as asked by the mainters
aditya292002 Feb 13, 2024
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- updated authors file and changelog,
aditya292002 Feb 23, 2024
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updated authors file and changed log and changed assert_array_almost_…
aditya292002 Feb 23, 2024
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corrected error
aditya292002 Feb 23, 2024
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corrected changelog entry
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corrected changelog entry
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Merge branch 'develop' into develop
orbeckst Feb 23, 2024
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corrected updated changelog in right format
aditya292002 Feb 24, 2024
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5 changes: 3 additions & 2 deletions package/MDAnalysis/visualization/streamlines_3D.py
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Original file line number Diff line number Diff line change
Expand Up @@ -245,10 +245,11 @@
cube_half_side_length = scipy.spatial.distance.pdist(array_cube_vertices, 'euclidean').min() / 2.0
array_cube_vertex_distances_from_centroid = scipy.spatial.distance.cdist(array_cube_vertices,
cube_centroid[np.newaxis, :])
np.testing.assert_almost_equal(array_cube_vertex_distances_from_centroid.min(),
array_cube_vertex_distances_from_centroid.max(), decimal=4,
np.testing.assert_allclose(array_cube_vertex_distances_from_centroid.min(),

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Added line #L248 was not covered by tests
array_cube_vertex_distances_from_centroid.max(), rtol=0, atol=1.5*(1e-4),
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Write floats as 1.5e-4 and not as 1.5*(1e-4).

This applies to all floats with powers of ten throughout.

err_msg="not all cube vertex to centroid distances are the same, "
"so not a true cube")

absolute_delta_coords = np.absolute(np.subtract(array_point_coordinates, cube_centroid))
absolute_delta_x_coords = absolute_delta_coords[..., 0]
indices_delta_x_acceptable = np.where(absolute_delta_x_coords <= cube_half_side_length)
Expand Down
88 changes: 50 additions & 38 deletions testsuite/MDAnalysisTests/analysis/test_align.py
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Original file line number Diff line number Diff line change
Expand Up @@ -167,7 +167,8 @@ 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_almost_equal(rmsd[1], 0.0, decimal=9)
assert_allclose(rmsd[1], 0.0, rtol=0, atol=1.5*1e-9)
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I think we can remove the commented old version


def test_no_atom_masses(self, universe):
#if no masses are present
Expand Down Expand Up @@ -199,43 +200,49 @@ 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")

assert_allclose(rms.rmsd(first_frame, first_frame), 0.0, rtol=0, atol=1.5*1e-5,
err_msg="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.
rmsd = rms.rmsd(first_frame, last_frame, superposition=True)
assert_almost_equal(
rms.rmsd(last_frame, first_frame, superposition=True), rmsd, 6,

assert_allclose(
rms.rmsd(last_frame, first_frame, superposition=True), rmsd, rtol=0, atol=1.5*1e-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_allclose(rmsd, 6.820321761927005, rtol=0, atol=1.5*(1e-5),
err_msg="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)
superposition=True)
assert_allclose(rmsd[1], rmsd_sup_weight, rtol=0, atol=1.5*(1e-6))

def test_rmsd_custom_mass_weights(self, universe, reference):
last_atoms_weight = universe.atoms.masses
A = universe.trajectory[0]
B = reference.trajectory[-1]
rmsd = align.alignto(universe, reference,
weights=reference.atoms.masses)
weights=reference.atoms.masses)
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some of the whitespace changes don't seem useful?

rmsd_sup_weight = rms.rmsd(A, B, weights=last_atoms_weight, center=True,
superposition=True)
assert_almost_equal(rmsd[1], rmsd_sup_weight, 6)
superposition=True)
assert_allclose(rmsd[1], rmsd_sup_weight, rtol=0, atol=1.5*(1e-6))

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_allclose(rmsd[1], rmsd_weights[1], rtol=0, atol=1.5*(1e-6))

def test_AlignTraj_outfile_default(self, universe, reference, tmpdir):
with tmpdir.as_cwd():
Expand Down Expand Up @@ -285,8 +292,8 @@ 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_allclose(x.results.rmsd[0], 6.9290, rtol=0, atol=1.5*(1e-3))
assert_allclose(x.results.rmsd[-1], 5.2797e-07, rtol=0, atol=1.5*(1e-3))

# RMSD against the reference frame
# calculated on Mac OS X x86 with MDA 0.7.2 r689
Expand All @@ -299,13 +306,13 @@ 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_allclose(x.results.rmsd[0], 0, rtol=0, atol=1.5*(1e-3))
assert_allclose(x.results.rmsd[-1], 6.9033, rtol=0, atol=1.5*(1e-3))

self._assert_rmsd(reference, fitted, 0, 0.0,
weights=universe.atoms.masses)
weights=universe.atoms.masses)
self._assert_rmsd(reference, fitted, -1, 6.929083032629219,
weights=universe.atoms.masses)
weights=universe.atoms.masses)

def test_AlignTraj_custom_weights(self, universe, reference, tmpdir):
weights = np.zeros(universe.atoms.n_atoms)
Expand All @@ -327,13 +334,13 @@ def test_AlignTraj_custom_mass_weights(self, universe, reference, tmpdir):
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_allclose(x.results.rmsd[0], 0, rtol=0, atol=1.5*(1e-3))
assert_allclose(x.results.rmsd[-1], 6.9033, rtol=0, atol=1.5*(1e-3))

self._assert_rmsd(reference, fitted, 0, 0.0,
weights=universe.atoms.masses)
weights=universe.atoms.masses)
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undo indent

self._assert_rmsd(reference, fitted, -1, 6.929083032629219,
weights=universe.atoms.masses)
weights=universe.atoms.masses)
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undo indent


def test_AlignTraj_partial_fit(self, universe, reference, tmpdir):
outfile = str(tmpdir.join('align_test.dcd'))
Expand All @@ -348,20 +355,21 @@ 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_allclose(x.results.rmsd[0], 6.9290, rtol=0, atol=1.5*(1e-3))
assert_allclose(x.results.rmsd[-1], 5.2797e-07, rtol=0, atol=1.5*(1e-3))

# check in memory trajectory
self._assert_rmsd(reference, universe, 0, 6.929083044751061)
self._assert_rmsd(reference, universe, -1, 0.0)

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,
err_msg="frame {0:d} of fit does not have "
"expected RMSD".format(frame))
fitted.trajectory[frame]
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You still have unwanted whitespace changes here and elsewhere, please re-read the entire diff line-by-line and make sure those changes are not present (since I'm spending time doing the same).

rmsd = rms.rmsd(reference.atoms.positions, fitted.atoms.positions,
superposition=True)
np.testing.assert_allclose(rmsd, desired, rtol=0, atol=1.5*(1e-5),
err_msg="frame {0:d} of fit does not have "
"expected RMSD".format(frame))


def test_alignto_checks_selections(self, universe, reference):
"""Testing that alignto() fails if selections do not
Expand All @@ -388,7 +396,6 @@ def test_alignto_partial_universe(self, universe, reference):
u_bound = mda.Universe(ALIGN_BOUND)
u_free = mda.Universe(ALIGN_UNBOUND)
selection = 'segid B'

segB_bound = u_bound.select_atoms(selection)
segB_free = u_free.select_atoms(selection)
segB_free.translate(segB_bound.centroid() - segB_free.centroid())
Expand All @@ -398,6 +405,7 @@ def test_alignto_partial_universe(self, universe, reference):
decimal=3)



def _get_aligned_average_positions(ref_files, ref, select="all", **kwargs):
u = mda.Universe(*ref_files, in_memory=True)
prealigner = align.AlignTraj(u, ref, select=select, **kwargs).run()
Expand Down Expand Up @@ -485,15 +493,19 @@ 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,
rtol=0, atol=1.5*(1e-4),
err_msg="assert_allclose failed for positions")
assert_allclose(avg.results.rmsd, rmsd,
rtol=0, atol=1.5*(1e-4),
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Don't you want 1e-7 since assert_almost_equal is using default arguments in the original here?

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Yeah, that's a mistake. I will correct this.

err_msg="assert_allclose failed for rmsd")
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fwiw, I don't think these custom messages are worth it in this context, but that may just be based on the style of the projects I usually maintain


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=0, atol=1.5*(1e-4),
err_msg="assert_allclose failed for positions")
assert avg.filename is None


Expand Down Expand Up @@ -603,4 +615,4 @@ def test_alignto_reorder_atomgroups():
mobile = u.atoms[:4]
ref = u.atoms[[3, 2, 1, 0]]
rmsd = align.alignto(mobile, ref, select='bynum 1-4')
assert_allclose(rmsd, (0.0, 0.0))
assert_allclose(rmsd, (0.0, 0.0))
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