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Fixes #3743: Modernize test assertions in test_msd.py #5171

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Fixes #3743: Modernize test assertions in test_msd.py #5171

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9e2455f
removed build error
tanii1125 Dec 8, 2025
2edd8a5
Merge branch 'MDAnalysis:develop' into modernize-test-msd-3743
tanii1125 Dec 8, 2025
774d059
resolved Black error
tanii1125 Dec 8, 2025
c842b26
resolved formatting error
tanii1125 Dec 8, 2025
665c628
Merge branch 'modernize-test-msd-3744' of https://github.com/tanii112…
tanii1125 Dec 8, 2025
9190efd
Re-trigger CI
tanii1125 Dec 10, 2025
0c49e61
Re-trigger CI
tanii1125 Dec 10, 2025
4ad7959
Added Tanisha Dubey to authors
tanii1125 Dec 13, 2025
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1 change: 1 addition & 0 deletions package/AUTHORS
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Original file line number Diff line number Diff line change
Expand Up @@ -265,6 +265,7 @@ Chronological list of authors
- Raúl Lois-Cuns
- Pranay Pelapkar
- Shreejan Dolai
- Tanisha Dubey

External code
-------------
Expand Down
27 changes: 11 additions & 16 deletions testsuite/MDAnalysisTests/analysis/test_msd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,11 +21,10 @@
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#


from MDAnalysis.analysis.msd import EinsteinMSD as MSD
import MDAnalysis as mda

from numpy.testing import assert_almost_equal, assert_equal, assert_allclose
from numpy.testing import assert_allclose, assert_equal
import numpy as np

from MDAnalysisTests.datafiles import (
Expand Down Expand Up @@ -143,7 +142,7 @@ def test_simple_step_traj_all_dims(
m_simple = MSD(step_traj, "all", msd_type=dim, fft=False)
m_simple.run()
poly = characteristic_poly(NSTEP, dim_factor)
assert_almost_equal(m_simple.results.timeseries, poly, decimal=4)
assert_allclose(m_simple.results.timeseries, poly, rtol=1e-4)

@pytest.mark.parametrize(
"dim, dim_factor",
Expand All @@ -166,17 +165,15 @@ def test_simple_start_stop_step_all_dims(
m_simple.run(start=10, stop=1000, step=10)
poly = characteristic_poly(NSTEP, dim_factor)
# polynomial must take offset start into account
assert_almost_equal(
m_simple.results.timeseries, poly[0:990:10], decimal=4
)
assert_allclose(m_simple.results.timeseries, poly[0:990:10], rtol=1e-4)

def test_random_walk_u_simple(self, random_walk_u):
# regress against random_walk test data
msd_rw = MSD(random_walk_u, "all", msd_type="xyz", fft=False)
msd_rw.run()
norm = np.linalg.norm(msd_rw.results.timeseries)
val = 3932.39927487146
assert_almost_equal(norm, val, decimal=5)
assert norm == pytest.approx(val, rel=1e-5)


@pytest.mark.skipif(
Expand All @@ -196,13 +193,13 @@ def test_fft_vs_simple_default(self, msd, msd_fft):
# testing on the PSF, DCD trajectory
timeseries_simple = msd.results.timeseries
timeseries_fft = msd_fft.results.timeseries
assert_almost_equal(timeseries_simple, timeseries_fft, decimal=4)
assert_allclose(timeseries_simple, timeseries_fft, rtol=1e-4)

def test_fft_vs_simple_default_per_particle(self, msd, msd_fft):
# check fft and simple give same result per particle
per_particle_simple = msd.results.msds_by_particle
per_particle_fft = msd_fft.results.msds_by_particle
assert_almost_equal(per_particle_simple, per_particle_fft, decimal=4)
assert_allclose(per_particle_simple, per_particle_fft, rtol=1e-4)

@pytest.mark.parametrize("dim", ["xyz", "xy", "xz", "yz", "x", "y", "z"])
def test_fft_vs_simple_all_dims(self, u, SELECTION, dim):
Expand All @@ -213,7 +210,7 @@ def test_fft_vs_simple_all_dims(self, u, SELECTION, dim):
m_fft = MSD(u, SELECTION, msd_type=dim, fft=True)
m_fft.run()
timeseries_fft = m_fft.results.timeseries
assert_almost_equal(timeseries_simple, timeseries_fft, decimal=4)
assert_allclose(timeseries_simple, timeseries_fft, rtol=1e-4)

@pytest.mark.parametrize("dim", ["xyz", "xy", "xz", "yz", "x", "y", "z"])
def test_fft_vs_simple_all_dims_per_particle(self, u, SELECTION, dim):
Expand All @@ -225,7 +222,7 @@ def test_fft_vs_simple_all_dims_per_particle(self, u, SELECTION, dim):
m_fft = MSD(u, SELECTION, msd_type=dim, fft=True)
m_fft.run()
per_particle_fft = m_fft.results.msds_by_particle
assert_almost_equal(per_particle_simple, per_particle_fft, decimal=4)
assert_allclose(per_particle_simple, per_particle_fft, rtol=1e-4)

@pytest.mark.parametrize(
"dim, dim_factor",
Expand All @@ -249,7 +246,7 @@ def test_fft_step_traj_all_dims(self, step_traj, NSTEP, dim, dim_factor):
m_simple.run()
poly = characteristic_poly(NSTEP, dim_factor)
# this was relaxed from decimal=4 for numpy=1.13 test
assert_almost_equal(m_simple.results.timeseries, poly, decimal=3)
assert_allclose(m_simple.results.timeseries, poly, rtol=1e-3)

@pytest.mark.parametrize(
"dim, dim_factor",
Expand All @@ -272,17 +269,15 @@ def test_fft_start_stop_step_all_dims(
m_simple.run(start=10, stop=1000, step=10)
poly = characteristic_poly(NSTEP, dim_factor)
# polynomial must take offset start into account
assert_almost_equal(
m_simple.results.timeseries, poly[0:990:10], decimal=3
)
assert_allclose(m_simple.results.timeseries, poly[0:990:10], rtol=1e-3)

def test_random_walk_u_fft(self, random_walk_u):
# regress against random_walk test data
msd_rw = MSD(random_walk_u, "all", msd_type="xyz", fft=True)
msd_rw.run()
norm = np.linalg.norm(msd_rw.results.timeseries)
val = 3932.39927487146
assert_almost_equal(norm, val, decimal=5)
assert norm == pytest.approx(val, rel=1e-4)


class TestMSDNonLinear:
Expand Down
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