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tests: modernize deprecated numpy assertions in test_helix_analysis.p… #5408

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tests: modernize deprecated numpy assertions in test_helix_analysis.p…
AnimeshPriyanshu Jun 22, 2026
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AnimeshPriyanshu Jun 23, 2026
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3 changes: 2 additions & 1 deletion package/AUTHORS
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Original file line number Diff line number Diff line change
Expand Up @@ -281,6 +281,7 @@ Chronological list of authors
- Shubham Mittal
- Charity Grey
- Sai Udayagiri
- Animesh Priyanshu

External code
-------------
Expand Down Expand Up @@ -328,4 +329,4 @@ Logo

The MDAnalysis 'Atom' logo was designed by Christian Beckstein; it is
Copyright (c) 2011 Christian Beckstein and made available under a
Creative Commons Attribution-NoDerivs 3.0 Unported License.
Creative Commons Attribution-NoDerivs 3.0 Unported License.
114 changes: 57 additions & 57 deletions testsuite/MDAnalysisTests/analysis/test_helix_analysis.py
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Expand Up @@ -24,7 +24,7 @@

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

import MDAnalysis as mda
from MDAnalysis.analysis import helix_analysis as hel
Expand Down Expand Up @@ -167,7 +167,7 @@ def test_local_screw_angles_plane_circle():
screw = hel.local_screw_angles([1, 0, 0], [0, 1, 0], xyz)
correct = np.zeros_like(angdeg)
correct[(angdeg > 180)] = 180
assert_almost_equal(screw, correct)
assert_allclose(screw, correct)


def test_local_screw_angles_ortho_circle():
Expand All @@ -187,7 +187,7 @@ def test_local_screw_angles_ortho_circle():
correct[(angdeg < 180)] = 90
correct[(angdeg > 180)] = -90
correct[0] = correct[15] = 0
assert_almost_equal(screw, correct)
assert_allclose(screw, correct)


def test_local_screw_angles_around_circle():
Expand All @@ -203,7 +203,7 @@ def test_local_screw_angles_around_circle():
screw = hel.local_screw_angles([0, 1, 0], [1, 0, 0], xyz)
angdeg[-14:] = -angdeg[1:15][::-1]
angdeg[-15] = 180
assert_almost_equal(screw, angdeg)
assert_allclose(screw, angdeg)


def test_local_screw_angles_around_circle_rising():
Expand All @@ -221,7 +221,7 @@ def test_local_screw_angles_around_circle_rising():
screw = hel.local_screw_angles([0, 1, 0], [1, 0, 0], xyz)
angdeg[-14:] = -angdeg[1:15][::-1]
angdeg[-15] = 180
assert_almost_equal(screw, angdeg)
assert_allclose(screw, angdeg)


def test_local_screw_angles_parallel_axes():
Expand All @@ -233,7 +233,7 @@ def test_local_screw_angles_parallel_axes():
"""
xyz = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
angles = hel.local_screw_angles([1, 0, 0], [-1, 0, 0], xyz)
assert_almost_equal(angles, [0, 90, 0])
assert_allclose(angles, [0, 90, 0])


@pytest.fixture()
Expand Down Expand Up @@ -288,27 +288,27 @@ def zigzag():
)
def test_helix_analysis_zigzag(zigzag, ref_axis, screw_angles):
properties = hel.helix_analysis(zigzag.atoms.positions, ref_axis=ref_axis)
assert_almost_equal(properties["local_twists"], 180, decimal=4)
assert_almost_equal(properties["local_nres_per_turn"], 2, decimal=4)
assert_almost_equal(properties["global_axis"], [0, 0, -1], decimal=4)
assert_allclose(properties["local_twists"], 180, atol=1e-4)
assert_allclose(properties["local_nres_per_turn"], 2, atol=1e-4)
assert_allclose(properties["global_axis"], [0, 0, -1], atol=1e-4)
# all 0 vectors
assert_almost_equal(properties["local_axes"], 0, decimal=4)
assert_almost_equal(properties["local_bends"], 0, decimal=4)
assert_almost_equal(properties["all_bends"], 0, decimal=4)
assert_almost_equal(properties["local_heights"], 0, decimal=4)
assert_almost_equal(
assert_allclose(properties["local_axes"], 0, atol=1e-4)
assert_allclose(properties["local_bends"], 0, atol=1e-4)
assert_allclose(properties["all_bends"], 0, atol=1e-4)
assert_allclose(properties["local_heights"], 0, atol=1e-4)
assert_allclose(
properties["local_helix_directions"][0::2],
[[-1, 0, 0]] * 49,
decimal=4,
atol=1e-4,
)
assert_almost_equal(
properties["local_helix_directions"][1::2], [[1, 0, 0]] * 49, decimal=4
assert_allclose(
properties["local_helix_directions"][1::2], [[1, 0, 0]] * 49, atol=1e-4
)
origins = zigzag.atoms.positions[1:-1].copy()
origins[:, 0] = 0
assert_almost_equal(properties["local_origins"], origins, decimal=4)
assert_almost_equal(
properties["local_screw_angles"], screw_angles * 49, decimal=4
assert_allclose(properties["local_origins"], origins, atol=1e-4)
assert_allclose(
properties["local_screw_angles"], screw_angles * 49, atol=1e-4
)


Expand Down Expand Up @@ -348,19 +348,19 @@ def test_helix_analysis_square_oct():
properties = hel.helix_analysis(u.atoms.positions, ref_axis=[0, 0, 1])
twist_trans = [102.76438, 32.235607]
twists = ([90] * 2 + twist_trans + [45] * 6 + twist_trans[::-1]) * n_rep
assert_almost_equal(
properties["local_twists"], twists[: n_atoms - 3], decimal=4
assert_allclose(
properties["local_twists"], twists[: n_atoms - 3], atol=1e-4
)
res_trans = [3.503159, 11.167775]
res = ([4] * 2 + res_trans + [8] * 6 + res_trans[::-1]) * n_rep
assert_almost_equal(
properties["local_nres_per_turn"], res[: n_atoms - 3], decimal=4
assert_allclose(
properties["local_nres_per_turn"], res[: n_atoms - 3], atol=1e-4
)
assert_almost_equal(properties["global_axis"], [-1, 0, 0], decimal=3)
assert_almost_equal(properties["local_axes"] - [1, 0, 0], 0, decimal=4)
assert_almost_equal(properties["local_bends"], 0, decimal=4)
assert_almost_equal(properties["all_bends"], 0, decimal=4)
assert_almost_equal(properties["local_heights"], 1, decimal=4)
assert_allclose(properties["global_axis"], [-1, 0, 0], atol=1e-3)
assert_allclose(properties["local_axes"] - [1, 0, 0], 0, atol=1e-4)
assert_allclose(properties["local_bends"], 0, atol=1e-4)
assert_allclose(properties["all_bends"], 0, atol=1e-4)
assert_allclose(properties["local_heights"], 1, atol=1e-4)

loc_rot = [
[0.0, 0.0, 1.0],
Expand All @@ -376,8 +376,8 @@ def test_helix_analysis_square_oct():
[0.0, 0.70710677, -0.70710677],
[0.0, 0.97528684, -0.2209424],
] * n_rep
assert_almost_equal(
properties["local_helix_directions"], loc_rot[: n_atoms - 2], decimal=4
assert_allclose(
properties["local_helix_directions"], loc_rot[: n_atoms - 2], atol=1e-4
)

origins = u.atoms.positions.copy()[1:-1]
Expand All @@ -398,7 +398,7 @@ def test_helix_analysis_square_oct():
]
* n_rep
)[: len(origins)]
assert_almost_equal(properties["local_origins"], origins, decimal=4)
assert_allclose(properties["local_origins"], origins, atol=1e-4)

# calculated to the x-y plane
# all input vectors (loc_rot) are in y-z plane
Expand All @@ -418,8 +418,8 @@ def test_helix_analysis_square_oct():
] * n_rep

# not quite 0, comes out as 1.32e-06
assert_almost_equal(
properties["local_screw_angles"], screw[:-2], decimal=3
assert_allclose(
properties["local_screw_angles"], screw[:-2], atol=1e-3
)


Expand All @@ -441,14 +441,14 @@ def helanal(self, psf_ca):
def test_regression_summary(self, helanal):
bends = helanal.results.summary["all_bends"]
old_helanal = read_bending_matrix(HELANAL_BENDING_MATRIX_SUBSET)
assert_almost_equal(
np.triu(bends["mean"], 1), old_helanal["Mean"], decimal=1
assert_allclose(
np.triu(bends["mean"], 1), old_helanal["Mean"], atol=0.1
)
assert_almost_equal(
np.triu(bends["sample_sd"], 1), old_helanal["SD"], decimal=1
assert_allclose(
np.triu(bends["sample_sd"], 1), old_helanal["SD"], atol=0.1
)
assert_almost_equal(
np.triu(bends["abs_dev"], 1), old_helanal["ABDEV"], decimal=1
assert_allclose(
np.triu(bends["abs_dev"], 1), old_helanal["ABDEV"], atol=0.1
)

def test_regression_values(self):
Expand All @@ -470,8 +470,8 @@ def test_regression_values(self):
calculated = ha.results[key][0]

msg = "Mismatch between calculated and reference {}"
assert_almost_equal(
calculated, value, decimal=4, err_msg=msg.format(key)
assert_allclose(
calculated, value, atol=1e-4, err_msg=msg.format(key)
)

def test_multiple_selections(self, psf_ca):
Expand Down Expand Up @@ -562,29 +562,29 @@ def test_helanal_zigzag(self, zigzag, ref_axis, screw_angles):
ha = hel.HELANAL(
zigzag, select="all", ref_axis=ref_axis, flatten_single_helix=True
).run()
assert_almost_equal(ha.results.local_twists, 180, decimal=4)
assert_almost_equal(ha.results.local_nres_per_turn, 2, decimal=4)
assert_almost_equal(ha.results.global_axis, [[0, 0, -1]], decimal=4)
assert_allclose(ha.results.local_twists, 180, atol=1e-4)
assert_allclose(ha.results.local_nres_per_turn, 2, atol=1e-4)
assert_allclose(ha.results.global_axis, [[0, 0, -1]], atol=1e-4)
# all 0 vectors
assert_almost_equal(ha.results.local_axes, 0, decimal=4)
assert_almost_equal(ha.results.local_bends, 0, decimal=4)
assert_almost_equal(ha.results.all_bends, 0, decimal=4)
assert_almost_equal(ha.results.local_heights, 0, decimal=4)
assert_almost_equal(
assert_allclose(ha.results.local_axes, 0, atol=1e-4)
assert_allclose(ha.results.local_bends, 0, atol=1e-4)
assert_allclose(ha.results.all_bends, 0, atol=1e-4)
assert_allclose(ha.results.local_heights, 0, atol=1e-4)
assert_allclose(
ha.results.local_helix_directions[0][0::2],
[[-1, 0, 0]] * 49,
decimal=4,
atol=1e-4,
)
assert_almost_equal(
assert_allclose(
ha.results.local_helix_directions[0][1::2],
[[1, 0, 0]] * 49,
decimal=4,
atol=1e-4,
)
origins = zigzag.atoms.positions[1:-1].copy()
origins[:, 0] = 0
assert_almost_equal(ha.results.local_origins[0], origins, decimal=4)
assert_almost_equal(
ha.results.local_screw_angles[0], screw_angles * 49, decimal=4
assert_allclose(ha.results.local_origins[0], origins, atol=1e-4)
assert_allclose(
ha.results.local_screw_angles[0], screw_angles * 49, atol=1e-4
)


Expand All @@ -597,4 +597,4 @@ def test_vector_of_best_fit():

vector = hel.vector_of_best_fit(data)
cos = np.dot(vector, unit)
assert_almost_equal(abs(cos), 1.0, decimal=5)
assert abs(cos) == pytest.approx(1.0, abs=1e-5)
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