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Modernize assertions in test_distances.py (part of #3743) #5158

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Nov 27, 2025
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Modernize assertions in test_distances.py (part of #3743) #5158

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17 changes: 7 additions & 10 deletions testsuite/MDAnalysisTests/analysis/test_distances.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
import pytest
import scipy
import scipy.spatial

import MDAnalysis
Expand All @@ -30,12 +29,10 @@
import MDAnalysis.analysis.distances

from numpy.testing import (
assert_equal,
assert_array_equal,
assert_almost_equal,
assert_array_almost_equal,
assert_allclose,
)

import numpy as np


Expand Down Expand Up @@ -99,7 +96,7 @@ def test_np(self, coord, shape, res_no_pbc):
assert contacts.shape == shape, "wrong shape (should be {0})".format(
shape
)
assert_equal(contacts, res_no_pbc)
assert_array_equal(contacts, res_no_pbc)

def test_sparse(self, coord, shape, res_no_pbc):
contacts = MDAnalysis.analysis.distances.contact_matrix(
Expand All @@ -108,7 +105,7 @@ def test_sparse(self, coord, shape, res_no_pbc):
assert contacts.shape == shape, "wrong shape (should be {0})".format(
shape
)
assert_equal(contacts.toarray(), res_no_pbc)
assert_array_equal(contacts.toarray(), res_no_pbc)

def test_box_numpy(self, coord, box, shape, res_pbc):
contacts = MDAnalysis.analysis.distances.contact_matrix(
Expand All @@ -117,7 +114,7 @@ def test_box_numpy(self, coord, box, shape, res_pbc):
assert contacts.shape == shape, "wrong shape (should be {0})".format(
shape
)
assert_equal(contacts, res_pbc)
assert_array_equal(contacts, res_pbc)

def test_box_sparse(self, coord, box, shape, res_pbc):
contacts = MDAnalysis.analysis.distances.contact_matrix(
Expand All @@ -126,7 +123,7 @@ def test_box_sparse(self, coord, box, shape, res_pbc):
assert contacts.shape == shape, "wrong shape (should be {0})".format(
shape
)
assert_equal(contacts.toarray(), res_pbc)
assert_array_equal(contacts.toarray(), res_pbc)


class TestDist(object):
Expand Down Expand Up @@ -187,7 +184,7 @@ def test_pairwise_dist_offset_effect(self, ag, ag2, expected):
def test_offset_calculation(self, ag, ag2):
"""Test that offsets fed to dist() are correctly calculated."""
actual = MDAnalysis.analysis.distances.dist(ag, ag2, offset=33)[:2]
assert_equal(
assert_array_equal(
actual, np.array([ag.atoms.resids + 33, ag2.atoms.resids + 33])
)

Expand Down Expand Up @@ -242,7 +239,7 @@ def test_between_simple_case_indices_only(self, group, ag, ag2, expected):
actual = MDAnalysis.analysis.distances.between(
group, ag, ag2, self.distance
).indices
assert_equal(actual, expected)
assert_array_equal(actual, expected)

@pytest.mark.parametrize("dists", [5.9, 0.0])
def test_between_return_type(self, dists, group, ag, ag2):
Expand Down
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