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Fix #3743: Modernize deprecated test assertions in hydrogen bond tests #5400

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Fix #3743: Modernize deprecated test assertions in hydrogen bond tests #5400

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Address review feedback in hydrogen bond tests
ShivansGupta25 Jun 18, 2026
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ShivansGupta25 Jun 19, 2026
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17 changes: 8 additions & 9 deletions testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,9 +28,7 @@
from numpy.testing import (
assert_allclose,
assert_equal,
assert_array_almost_equal,
assert_array_equal,
assert_almost_equal,
)

import MDAnalysis
Expand Down Expand Up @@ -108,7 +106,7 @@ def test_count_by_time(self, h):
ref_counts = np.array([3, 2, 4, 4, 4, 4, 3, 2, 3, 3])

counts = h.count_by_time()
assert_array_almost_equal(h.times, ref_times)
assert_allclose(h.times, ref_times)

@Dreamstick9 Dreamstick9 Jun 20, 2026

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assert_allclose without args is actually stricter than the old assert_array_almost_equal. In a similar PR (#5156), the fix was to add atol=1e-6, rtol=0 to match the old tolerance. Might be worth doing the same here

Suggested change
assert_allclose(h.times, ref_times)
assert_allclose(h.times, ref_times, atol=1e-6, rtol=0)

assert_array_equal(counts, ref_counts)

def test_count_by_type(self, h):
Expand Down Expand Up @@ -241,7 +239,7 @@ def test_no_bond_info_exception(self, universe):
u.add_TopologyAttr("mass", [15.999, 1.008, 1.008] * n_residues)
u.add_TopologyAttr("charge", [-1.04, 0.52, 0.52] * n_residues)
with pytest.raises(NoDataError, match="no bond information"):
h = HydrogenBondAnalysis(u, **kwargs)
HydrogenBondAnalysis(u, **kwargs)

def test_no_bond_donor_sel(self, universe):

Expand All @@ -258,7 +256,7 @@ def test_no_bond_donor_sel(self, universe):
u.add_TopologyAttr("mass", [15.999, 1.008, 1.008] * n_residues)
u.add_TopologyAttr("charge", [-1.04, 0.52, 0.52] * n_residues)
h = HydrogenBondAnalysis(u, **kwargs)
donors = u.select_atoms(h.guess_donors())
u.select_atoms(h.guess_donors())

def test_first_hbond(self, hydrogen_bonds):
assert len(hydrogen_bonds.results.hbonds) == 2
Expand All @@ -273,15 +271,16 @@ def test_first_hbond(self, hydrogen_bonds):
assert_equal(donor_index, 0)
assert_equal(hydrogen_index, 2)
assert_equal(acceptor_index, 3)
assert_almost_equal(da_dst, 2.5)
assert_almost_equal(angle, 180)
assert da_dst == pytest.approx(2.5)
assert angle == pytest.approx(180)


def test_count_by_time(self, hydrogen_bonds):
ref_times = np.array([0, 1, 2]) # u.trajectory.dt is 1
ref_counts = np.array([1, 0, 1])

counts = hydrogen_bonds.count_by_time()
assert_array_almost_equal(hydrogen_bonds.times, ref_times)
assert_allclose(hydrogen_bonds.times, ref_times)
assert_array_equal(counts, ref_counts)

def test_hydrogen_bond_lifetime(self, hydrogen_bonds):
Expand Down Expand Up @@ -716,7 +715,7 @@ def test_count_by_time(self, h):
ref_counts = np.array([2, 4, 4, 2, 3])

counts = h.count_by_time()
assert_array_almost_equal(h.times, ref_times)
assert_allclose(h.times, ref_times)
assert_array_equal(counts, ref_counts)

def test_count_by_type(self, h):
Expand Down
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