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Fixed #1175 Migrate tests/test_aamp_motifs.py to npt.assert_allclose #1181

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Merged
seanlaw merged 2 commits into from
Aug 14, 2026
Merged

Fixed #1175 Migrate tests/test_aamp_motifs.py to npt.assert_allclose #1181

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9a014be
Migrate tests/test_aamp_motifs.py from npt.assert_almost_equal to npt…
viknesh-ai Aug 13, 2026
e59b3f5
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viknesh-ai Aug 13, 2026
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62 changes: 37 additions & 25 deletions tests/test_aamp_motifs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,12 +51,12 @@ def test_aamp_motifs_one_motif():
m = 3
max_motifs = 1

left_indices = [[0, 5]]
left_profile_values = [[0.0, 0.0]]
ref_indices = [[0, 5]]
ref_profile_values = [[0.0, 0.0]]

for p in [1.0, 2.0, 3.0]:
mp = naive.aamp(T, m, p=p)
right_distance_values, right_indices = aamp_motifs(
cmp_distance_values, cmp_indices = aamp_motifs(
T,
mp[:, 0],
max_motifs=max_motifs,
Expand All @@ -65,8 +65,8 @@ def test_aamp_motifs_one_motif():
p=p,
)

npt.assert_array_equal(left_indices, right_indices)
npt.assert_almost_equal(left_profile_values, right_distance_values, decimal=4)
npt.assert_array_equal(cmp_indices, ref_indices)
npt.assert_allclose(cmp_distance_values, ref_profile_values, atol=1.5e-04)


def test_aamp_motifs_two_motifs():
Expand Down Expand Up @@ -105,16 +105,16 @@ def test_aamp_motifs_two_motifs():

mp = naive.aamp(T, m)

# left_indices = [[70, 170], [10, 210]]
left_profile_values = [
# ref_indices = [[70, 170], [10, 210]]
ref_profile_values = [
[0.0, 0.0],
[
0.0,
naive.distance(T[10:30], T[210:230]),
],
]

right_distance_values, right_indices = aamp_motifs(
cmp_distance_values, cmp_indices = aamp_motifs(
T,
mp[:, 0],
max_motifs=max_motifs,
Expand All @@ -124,7 +124,7 @@ def test_aamp_motifs_two_motifs():

# We ignore indices because of sorting ambiguities for equal distances.
# As long as the distances are correct, the indices will be too.
npt.assert_almost_equal(left_profile_values, right_distance_values, decimal=6)
npt.assert_allclose(cmp_distance_values, ref_profile_values, atol=1.5e-06)


def test_aamp_naive_match_exact():
Expand All @@ -135,8 +135,8 @@ def test_aamp_naive_match_exact():
excl_zone = int(np.ceil(m / 4))

for p in [1.0, 2.0, 3.0]:
left = [[0, 0], [0, 5]]
right = list(
ref = [[0, 0], [0, 5]]
cmp = list(
naive_aamp_match(
Q,
T,
Expand All @@ -147,9 +147,13 @@ def test_aamp_naive_match_exact():
)
# To avoid sorting errors we first sort based on distance and then based on
# indices
right.sort(key=lambda x: (x[1], x[0]))
cmp.sort(key=lambda x: (x[1], x[0]))

npt.assert_almost_equal(left, right)
npt.assert_allclose(
np.array(cmp).astype(np.float64),
np.array(ref).astype(np.float64),
atol=1.5e-07,
)


def test_aamp_naive_match_exclusion_zone():
Expand All @@ -166,11 +170,11 @@ def test_aamp_naive_match_exclusion_zone():
excl_zone = m

for p in [1.0, 2.0, 3.0]:
left = [
ref = [
[0, 3],
[naive.distance(Q, T[7 : 7 + m], p=p), 7],
]
right = list(
cmp = list(
naive_aamp_match(
Q,
T,
Expand All @@ -181,9 +185,13 @@ def test_aamp_naive_match_exclusion_zone():
)
# To avoid sorting errors we first sort based on distance and then based on
# indices
right.sort(key=lambda x: (x[0], x[1]))
cmp.sort(key=lambda x: (x[0], x[1]))

npt.assert_almost_equal(left, right)
npt.assert_allclose(
np.array(cmp).astype(np.float64),
np.array(ref).astype(np.float64),
atol=1.5e-07,
)


@pytest.mark.parametrize("Q, T", test_data)
Expand All @@ -193,23 +201,25 @@ def test_aamp_match(Q, T):
max_distance = 0.3

for p in [1.0, 2.0, 3.0]:
left = naive_aamp_match(
ref = naive_aamp_match(
Q,
T,
p=p,
excl_zone=excl_zone,
max_distance=max_distance,
)

right = aamp_match(
cmp = aamp_match(
Q,
T,
p=p,
max_matches=None,
max_distance=max_distance,
)

npt.assert_almost_equal(left, right)
npt.assert_allclose(
cmp.astype(np.float64), ref.astype(np.float64), atol=1.5e-07
)


@pytest.mark.parametrize("Q, T", test_data)
Expand All @@ -220,15 +230,15 @@ def test_aamp_match_T_subseq_isfinite(Q, T):
T, T_subseq_isfinite = core.preprocess_non_normalized(T, len(Q))

for p in [1.0, 2.0, 3.0]:
left = naive_aamp_match(
ref = naive_aamp_match(
Q,
T,
p=p,
excl_zone=excl_zone,
max_distance=max_distance,
)

right = aamp_match(
cmp = aamp_match(
Q,
T,
T_subseq_isfinite,
Expand All @@ -237,7 +247,9 @@ def test_aamp_match_T_subseq_isfinite(Q, T):
max_distance=max_distance,
)

npt.assert_almost_equal(left, right)
npt.assert_allclose(
cmp.astype(np.float64), ref.astype(np.float64), atol=1.5e-07
)


def test_aamp_match_query_idx():
Expand All @@ -248,12 +260,12 @@ def test_aamp_match_query_idx():

# `mass_absolute` zeroes the self-match distance when told where `Q` lives.
D = core.mass_absolute(Q, T, query_idx=query_idx)
npt.assert_almost_equal(D[query_idx], 0.0)
npt.assert_allclose(D[query_idx], 0.0, atol=1.5e-07)

# A `Q` that is not the subsequence at `query_idx` must still return the
# self-match first, and must warn, exactly as `stumpy.match` does.
with pytest.warns(UserWarning):
out = aamp_match(Q + 0.5, T, query_idx=query_idx, max_distance=1.0)

assert out[0, 1] == query_idx
npt.assert_almost_equal(out[0, 0], 0.0)
npt.assert_allclose(out[0, 0], 0.0, atol=1.5e-07)
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