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Migrate tests from npt.assert_almost_equal to npt.assert_allclose #1178

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20 changes: 15 additions & 5 deletions tests/test_aamp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -132,13 +132,17 @@ def test_aamp_identical_subsequence_self_join():
naive.replace_inf(ref_mp)
naive.replace_inf(comp_mp)
npt.assert_almost_equal(

@seanlaw seanlaw Aug 9, 2026

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Why is npt.assert_almost_equal still being used here instead of npt.assert_allclose?

ref_mp[:, 0], comp_mp[:, 0], decimal=config.STUMPY_TEST_PRECISION
ref_mp[:, 0],
comp_mp[:, 0],
decimal=config.STUMPY_TEST_PRECISION,
) # ignore indices

comp_mp = aamp(pd.Series(T_A), m, ignore_trivial=True)
naive.replace_inf(comp_mp)
npt.assert_almost_equal(

@seanlaw seanlaw Aug 9, 2026

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Why is npt.assert_almost_equal still being used here instead of npt.assert_allclose?

ref_mp[:, 0], comp_mp[:, 0], decimal=config.STUMPY_TEST_PRECISION
ref_mp[:, 0],
comp_mp[:, 0],
decimal=config.STUMPY_TEST_PRECISION,
) # ignore indices


Expand All @@ -154,13 +158,17 @@ def test_aamp_identical_subsequence_A_B_join():
naive.replace_inf(ref_mp)
naive.replace_inf(comp_mp)
npt.assert_almost_equal(

@seanlaw seanlaw Aug 9, 2026

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Why is npt.assert_almost_equal still being used here instead of npt.assert_allclose?

ref_mp[:, 0], comp_mp[:, 0], config.STUMPY_TEST_PRECISION
ref_mp[:, 0],
comp_mp[:, 0],
decimal=config.STUMPY_TEST_PRECISION,
) # ignore indices

comp_mp = aamp(pd.Series(T_A), m, pd.Series(T_B), ignore_trivial=False)
naive.replace_inf(comp_mp)
npt.assert_almost_equal(

@seanlaw seanlaw Aug 9, 2026

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Why is npt.assert_almost_equal still being used here instead of npt.assert_allclose?

ref_mp[:, 0], comp_mp[:, 0], config.STUMPY_TEST_PRECISION
ref_mp[:, 0],
comp_mp[:, 0],
decimal=config.STUMPY_TEST_PRECISION,
) # ignore indices

# Swap inputs
Expand All @@ -169,7 +177,9 @@ def test_aamp_identical_subsequence_A_B_join():
naive.replace_inf(ref_mp)
naive.replace_inf(comp_mp)
npt.assert_almost_equal(

@seanlaw seanlaw Aug 9, 2026

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Why is npt.assert_almost_equal still being used here instead of npt.assert_allclose?

ref_mp[:, 0], comp_mp[:, 0], config.STUMPY_TEST_PRECISION
ref_mp[:, 0],
comp_mp[:, 0],
decimal=config.STUMPY_TEST_PRECISION,
) # ignore indices


Expand Down
12 changes: 8 additions & 4 deletions tests/test_aamp_motifs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,9 @@ def test_aamp_motifs_one_motif():
)

npt.assert_array_equal(left_indices, right_indices)
npt.assert_almost_equal(left_profile_values, right_distance_values, decimal=4)
npt.assert_allclose(
left_profile_values, right_distance_values, atol=1.5e-04, rtol=0
)


def test_aamp_motifs_two_motifs():
Expand Down Expand Up @@ -124,7 +126,9 @@ 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(
left_profile_values, right_distance_values, atol=1.5e-06, rtol=0
)


def test_aamp_naive_match_exact():
Expand Down Expand Up @@ -248,12 +252,12 @@ 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, rtol=0)

# 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, rtol=0)
48 changes: 30 additions & 18 deletions tests/test_aamp_ostinato.py
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Expand Up @@ -33,9 +33,9 @@ def test_random_ostinato(runs):
ref_radius, ref_Ts_idx, ref_subseq_idx = naive.aamp_ostinato(Ts, m)
comp_radius, comp_Ts_idx, comp_subseq_idx = aamp_ostinato(Ts, m)

npt.assert_almost_equal(ref_radius, comp_radius)
npt.assert_almost_equal(ref_Ts_idx, comp_Ts_idx)
npt.assert_almost_equal(ref_subseq_idx, comp_subseq_idx)
npt.assert_allclose(ref_radius, comp_radius, atol=1.5e-07, rtol=0)
npt.assert_allclose(ref_Ts_idx, comp_Ts_idx, atol=1.5e-07, rtol=0)
npt.assert_allclose(ref_subseq_idx, comp_subseq_idx, atol=1.5e-07, rtol=0)


@pytest.mark.parametrize("seed", [41, 88, 290, 292, 310, 328, 538, 556, 563, 570])
Expand All @@ -49,9 +49,9 @@ def test_deterministic_ostinato(seed):
ref_radius, ref_Ts_idx, ref_subseq_idx = naive.aamp_ostinato(Ts, m, p=p)
comp_radius, comp_Ts_idx, comp_subseq_idx = aamp_ostinato(Ts, m, p=p)

npt.assert_almost_equal(ref_radius, comp_radius)
npt.assert_almost_equal(ref_Ts_idx, comp_Ts_idx)
npt.assert_almost_equal(ref_subseq_idx, comp_subseq_idx)
npt.assert_allclose(ref_radius, comp_radius, atol=1.5e-07, rtol=0)
npt.assert_allclose(ref_Ts_idx, comp_Ts_idx, atol=1.5e-07, rtol=0)
npt.assert_allclose(ref_subseq_idx, comp_subseq_idx, atol=1.5e-07, rtol=0)


@pytest.mark.parametrize("runs", range(25))
Expand All @@ -63,9 +63,9 @@ def test_random_ostinatoed(runs, dask_cluster):
ref_radius, ref_Ts_idx, ref_subseq_idx = naive.aamp_ostinato(Ts, m)
comp_radius, comp_Ts_idx, comp_subseq_idx = aamp_ostinatoed(dask_client, Ts, m)

npt.assert_almost_equal(ref_radius, comp_radius)
npt.assert_almost_equal(ref_Ts_idx, comp_Ts_idx)
npt.assert_almost_equal(ref_subseq_idx, comp_subseq_idx)
npt.assert_allclose(ref_radius, comp_radius, atol=1.5e-07, rtol=0)
npt.assert_allclose(ref_Ts_idx, comp_Ts_idx, atol=1.5e-07, rtol=0)
npt.assert_allclose(ref_subseq_idx, comp_subseq_idx, atol=1.5e-07, rtol=0)


@pytest.mark.parametrize("seed", [41, 88, 290, 292, 310, 328, 538, 556, 563, 570])
Expand All @@ -82,9 +82,11 @@ def test_deterministic_ostinatoed(seed, dask_cluster):
dask_client, Ts, m, p=p
)

npt.assert_almost_equal(ref_radius, comp_radius)
npt.assert_almost_equal(ref_Ts_idx, comp_Ts_idx)
npt.assert_almost_equal(ref_subseq_idx, comp_subseq_idx)
npt.assert_allclose(ref_radius, comp_radius, atol=1.5e-07, rtol=0)
npt.assert_allclose(ref_Ts_idx, comp_Ts_idx, atol=1.5e-07, rtol=0)
npt.assert_allclose(
ref_subseq_idx, comp_subseq_idx, atol=1.5e-07, rtol=0
)


def test_input_not_overwritten_ostinato():
Expand All @@ -102,7 +104,9 @@ def test_input_not_overwritten_ostinato():
for i in range(len(Ts)):
T_ref = Ts[i]
T_comp = Ts_input[i]
npt.assert_almost_equal(T_ref[np.isfinite(T_ref)], T_comp[np.isfinite(T_comp)])
npt.assert_allclose(
T_ref[np.isfinite(T_ref)], T_comp[np.isfinite(T_comp)], atol=1.5e-07, rtol=0
)


def test_extract_several_consensus_ostinato():
Expand Down Expand Up @@ -135,8 +139,11 @@ def test_extract_several_consensus_ostinato():
Ts_comp[i][idx : idx + m] = np.nan
Ts_ref[i][idx : idx + m] = np.nan

npt.assert_almost_equal(
Ts_ref[i][np.isfinite(Ts_ref[i])], Ts_comp[i][np.isfinite(Ts_comp[i])]
npt.assert_allclose(
Ts_ref[i][np.isfinite(Ts_ref[i])],
Ts_comp[i][np.isfinite(Ts_comp[i])],
atol=1.5e-07,
rtol=0,
)


Expand All @@ -156,8 +163,11 @@ def test_input_not_overwritten_ostinatoed(dask_cluster):
for i in range(len(Ts)):
T_ref = Ts[i]
T_comp = Ts_input[i]
npt.assert_almost_equal(
T_ref[np.isfinite(T_ref)], T_comp[np.isfinite(T_comp)]
npt.assert_allclose(
T_ref[np.isfinite(T_ref)],
T_comp[np.isfinite(T_comp)],
atol=1.5e-07,
rtol=0,
)


Expand Down Expand Up @@ -195,7 +205,9 @@ def test_extract_several_consensus_ostinatoed(dask_cluster):
Ts_comp[i][idx : idx + m] = np.nan
Ts_ref[i][idx : idx + m] = np.nan

npt.assert_almost_equal(
npt.assert_allclose(
Ts_ref[i][np.isfinite(Ts_ref[i])],
Ts_comp[i][np.isfinite(Ts_comp[i])],
atol=1.5e-07,
rtol=0,
)
16 changes: 8 additions & 8 deletions tests/test_aamp_stimp.py
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Expand Up @@ -68,7 +68,7 @@ def test_aamp_stimp_1_percent(T):
naive.replace_inf(ref_PAN)
naive.replace_inf(cmp_PAN)

npt.assert_almost_equal(ref_PAN, cmp_PAN)
npt.assert_allclose(ref_PAN, cmp_PAN, atol=1.5e-07, rtol=0)

# Compare transformed pan
cmp_pan = pan.PAN_
Expand All @@ -85,7 +85,7 @@ def test_aamp_stimp_1_percent(T):
naive.replace_inf(ref_pan)
naive.replace_inf(cmp_pan)

npt.assert_almost_equal(ref_pan, cmp_pan)
npt.assert_allclose(ref_pan, cmp_pan, atol=1.5e-07, rtol=0)


@pytest.mark.parametrize("T", T)
Expand Down Expand Up @@ -126,7 +126,7 @@ def test_aamp_stimp_max_m(T):
naive.replace_inf(ref_PAN)
naive.replace_inf(cmp_PAN)

npt.assert_almost_equal(ref_PAN, cmp_PAN)
npt.assert_allclose(ref_PAN, cmp_PAN, atol=1.5e-07, rtol=0)

# Compare transformed pan
cmp_pan = pan.PAN_
Expand All @@ -143,7 +143,7 @@ def test_aamp_stimp_max_m(T):
naive.replace_inf(ref_pan)
naive.replace_inf(cmp_pan)

npt.assert_almost_equal(ref_pan, cmp_pan)
npt.assert_allclose(ref_pan, cmp_pan, atol=1.5e-07, rtol=0)


@pytest.mark.parametrize("T", T)
Expand Down Expand Up @@ -178,7 +178,7 @@ def test_aamp_stimp_100_percent(T):
naive.replace_inf(ref_PAN)
naive.replace_inf(cmp_PAN)

npt.assert_almost_equal(ref_PAN, cmp_PAN)
npt.assert_allclose(ref_PAN, cmp_PAN, atol=1.5e-07, rtol=0)

# Compare transformed pan
cmp_pan = pan.PAN_
Expand All @@ -195,7 +195,7 @@ def test_aamp_stimp_100_percent(T):
naive.replace_inf(ref_pan)
naive.replace_inf(cmp_pan)

npt.assert_almost_equal(ref_pan, cmp_pan)
npt.assert_allclose(ref_pan, cmp_pan, atol=1.5e-07, rtol=0)


@pytest.mark.parametrize("T", T)
Expand Down Expand Up @@ -264,7 +264,7 @@ def test_aamp_stimped(T, dask_cluster):
naive.replace_inf(ref_PAN)
naive.replace_inf(cmp_PAN)

npt.assert_almost_equal(ref_PAN, cmp_PAN)
npt.assert_allclose(ref_PAN, cmp_PAN, atol=1.5e-07, rtol=0)

# Compare transformed pan
cmp_pan = pan.PAN_
Expand All @@ -281,4 +281,4 @@ def test_aamp_stimped(T, dask_cluster):
naive.replace_inf(ref_pan)
naive.replace_inf(cmp_pan)

npt.assert_almost_equal(ref_pan, cmp_pan)
npt.assert_allclose(ref_pan, cmp_pan, atol=1.5e-07, rtol=0)
14 changes: 7 additions & 7 deletions tests/test_aampdist.py
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Expand Up @@ -46,7 +46,7 @@ def test_aampdist_vect(T_A, T_B):
ref_aampdist_vect = naive.aampdist_vect(T_A, T_B, m, p=p)
comp_aampdist_vect = _aampdist_vect(T_A, T_B, m, p=p)

npt.assert_almost_equal(ref_aampdist_vect, comp_aampdist_vect)
npt.assert_allclose(ref_aampdist_vect, comp_aampdist_vect, atol=1.5e-07, rtol=0)


@pytest.mark.parametrize("T_A, T_B", test_data)
Expand All @@ -56,7 +56,7 @@ def test_aampdist_vect_percentage(T_A, T_B, percentage):
ref_aampdist_vect = naive.aampdist_vect(T_A, T_B, m, percentage=percentage)
comp_aampdist_vect = _aampdist_vect(T_A, T_B, m, percentage=percentage)

npt.assert_almost_equal(ref_aampdist_vect, comp_aampdist_vect)
npt.assert_allclose(ref_aampdist_vect, comp_aampdist_vect, atol=1.5e-07, rtol=0)


@pytest.mark.parametrize("T_A, T_B", test_data)
Expand All @@ -66,7 +66,7 @@ def test_aampdist_vect_k(T_A, T_B, k):
ref_aampdist_vect = naive.aampdist_vect(T_A, T_B, m, k=k)
comp_aampdist_vect = _aampdist_vect(T_A, T_B, m, k=k)

npt.assert_almost_equal(ref_aampdist_vect, comp_aampdist_vect)
npt.assert_allclose(ref_aampdist_vect, comp_aampdist_vect, atol=1.5e-07, rtol=0)


@pytest.mark.parametrize("T_A, T_B", test_data)
Expand All @@ -76,7 +76,7 @@ def test_aampdist(T_A, T_B):
ref_mpdist = naive.aampdist(T_A, T_B, m, p=p)
comp_mpdist = aampdist(T_A, T_B, m, p=p)

npt.assert_almost_equal(ref_mpdist, comp_mpdist)
npt.assert_allclose(ref_mpdist, comp_mpdist, atol=1.5e-07, rtol=0)


@pytest.mark.parametrize("T_A, T_B", test_data)
Expand All @@ -86,7 +86,7 @@ def test_aampdist_percentage(T_A, T_B, percentage):
ref_mpdist = naive.aampdist(T_A, T_B, m, percentage=percentage)
comp_mpdist = aampdist(T_A, T_B, m, percentage=percentage)

npt.assert_almost_equal(ref_mpdist, comp_mpdist)
npt.assert_allclose(ref_mpdist, comp_mpdist, atol=1.5e-07, rtol=0)


@pytest.mark.parametrize("T_A, T_B", test_data)
Expand All @@ -96,7 +96,7 @@ def test_aampdist_k(T_A, T_B, k):
ref_mpdist = naive.aampdist(T_A, T_B, m, k=k)
comp_mpdist = aampdist(T_A, T_B, m, k=k)

npt.assert_almost_equal(ref_mpdist, comp_mpdist)
npt.assert_allclose(ref_mpdist, comp_mpdist, atol=1.5e-07, rtol=0)


@pytest.mark.filterwarnings("ignore:numpy.dtype size changed")
Expand All @@ -111,4 +111,4 @@ def test_aampdisted(T_A, T_B, dask_cluster):
ref_mpdist = naive.aampdist(T_A, T_B, m, p=p)
comp_mpdist = aampdisted(dask_client, T_A, T_B, m, p=p)

npt.assert_almost_equal(ref_mpdist, comp_mpdist)
npt.assert_allclose(ref_mpdist, comp_mpdist, atol=1.5e-07, rtol=0)
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