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Migrate tests/test_maamp.py to npt.assert_allclose #1198

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Merged
seanlaw merged 1 commit into from
Aug 25, 2026
Merged

Migrate tests/test_maamp.py to npt.assert_allclose #1198

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122 changes: 63 additions & 59 deletions tests/test_maamp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,11 +37,11 @@ def test_multi_mass_absolute_seeded():
ref = naive.multi_mass_absolute(Q, T, m)

T, T_subseq_isfinite = core.preprocess_non_normalized(T, m)
comp = _multi_mass_absolute(
cmp = _multi_mass_absolute(
Q, T, m, T_subseq_isfinite[:, trivial_idx], T_subseq_isfinite
)

npt.assert_almost_equal(ref, comp, decimal=config.STUMPY_TEST_PRECISION)
npt.assert_allclose(cmp, ref, atol=1.5 * 10**-config.STUMPY_TEST_PRECISION)


@pytest.mark.parametrize("T, m", test_data)
Expand All @@ -54,11 +54,11 @@ def test_multi_mass_absolute(T, m):
ref = naive.multi_mass_absolute(Q, T, m, p=p)

_T, T_subseq_isfinite = core.preprocess_non_normalized(T, m)
comp = _multi_mass_absolute(
cmp = _multi_mass_absolute(
Q, _T, m, T_subseq_isfinite[:, trivial_idx], T_subseq_isfinite, p=p
)

npt.assert_almost_equal(ref, comp, decimal=config.STUMPY_TEST_PRECISION)
npt.assert_allclose(cmp, ref, atol=1.5 * 10**-config.STUMPY_TEST_PRECISION)


@pytest.mark.parametrize("T, m", test_data)
Expand All @@ -68,9 +68,9 @@ def test_maamp_multi_distance_profile(T, m):
for query_idx in range(_T.shape[0] - m + 1):
ref_D = naive.maamp_multi_distance_profile(query_idx, _T, m, p=p)

comp_D = maamp_multi_distance_profile(query_idx, _T, m, p=p)
cmp_D = maamp_multi_distance_profile(query_idx, _T, m, p=p)

npt.assert_almost_equal(ref_D, comp_D)
npt.assert_allclose(cmp_D, ref_D, atol=1.5e-07)


@pytest.mark.parametrize("T, m", test_data)
Expand All @@ -84,12 +84,12 @@ def test_get_first_maamp_profile(T, m):
ref_I = ref_I[:, start]

_T, T_subseq_isfinite = core.preprocess_non_normalized(T, m)
comp_P, comp_I = _get_first_maamp_profile(
cmp_P, cmp_I = _get_first_maamp_profile(
start, _T, _T, m, excl_zone, T_subseq_isfinite, p=p
)

npt.assert_almost_equal(ref_P, comp_P)
npt.assert_equal(ref_I, comp_I)
npt.assert_allclose(cmp_P, ref_P, atol=1.5e-07)
npt.assert_equal(ref_I, cmp_I)


@pytest.mark.parametrize("T, m", test_data)
Expand All @@ -100,8 +100,8 @@ def test_maamp_subspace(T, m):
for p in [1.0, 2.0, 3.0]:
for k in range(T.shape[0]):
ref_S = naive.maamp_subspace(T, m, motif_idx, nn_idx, k, p=p)
comp_S = maamp_subspace(T, m, motif_idx, nn_idx, k, p=p)
npt.assert_almost_equal(ref_S, comp_S)
cmp_S = maamp_subspace(T, m, motif_idx, nn_idx, k, p=p)
npt.assert_allclose(cmp_S, ref_S, atol=1.5e-07)


@pytest.mark.parametrize("T, m", test_data)
Expand All @@ -114,8 +114,8 @@ def test_maamp_subspace_include(T, m):

for k in range(T.shape[0]):
ref_S = naive.maamp_subspace(T, m, motif_idx, nn_idx, k, include)
comp_S = maamp_subspace(T, m, motif_idx, nn_idx, k, include)
npt.assert_almost_equal(ref_S, comp_S)
cmp_S = maamp_subspace(T, m, motif_idx, nn_idx, k, include)
npt.assert_allclose(cmp_S, ref_S, atol=1.5e-07)


@pytest.mark.parametrize("T, m", test_data)
Expand All @@ -125,8 +125,8 @@ def test_maamp_subspace_discords(T, m):

for k in range(T.shape[0]):
ref_S = naive.maamp_subspace(T, m, discord_idx, nn_idx, k, discords=True)
comp_S = maamp_subspace(T, m, discord_idx, nn_idx, k, discords=True)
npt.assert_almost_equal(ref_S, comp_S)
cmp_S = maamp_subspace(T, m, discord_idx, nn_idx, k, discords=True)
npt.assert_allclose(cmp_S, ref_S, atol=1.5e-07)


@pytest.mark.parametrize("T, m", test_data)
Expand All @@ -141,10 +141,10 @@ def test_maamp_subspace_include_discords(T, m):
ref_S = naive.maamp_subspace(
T, m, discord_idx, nn_idx, k, include, discords=True
)
comp_S = maamp_subspace(
cmp_S = maamp_subspace(
T, m, discord_idx, nn_idx, k, include, discords=True
)
npt.assert_almost_equal(ref_S, comp_S)
npt.assert_allclose(cmp_S, ref_S, atol=1.5e-07)


@pytest.mark.parametrize("T, m", test_data)
Expand All @@ -154,11 +154,11 @@ def test_maamp_mdl(T, m):

for p in [1.0, 2.0, 3.0]:
ref_MDL, ref_S = naive.maamp_mdl(T, m, subseq_idx, nn_idx, p=p)
comp_MDL, comp_S = maamp_mdl(T, m, subseq_idx, nn_idx, p=p)
npt.assert_almost_equal(ref_MDL, comp_MDL)
cmp_MDL, cmp_S = maamp_mdl(T, m, subseq_idx, nn_idx, p=p)
npt.assert_allclose(cmp_MDL, ref_MDL, atol=1.5e-07)

for ref, cmp in zip(ref_S, comp_S):
npt.assert_almost_equal(ref, cmp)
for ref, cmp in zip(ref_S, cmp_S):
npt.assert_allclose(cmp, ref, atol=1.5e-07)


def test_naive_maamp():
Expand All @@ -171,10 +171,14 @@ def test_naive_maamp():
ref_P = ref_mp[np.newaxis, :, 0]
ref_I = ref_mp[np.newaxis, :, 1]

comp_P, comp_I = naive.maamp(T, m, zone)
cmp_P, cmp_I = naive.maamp(T, m, zone)

npt.assert_almost_equal(ref_P, comp_P)
npt.assert_almost_equal(ref_I, comp_I)
npt.assert_allclose(
cmp_P.astype(np.float64), ref_P.astype(np.float64), atol=1.5e-07
)
npt.assert_allclose(
cmp_I.astype(np.float64), ref_I.astype(np.float64), atol=1.5e-07
)


def test_maamp_int_input():
Expand All @@ -188,10 +192,10 @@ def test_maamp(T, m):

for p in [1.0, 2.0, 3.0]:
ref_P, ref_I = naive.maamp(T, m, excl_zone, p=p)
comp_P, comp_I = maamp(T, m, p=p)
cmp_P, cmp_I = maamp(T, m, p=p)

npt.assert_almost_equal(ref_P, comp_P)
npt.assert_almost_equal(ref_I, comp_I)
npt.assert_allclose(cmp_P, ref_P, atol=1.5e-07)
npt.assert_allclose(cmp_I, ref_I, atol=1.5e-07)


@pytest.mark.parametrize("T, m", test_data)
Expand All @@ -202,21 +206,21 @@ def test_maamp_include(T, m):
excl_zone = int(np.ceil(m / 4))

ref_P, ref_I = naive.maamp(T, m, excl_zone, include)
comp_P, comp_I = maamp(T, m, include)
cmp_P, cmp_I = maamp(T, m, include)

npt.assert_almost_equal(ref_P, comp_P)
npt.assert_almost_equal(ref_I, comp_I)
npt.assert_allclose(cmp_P, ref_P, atol=1.5e-07)
npt.assert_allclose(cmp_I, ref_I, atol=1.5e-07)


@pytest.mark.parametrize("T, m", test_data)
def test_maamp_discords(T, m):
excl_zone = int(np.ceil(m / 4))

ref_P, ref_I = naive.maamp(T, m, excl_zone, discords=True)
comp_P, comp_I = maamp(T, m, discords=True)
cmp_P, cmp_I = maamp(T, m, discords=True)

npt.assert_almost_equal(ref_P, comp_P)
npt.assert_almost_equal(ref_I, comp_I)
npt.assert_allclose(cmp_P, ref_P, atol=1.5e-07)
npt.assert_allclose(cmp_I, ref_I, atol=1.5e-07)


@pytest.mark.parametrize("T, m", test_data)
Expand All @@ -228,27 +232,27 @@ def test_maamp_include_discords(T, m):
excl_zone = int(np.ceil(m / 4))

ref_P, ref_I = naive.maamp(T, m, excl_zone, include, discords=True)
comp_P, comp_I = maamp(T, m, include, discords=True)
cmp_P, cmp_I = maamp(T, m, include, discords=True)

npt.assert_almost_equal(ref_P, comp_P)
npt.assert_almost_equal(ref_I, comp_I)
npt.assert_allclose(cmp_P, ref_P, atol=1.5e-07)
npt.assert_allclose(cmp_I, ref_I, atol=1.5e-07)


@pytest.mark.parametrize("T, m", test_data)
def test_maamp_wrapper(T, m):
excl_zone = int(np.ceil(m / 4))

ref_P, ref_I = naive.maamp(T, m, excl_zone)
comp_P, comp_I = maamp(T, m)
cmp_P, cmp_I = maamp(T, m)

npt.assert_almost_equal(ref_P, comp_P)
npt.assert_almost_equal(ref_I, comp_I)
npt.assert_allclose(cmp_P, ref_P, atol=1.5e-07)
npt.assert_allclose(cmp_I, ref_I, atol=1.5e-07)

df = pd.DataFrame(T.T)
comp_P, comp_I = maamp(df, m)
cmp_P, cmp_I = maamp(df, m)

npt.assert_almost_equal(ref_P, comp_P)
npt.assert_almost_equal(ref_I, comp_I)
npt.assert_allclose(cmp_P, ref_P, atol=1.5e-07)
npt.assert_allclose(cmp_I, ref_I, atol=1.5e-07)


@pytest.mark.parametrize("T, m", test_data)
Expand All @@ -260,16 +264,16 @@ def test_maamp_wrapper_include(T, m):
excl_zone = int(np.ceil(m / 4))

ref_P, ref_I = naive.maamp(T, m, excl_zone, include)
comp_P, comp_I = maamp(T, m, include)
cmp_P, cmp_I = maamp(T, m, include)

npt.assert_almost_equal(ref_P, comp_P)
npt.assert_almost_equal(ref_I, comp_I)
npt.assert_allclose(cmp_P, ref_P, atol=1.5e-07)
npt.assert_allclose(cmp_I, ref_I, atol=1.5e-07)

df = pd.DataFrame(T.T)
comp_P, comp_I = maamp(df, m, include)
cmp_P, cmp_I = maamp(df, m, include)

npt.assert_almost_equal(ref_P, comp_P)
npt.assert_almost_equal(ref_I, comp_I)
npt.assert_allclose(cmp_P, ref_P, atol=1.5e-07)
npt.assert_allclose(cmp_I, ref_I, atol=1.5e-07)


def test_constant_subsequence_self_join():
Expand All @@ -280,9 +284,9 @@ def test_constant_subsequence_self_join():
excl_zone = int(np.ceil(m / 4))

ref_P, ref_I = naive.maamp(T, m, excl_zone)
comp_P, comp_I = maamp(T, m)
cmp_P, cmp_I = maamp(T, m)

npt.assert_almost_equal(ref_P, comp_P) # ignore indices
npt.assert_allclose(cmp_P, ref_P, atol=1.5e-07) # ignore indices


def test_identical_subsequence_self_join():
Expand All @@ -296,10 +300,10 @@ def test_identical_subsequence_self_join():
excl_zone = int(np.ceil(m / 4))

ref_P, ref_I = naive.maamp(T, m, excl_zone)
comp_P, comp_I = maamp(T, m)
cmp_P, cmp_I = maamp(T, m)

npt.assert_almost_equal(
ref_P, comp_P, decimal=config.STUMPY_TEST_PRECISION
npt.assert_allclose(
cmp_P, ref_P, atol=1.5 * 10**-config.STUMPY_TEST_PRECISION
) # ignore indices


Expand All @@ -318,10 +322,10 @@ def test_maamp_nan_inf_self_join_first_dimension(
T_sub[0, substitution_location] = substitute

ref_P, ref_I = naive.maamp(T_sub, m, excl_zone)
comp_P, comp_I = maamp(T_sub, m)
cmp_P, cmp_I = maamp(T_sub, m)

npt.assert_almost_equal(ref_P, comp_P)
npt.assert_almost_equal(ref_I, comp_I)
npt.assert_allclose(cmp_P, ref_P, atol=1.5e-07)
npt.assert_allclose(cmp_I, ref_I, atol=1.5e-07)


@pytest.mark.parametrize("T, m", test_data)
Expand All @@ -337,7 +341,7 @@ def test_maamp_nan_self_join_all_dimensions(T, m, substitute, substitution_locat
T_sub[:, substitution_location] = substitute

ref_P, ref_I = naive.maamp(T_sub, m, excl_zone)
comp_P, comp_I = maamp(T_sub, m)
cmp_P, cmp_I = maamp(T_sub, m)

npt.assert_almost_equal(ref_P, comp_P)
npt.assert_almost_equal(ref_I, comp_I)
npt.assert_allclose(cmp_P, ref_P, atol=1.5e-07)
npt.assert_allclose(cmp_I, ref_I, atol=1.5e-07)
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