Skip to content

Migrate tests/test_mmotifs.py to NumPy array comparisons #1212

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
karthiksenv wants to merge 2 commits into
base: main
Choose a base branch
from
Open

Migrate tests/test_mmotifs.py to NumPy array comparisons #1212

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
3501ed5
Migrate multidimensional motif test comparisons
karthiksenv Nov 5, 2026
9bbe330
Align mmotifs assertions with migration conventions
karthiksenv Nov 6, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
170 changes: 85 additions & 85 deletions tests/test_mmotifs.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -52,128 +52,128 @@

@pytest.mark.parametrize("T", test_data)
def test_mmotifs_with_default_parameters(T):
motif_distances_ref = np.array([[0.0000000e00, 1.1151008e-07]])
motif_indices_ref = np.array([[2, 9]])
motif_subspaces_ref = [np.array([1])]
motif_mdls_ref = [np.array([232.0, 250.57542476, 260.0, 271.3509059])]
ref_motif_distances = np.array([[0.0000000e00, 1.1151008e-07]])
ref_motif_indices = np.array([[2, 9]])
ref_motif_subspaces = [np.array([1])]
ref_motif_mdls = [np.array([232.0, 250.57542476, 260.0, 271.3509059])]

m = 4
excl_zone = int(np.ceil(m / config.STUMPY_EXCL_ZONE_DENOM))
P, I = naive.mstump(T, m, excl_zone)
(
motif_distances_cmp,
motif_indices_cmp,
motif_subspaces_cmp,
motif_mdls_cmp,
cmp_motif_distances,
cmp_motif_indices,
cmp_motif_subspaces,
cmp_motif_mdls,
) = mmotifs(T, P, I)

npt.assert_array_almost_equal(motif_distances_ref, motif_distances_cmp)
npt.assert_array_almost_equal(motif_indices_ref, motif_indices_cmp)
npt.assert_array_almost_equal(motif_subspaces_ref, motif_subspaces_cmp)
npt.assert_array_almost_equal(motif_mdls_ref, motif_mdls_cmp)
npt.assert_allclose(cmp_motif_distances, ref_motif_distances, atol=1.5e-07)
npt.assert_allclose(cmp_motif_indices, ref_motif_indices, atol=1.5e-07)
npt.assert_allclose(cmp_motif_subspaces, ref_motif_subspaces, atol=1.5e-07)
npt.assert_allclose(cmp_motif_mdls, ref_motif_mdls, atol=1.5e-07)


@pytest.mark.parametrize("T", test_data)
def test_mmotifs_max_matches_none(T):
motif_distances_ref = np.array([[0.0000000e00, 1.1151008e-07]])
motif_indices_ref = np.array([[2, 9]])
motif_subspaces_ref = [np.array([1])]
motif_mdls_ref = [np.array([232.0, 250.57542476, 260.0, 271.3509059])]
ref_motif_distances = np.array([[0.0000000e00, 1.1151008e-07]])
ref_motif_indices = np.array([[2, 9]])
ref_motif_subspaces = [np.array([1])]
ref_motif_mdls = [np.array([232.0, 250.57542476, 260.0, 271.3509059])]

m = 4
excl_zone = int(np.ceil(m / config.STUMPY_EXCL_ZONE_DENOM))
P, I = naive.mstump(T, m, excl_zone)
(
motif_distances_cmp,
motif_indices_cmp,
motif_subspaces_cmp,
motif_mdls_cmp,
cmp_motif_distances,
cmp_motif_indices,
cmp_motif_subspaces,
cmp_motif_mdls,
) = mmotifs(T, P, I, max_matches=None)

npt.assert_array_almost_equal(motif_distances_ref, motif_distances_cmp)
npt.assert_array_almost_equal(motif_indices_ref, motif_indices_cmp)
npt.assert_array_almost_equal(motif_subspaces_ref, motif_subspaces_cmp)
npt.assert_array_almost_equal(motif_mdls_ref, motif_mdls_cmp)
npt.assert_allclose(cmp_motif_distances, ref_motif_distances, atol=1.5e-07)
npt.assert_allclose(cmp_motif_indices, ref_motif_indices, atol=1.5e-07)
npt.assert_allclose(cmp_motif_subspaces, ref_motif_subspaces, atol=1.5e-07)
npt.assert_allclose(cmp_motif_mdls, ref_motif_mdls, atol=1.5e-07)


@pytest.mark.parametrize("T", test_data)
def test_mmotifs_more_motifs_when_cutoffs_3(T):
motif_distances_ref = np.array([[0.0000000e00, 1.1151008e-07]])
motif_indices_ref = np.array([[2, 9]])
motif_subspaces_ref = [np.array([1])]
motif_mdls_ref = [np.array([232.0, 250.57542476, 260.0, 271.3509059])]
ref_motif_distances = np.array([[0.0000000e00, 1.1151008e-07]])
ref_motif_indices = np.array([[2, 9]])
ref_motif_subspaces = [np.array([1])]
ref_motif_mdls = [np.array([232.0, 250.57542476, 260.0, 271.3509059])]

m = 4
excl_zone = int(np.ceil(m / config.STUMPY_EXCL_ZONE_DENOM))
P, I = naive.mstump(T, m, excl_zone)
(
motif_distances_cmp,
motif_indices_cmp,
motif_subspaces_cmp,
motif_mdls_cmp,
cmp_motif_distances,
cmp_motif_indices,
cmp_motif_subspaces,
cmp_motif_mdls,
) = mmotifs(T, P, I, cutoffs=3, max_motifs=10)

npt.assert_array_almost_equal(motif_distances_ref, motif_distances_cmp)
npt.assert_array_almost_equal(motif_indices_ref, motif_indices_cmp)
npt.assert_array_almost_equal(motif_subspaces_ref, motif_subspaces_cmp)
npt.assert_array_almost_equal(motif_mdls_ref, motif_mdls_cmp)
npt.assert_allclose(cmp_motif_distances, ref_motif_distances, atol=1.5e-07)
npt.assert_allclose(cmp_motif_indices, ref_motif_indices, atol=1.5e-07)
npt.assert_allclose(cmp_motif_subspaces, ref_motif_subspaces, atol=1.5e-07)
npt.assert_allclose(cmp_motif_mdls, ref_motif_mdls, atol=1.5e-07)


@pytest.mark.parametrize("T", test_data)
def test_mmotifs_more_motifs_cutoffs_is_list(T):
motif_distances_ref = np.array([[0.0000000e00, 1.1151008e-07]])
motif_indices_ref = np.array([[2, 9]])
motif_subspaces_ref = [np.array([1])]
motif_mdls_ref = [np.array([232.0, 250.57542476, 260.0, 271.3509059])]
ref_motif_distances = np.array([[0.0000000e00, 1.1151008e-07]])
ref_motif_indices = np.array([[2, 9]])
ref_motif_subspaces = [np.array([1])]
ref_motif_mdls = [np.array([232.0, 250.57542476, 260.0, 271.3509059])]

m = 4
cutoffs = [2, 3, 4, 5]
excl_zone = int(np.ceil(m / config.STUMPY_EXCL_ZONE_DENOM))
P, I = naive.mstump(T, m, excl_zone)
(
motif_distances_cmp,
motif_indices_cmp,
motif_subspaces_cmp,
motif_mdls_cmp,
cmp_motif_distances,
cmp_motif_indices,
cmp_motif_subspaces,
cmp_motif_mdls,
) = mmotifs(T, P, I, cutoffs=cutoffs, max_motifs=10)

npt.assert_array_almost_equal(motif_distances_ref, motif_distances_cmp)
npt.assert_array_almost_equal(motif_indices_ref, motif_indices_cmp)
npt.assert_array_almost_equal(motif_subspaces_ref, motif_subspaces_cmp)
npt.assert_array_almost_equal(motif_mdls_ref, motif_mdls_cmp)
npt.assert_allclose(cmp_motif_distances, ref_motif_distances, atol=1.5e-07)
npt.assert_allclose(cmp_motif_indices, ref_motif_indices, atol=1.5e-07)
npt.assert_allclose(cmp_motif_subspaces, ref_motif_subspaces, atol=1.5e-07)
npt.assert_allclose(cmp_motif_mdls, ref_motif_mdls, atol=1.5e-07)


@pytest.mark.parametrize("T", test_data)
def test_mmotifs_max_matches_2_k_1(T):
motif_distances_ref = np.array([[0.0, 0.20948156]])
motif_indices_ref = np.array([[2, 9]])
motif_subspaces_ref = [np.array([1, 3])]
motif_mdls_ref = [np.array([232.0, 250.57542476, 260.0, 271.3509059])]
ref_motif_distances = np.array([[0.0, 0.20948156]])
ref_motif_indices = np.array([[2, 9]])
ref_motif_subspaces = [np.array([1, 3])]
ref_motif_mdls = [np.array([232.0, 250.57542476, 260.0, 271.3509059])]

m = 4
excl_zone = int(np.ceil(m / config.STUMPY_EXCL_ZONE_DENOM))
P, I = naive.mstump(T, m, excl_zone)
(
motif_distances_cmp,
motif_indices_cmp,
motif_subspaces_cmp,
motif_mdls_cmp,
cmp_motif_distances,
cmp_motif_indices,
cmp_motif_subspaces,
cmp_motif_mdls,
) = mmotifs(T, P, I, max_distance=np.inf, max_matches=2, k=1)

npt.assert_array_almost_equal(motif_distances_ref, motif_distances_cmp)
npt.assert_array_almost_equal(motif_indices_ref, motif_indices_cmp)
npt.assert_array_almost_equal(motif_subspaces_ref, motif_subspaces_cmp)
npt.assert_array_almost_equal(motif_mdls_ref, motif_mdls_cmp)
npt.assert_allclose(cmp_motif_distances, ref_motif_distances, atol=1.5e-07)
npt.assert_allclose(cmp_motif_indices, ref_motif_indices, atol=1.5e-07)
npt.assert_allclose(cmp_motif_subspaces, ref_motif_subspaces, atol=1.5e-07)
npt.assert_allclose(cmp_motif_mdls, ref_motif_mdls, atol=1.5e-07)


@pytest.mark.parametrize("T", test_data)
def test_mmotifs_two_motif_pairs_max_motifs_2(T):
motif_distances_ref = np.array(
[[0.00000000e00, 1.11510080e-07], [1.68587394e-07, 2.58694429e-01]]
ref_motif_distances = np.array(
[[0.00000000e00, 1.11510080e-07], [0.00000000e00, 2.58694429e-01]]
)
motif_indices_ref = np.array([[2, 9], [6, 1]])
motif_subspaces_ref = [np.array([1]), np.array([2])]
motif_mdls_ref = [
ref_motif_indices = np.array([[2, 9], [6, 1]])
ref_motif_subspaces = [np.array([1]), np.array([2])]
ref_motif_mdls = [
np.array([232.0, 250.57542476, 260.0, 271.3509059]),
np.array([264.0, 280.0, 299.01955001, 310.51024953]),
]
Expand All @@ -182,26 +182,26 @@ def test_mmotifs_two_motif_pairs_max_motifs_2(T):
excl_zone = int(np.ceil(m / config.STUMPY_EXCL_ZONE_DENOM))
P, I = naive.mstump(T, m, excl_zone)
(
motif_distances_cmp,
motif_indices_cmp,
motif_subspaces_cmp,
motif_mdls_cmp,
cmp_motif_distances,
cmp_motif_indices,
cmp_motif_subspaces,
cmp_motif_mdls,
) = mmotifs(
T, P, I, cutoffs=np.inf, max_motifs=2, max_distance=np.inf, max_matches=2
)

npt.assert_array_almost_equal(motif_distances_ref, motif_distances_cmp)
npt.assert_array_almost_equal(motif_indices_ref, motif_indices_cmp)
npt.assert_array_almost_equal(motif_subspaces_ref, motif_subspaces_cmp)
npt.assert_array_almost_equal(motif_mdls_ref, motif_mdls_cmp)
npt.assert_allclose(cmp_motif_distances, ref_motif_distances, atol=1.5e-07)
npt.assert_allclose(cmp_motif_indices, ref_motif_indices, atol=1.5e-07)
npt.assert_allclose(cmp_motif_subspaces, ref_motif_subspaces, atol=1.5e-07)
npt.assert_allclose(cmp_motif_mdls, ref_motif_mdls, atol=1.5e-07)


@pytest.mark.parametrize("T", test_data)
def test_mmotifs_with_default_parameters_with_isconstant(T):
motif_distances_ref = np.array([[0.0000000e00, 1.1151008e-07]])
motif_indices_ref = np.array([[2, 9]])
motif_subspaces_ref = [np.array([1])]
motif_mdls_ref = [np.array([232.0, 250.57542476, 260.0, 271.3509059])]
ref_motif_distances = np.array([[0.0000000e00, 1.1151008e-07]])
ref_motif_indices = np.array([[2, 9]])
ref_motif_subspaces = [np.array([1])]
ref_motif_mdls = [np.array([232.0, 250.57542476, 260.0, 271.3509059])]

m = 4
excl_zone = int(np.ceil(m / config.STUMPY_EXCL_ZONE_DENOM))
Expand All @@ -218,13 +218,13 @@ def test_mmotifs_with_default_parameters_with_isconstant(T):

P, I = naive.mstump(T, m, excl_zone, T_subseq_isconstant=T_subseq_isconstant)
(
motif_distances_cmp,
motif_indices_cmp,
motif_subspaces_cmp,
motif_mdls_cmp,
cmp_motif_distances,
cmp_motif_indices,
cmp_motif_subspaces,
cmp_motif_mdls,
) = mmotifs(T, P, I, T_subseq_isconstant=T_subseq_isconstant)

npt.assert_array_almost_equal(motif_distances_ref, motif_distances_cmp)
npt.assert_array_almost_equal(motif_indices_ref, motif_indices_cmp)
npt.assert_array_almost_equal(motif_subspaces_ref, motif_subspaces_cmp)
npt.assert_array_almost_equal(motif_mdls_ref, motif_mdls_cmp)
npt.assert_allclose(cmp_motif_distances, ref_motif_distances, atol=1.5e-07)
npt.assert_allclose(cmp_motif_indices, ref_motif_indices, atol=1.5e-07)
npt.assert_allclose(cmp_motif_subspaces, ref_motif_subspaces, atol=1.5e-07)
npt.assert_allclose(cmp_motif_mdls, ref_motif_mdls, atol=1.5e-07)