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MAINT Handle deprecation of sokalmichener metric #30004

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Merged
merged 4 commits into from
Oct 8, 2024
Merged

MAINT Handle deprecation of sokalmichener metric #30004

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cdfb17c
MAINT handle the deprecation of sokalmichener in scipy cdist/pdist
ogrisel Oct 3, 2024
bbd87e6
Trigger [scipy-dev] CI
ogrisel Oct 3, 2024
c261023
Update sklearn/neighbors/tests/test_neighbors.py
glemaitre Oct 8, 2024
748bc68
Update sklearn/neighbors/tests/test_neighbors.py
glemaitre Oct 8, 2024
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11 changes: 10 additions & 1 deletion sklearn/metrics/_dist_metrics.pyx.tp
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Original file line number Diff line number Diff line change
Expand Up @@ -42,15 +42,24 @@ BOOL_METRICS = [
"dice",
"rogerstanimoto",
"russellrao",
"sokalmichener",
"sokalsneath",
]
DEPRECATED_METRICS = []
if sp_base_version < parse_version("1.17"):
# Deprecated in SciPy 1.15 and removed in SciPy 1.17
BOOL_METRICS += ["sokalmichener"]
if sp_base_version >= parse_version("1.15"):
DEPRECATED_METRICS.append("sokalmichener")
if sp_base_version < parse_version("1.11"):
# Deprecated in SciPy 1.9 and removed in SciPy 1.11
BOOL_METRICS += ["kulsinski"]
if sp_base_version >= parse_version("1.9"):
DEPRECATED_METRICS.append("kulsinski")
if sp_base_version < parse_version("1.9"):
# Deprecated in SciPy 1.0 and removed in SciPy 1.9
BOOL_METRICS += ["matching"]
if sp_base_version >= parse_version("1.0"):
DEPRECATED_METRICS.append("matching")

def get_valid_metric_ids(L):
"""Given an iterable of metric class names or class identifiers,
Expand Down
8 changes: 6 additions & 2 deletions sklearn/metrics/pairwise.py
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Original file line number Diff line number Diff line change
Expand Up @@ -693,14 +693,16 @@ def _argmin_reduce(dist, start):
"rogerstanimoto",
"russellrao",
"seuclidean",
"sokalmichener",
"sokalsneath",
"sqeuclidean",
"yule",
"wminkowski",
"nan_euclidean",
"haversine",
]
if sp_base_version < parse_version("1.17"): # pragma: no cover
# Deprecated in SciPy 1.15 and removed in SciPy 1.17
_VALID_METRICS += ["sokalmichener"]
if sp_base_version < parse_version("1.11"): # pragma: no cover
# Deprecated in SciPy 1.9 and removed in SciPy 1.11
_VALID_METRICS += ["kulsinski"]
Expand Down Expand Up @@ -2482,10 +2484,12 @@ def pairwise_distances(
"jaccard",
"rogerstanimoto",
"russellrao",
"sokalmichener",
"sokalsneath",
"yule",
]
if sp_base_version < parse_version("1.17"):
# Deprecated in SciPy 1.15 and removed in SciPy 1.17
PAIRWISE_BOOLEAN_FUNCTIONS += ["sokalmichener"]
if sp_base_version < parse_version("1.11"):
# Deprecated in SciPy 1.9 and removed in SciPy 1.11
PAIRWISE_BOOLEAN_FUNCTIONS += ["kulsinski"]
Expand Down
28 changes: 25 additions & 3 deletions sklearn/metrics/tests/test_dist_metrics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,11 +9,16 @@
from sklearn.metrics import DistanceMetric
from sklearn.metrics._dist_metrics import (
BOOL_METRICS,
DEPRECATED_METRICS,
DistanceMetric32,
DistanceMetric64,
)
from sklearn.utils import check_random_state
from sklearn.utils._testing import assert_allclose, create_memmap_backed_data
from sklearn.utils._testing import (
assert_allclose,
create_memmap_backed_data,
ignore_warnings,
)
from sklearn.utils.fixes import CSR_CONTAINERS, parse_version, sp_version


Expand Down Expand Up @@ -112,7 +117,15 @@ def test_cdist(metric_param_grid, X, Y, csr_container):
)
@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
def test_cdist_bool_metric(metric, X_bool, Y_bool, csr_container):
D_scipy_cdist = cdist(X_bool, Y_bool, metric)
if metric in DEPRECATED_METRICS:
with ignore_warnings(category=DeprecationWarning):
# Some metrics can be deprecated depending on the scipy version.
# But if they are present, we still want to test wether
# scikit-learn gives the same result, whether or not they are
# deprecated.
D_scipy_cdist = cdist(X_bool, Y_bool, metric)
else:
D_scipy_cdist = cdist(X_bool, Y_bool, metric)

dm = DistanceMetric.get_metric(metric)
D_sklearn = dm.pairwise(X_bool, Y_bool)
Expand Down Expand Up @@ -219,7 +232,16 @@ def test_distance_metrics_dtype_consistency(metric_param_grid):
@pytest.mark.parametrize("X_bool", [X_bool, X_bool_mmap])
@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
def test_pdist_bool_metrics(metric, X_bool, csr_container):
D_scipy_pdist = cdist(X_bool, X_bool, metric)
if metric in DEPRECATED_METRICS:
with ignore_warnings(category=DeprecationWarning):
# Some metrics can be deprecated depending on the scipy version.
# But if they are present, we still want to test wether
# scikit-learn gives the same result, whether or not they are
# deprecated.
D_scipy_pdist = cdist(X_bool, X_bool, metric)
else:
D_scipy_pdist = cdist(X_bool, X_bool, metric)

dm = DistanceMetric.get_metric(metric)
D_sklearn = dm.pairwise(X_bool)
assert_allclose(D_sklearn, D_scipy_pdist)
Expand Down
3 changes: 3 additions & 0 deletions sklearn/metrics/tests/test_pairwise.py
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Expand Up @@ -212,6 +212,9 @@ def test_pairwise_distances_for_sparse_data(
pairwise_distances(X, Y_sparse, metric="minkowski")


# Some scipy metrics are deprecated (depending on the scipy version) but we
# still want to test them.
@ignore_warnings(category=DeprecationWarning)
@pytest.mark.parametrize("metric", PAIRWISE_BOOLEAN_FUNCTIONS)
def test_pairwise_boolean_distance(metric):
# test that we convert to boolean arrays for boolean distances
Expand Down
4 changes: 3 additions & 1 deletion sklearn/neighbors/_base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,11 +48,13 @@
"rogerstanimoto",
"russellrao",
"seuclidean",
"sokalmichener",
"sokalsneath",
"sqeuclidean",
"yule",
]
if sp_base_version < parse_version("1.17"):
# Deprecated in SciPy 1.15 and removed in SciPy 1.17
SCIPY_METRICS += ["sokalmichener"]
if sp_base_version < parse_version("1.11"):
# Deprecated in SciPy 1.9 and removed in SciPy 1.11
SCIPY_METRICS += ["kulsinski"]
Expand Down
8 changes: 8 additions & 0 deletions sklearn/neighbors/tests/test_neighbors.py
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Expand Up @@ -1721,6 +1721,10 @@ def test_neighbors_metrics(
assert_array_equal(ball_tree_idx, kd_tree_idx)


# TODO: Remove ignore_warnings when minimum supported SciPy version is 1.17
# Some scipy metrics are deprecated (depending on the scipy version) but we
# still want to test them.
@ignore_warnings(category=DeprecationWarning)
@pytest.mark.parametrize(
"metric", sorted(set(neighbors.VALID_METRICS["brute"]) - set(["precomputed"]))
)
Expand Down Expand Up @@ -2243,6 +2247,10 @@ def test_auto_algorithm(X, metric, metric_params, expected_algo):
assert model._fit_method == expected_algo


# TODO: Remove ignore_warnings when minimum supported SciPy version is 1.17
# Some scipy metrics are deprecated (depending on the scipy version) but we
# still want to test them.
@ignore_warnings(category=DeprecationWarning)
@pytest.mark.parametrize(
"metric", sorted(set(neighbors.VALID_METRICS["brute"]) - set(["precomputed"]))
)
Expand Down