FIX ‘sparse’ kwarg was not used by fowlkes_mallows_score (scikit-learn#28981)

Co-authored-by: Jérémie du Boisberranger <jeremie@probabl.ai>

Author: cynddl

doc/whats_new/upcoming_changes/sklearn.metrics/28981.api.rst

@@ -0,0 +1,3 @@
+- The `sparse` parameter of :func:`metrics.fowlkes_mallows_score` is deprecated and
+  will be removed in 1.9. It has no effect.
+  By :user:`Luc Rocher <cynddl>`.

sklearn/metrics/cluster/_supervised.py

@@ -15,7 +15,7 @@
 from scipy import sparse as sp
 
 from ...utils._array_api import _max_precision_float_dtype, get_namespace_and_device
-from ...utils._param_validation import Interval, StrOptions, validate_params
+from ...utils._param_validation import Hidden, Interval, StrOptions, validate_params
 from ...utils.multiclass import type_of_target
 from ...utils.validation import check_array, check_consistent_length
 from ._expected_mutual_info_fast import expected_mutual_information
@@ -1178,11 +1178,11 @@ def normalized_mutual_info_score(
     {
         "labels_true": ["array-like"],
         "labels_pred": ["array-like"],
-        "sparse": ["boolean"],
+        "sparse": ["boolean", Hidden(StrOptions({"deprecated"}))],
     },
     prefer_skip_nested_validation=True,
 )
-def fowlkes_mallows_score(labels_true, labels_pred, *, sparse=False):
+def fowlkes_mallows_score(labels_true, labels_pred, *, sparse="deprecated"):
     """Measure the similarity of two clusterings of a set of points.
 
     .. versionadded:: 0.18
@@ -1216,6 +1216,10 @@ def fowlkes_mallows_score(labels_true, labels_pred, *, sparse=False):
     sparse : bool, default=False
         Compute contingency matrix internally with sparse matrix.
 
+        .. deprecated:: 1.7
+            The ``sparse`` parameter is deprecated and will be removed in 1.9. It has
+            no effect.
+
     Returns
     -------
     score : float
@@ -1249,6 +1253,14 @@ def fowlkes_mallows_score(labels_true, labels_pred, *, sparse=False):
       >>> fowlkes_mallows_score([0, 0, 0, 0], [0, 1, 2, 3])
       0.0
     """
+    # TODO(1.9): remove the sparse parameter
+    if sparse != "deprecated":
+        warnings.warn(
+            "The 'sparse' parameter was deprecated in 1.7 and will be removed in 1.9. "
+            "It has no effect. Leave it to its default value to silence this warning.",
+            FutureWarning,
+        )
+
     labels_true, labels_pred = check_clusterings(labels_true, labels_pred)
     (n_samples,) = labels_true.shape
 

sklearn/metrics/cluster/tests/test_supervised.py

@@ -510,3 +510,13 @@ def test_normalized_mutual_info_score_bounded(average_method):
     # non constant, non perfect matching labels
     nmi = normalized_mutual_info_score(labels2, labels3, average_method=average_method)
     assert 0 <= nmi < 1
+
+
+# TODO(1.9): remove
+@pytest.mark.parametrize("sparse", [True, False])
+def test_fowlkes_mallows_sparse_deprecated(sparse):
+    """Check deprecation warning for 'sparse' parameter of fowlkes_mallows_score."""
+    with pytest.warns(
+        FutureWarning, match="The 'sparse' parameter was deprecated in 1.7"
+    ):
+        fowlkes_mallows_score([0, 1], [1, 1], sparse=sparse)