reconnect moved files to git repo

venv/lib/python3.11/site-packages/sklearn/metrics/cluster/tests/test_bicluster.py

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+"""Testing for bicluster metrics module"""
+
+import numpy as np
+
+from sklearn.metrics import consensus_score
+from sklearn.metrics.cluster._bicluster import _jaccard
+from sklearn.utils._testing import assert_almost_equal
+
+
+def test_jaccard():
+    a1 = np.array([True, True, False, False])
+    a2 = np.array([True, True, True, True])
+    a3 = np.array([False, True, True, False])
+    a4 = np.array([False, False, True, True])
+
+    assert _jaccard(a1, a1, a1, a1) == 1
+    assert _jaccard(a1, a1, a2, a2) == 0.25
+    assert _jaccard(a1, a1, a3, a3) == 1.0 / 7
+    assert _jaccard(a1, a1, a4, a4) == 0
+
+
+def test_consensus_score():
+    a = [[True, True, False, False], [False, False, True, True]]
+    b = a[::-1]
+
+    assert consensus_score((a, a), (a, a)) == 1
+    assert consensus_score((a, a), (b, b)) == 1
+    assert consensus_score((a, b), (a, b)) == 1
+    assert consensus_score((a, b), (b, a)) == 1
+
+    assert consensus_score((a, a), (b, a)) == 0
+    assert consensus_score((a, a), (a, b)) == 0
+    assert consensus_score((b, b), (a, b)) == 0
+    assert consensus_score((b, b), (b, a)) == 0
+
+
+def test_consensus_score_issue2445():
+    """Different number of biclusters in A and B"""
+    a_rows = np.array(
+        [
+            [True, True, False, False],
+            [False, False, True, True],
+            [False, False, False, True],
+        ]
+    )
+    a_cols = np.array(
+        [
+            [True, True, False, False],
+            [False, False, True, True],
+            [False, False, False, True],
+        ]
+    )
+    idx = [0, 2]
+    s = consensus_score((a_rows, a_cols), (a_rows[idx], a_cols[idx]))
+    # B contains 2 of the 3 biclusters in A, so score should be 2/3
+    assert_almost_equal(s, 2.0 / 3.0)

venv/lib/python3.11/site-packages/sklearn/metrics/cluster/tests/test_common.py

@@ -0,0 +1,219 @@
+from functools import partial
+from itertools import chain
+
+import numpy as np
+import pytest
+
+from sklearn.metrics.cluster import (
+    adjusted_mutual_info_score,
+    adjusted_rand_score,
+    calinski_harabasz_score,
+    completeness_score,
+    davies_bouldin_score,
+    fowlkes_mallows_score,
+    homogeneity_score,
+    mutual_info_score,
+    normalized_mutual_info_score,
+    rand_score,
+    silhouette_score,
+    v_measure_score,
+)
+from sklearn.utils._testing import assert_allclose
+
+# Dictionaries of metrics
+# ------------------------
+# The goal of having those dictionaries is to have an easy way to call a
+# particular metric and associate a name to each function:
+#   - SUPERVISED_METRICS: all supervised cluster metrics - (when given a
+# ground truth value)
+#   - UNSUPERVISED_METRICS: all unsupervised cluster metrics
+#
+# Those dictionaries will be used to test systematically some invariance
+# properties, e.g. invariance toward several input layout.
+#
+
+SUPERVISED_METRICS = {
+    "adjusted_mutual_info_score": adjusted_mutual_info_score,
+    "adjusted_rand_score": adjusted_rand_score,
+    "rand_score": rand_score,
+    "completeness_score": completeness_score,
+    "homogeneity_score": homogeneity_score,
+    "mutual_info_score": mutual_info_score,
+    "normalized_mutual_info_score": normalized_mutual_info_score,
+    "v_measure_score": v_measure_score,
+    "fowlkes_mallows_score": fowlkes_mallows_score,
+}
+
+UNSUPERVISED_METRICS = {
+    "silhouette_score": silhouette_score,
+    "silhouette_manhattan": partial(silhouette_score, metric="manhattan"),
+    "calinski_harabasz_score": calinski_harabasz_score,
+    "davies_bouldin_score": davies_bouldin_score,
+}
+
+# Lists of metrics with common properties
+# ---------------------------------------
+# Lists of metrics with common properties are used to test systematically some
+# functionalities and invariance, e.g. SYMMETRIC_METRICS lists all metrics
+# that are symmetric with respect to their input argument y_true and y_pred.
+#
+# --------------------------------------------------------------------
+# Symmetric with respect to their input arguments y_true and y_pred.
+# Symmetric metrics only apply to supervised clusters.
+SYMMETRIC_METRICS = [
+    "adjusted_rand_score",
+    "rand_score",
+    "v_measure_score",
+    "mutual_info_score",
+    "adjusted_mutual_info_score",
+    "normalized_mutual_info_score",
+    "fowlkes_mallows_score",
+]
+
+NON_SYMMETRIC_METRICS = ["homogeneity_score", "completeness_score"]
+
+# Metrics whose upper bound is 1
+NORMALIZED_METRICS = [
+    "adjusted_rand_score",
+    "rand_score",
+    "homogeneity_score",
+    "completeness_score",
+    "v_measure_score",
+    "adjusted_mutual_info_score",
+    "fowlkes_mallows_score",
+    "normalized_mutual_info_score",
+]
+
+
+rng = np.random.RandomState(0)
+y1 = rng.randint(3, size=30)
+y2 = rng.randint(3, size=30)
+
+
+def test_symmetric_non_symmetric_union():
+    assert sorted(SYMMETRIC_METRICS + NON_SYMMETRIC_METRICS) == sorted(
+        SUPERVISED_METRICS
+    )
+
+
+# 0.22 AMI and NMI changes
+@pytest.mark.filterwarnings("ignore::FutureWarning")
+@pytest.mark.parametrize(
+    "metric_name, y1, y2", [(name, y1, y2) for name in SYMMETRIC_METRICS]
+)
+def test_symmetry(metric_name, y1, y2):
+    metric = SUPERVISED_METRICS[metric_name]
+    assert metric(y1, y2) == pytest.approx(metric(y2, y1))
+
+
+@pytest.mark.parametrize(
+    "metric_name, y1, y2", [(name, y1, y2) for name in NON_SYMMETRIC_METRICS]
+)
+def test_non_symmetry(metric_name, y1, y2):
+    metric = SUPERVISED_METRICS[metric_name]
+    assert metric(y1, y2) != pytest.approx(metric(y2, y1))
+
+
+# 0.22 AMI and NMI changes
+@pytest.mark.filterwarnings("ignore::FutureWarning")
+@pytest.mark.parametrize("metric_name", NORMALIZED_METRICS)
+def test_normalized_output(metric_name):
+    upper_bound_1 = [0, 0, 0, 1, 1, 1]
+    upper_bound_2 = [0, 0, 0, 1, 1, 1]
+    metric = SUPERVISED_METRICS[metric_name]
+    assert metric([0, 0, 0, 1, 1], [0, 0, 0, 1, 2]) > 0.0
+    assert metric([0, 0, 1, 1, 2], [0, 0, 1, 1, 1]) > 0.0
+    assert metric([0, 0, 0, 1, 2], [0, 1, 1, 1, 1]) < 1.0
+    assert metric([0, 0, 0, 1, 2], [0, 1, 1, 1, 1]) < 1.0
+    assert metric(upper_bound_1, upper_bound_2) == pytest.approx(1.0)
+
+    lower_bound_1 = [0, 0, 0, 0, 0, 0]
+    lower_bound_2 = [0, 1, 2, 3, 4, 5]
+    score = np.array(
+        [metric(lower_bound_1, lower_bound_2), metric(lower_bound_2, lower_bound_1)]
+    )
+    assert not (score < 0).any()
+
+
+# 0.22 AMI and NMI changes
+@pytest.mark.filterwarnings("ignore::FutureWarning")
+@pytest.mark.parametrize("metric_name", chain(SUPERVISED_METRICS, UNSUPERVISED_METRICS))
+def test_permute_labels(metric_name):
+    # All clustering metrics do not change score due to permutations of labels
+    # that is when 0 and 1 exchanged.
+    y_label = np.array([0, 0, 0, 1, 1, 0, 1])
+    y_pred = np.array([1, 0, 1, 0, 1, 1, 0])
+    if metric_name in SUPERVISED_METRICS:
+        metric = SUPERVISED_METRICS[metric_name]
+        score_1 = metric(y_pred, y_label)
+        assert_allclose(score_1, metric(1 - y_pred, y_label))
+        assert_allclose(score_1, metric(1 - y_pred, 1 - y_label))
+        assert_allclose(score_1, metric(y_pred, 1 - y_label))
+    else:
+        metric = UNSUPERVISED_METRICS[metric_name]
+        X = np.random.randint(10, size=(7, 10))
+        score_1 = metric(X, y_pred)
+        assert_allclose(score_1, metric(X, 1 - y_pred))
+
+
+# 0.22 AMI and NMI changes
+@pytest.mark.filterwarnings("ignore::FutureWarning")
+@pytest.mark.parametrize("metric_name", chain(SUPERVISED_METRICS, UNSUPERVISED_METRICS))
+# For all clustering metrics Input parameters can be both
+# in the form of arrays lists, positive, negative or string
+def test_format_invariance(metric_name):
+    y_true = [0, 0, 0, 0, 1, 1, 1, 1]
+    y_pred = [0, 1, 2, 3, 4, 5, 6, 7]
+
+    def generate_formats(y):
+        y = np.array(y)
+        yield y, "array of ints"
+        yield y.tolist(), "list of ints"
+        yield [str(x) + "-a" for x in y.tolist()], "list of strs"
+        yield (
+            np.array([str(x) + "-a" for x in y.tolist()], dtype=object),
+            "array of strs",
+        )
+        yield y - 1, "including negative ints"
+        yield y + 1, "strictly positive ints"
+
+    if metric_name in SUPERVISED_METRICS:
+        metric = SUPERVISED_METRICS[metric_name]
+        score_1 = metric(y_true, y_pred)
+        y_true_gen = generate_formats(y_true)
+        y_pred_gen = generate_formats(y_pred)
+        for (y_true_fmt, fmt_name), (y_pred_fmt, _) in zip(y_true_gen, y_pred_gen):
+            assert score_1 == metric(y_true_fmt, y_pred_fmt)
+    else:
+        metric = UNSUPERVISED_METRICS[metric_name]
+        X = np.random.randint(10, size=(8, 10))
+        score_1 = metric(X, y_true)
+        assert score_1 == metric(X.astype(float), y_true)
+        y_true_gen = generate_formats(y_true)
+        for y_true_fmt, fmt_name in y_true_gen:
+            assert score_1 == metric(X, y_true_fmt)
+
+
+@pytest.mark.parametrize("metric", SUPERVISED_METRICS.values())
+def test_single_sample(metric):
+    # only the supervised metrics support single sample
+    for i, j in [(0, 0), (0, 1), (1, 0), (1, 1)]:
+        metric([i], [j])
+
+
+@pytest.mark.parametrize(
+    "metric_name, metric_func", dict(SUPERVISED_METRICS, **UNSUPERVISED_METRICS).items()
+)
+def test_inf_nan_input(metric_name, metric_func):
+    if metric_name in SUPERVISED_METRICS:
+        invalids = [
+            ([0, 1], [np.inf, np.inf]),
+            ([0, 1], [np.nan, np.nan]),
+            ([0, 1], [np.nan, np.inf]),
+        ]
+    else:
+        X = np.random.randint(10, size=(2, 10))
+        invalids = [(X, [np.inf, np.inf]), (X, [np.nan, np.nan]), (X, [np.nan, np.inf])]
+    with pytest.raises(ValueError, match=r"contains (NaN|infinity)"):
+        for args in invalids:
+            metric_func(*args)

venv/lib/python3.11/site-packages/sklearn/metrics/cluster/tests/test_supervised.py

@@ -0,0 +1,482 @@
+import warnings
+
+import numpy as np
+import pytest
+from numpy.testing import assert_allclose, assert_array_almost_equal, assert_array_equal
+
+from sklearn.metrics.cluster import (
+    adjusted_mutual_info_score,
+    adjusted_rand_score,
+    completeness_score,
+    contingency_matrix,
+    entropy,
+    expected_mutual_information,
+    fowlkes_mallows_score,
+    homogeneity_completeness_v_measure,
+    homogeneity_score,
+    mutual_info_score,
+    normalized_mutual_info_score,
+    pair_confusion_matrix,
+    rand_score,
+    v_measure_score,
+)
+from sklearn.metrics.cluster._supervised import _generalized_average, check_clusterings
+from sklearn.utils import assert_all_finite
+from sklearn.utils._testing import assert_almost_equal
+
+score_funcs = [
+    adjusted_rand_score,
+    rand_score,
+    homogeneity_score,
+    completeness_score,
+    v_measure_score,
+    adjusted_mutual_info_score,
+    normalized_mutual_info_score,
+]
+
+
+def test_error_messages_on_wrong_input():
+    for score_func in score_funcs:
+        expected = (
+            r"Found input variables with inconsistent numbers " r"of samples: \[2, 3\]"
+        )
+        with pytest.raises(ValueError, match=expected):
+            score_func([0, 1], [1, 1, 1])
+
+        expected = r"labels_true must be 1D: shape is \(2"
+        with pytest.raises(ValueError, match=expected):
+            score_func([[0, 1], [1, 0]], [1, 1, 1])
+
+        expected = r"labels_pred must be 1D: shape is \(2"
+        with pytest.raises(ValueError, match=expected):
+            score_func([0, 1, 0], [[1, 1], [0, 0]])
+
+
+def test_generalized_average():
+    a, b = 1, 2
+    methods = ["min", "geometric", "arithmetic", "max"]
+    means = [_generalized_average(a, b, method) for method in methods]
+    assert means[0] <= means[1] <= means[2] <= means[3]
+    c, d = 12, 12
+    means = [_generalized_average(c, d, method) for method in methods]
+    assert means[0] == means[1] == means[2] == means[3]
+
+
+def test_perfect_matches():
+    for score_func in score_funcs:
+        assert score_func([], []) == pytest.approx(1.0)
+        assert score_func([0], [1]) == pytest.approx(1.0)
+        assert score_func([0, 0, 0], [0, 0, 0]) == pytest.approx(1.0)
+        assert score_func([0, 1, 0], [42, 7, 42]) == pytest.approx(1.0)
+        assert score_func([0.0, 1.0, 0.0], [42.0, 7.0, 42.0]) == pytest.approx(1.0)
+        assert score_func([0.0, 1.0, 2.0], [42.0, 7.0, 2.0]) == pytest.approx(1.0)
+        assert score_func([0, 1, 2], [42, 7, 2]) == pytest.approx(1.0)
+    score_funcs_with_changing_means = [
+        normalized_mutual_info_score,
+        adjusted_mutual_info_score,
+    ]
+    means = {"min", "geometric", "arithmetic", "max"}
+    for score_func in score_funcs_with_changing_means:
+        for mean in means:
+            assert score_func([], [], average_method=mean) == pytest.approx(1.0)
+            assert score_func([0], [1], average_method=mean) == pytest.approx(1.0)
+            assert score_func(
+                [0, 0, 0], [0, 0, 0], average_method=mean
+            ) == pytest.approx(1.0)
+            assert score_func(
+                [0, 1, 0], [42, 7, 42], average_method=mean
+            ) == pytest.approx(1.0)
+            assert score_func(
+                [0.0, 1.0, 0.0], [42.0, 7.0, 42.0], average_method=mean
+            ) == pytest.approx(1.0)
+            assert score_func(
+                [0.0, 1.0, 2.0], [42.0, 7.0, 2.0], average_method=mean
+            ) == pytest.approx(1.0)
+            assert score_func(
+                [0, 1, 2], [42, 7, 2], average_method=mean
+            ) == pytest.approx(1.0)
+
+
+def test_homogeneous_but_not_complete_labeling():
+    # homogeneous but not complete clustering
+    h, c, v = homogeneity_completeness_v_measure([0, 0, 0, 1, 1, 1], [0, 0, 0, 1, 2, 2])
+    assert_almost_equal(h, 1.00, 2)
+    assert_almost_equal(c, 0.69, 2)
+    assert_almost_equal(v, 0.81, 2)
+
+
+def test_complete_but_not_homogeneous_labeling():
+    # complete but not homogeneous clustering
+    h, c, v = homogeneity_completeness_v_measure([0, 0, 1, 1, 2, 2], [0, 0, 1, 1, 1, 1])
+    assert_almost_equal(h, 0.58, 2)
+    assert_almost_equal(c, 1.00, 2)
+    assert_almost_equal(v, 0.73, 2)
+
+
+def test_not_complete_and_not_homogeneous_labeling():
+    # neither complete nor homogeneous but not so bad either
+    h, c, v = homogeneity_completeness_v_measure([0, 0, 0, 1, 1, 1], [0, 1, 0, 1, 2, 2])
+    assert_almost_equal(h, 0.67, 2)
+    assert_almost_equal(c, 0.42, 2)
+    assert_almost_equal(v, 0.52, 2)
+
+
+def test_beta_parameter():
+    # test for when beta passed to
+    # homogeneity_completeness_v_measure
+    # and v_measure_score
+    beta_test = 0.2
+    h_test = 0.67
+    c_test = 0.42
+    v_test = (1 + beta_test) * h_test * c_test / (beta_test * h_test + c_test)
+
+    h, c, v = homogeneity_completeness_v_measure(
+        [0, 0, 0, 1, 1, 1], [0, 1, 0, 1, 2, 2], beta=beta_test
+    )
+    assert_almost_equal(h, h_test, 2)
+    assert_almost_equal(c, c_test, 2)
+    assert_almost_equal(v, v_test, 2)
+
+    v = v_measure_score([0, 0, 0, 1, 1, 1], [0, 1, 0, 1, 2, 2], beta=beta_test)
+    assert_almost_equal(v, v_test, 2)
+
+
+def test_non_consecutive_labels():
+    # regression tests for labels with gaps
+    h, c, v = homogeneity_completeness_v_measure([0, 0, 0, 2, 2, 2], [0, 1, 0, 1, 2, 2])
+    assert_almost_equal(h, 0.67, 2)
+    assert_almost_equal(c, 0.42, 2)
+    assert_almost_equal(v, 0.52, 2)
+
+    h, c, v = homogeneity_completeness_v_measure([0, 0, 0, 1, 1, 1], [0, 4, 0, 4, 2, 2])
+    assert_almost_equal(h, 0.67, 2)
+    assert_almost_equal(c, 0.42, 2)
+    assert_almost_equal(v, 0.52, 2)
+
+    ari_1 = adjusted_rand_score([0, 0, 0, 1, 1, 1], [0, 1, 0, 1, 2, 2])
+    ari_2 = adjusted_rand_score([0, 0, 0, 1, 1, 1], [0, 4, 0, 4, 2, 2])
+    assert_almost_equal(ari_1, 0.24, 2)
+    assert_almost_equal(ari_2, 0.24, 2)
+
+    ri_1 = rand_score([0, 0, 0, 1, 1, 1], [0, 1, 0, 1, 2, 2])
+    ri_2 = rand_score([0, 0, 0, 1, 1, 1], [0, 4, 0, 4, 2, 2])
+    assert_almost_equal(ri_1, 0.66, 2)
+    assert_almost_equal(ri_2, 0.66, 2)
+
+
+def uniform_labelings_scores(score_func, n_samples, k_range, n_runs=10, seed=42):
+    # Compute score for random uniform cluster labelings
+    random_labels = np.random.RandomState(seed).randint
+    scores = np.zeros((len(k_range), n_runs))
+    for i, k in enumerate(k_range):
+        for j in range(n_runs):
+            labels_a = random_labels(low=0, high=k, size=n_samples)
+            labels_b = random_labels(low=0, high=k, size=n_samples)
+            scores[i, j] = score_func(labels_a, labels_b)
+    return scores
+
+
+def test_adjustment_for_chance():
+    # Check that adjusted scores are almost zero on random labels
+    n_clusters_range = [2, 10, 50, 90]
+    n_samples = 100
+    n_runs = 10
+
+    scores = uniform_labelings_scores(
+        adjusted_rand_score, n_samples, n_clusters_range, n_runs
+    )
+
+    max_abs_scores = np.abs(scores).max(axis=1)
+    assert_array_almost_equal(max_abs_scores, [0.02, 0.03, 0.03, 0.02], 2)
+
+
+def test_adjusted_mutual_info_score():
+    # Compute the Adjusted Mutual Information and test against known values
+    labels_a = np.array([1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3])
+    labels_b = np.array([1, 1, 1, 1, 2, 1, 2, 2, 2, 2, 3, 1, 3, 3, 3, 2, 2])
+    # Mutual information
+    mi = mutual_info_score(labels_a, labels_b)
+    assert_almost_equal(mi, 0.41022, 5)
+    # with provided sparse contingency
+    C = contingency_matrix(labels_a, labels_b, sparse=True)
+    mi = mutual_info_score(labels_a, labels_b, contingency=C)
+    assert_almost_equal(mi, 0.41022, 5)
+    # with provided dense contingency
+    C = contingency_matrix(labels_a, labels_b)
+    mi = mutual_info_score(labels_a, labels_b, contingency=C)
+    assert_almost_equal(mi, 0.41022, 5)
+    # Expected mutual information
+    n_samples = C.sum()
+    emi = expected_mutual_information(C, n_samples)
+    assert_almost_equal(emi, 0.15042, 5)
+    # Adjusted mutual information
+    ami = adjusted_mutual_info_score(labels_a, labels_b)
+    assert_almost_equal(ami, 0.27821, 5)
+    ami = adjusted_mutual_info_score([1, 1, 2, 2], [2, 2, 3, 3])
+    assert ami == pytest.approx(1.0)
+    # Test with a very large array
+    a110 = np.array([list(labels_a) * 110]).flatten()
+    b110 = np.array([list(labels_b) * 110]).flatten()
+    ami = adjusted_mutual_info_score(a110, b110)
+    assert_almost_equal(ami, 0.38, 2)
+
+
+def test_expected_mutual_info_overflow():
+    # Test for regression where contingency cell exceeds 2**16
+    # leading to overflow in np.outer, resulting in EMI > 1
+    assert expected_mutual_information(np.array([[70000]]), 70000) <= 1
+
+
+def test_int_overflow_mutual_info_fowlkes_mallows_score():
+    # Test overflow in mutual_info_classif and fowlkes_mallows_score
+    x = np.array(
+        [1] * (52632 + 2529)
+        + [2] * (14660 + 793)
+        + [3] * (3271 + 204)
+        + [4] * (814 + 39)
+        + [5] * (316 + 20)
+    )
+    y = np.array(
+        [0] * 52632
+        + [1] * 2529
+        + [0] * 14660
+        + [1] * 793
+        + [0] * 3271
+        + [1] * 204
+        + [0] * 814
+        + [1] * 39
+        + [0] * 316
+        + [1] * 20
+    )
+
+    assert_all_finite(mutual_info_score(x, y))
+    assert_all_finite(fowlkes_mallows_score(x, y))
+
+
+def test_entropy():
+    ent = entropy([0, 0, 42.0])
+    assert_almost_equal(ent, 0.6365141, 5)
+    assert_almost_equal(entropy([]), 1)
+    assert entropy([1, 1, 1, 1]) == 0
+
+
+def test_contingency_matrix():
+    labels_a = np.array([1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3])
+    labels_b = np.array([1, 1, 1, 1, 2, 1, 2, 2, 2, 2, 3, 1, 3, 3, 3, 2, 2])
+    C = contingency_matrix(labels_a, labels_b)
+    C2 = np.histogram2d(labels_a, labels_b, bins=(np.arange(1, 5), np.arange(1, 5)))[0]
+    assert_array_almost_equal(C, C2)
+    C = contingency_matrix(labels_a, labels_b, eps=0.1)
+    assert_array_almost_equal(C, C2 + 0.1)
+
+
+def test_contingency_matrix_sparse():
+    labels_a = np.array([1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3])
+    labels_b = np.array([1, 1, 1, 1, 2, 1, 2, 2, 2, 2, 3, 1, 3, 3, 3, 2, 2])
+    C = contingency_matrix(labels_a, labels_b)
+    C_sparse = contingency_matrix(labels_a, labels_b, sparse=True).toarray()
+    assert_array_almost_equal(C, C_sparse)
+    with pytest.raises(ValueError, match="Cannot set 'eps' when sparse=True"):
+        contingency_matrix(labels_a, labels_b, eps=1e-10, sparse=True)
+
+
+def test_exactly_zero_info_score():
+    # Check numerical stability when information is exactly zero
+    for i in np.logspace(1, 4, 4).astype(int):
+        labels_a, labels_b = (np.ones(i, dtype=int), np.arange(i, dtype=int))
+        assert normalized_mutual_info_score(labels_a, labels_b) == pytest.approx(0.0)
+        assert v_measure_score(labels_a, labels_b) == pytest.approx(0.0)
+        assert adjusted_mutual_info_score(labels_a, labels_b) == pytest.approx(0.0)
+        assert normalized_mutual_info_score(labels_a, labels_b) == pytest.approx(0.0)
+        for method in ["min", "geometric", "arithmetic", "max"]:
+            assert adjusted_mutual_info_score(
+                labels_a, labels_b, average_method=method
+            ) == pytest.approx(0.0)
+            assert normalized_mutual_info_score(
+                labels_a, labels_b, average_method=method
+            ) == pytest.approx(0.0)
+
+
+def test_v_measure_and_mutual_information(seed=36):
+    # Check relation between v_measure, entropy and mutual information
+    for i in np.logspace(1, 4, 4).astype(int):
+        random_state = np.random.RandomState(seed)
+        labels_a, labels_b = (
+            random_state.randint(0, 10, i),
+            random_state.randint(0, 10, i),
+        )
+        assert_almost_equal(
+            v_measure_score(labels_a, labels_b),
+            2.0
+            * mutual_info_score(labels_a, labels_b)
+            / (entropy(labels_a) + entropy(labels_b)),
+            0,
+        )
+        avg = "arithmetic"
+        assert_almost_equal(
+            v_measure_score(labels_a, labels_b),
+            normalized_mutual_info_score(labels_a, labels_b, average_method=avg),
+        )
+
+
+def test_fowlkes_mallows_score():
+    # General case
+    score = fowlkes_mallows_score([0, 0, 0, 1, 1, 1], [0, 0, 1, 1, 2, 2])
+    assert_almost_equal(score, 4.0 / np.sqrt(12.0 * 6.0))
+
+    # Perfect match but where the label names changed
+    perfect_score = fowlkes_mallows_score([0, 0, 0, 1, 1, 1], [1, 1, 1, 0, 0, 0])
+    assert_almost_equal(perfect_score, 1.0)
+
+    # Worst case
+    worst_score = fowlkes_mallows_score([0, 0, 0, 0, 0, 0], [0, 1, 2, 3, 4, 5])
+    assert_almost_equal(worst_score, 0.0)
+
+
+def test_fowlkes_mallows_score_properties():
+    # handcrafted example
+    labels_a = np.array([0, 0, 0, 1, 1, 2])
+    labels_b = np.array([1, 1, 2, 2, 0, 0])
+    expected = 1.0 / np.sqrt((1.0 + 3.0) * (1.0 + 2.0))
+    # FMI = TP / sqrt((TP + FP) * (TP + FN))
+
+    score_original = fowlkes_mallows_score(labels_a, labels_b)
+    assert_almost_equal(score_original, expected)
+
+    # symmetric property
+    score_symmetric = fowlkes_mallows_score(labels_b, labels_a)
+    assert_almost_equal(score_symmetric, expected)
+
+    # permutation property
+    score_permuted = fowlkes_mallows_score((labels_a + 1) % 3, labels_b)
+    assert_almost_equal(score_permuted, expected)
+
+    # symmetric and permutation(both together)
+    score_both = fowlkes_mallows_score(labels_b, (labels_a + 2) % 3)
+    assert_almost_equal(score_both, expected)
+
+
+@pytest.mark.parametrize(
+    "labels_true, labels_pred",
+    [
+        (["a"] * 6, [1, 1, 0, 0, 1, 1]),
+        ([1] * 6, [1, 1, 0, 0, 1, 1]),
+        ([1, 1, 0, 0, 1, 1], ["a"] * 6),
+        ([1, 1, 0, 0, 1, 1], [1] * 6),
+        (["a"] * 6, ["a"] * 6),
+    ],
+)
+def test_mutual_info_score_positive_constant_label(labels_true, labels_pred):
+    # Check that MI = 0 when one or both labelling are constant
+    # non-regression test for #16355
+    assert mutual_info_score(labels_true, labels_pred) == 0
+
+
+def test_check_clustering_error():
+    # Test warning message for continuous values
+    rng = np.random.RandomState(42)
+    noise = rng.rand(500)
+    wavelength = np.linspace(0.01, 1, 500) * 1e-6
+    msg = (
+        "Clustering metrics expects discrete values but received "
+        "continuous values for label, and continuous values for "
+        "target"
+    )
+
+    with pytest.warns(UserWarning, match=msg):
+        check_clusterings(wavelength, noise)
+
+
+def test_pair_confusion_matrix_fully_dispersed():
+    # edge case: every element is its own cluster
+    N = 100
+    clustering1 = list(range(N))
+    clustering2 = clustering1
+    expected = np.array([[N * (N - 1), 0], [0, 0]])
+    assert_array_equal(pair_confusion_matrix(clustering1, clustering2), expected)
+
+
+def test_pair_confusion_matrix_single_cluster():
+    # edge case: only one cluster
+    N = 100
+    clustering1 = np.zeros((N,))
+    clustering2 = clustering1
+    expected = np.array([[0, 0], [0, N * (N - 1)]])
+    assert_array_equal(pair_confusion_matrix(clustering1, clustering2), expected)
+
+
+def test_pair_confusion_matrix():
+    # regular case: different non-trivial clusterings
+    n = 10
+    N = n**2
+    clustering1 = np.hstack([[i + 1] * n for i in range(n)])
+    clustering2 = np.hstack([[i + 1] * (n + 1) for i in range(n)])[:N]
+    # basic quadratic implementation
+    expected = np.zeros(shape=(2, 2), dtype=np.int64)
+    for i in range(len(clustering1)):
+        for j in range(len(clustering2)):
+            if i != j:
+                same_cluster_1 = int(clustering1[i] == clustering1[j])
+                same_cluster_2 = int(clustering2[i] == clustering2[j])
+                expected[same_cluster_1, same_cluster_2] += 1
+    assert_array_equal(pair_confusion_matrix(clustering1, clustering2), expected)
+
+
+@pytest.mark.parametrize(
+    "clustering1, clustering2",
+    [(list(range(100)), list(range(100))), (np.zeros((100,)), np.zeros((100,)))],
+)
+def test_rand_score_edge_cases(clustering1, clustering2):
+    # edge case 1: every element is its own cluster
+    # edge case 2: only one cluster
+    assert_allclose(rand_score(clustering1, clustering2), 1.0)
+
+
+def test_rand_score():
+    # regular case: different non-trivial clusterings
+    clustering1 = [0, 0, 0, 1, 1, 1]
+    clustering2 = [0, 1, 0, 1, 2, 2]
+    # pair confusion matrix
+    D11 = 2 * 2  # ordered pairs (1, 3), (5, 6)
+    D10 = 2 * 4  # ordered pairs (1, 2), (2, 3), (4, 5), (4, 6)
+    D01 = 2 * 1  # ordered pair (2, 4)
+    D00 = 5 * 6 - D11 - D01 - D10  # the remaining pairs
+    # rand score
+    expected_numerator = D00 + D11
+    expected_denominator = D00 + D01 + D10 + D11
+    expected = expected_numerator / expected_denominator
+    assert_allclose(rand_score(clustering1, clustering2), expected)
+
+
+def test_adjusted_rand_score_overflow():
+    """Check that large amount of data will not lead to overflow in
+    `adjusted_rand_score`.
+    Non-regression test for:
+    https://github.com/scikit-learn/scikit-learn/issues/20305
+    """
+    rng = np.random.RandomState(0)
+    y_true = rng.randint(0, 2, 100_000, dtype=np.int8)
+    y_pred = rng.randint(0, 2, 100_000, dtype=np.int8)
+    with warnings.catch_warnings():
+        warnings.simplefilter("error", RuntimeWarning)
+        adjusted_rand_score(y_true, y_pred)
+
+
+@pytest.mark.parametrize("average_method", ["min", "arithmetic", "geometric", "max"])
+def test_normalized_mutual_info_score_bounded(average_method):
+    """Check that nmi returns a score between 0 (included) and 1 (excluded
+    for non-perfect match)
+
+    Non-regression test for issue #13836
+    """
+    labels1 = [0] * 469
+    labels2 = [1] + labels1[1:]
+    labels3 = [0, 1] + labels1[2:]
+
+    # labels1 is constant. The mutual info between labels1 and any other labelling is 0.
+    nmi = normalized_mutual_info_score(labels1, labels2, average_method=average_method)
+    assert nmi == 0
+
+    # non constant, non perfect matching labels
+    nmi = normalized_mutual_info_score(labels2, labels3, average_method=average_method)
+    assert 0 <= nmi < 1

venv/lib/python3.11/site-packages/sklearn/metrics/cluster/tests/test_unsupervised.py

@@ -0,0 +1,413 @@
+import warnings
+
+import numpy as np
+import pytest
+from numpy.testing import assert_allclose
+from scipy.sparse import issparse
+
+from sklearn import datasets
+from sklearn.metrics import pairwise_distances
+from sklearn.metrics.cluster import (
+    calinski_harabasz_score,
+    davies_bouldin_score,
+    silhouette_samples,
+    silhouette_score,
+)
+from sklearn.metrics.cluster._unsupervised import _silhouette_reduce
+from sklearn.utils._testing import assert_array_equal
+from sklearn.utils.fixes import (
+    CSC_CONTAINERS,
+    CSR_CONTAINERS,
+    DOK_CONTAINERS,
+    LIL_CONTAINERS,
+)
+
+
+@pytest.mark.parametrize(
+    "sparse_container",
+    [None] + CSR_CONTAINERS + CSC_CONTAINERS + DOK_CONTAINERS + LIL_CONTAINERS,
+)
+@pytest.mark.parametrize("sample_size", [None, "half"])
+def test_silhouette(sparse_container, sample_size):
+    # Tests the Silhouette Coefficient.
+    dataset = datasets.load_iris()
+    X, y = dataset.data, dataset.target
+    if sparse_container is not None:
+        X = sparse_container(X)
+    sample_size = int(X.shape[0] / 2) if sample_size == "half" else sample_size
+
+    D = pairwise_distances(X, metric="euclidean")
+    # Given that the actual labels are used, we can assume that S would be positive.
+    score_precomputed = silhouette_score(
+        D, y, metric="precomputed", sample_size=sample_size, random_state=0
+    )
+    score_euclidean = silhouette_score(
+        X, y, metric="euclidean", sample_size=sample_size, random_state=0
+    )
+    assert score_precomputed > 0
+    assert score_euclidean > 0
+    assert score_precomputed == pytest.approx(score_euclidean)
+
+
+def test_cluster_size_1():
+    # Assert Silhouette Coefficient == 0 when there is 1 sample in a cluster
+    # (cluster 0). We also test the case where there are identical samples
+    # as the only members of a cluster (cluster 2). To our knowledge, this case
+    # is not discussed in reference material, and we choose for it a sample
+    # score of 1.
+    X = [[0.0], [1.0], [1.0], [2.0], [3.0], [3.0]]
+    labels = np.array([0, 1, 1, 1, 2, 2])
+
+    # Cluster 0: 1 sample -> score of 0 by Rousseeuw's convention
+    # Cluster 1: intra-cluster = [.5, .5, 1]
+    #            inter-cluster = [1, 1, 1]
+    #            silhouette    = [.5, .5, 0]
+    # Cluster 2: intra-cluster = [0, 0]
+    #            inter-cluster = [arbitrary, arbitrary]
+    #            silhouette    = [1., 1.]
+
+    silhouette = silhouette_score(X, labels)
+    assert not np.isnan(silhouette)
+    ss = silhouette_samples(X, labels)
+    assert_array_equal(ss, [0, 0.5, 0.5, 0, 1, 1])
+
+
+def test_silhouette_paper_example():
+    # Explicitly check per-sample results against Rousseeuw (1987)
+    # Data from Table 1
+    lower = [
+        5.58,
+        7.00,
+        6.50,
+        7.08,
+        7.00,
+        3.83,
+        4.83,
+        5.08,
+        8.17,
+        5.83,
+        2.17,
+        5.75,
+        6.67,
+        6.92,
+        4.92,
+        6.42,
+        5.00,
+        5.58,
+        6.00,
+        4.67,
+        6.42,
+        3.42,
+        5.50,
+        6.42,
+        6.42,
+        5.00,
+        3.92,
+        6.17,
+        2.50,
+        4.92,
+        6.25,
+        7.33,
+        4.50,
+        2.25,
+        6.33,
+        2.75,
+        6.08,
+        6.67,
+        4.25,
+        2.67,
+        6.00,
+        6.17,
+        6.17,
+        6.92,
+        6.17,
+        5.25,
+        6.83,
+        4.50,
+        3.75,
+        5.75,
+        5.42,
+        6.08,
+        5.83,
+        6.67,
+        3.67,
+        4.75,
+        3.00,
+        6.08,
+        6.67,
+        5.00,
+        5.58,
+        4.83,
+        6.17,
+        5.67,
+        6.50,
+        6.92,
+    ]
+    D = np.zeros((12, 12))
+    D[np.tril_indices(12, -1)] = lower
+    D += D.T
+
+    names = [
+        "BEL",
+        "BRA",
+        "CHI",
+        "CUB",
+        "EGY",
+        "FRA",
+        "IND",
+        "ISR",
+        "USA",
+        "USS",
+        "YUG",
+        "ZAI",
+    ]
+
+    # Data from Figure 2
+    labels1 = [1, 1, 2, 2, 1, 1, 2, 1, 1, 2, 2, 1]
+    expected1 = {
+        "USA": 0.43,
+        "BEL": 0.39,
+        "FRA": 0.35,
+        "ISR": 0.30,
+        "BRA": 0.22,
+        "EGY": 0.20,
+        "ZAI": 0.19,
+        "CUB": 0.40,
+        "USS": 0.34,
+        "CHI": 0.33,
+        "YUG": 0.26,
+        "IND": -0.04,
+    }
+    score1 = 0.28
+
+    # Data from Figure 3
+    labels2 = [1, 2, 3, 3, 1, 1, 2, 1, 1, 3, 3, 2]
+    expected2 = {
+        "USA": 0.47,
+        "FRA": 0.44,
+        "BEL": 0.42,
+        "ISR": 0.37,
+        "EGY": 0.02,
+        "ZAI": 0.28,
+        "BRA": 0.25,
+        "IND": 0.17,
+        "CUB": 0.48,
+        "USS": 0.44,
+        "YUG": 0.31,
+        "CHI": 0.31,
+    }
+    score2 = 0.33
+
+    for labels, expected, score in [
+        (labels1, expected1, score1),
+        (labels2, expected2, score2),
+    ]:
+        expected = [expected[name] for name in names]
+        # we check to 2dp because that's what's in the paper
+        pytest.approx(
+            expected,
+            silhouette_samples(D, np.array(labels), metric="precomputed"),
+            abs=1e-2,
+        )
+        pytest.approx(
+            score, silhouette_score(D, np.array(labels), metric="precomputed"), abs=1e-2
+        )
+
+
+def test_correct_labelsize():
+    # Assert 1 < n_labels < n_samples
+    dataset = datasets.load_iris()
+    X = dataset.data
+
+    # n_labels = n_samples
+    y = np.arange(X.shape[0])
+    err_msg = (
+        r"Number of labels is %d\. Valid values are 2 "
+        r"to n_samples - 1 \(inclusive\)" % len(np.unique(y))
+    )
+    with pytest.raises(ValueError, match=err_msg):
+        silhouette_score(X, y)
+
+    # n_labels = 1
+    y = np.zeros(X.shape[0])
+    err_msg = (
+        r"Number of labels is %d\. Valid values are 2 "
+        r"to n_samples - 1 \(inclusive\)" % len(np.unique(y))
+    )
+    with pytest.raises(ValueError, match=err_msg):
+        silhouette_score(X, y)
+
+
+def test_non_encoded_labels():
+    dataset = datasets.load_iris()
+    X = dataset.data
+    labels = dataset.target
+    assert silhouette_score(X, labels * 2 + 10) == silhouette_score(X, labels)
+    assert_array_equal(
+        silhouette_samples(X, labels * 2 + 10), silhouette_samples(X, labels)
+    )
+
+
+def test_non_numpy_labels():
+    dataset = datasets.load_iris()
+    X = dataset.data
+    y = dataset.target
+    assert silhouette_score(list(X), list(y)) == silhouette_score(X, y)
+
+
+@pytest.mark.parametrize("dtype", (np.float32, np.float64))
+def test_silhouette_nonzero_diag(dtype):
+    # Make sure silhouette_samples requires diagonal to be zero.
+    # Non-regression test for #12178
+
+    # Construct a zero-diagonal matrix
+    dists = pairwise_distances(
+        np.array([[0.2, 0.1, 0.12, 1.34, 1.11, 1.6]], dtype=dtype).T
+    )
+    labels = [0, 0, 0, 1, 1, 1]
+
+    # small values on the diagonal are OK
+    dists[2][2] = np.finfo(dists.dtype).eps * 10
+    silhouette_samples(dists, labels, metric="precomputed")
+
+    # values bigger than eps * 100 are not
+    dists[2][2] = np.finfo(dists.dtype).eps * 1000
+    with pytest.raises(ValueError, match="contains non-zero"):
+        silhouette_samples(dists, labels, metric="precomputed")
+
+
+@pytest.mark.parametrize(
+    "sparse_container",
+    CSC_CONTAINERS + CSR_CONTAINERS + DOK_CONTAINERS + LIL_CONTAINERS,
+)
+def test_silhouette_samples_precomputed_sparse(sparse_container):
+    """Check that silhouette_samples works for sparse matrices correctly."""
+    X = np.array([[0.2, 0.1, 0.1, 0.2, 0.1, 1.6, 0.2, 0.1]], dtype=np.float32).T
+    y = [0, 0, 0, 0, 1, 1, 1, 1]
+    pdist_dense = pairwise_distances(X)
+    pdist_sparse = sparse_container(pdist_dense)
+    assert issparse(pdist_sparse)
+    output_with_sparse_input = silhouette_samples(pdist_sparse, y, metric="precomputed")
+    output_with_dense_input = silhouette_samples(pdist_dense, y, metric="precomputed")
+    assert_allclose(output_with_sparse_input, output_with_dense_input)
+
+
+@pytest.mark.parametrize(
+    "sparse_container",
+    CSC_CONTAINERS + CSR_CONTAINERS + DOK_CONTAINERS + LIL_CONTAINERS,
+)
+def test_silhouette_samples_euclidean_sparse(sparse_container):
+    """Check that silhouette_samples works for sparse matrices correctly."""
+    X = np.array([[0.2, 0.1, 0.1, 0.2, 0.1, 1.6, 0.2, 0.1]], dtype=np.float32).T
+    y = [0, 0, 0, 0, 1, 1, 1, 1]
+    pdist_dense = pairwise_distances(X)
+    pdist_sparse = sparse_container(pdist_dense)
+    assert issparse(pdist_sparse)
+    output_with_sparse_input = silhouette_samples(pdist_sparse, y)
+    output_with_dense_input = silhouette_samples(pdist_dense, y)
+    assert_allclose(output_with_sparse_input, output_with_dense_input)
+
+
+@pytest.mark.parametrize(
+    "sparse_container", CSC_CONTAINERS + DOK_CONTAINERS + LIL_CONTAINERS
+)
+def test_silhouette_reduce(sparse_container):
+    """Check for non-CSR input to private method `_silhouette_reduce`."""
+    X = np.array([[0.2, 0.1, 0.1, 0.2, 0.1, 1.6, 0.2, 0.1]], dtype=np.float32).T
+    pdist_dense = pairwise_distances(X)
+    pdist_sparse = sparse_container(pdist_dense)
+    y = [0, 0, 0, 0, 1, 1, 1, 1]
+    label_freqs = np.bincount(y)
+    with pytest.raises(
+        TypeError,
+        match="Expected CSR matrix. Please pass sparse matrix in CSR format.",
+    ):
+        _silhouette_reduce(pdist_sparse, start=0, labels=y, label_freqs=label_freqs)
+
+
+def assert_raises_on_only_one_label(func):
+    """Assert message when there is only one label"""
+    rng = np.random.RandomState(seed=0)
+    with pytest.raises(ValueError, match="Number of labels is"):
+        func(rng.rand(10, 2), np.zeros(10))
+
+
+def assert_raises_on_all_points_same_cluster(func):
+    """Assert message when all point are in different clusters"""
+    rng = np.random.RandomState(seed=0)
+    with pytest.raises(ValueError, match="Number of labels is"):
+        func(rng.rand(10, 2), np.arange(10))
+
+
+def test_calinski_harabasz_score():
+    assert_raises_on_only_one_label(calinski_harabasz_score)
+
+    assert_raises_on_all_points_same_cluster(calinski_harabasz_score)
+
+    # Assert the value is 1. when all samples are equals
+    assert 1.0 == calinski_harabasz_score(np.ones((10, 2)), [0] * 5 + [1] * 5)
+
+    # Assert the value is 0. when all the mean cluster are equal
+    assert 0.0 == calinski_harabasz_score([[-1, -1], [1, 1]] * 10, [0] * 10 + [1] * 10)
+
+    # General case (with non numpy arrays)
+    X = (
+        [[0, 0], [1, 1]] * 5
+        + [[3, 3], [4, 4]] * 5
+        + [[0, 4], [1, 3]] * 5
+        + [[3, 1], [4, 0]] * 5
+    )
+    labels = [0] * 10 + [1] * 10 + [2] * 10 + [3] * 10
+    pytest.approx(calinski_harabasz_score(X, labels), 45 * (40 - 4) / (5 * (4 - 1)))
+
+
+def test_davies_bouldin_score():
+    assert_raises_on_only_one_label(davies_bouldin_score)
+    assert_raises_on_all_points_same_cluster(davies_bouldin_score)
+
+    # Assert the value is 0. when all samples are equals
+    assert davies_bouldin_score(np.ones((10, 2)), [0] * 5 + [1] * 5) == pytest.approx(
+        0.0
+    )
+
+    # Assert the value is 0. when all the mean cluster are equal
+    assert davies_bouldin_score(
+        [[-1, -1], [1, 1]] * 10, [0] * 10 + [1] * 10
+    ) == pytest.approx(0.0)
+
+    # General case (with non numpy arrays)
+    X = (
+        [[0, 0], [1, 1]] * 5
+        + [[3, 3], [4, 4]] * 5
+        + [[0, 4], [1, 3]] * 5
+        + [[3, 1], [4, 0]] * 5
+    )
+    labels = [0] * 10 + [1] * 10 + [2] * 10 + [3] * 10
+    pytest.approx(davies_bouldin_score(X, labels), 2 * np.sqrt(0.5) / 3)
+
+    # Ensure divide by zero warning is not raised in general case
+    with warnings.catch_warnings():
+        warnings.simplefilter("error", RuntimeWarning)
+        davies_bouldin_score(X, labels)
+
+    # General case - cluster have one sample
+    X = [[0, 0], [2, 2], [3, 3], [5, 5]]
+    labels = [0, 0, 1, 2]
+    pytest.approx(davies_bouldin_score(X, labels), (5.0 / 4) / 3)
+
+
+def test_silhouette_score_integer_precomputed():
+    """Check that silhouette_score works for precomputed metrics that are integers.
+
+    Non-regression test for #22107.
+    """
+    result = silhouette_score(
+        [[0, 1, 2], [1, 0, 1], [2, 1, 0]], [0, 0, 1], metric="precomputed"
+    )
+    assert result == pytest.approx(1 / 6)
+
+    # non-zero on diagonal for ints raises an error
+    with pytest.raises(ValueError, match="contains non-zero"):
+        silhouette_score(
+            [[1, 1, 2], [1, 0, 1], [2, 1, 0]], [0, 0, 1], metric="precomputed"
+        )