venv/lib/python3.10/site-packages/sklearn/utils/tests/test_extmath.py

# Authors: Olivier Grisel <[email protected]>
#          Mathieu Blondel <[email protected]>
#          Denis Engemann <[email protected]>
#
# License: BSD 3 clause
import numpy as np
import pytest
from scipy import linalg, sparse
from scipy.linalg import eigh
from scipy.sparse.linalg import eigsh
from scipy.special import expit

from sklearn.datasets import make_low_rank_matrix, make_sparse_spd_matrix
from sklearn.utils import gen_batches
from sklearn.utils._arpack import _init_arpack_v0
from sklearn.utils._testing import (
    assert_allclose,
    assert_allclose_dense_sparse,
    assert_almost_equal,
    assert_array_almost_equal,
    assert_array_equal,
    skip_if_32bit,
)
from sklearn.utils.extmath import (
    _deterministic_vector_sign_flip,
    _incremental_mean_and_var,
    _randomized_eigsh,
    _safe_accumulator_op,
    cartesian,
    density,
    log_logistic,
    randomized_svd,
    row_norms,
    safe_sparse_dot,
    softmax,
    stable_cumsum,
    svd_flip,
    weighted_mode,
)
from sklearn.utils.fixes import (
    COO_CONTAINERS,
    CSC_CONTAINERS,
    CSR_CONTAINERS,
    DOK_CONTAINERS,
    LIL_CONTAINERS,
    _mode,
)


@pytest.mark.parametrize(
    "sparse_container",
    COO_CONTAINERS + CSC_CONTAINERS + CSR_CONTAINERS + LIL_CONTAINERS,
)
def test_density(sparse_container):
    rng = np.random.RandomState(0)
    X = rng.randint(10, size=(10, 5))
    X[1, 2] = 0
    X[5, 3] = 0

    assert density(sparse_container(X)) == density(X)


def test_uniform_weights():
    # with uniform weights, results should be identical to stats.mode
    rng = np.random.RandomState(0)
    x = rng.randint(10, size=(10, 5))
    weights = np.ones(x.shape)

    for axis in (None, 0, 1):
        mode, score = _mode(x, axis)
        mode2, score2 = weighted_mode(x, weights, axis=axis)

        assert_array_equal(mode, mode2)
        assert_array_equal(score, score2)


def test_random_weights():
    # set this up so that each row should have a weighted mode of 6,
    # with a score that is easily reproduced
    mode_result = 6

    rng = np.random.RandomState(0)
    x = rng.randint(mode_result, size=(100, 10))
    w = rng.random_sample(x.shape)

    x[:, :5] = mode_result
    w[:, :5] += 1

    mode, score = weighted_mode(x, w, axis=1)

    assert_array_equal(mode, mode_result)
    assert_array_almost_equal(score.ravel(), w[:, :5].sum(1))


@pytest.mark.parametrize("dtype", (np.int32, np.int64, np.float32, np.float64))
def test_randomized_svd_low_rank_all_dtypes(dtype):
    # Check that extmath.randomized_svd is consistent with linalg.svd
    n_samples = 100
    n_features = 500
    rank = 5
    k = 10
    decimal = 5 if dtype == np.float32 else 7
    dtype = np.dtype(dtype)

    # generate a matrix X of approximate effective rank `rank` and no noise
    # component (very structured signal):
    X = make_low_rank_matrix(
        n_samples=n_samples,
        n_features=n_features,
        effective_rank=rank,
        tail_strength=0.0,
        random_state=0,
    ).astype(dtype, copy=False)
    assert X.shape == (n_samples, n_features)

    # compute the singular values of X using the slow exact method
    U, s, Vt = linalg.svd(X, full_matrices=False)

    # Convert the singular values to the specific dtype
    U = U.astype(dtype, copy=False)
    s = s.astype(dtype, copy=False)
    Vt = Vt.astype(dtype, copy=False)

    for normalizer in ["auto", "LU", "QR"]:  # 'none' would not be stable
        # compute the singular values of X using the fast approximate method
        Ua, sa, Va = randomized_svd(
            X, k, power_iteration_normalizer=normalizer, random_state=0
        )

        # If the input dtype is float, then the output dtype is float of the
        # same bit size (f32 is not upcast to f64)
        # But if the input dtype is int, the output dtype is float64
        if dtype.kind == "f":
            assert Ua.dtype == dtype
            assert sa.dtype == dtype
            assert Va.dtype == dtype
        else:
            assert Ua.dtype == np.float64
            assert sa.dtype == np.float64
            assert Va.dtype == np.float64

        assert Ua.shape == (n_samples, k)
        assert sa.shape == (k,)
        assert Va.shape == (k, n_features)

        # ensure that the singular values of both methods are equal up to the
        # real rank of the matrix
        assert_almost_equal(s[:k], sa, decimal=decimal)

        # check the singular vectors too (while not checking the sign)
        assert_almost_equal(
            np.dot(U[:, :k], Vt[:k, :]), np.dot(Ua, Va), decimal=decimal
        )

        # check the sparse matrix representation
        for csr_container in CSR_CONTAINERS:
            X = csr_container(X)

            # compute the singular values of X using the fast approximate method
            Ua, sa, Va = randomized_svd(
                X, k, power_iteration_normalizer=normalizer, random_state=0
            )
            if dtype.kind == "f":
                assert Ua.dtype == dtype
                assert sa.dtype == dtype
                assert Va.dtype == dtype
            else:
                assert Ua.dtype.kind == "f"
                assert sa.dtype.kind == "f"
                assert Va.dtype.kind == "f"

            assert_almost_equal(s[:rank], sa[:rank], decimal=decimal)


@pytest.mark.parametrize("dtype", (np.int32, np.int64, np.float32, np.float64))
def test_randomized_eigsh(dtype):
    """Test that `_randomized_eigsh` returns the appropriate components"""

    rng = np.random.RandomState(42)
    X = np.diag(np.array([1.0, -2.0, 0.0, 3.0], dtype=dtype))
    # random rotation that preserves the eigenvalues of X
    rand_rot = np.linalg.qr(rng.normal(size=X.shape))[0]
    X = rand_rot @ X @ rand_rot.T

    # with 'module' selection method, the negative eigenvalue shows up
    eigvals, eigvecs = _randomized_eigsh(X, n_components=2, selection="module")
    # eigenvalues
    assert eigvals.shape == (2,)
    assert_array_almost_equal(eigvals, [3.0, -2.0])  # negative eigenvalue here
    # eigenvectors
    assert eigvecs.shape == (4, 2)

    # with 'value' selection method, the negative eigenvalue does not show up
    with pytest.raises(NotImplementedError):
        _randomized_eigsh(X, n_components=2, selection="value")


@pytest.mark.parametrize("k", (10, 50, 100, 199, 200))
def test_randomized_eigsh_compared_to_others(k):
    """Check that `_randomized_eigsh` is similar to other `eigsh`

    Tests that for a random PSD matrix, `_randomized_eigsh` provides results
    comparable to LAPACK (scipy.linalg.eigh) and ARPACK
    (scipy.sparse.linalg.eigsh).

    Note: some versions of ARPACK do not support k=n_features.
    """

    # make a random PSD matrix
    n_features = 200
    X = make_sparse_spd_matrix(n_features, random_state=0)

    # compare two versions of randomized
    # rough and fast
    eigvals, eigvecs = _randomized_eigsh(
        X, n_components=k, selection="module", n_iter=25, random_state=0
    )
    # more accurate but slow (TODO find realistic settings here)
    eigvals_qr, eigvecs_qr = _randomized_eigsh(
        X,
        n_components=k,
        n_iter=25,
        n_oversamples=20,
        random_state=0,
        power_iteration_normalizer="QR",
        selection="module",
    )

    # with LAPACK
    eigvals_lapack, eigvecs_lapack = eigh(
        X, subset_by_index=(n_features - k, n_features - 1)
    )
    indices = eigvals_lapack.argsort()[::-1]
    eigvals_lapack = eigvals_lapack[indices]
    eigvecs_lapack = eigvecs_lapack[:, indices]

    # -- eigenvalues comparison
    assert eigvals_lapack.shape == (k,)
    # comparison precision
    assert_array_almost_equal(eigvals, eigvals_lapack, decimal=6)
    assert_array_almost_equal(eigvals_qr, eigvals_lapack, decimal=6)

    # -- eigenvectors comparison
    assert eigvecs_lapack.shape == (n_features, k)
    # flip eigenvectors' sign to enforce deterministic output
    dummy_vecs = np.zeros_like(eigvecs).T
    eigvecs, _ = svd_flip(eigvecs, dummy_vecs)
    eigvecs_qr, _ = svd_flip(eigvecs_qr, dummy_vecs)
    eigvecs_lapack, _ = svd_flip(eigvecs_lapack, dummy_vecs)
    assert_array_almost_equal(eigvecs, eigvecs_lapack, decimal=4)
    assert_array_almost_equal(eigvecs_qr, eigvecs_lapack, decimal=6)

    # comparison ARPACK ~ LAPACK (some ARPACK implems do not support k=n)
    if k < n_features:
        v0 = _init_arpack_v0(n_features, random_state=0)
        # "LA" largest algebraic <=> selection="value" in randomized_eigsh
        eigvals_arpack, eigvecs_arpack = eigsh(
            X, k, which="LA", tol=0, maxiter=None, v0=v0
        )
        indices = eigvals_arpack.argsort()[::-1]
        # eigenvalues
        eigvals_arpack = eigvals_arpack[indices]
        assert_array_almost_equal(eigvals_lapack, eigvals_arpack, decimal=10)
        # eigenvectors
        eigvecs_arpack = eigvecs_arpack[:, indices]
        eigvecs_arpack, _ = svd_flip(eigvecs_arpack, dummy_vecs)
        assert_array_almost_equal(eigvecs_arpack, eigvecs_lapack, decimal=8)


@pytest.mark.parametrize(
    "n,rank",
    [
        (10, 7),
        (100, 10),
        (100, 80),
        (500, 10),
        (500, 250),
        (500, 400),
    ],
)
def test_randomized_eigsh_reconst_low_rank(n, rank):
    """Check that randomized_eigsh is able to reconstruct a low rank psd matrix

    Tests that the decomposition provided by `_randomized_eigsh` leads to
    orthonormal eigenvectors, and that a low rank PSD matrix can be effectively
    reconstructed with good accuracy using it.
    """
    assert rank < n

    # create a low rank PSD
    rng = np.random.RandomState(69)
    X = rng.randn(n, rank)
    A = X @ X.T

    # approximate A with the "right" number of components
    S, V = _randomized_eigsh(A, n_components=rank, random_state=rng)
    # orthonormality checks
    assert_array_almost_equal(np.linalg.norm(V, axis=0), np.ones(S.shape))
    assert_array_almost_equal(V.T @ V, np.diag(np.ones(S.shape)))
    # reconstruction
    A_reconstruct = V @ np.diag(S) @ V.T

    # test that the approximation is good
    assert_array_almost_equal(A_reconstruct, A, decimal=6)


@pytest.mark.parametrize("dtype", (np.float32, np.float64))
@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
def test_row_norms(dtype, csr_container):
    X = np.random.RandomState(42).randn(100, 100)
    if dtype is np.float32:
        precision = 4
    else:
        precision = 5

    X = X.astype(dtype, copy=False)
    sq_norm = (X**2).sum(axis=1)

    assert_array_almost_equal(sq_norm, row_norms(X, squared=True), precision)
    assert_array_almost_equal(np.sqrt(sq_norm), row_norms(X), precision)

    for csr_index_dtype in [np.int32, np.int64]:
        Xcsr = csr_container(X, dtype=dtype)
        # csr_matrix will use int32 indices by default,
        # up-casting those to int64 when necessary
        if csr_index_dtype is np.int64:
            Xcsr.indptr = Xcsr.indptr.astype(csr_index_dtype, copy=False)
            Xcsr.indices = Xcsr.indices.astype(csr_index_dtype, copy=False)
        assert Xcsr.indices.dtype == csr_index_dtype
        assert Xcsr.indptr.dtype == csr_index_dtype
        assert_array_almost_equal(sq_norm, row_norms(Xcsr, squared=True), precision)
        assert_array_almost_equal(np.sqrt(sq_norm), row_norms(Xcsr), precision)


def test_randomized_svd_low_rank_with_noise():
    # Check that extmath.randomized_svd can handle noisy matrices
    n_samples = 100
    n_features = 500
    rank = 5
    k = 10

    # generate a matrix X wity structure approximate rank `rank` and an
    # important noisy component
    X = make_low_rank_matrix(
        n_samples=n_samples,
        n_features=n_features,
        effective_rank=rank,
        tail_strength=0.1,
        random_state=0,
    )
    assert X.shape == (n_samples, n_features)

    # compute the singular values of X using the slow exact method
    _, s, _ = linalg.svd(X, full_matrices=False)

    for normalizer in ["auto", "none", "LU", "QR"]:
        # compute the singular values of X using the fast approximate
        # method without the iterated power method
        _, sa, _ = randomized_svd(
            X, k, n_iter=0, power_iteration_normalizer=normalizer, random_state=0
        )

        # the approximation does not tolerate the noise:
        assert np.abs(s[:k] - sa).max() > 0.01

        # compute the singular values of X using the fast approximate
        # method with iterated power method
        _, sap, _ = randomized_svd(
            X, k, power_iteration_normalizer=normalizer, random_state=0
        )

        # the iterated power method is helping getting rid of the noise:
        assert_almost_equal(s[:k], sap, decimal=3)


def test_randomized_svd_infinite_rank():
    # Check that extmath.randomized_svd can handle noisy matrices
    n_samples = 100
    n_features = 500
    rank = 5
    k = 10

    # let us try again without 'low_rank component': just regularly but slowly
    # decreasing singular values: the rank of the data matrix is infinite
    X = make_low_rank_matrix(
        n_samples=n_samples,
        n_features=n_features,
        effective_rank=rank,
        tail_strength=1.0,
        random_state=0,
    )
    assert X.shape == (n_samples, n_features)

    # compute the singular values of X using the slow exact method
    _, s, _ = linalg.svd(X, full_matrices=False)
    for normalizer in ["auto", "none", "LU", "QR"]:
        # compute the singular values of X using the fast approximate method
        # without the iterated power method
        _, sa, _ = randomized_svd(
            X, k, n_iter=0, power_iteration_normalizer=normalizer, random_state=0
        )

        # the approximation does not tolerate the noise:
        assert np.abs(s[:k] - sa).max() > 0.1

        # compute the singular values of X using the fast approximate method
        # with iterated power method
        _, sap, _ = randomized_svd(
            X, k, n_iter=5, power_iteration_normalizer=normalizer, random_state=0
        )

        # the iterated power method is still managing to get most of the
        # structure at the requested rank
        assert_almost_equal(s[:k], sap, decimal=3)


def test_randomized_svd_transpose_consistency():
    # Check that transposing the design matrix has limited impact
    n_samples = 100
    n_features = 500
    rank = 4
    k = 10

    X = make_low_rank_matrix(
        n_samples=n_samples,
        n_features=n_features,
        effective_rank=rank,
        tail_strength=0.5,
        random_state=0,
    )
    assert X.shape == (n_samples, n_features)

    U1, s1, V1 = randomized_svd(X, k, n_iter=3, transpose=False, random_state=0)
    U2, s2, V2 = randomized_svd(X, k, n_iter=3, transpose=True, random_state=0)
    U3, s3, V3 = randomized_svd(X, k, n_iter=3, transpose="auto", random_state=0)
    U4, s4, V4 = linalg.svd(X, full_matrices=False)

    assert_almost_equal(s1, s4[:k], decimal=3)
    assert_almost_equal(s2, s4[:k], decimal=3)
    assert_almost_equal(s3, s4[:k], decimal=3)

    assert_almost_equal(np.dot(U1, V1), np.dot(U4[:, :k], V4[:k, :]), decimal=2)
    assert_almost_equal(np.dot(U2, V2), np.dot(U4[:, :k], V4[:k, :]), decimal=2)

    # in this case 'auto' is equivalent to transpose
    assert_almost_equal(s2, s3)


def test_randomized_svd_power_iteration_normalizer():
    # randomized_svd with power_iteration_normalized='none' diverges for
    # large number of power iterations on this dataset
    rng = np.random.RandomState(42)
    X = make_low_rank_matrix(100, 500, effective_rank=50, random_state=rng)
    X += 3 * rng.randint(0, 2, size=X.shape)
    n_components = 50

    # Check that it diverges with many (non-normalized) power iterations
    U, s, Vt = randomized_svd(
        X, n_components, n_iter=2, power_iteration_normalizer="none", random_state=0
    )
    A = X - U.dot(np.diag(s).dot(Vt))
    error_2 = linalg.norm(A, ord="fro")
    U, s, Vt = randomized_svd(
        X, n_components, n_iter=20, power_iteration_normalizer="none", random_state=0
    )
    A = X - U.dot(np.diag(s).dot(Vt))
    error_20 = linalg.norm(A, ord="fro")
    assert np.abs(error_2 - error_20) > 100

    for normalizer in ["LU", "QR", "auto"]:
        U, s, Vt = randomized_svd(
            X,
            n_components,
            n_iter=2,
            power_iteration_normalizer=normalizer,
            random_state=0,
        )
        A = X - U.dot(np.diag(s).dot(Vt))
        error_2 = linalg.norm(A, ord="fro")

        for i in [5, 10, 50]:
            U, s, Vt = randomized_svd(
                X,
                n_components,
                n_iter=i,
                power_iteration_normalizer=normalizer,
                random_state=0,
            )
            A = X - U.dot(np.diag(s).dot(Vt))
            error = linalg.norm(A, ord="fro")
            assert 15 > np.abs(error_2 - error)


@pytest.mark.parametrize("sparse_container", DOK_CONTAINERS + LIL_CONTAINERS)
def test_randomized_svd_sparse_warnings(sparse_container):
    # randomized_svd throws a warning for lil and dok matrix
    rng = np.random.RandomState(42)
    X = make_low_rank_matrix(50, 20, effective_rank=10, random_state=rng)
    n_components = 5

    X = sparse_container(X)
    warn_msg = (
        "Calculating SVD of a {} is expensive. csr_matrix is more efficient.".format(
            sparse_container.__name__
        )
    )
    with pytest.warns(sparse.SparseEfficiencyWarning, match=warn_msg):
        randomized_svd(X, n_components, n_iter=1, power_iteration_normalizer="none")


def test_svd_flip():
    # Check that svd_flip works in both situations, and reconstructs input.
    rs = np.random.RandomState(1999)
    n_samples = 20
    n_features = 10
    X = rs.randn(n_samples, n_features)

    # Check matrix reconstruction
    U, S, Vt = linalg.svd(X, full_matrices=False)
    U1, V1 = svd_flip(U, Vt, u_based_decision=False)
    assert_almost_equal(np.dot(U1 * S, V1), X, decimal=6)

    # Check transposed matrix reconstruction
    XT = X.T
    U, S, Vt = linalg.svd(XT, full_matrices=False)
    U2, V2 = svd_flip(U, Vt, u_based_decision=True)
    assert_almost_equal(np.dot(U2 * S, V2), XT, decimal=6)

    # Check that different flip methods are equivalent under reconstruction
    U_flip1, V_flip1 = svd_flip(U, Vt, u_based_decision=True)
    assert_almost_equal(np.dot(U_flip1 * S, V_flip1), XT, decimal=6)
    U_flip2, V_flip2 = svd_flip(U, Vt, u_based_decision=False)
    assert_almost_equal(np.dot(U_flip2 * S, V_flip2), XT, decimal=6)


@pytest.mark.parametrize("n_samples, n_features", [(3, 4), (4, 3)])
def test_svd_flip_max_abs_cols(n_samples, n_features, global_random_seed):
    rs = np.random.RandomState(global_random_seed)
    X = rs.randn(n_samples, n_features)
    U, _, Vt = linalg.svd(X, full_matrices=False)

    U1, _ = svd_flip(U, Vt, u_based_decision=True)
    max_abs_U1_row_idx_for_col = np.argmax(np.abs(U1), axis=0)
    assert (U1[max_abs_U1_row_idx_for_col, np.arange(U1.shape[1])] >= 0).all()

    _, V2 = svd_flip(U, Vt, u_based_decision=False)
    max_abs_V2_col_idx_for_row = np.argmax(np.abs(V2), axis=1)
    assert (V2[np.arange(V2.shape[0]), max_abs_V2_col_idx_for_row] >= 0).all()


def test_randomized_svd_sign_flip():
    a = np.array([[2.0, 0.0], [0.0, 1.0]])
    u1, s1, v1 = randomized_svd(a, 2, flip_sign=True, random_state=41)
    for seed in range(10):
        u2, s2, v2 = randomized_svd(a, 2, flip_sign=True, random_state=seed)
        assert_almost_equal(u1, u2)
        assert_almost_equal(v1, v2)
        assert_almost_equal(np.dot(u2 * s2, v2), a)
        assert_almost_equal(np.dot(u2.T, u2), np.eye(2))
        assert_almost_equal(np.dot(v2.T, v2), np.eye(2))


def test_randomized_svd_sign_flip_with_transpose():
    # Check if the randomized_svd sign flipping is always done based on u
    # irrespective of transpose.
    # See https://github.com/scikit-learn/scikit-learn/issues/5608
    # for more details.
    def max_loading_is_positive(u, v):
        """
        returns bool tuple indicating if the values maximising np.abs
        are positive across all rows for u and across all columns for v.
        """
        u_based = (np.abs(u).max(axis=0) == u.max(axis=0)).all()
        v_based = (np.abs(v).max(axis=1) == v.max(axis=1)).all()
        return u_based, v_based

    mat = np.arange(10 * 8).reshape(10, -1)

    # Without transpose
    u_flipped, _, v_flipped = randomized_svd(mat, 3, flip_sign=True, random_state=0)
    u_based, v_based = max_loading_is_positive(u_flipped, v_flipped)
    assert u_based
    assert not v_based

    # With transpose
    u_flipped_with_transpose, _, v_flipped_with_transpose = randomized_svd(
        mat, 3, flip_sign=True, transpose=True, random_state=0
    )
    u_based, v_based = max_loading_is_positive(
        u_flipped_with_transpose, v_flipped_with_transpose
    )
    assert u_based
    assert not v_based


@pytest.mark.parametrize("n", [50, 100, 300])
@pytest.mark.parametrize("m", [50, 100, 300])
@pytest.mark.parametrize("k", [10, 20, 50])
@pytest.mark.parametrize("seed", range(5))
def test_randomized_svd_lapack_driver(n, m, k, seed):
    # Check that different SVD drivers provide consistent results

    # Matrix being compressed
    rng = np.random.RandomState(seed)
    X = rng.rand(n, m)

    # Number of components
    u1, s1, vt1 = randomized_svd(X, k, svd_lapack_driver="gesdd", random_state=0)
    u2, s2, vt2 = randomized_svd(X, k, svd_lapack_driver="gesvd", random_state=0)

    # Check shape and contents
    assert u1.shape == u2.shape
    assert_allclose(u1, u2, atol=0, rtol=1e-3)

    assert s1.shape == s2.shape
    assert_allclose(s1, s2, atol=0, rtol=1e-3)

    assert vt1.shape == vt2.shape
    assert_allclose(vt1, vt2, atol=0, rtol=1e-3)


def test_cartesian():
    # Check if cartesian product delivers the right results

    axes = (np.array([1, 2, 3]), np.array([4, 5]), np.array([6, 7]))

    true_out = np.array(
        [
            [1, 4, 6],
            [1, 4, 7],
            [1, 5, 6],
            [1, 5, 7],
            [2, 4, 6],
            [2, 4, 7],
            [2, 5, 6],
            [2, 5, 7],
            [3, 4, 6],
            [3, 4, 7],
            [3, 5, 6],
            [3, 5, 7],
        ]
    )

    out = cartesian(axes)
    assert_array_equal(true_out, out)

    # check single axis
    x = np.arange(3)
    assert_array_equal(x[:, np.newaxis], cartesian((x,)))


@pytest.mark.parametrize(
    "arrays, output_dtype",
    [
        (
            [np.array([1, 2, 3], dtype=np.int32), np.array([4, 5], dtype=np.int64)],
            np.dtype(np.int64),
        ),
        (
            [np.array([1, 2, 3], dtype=np.int32), np.array([4, 5], dtype=np.float64)],
            np.dtype(np.float64),
        ),
        (
            [np.array([1, 2, 3], dtype=np.int32), np.array(["x", "y"], dtype=object)],
            np.dtype(object),
        ),
    ],
)
def test_cartesian_mix_types(arrays, output_dtype):
    """Check that the cartesian product works with mixed types."""
    output = cartesian(arrays)

    assert output.dtype == output_dtype


# TODO(1.6): remove this test
def test_logistic_sigmoid():
    # Check correctness and robustness of logistic sigmoid implementation
    def naive_log_logistic(x):
        return np.log(expit(x))

    x = np.linspace(-2, 2, 50)
    warn_msg = "`log_logistic` is deprecated and will be removed"
    with pytest.warns(FutureWarning, match=warn_msg):
        assert_array_almost_equal(log_logistic(x), naive_log_logistic(x))

    extreme_x = np.array([-100.0, 100.0])
    with pytest.warns(FutureWarning, match=warn_msg):
        assert_array_almost_equal(log_logistic(extreme_x), [-100, 0])


@pytest.fixture()
def rng():
    return np.random.RandomState(42)


@pytest.mark.parametrize("dtype", [np.float32, np.float64])
def test_incremental_weighted_mean_and_variance_simple(rng, dtype):
    mult = 10
    X = rng.rand(1000, 20).astype(dtype) * mult
    sample_weight = rng.rand(X.shape[0]) * mult
    mean, var, _ = _incremental_mean_and_var(X, 0, 0, 0, sample_weight=sample_weight)

    expected_mean = np.average(X, weights=sample_weight, axis=0)
    expected_var = (
        np.average(X**2, weights=sample_weight, axis=0) - expected_mean**2
    )
    assert_almost_equal(mean, expected_mean)
    assert_almost_equal(var, expected_var)


@pytest.mark.parametrize("mean", [0, 1e7, -1e7])
@pytest.mark.parametrize("var", [1, 1e-8, 1e5])
@pytest.mark.parametrize(
    "weight_loc, weight_scale", [(0, 1), (0, 1e-8), (1, 1e-8), (10, 1), (1e7, 1)]
)
def test_incremental_weighted_mean_and_variance(
    mean, var, weight_loc, weight_scale, rng
):
    # Testing of correctness and numerical stability
    def _assert(X, sample_weight, expected_mean, expected_var):
        n = X.shape[0]
        for chunk_size in [1, n // 10 + 1, n // 4 + 1, n // 2 + 1, n]:
            last_mean, last_weight_sum, last_var = 0, 0, 0
            for batch in gen_batches(n, chunk_size):
                last_mean, last_var, last_weight_sum = _incremental_mean_and_var(
                    X[batch],
                    last_mean,
                    last_var,
                    last_weight_sum,
                    sample_weight=sample_weight[batch],
                )
            assert_allclose(last_mean, expected_mean)
            assert_allclose(last_var, expected_var, atol=1e-6)

    size = (100, 20)
    weight = rng.normal(loc=weight_loc, scale=weight_scale, size=size[0])

    # Compare to weighted average: np.average
    X = rng.normal(loc=mean, scale=var, size=size)
    expected_mean = _safe_accumulator_op(np.average, X, weights=weight, axis=0)
    expected_var = _safe_accumulator_op(
        np.average, (X - expected_mean) ** 2, weights=weight, axis=0
    )
    _assert(X, weight, expected_mean, expected_var)

    # Compare to unweighted mean: np.mean
    X = rng.normal(loc=mean, scale=var, size=size)
    ones_weight = np.ones(size[0])
    expected_mean = _safe_accumulator_op(np.mean, X, axis=0)
    expected_var = _safe_accumulator_op(np.var, X, axis=0)
    _assert(X, ones_weight, expected_mean, expected_var)


@pytest.mark.parametrize("dtype", [np.float32, np.float64])
def test_incremental_weighted_mean_and_variance_ignore_nan(dtype):
    old_means = np.array([535.0, 535.0, 535.0, 535.0])
    old_variances = np.array([4225.0, 4225.0, 4225.0, 4225.0])
    old_weight_sum = np.array([2, 2, 2, 2], dtype=np.int32)
    sample_weights_X = np.ones(3)
    sample_weights_X_nan = np.ones(4)

    X = np.array(
        [[170, 170, 170, 170], [430, 430, 430, 430], [300, 300, 300, 300]]
    ).astype(dtype)

    X_nan = np.array(
        [
            [170, np.nan, 170, 170],
            [np.nan, 170, 430, 430],
            [430, 430, np.nan, 300],
            [300, 300, 300, np.nan],
        ]
    ).astype(dtype)

    X_means, X_variances, X_count = _incremental_mean_and_var(
        X, old_means, old_variances, old_weight_sum, sample_weight=sample_weights_X
    )
    X_nan_means, X_nan_variances, X_nan_count = _incremental_mean_and_var(
        X_nan,
        old_means,
        old_variances,
        old_weight_sum,
        sample_weight=sample_weights_X_nan,
    )

    assert_allclose(X_nan_means, X_means)
    assert_allclose(X_nan_variances, X_variances)
    assert_allclose(X_nan_count, X_count)


def test_incremental_variance_update_formulas():
    # Test Youngs and Cramer incremental variance formulas.
    # Doggie data from https://www.mathsisfun.com/data/standard-deviation.html
    A = np.array(
        [
            [600, 470, 170, 430, 300],
            [600, 470, 170, 430, 300],
            [600, 470, 170, 430, 300],
            [600, 470, 170, 430, 300],
        ]
    ).T
    idx = 2
    X1 = A[:idx, :]
    X2 = A[idx:, :]

    old_means = X1.mean(axis=0)
    old_variances = X1.var(axis=0)
    old_sample_count = np.full(X1.shape[1], X1.shape[0], dtype=np.int32)
    final_means, final_variances, final_count = _incremental_mean_and_var(
        X2, old_means, old_variances, old_sample_count
    )
    assert_almost_equal(final_means, A.mean(axis=0), 6)
    assert_almost_equal(final_variances, A.var(axis=0), 6)
    assert_almost_equal(final_count, A.shape[0])


def test_incremental_mean_and_variance_ignore_nan():
    old_means = np.array([535.0, 535.0, 535.0, 535.0])
    old_variances = np.array([4225.0, 4225.0, 4225.0, 4225.0])
    old_sample_count = np.array([2, 2, 2, 2], dtype=np.int32)

    X = np.array([[170, 170, 170, 170], [430, 430, 430, 430], [300, 300, 300, 300]])

    X_nan = np.array(
        [
            [170, np.nan, 170, 170],
            [np.nan, 170, 430, 430],
            [430, 430, np.nan, 300],
            [300, 300, 300, np.nan],
        ]
    )

    X_means, X_variances, X_count = _incremental_mean_and_var(
        X, old_means, old_variances, old_sample_count
    )
    X_nan_means, X_nan_variances, X_nan_count = _incremental_mean_and_var(
        X_nan, old_means, old_variances, old_sample_count
    )

    assert_allclose(X_nan_means, X_means)
    assert_allclose(X_nan_variances, X_variances)
    assert_allclose(X_nan_count, X_count)


@skip_if_32bit
def test_incremental_variance_numerical_stability():
    # Test Youngs and Cramer incremental variance formulas.

    def np_var(A):
        return A.var(axis=0)

    # Naive one pass variance computation - not numerically stable
    # https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance
    def one_pass_var(X):
        n = X.shape[0]
        exp_x2 = (X**2).sum(axis=0) / n
        expx_2 = (X.sum(axis=0) / n) ** 2
        return exp_x2 - expx_2

    # Two-pass algorithm, stable.
    # We use it as a benchmark. It is not an online algorithm
    # https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance#Two-pass_algorithm
    def two_pass_var(X):
        mean = X.mean(axis=0)
        Y = X.copy()
        return np.mean((Y - mean) ** 2, axis=0)

    # Naive online implementation
    # https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance#Online_algorithm
    # This works only for chunks for size 1
    def naive_mean_variance_update(x, last_mean, last_variance, last_sample_count):
        updated_sample_count = last_sample_count + 1
        samples_ratio = last_sample_count / float(updated_sample_count)
        updated_mean = x / updated_sample_count + last_mean * samples_ratio
        updated_variance = (
            last_variance * samples_ratio
            + (x - last_mean) * (x - updated_mean) / updated_sample_count
        )
        return updated_mean, updated_variance, updated_sample_count

    # We want to show a case when one_pass_var has error > 1e-3 while
    # _batch_mean_variance_update has less.
    tol = 200
    n_features = 2
    n_samples = 10000
    x1 = np.array(1e8, dtype=np.float64)
    x2 = np.log(1e-5, dtype=np.float64)
    A0 = np.full((n_samples // 2, n_features), x1, dtype=np.float64)
    A1 = np.full((n_samples // 2, n_features), x2, dtype=np.float64)
    A = np.vstack((A0, A1))

    # Naive one pass var: >tol (=1063)
    assert np.abs(np_var(A) - one_pass_var(A)).max() > tol

    # Starting point for online algorithms: after A0

    # Naive implementation: >tol (436)
    mean, var, n = A0[0, :], np.zeros(n_features), n_samples // 2
    for i in range(A1.shape[0]):
        mean, var, n = naive_mean_variance_update(A1[i, :], mean, var, n)
    assert n == A.shape[0]
    # the mean is also slightly unstable
    assert np.abs(A.mean(axis=0) - mean).max() > 1e-6
    assert np.abs(np_var(A) - var).max() > tol

    # Robust implementation: <tol (177)
    mean, var = A0[0, :], np.zeros(n_features)
    n = np.full(n_features, n_samples // 2, dtype=np.int32)
    for i in range(A1.shape[0]):
        mean, var, n = _incremental_mean_and_var(
            A1[i, :].reshape((1, A1.shape[1])), mean, var, n
        )
    assert_array_equal(n, A.shape[0])
    assert_array_almost_equal(A.mean(axis=0), mean)
    assert tol > np.abs(np_var(A) - var).max()


def test_incremental_variance_ddof():
    # Test that degrees of freedom parameter for calculations are correct.
    rng = np.random.RandomState(1999)
    X = rng.randn(50, 10)
    n_samples, n_features = X.shape
    for batch_size in [11, 20, 37]:
        steps = np.arange(0, X.shape[0], batch_size)
        if steps[-1] != X.shape[0]:
            steps = np.hstack([steps, n_samples])

        for i, j in zip(steps[:-1], steps[1:]):
            batch = X[i:j, :]
            if i == 0:
                incremental_means = batch.mean(axis=0)
                incremental_variances = batch.var(axis=0)
                # Assign this twice so that the test logic is consistent
                incremental_count = batch.shape[0]
                sample_count = np.full(batch.shape[1], batch.shape[0], dtype=np.int32)
            else:
                result = _incremental_mean_and_var(
                    batch, incremental_means, incremental_variances, sample_count
                )
                (incremental_means, incremental_variances, incremental_count) = result
                sample_count += batch.shape[0]

            calculated_means = np.mean(X[:j], axis=0)
            calculated_variances = np.var(X[:j], axis=0)
            assert_almost_equal(incremental_means, calculated_means, 6)
            assert_almost_equal(incremental_variances, calculated_variances, 6)
            assert_array_equal(incremental_count, sample_count)


def test_vector_sign_flip():
    # Testing that sign flip is working & largest value has positive sign
    data = np.random.RandomState(36).randn(5, 5)
    max_abs_rows = np.argmax(np.abs(data), axis=1)
    data_flipped = _deterministic_vector_sign_flip(data)
    max_rows = np.argmax(data_flipped, axis=1)
    assert_array_equal(max_abs_rows, max_rows)
    signs = np.sign(data[range(data.shape[0]), max_abs_rows])
    assert_array_equal(data, data_flipped * signs[:, np.newaxis])


def test_softmax():
    rng = np.random.RandomState(0)
    X = rng.randn(3, 5)
    exp_X = np.exp(X)
    sum_exp_X = np.sum(exp_X, axis=1).reshape((-1, 1))
    assert_array_almost_equal(softmax(X), exp_X / sum_exp_X)


def test_stable_cumsum():
    assert_array_equal(stable_cumsum([1, 2, 3]), np.cumsum([1, 2, 3]))
    r = np.random.RandomState(0).rand(100000)
    with pytest.warns(RuntimeWarning):
        stable_cumsum(r, rtol=0, atol=0)

    # test axis parameter
    A = np.random.RandomState(36).randint(1000, size=(5, 5, 5))
    assert_array_equal(stable_cumsum(A, axis=0), np.cumsum(A, axis=0))
    assert_array_equal(stable_cumsum(A, axis=1), np.cumsum(A, axis=1))
    assert_array_equal(stable_cumsum(A, axis=2), np.cumsum(A, axis=2))


@pytest.mark.parametrize(
    "A_container",
    [np.array, *CSR_CONTAINERS],
    ids=["dense"] + [container.__name__ for container in CSR_CONTAINERS],
)
@pytest.mark.parametrize(
    "B_container",
    [np.array, *CSR_CONTAINERS],
    ids=["dense"] + [container.__name__ for container in CSR_CONTAINERS],
)
def test_safe_sparse_dot_2d(A_container, B_container):
    rng = np.random.RandomState(0)

    A = rng.random_sample((30, 10))
    B = rng.random_sample((10, 20))
    expected = np.dot(A, B)

    A = A_container(A)
    B = B_container(B)
    actual = safe_sparse_dot(A, B, dense_output=True)

    assert_allclose(actual, expected)


@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
def test_safe_sparse_dot_nd(csr_container):
    rng = np.random.RandomState(0)

    # dense ND / sparse
    A = rng.random_sample((2, 3, 4, 5, 6))
    B = rng.random_sample((6, 7))
    expected = np.dot(A, B)
    B = csr_container(B)
    actual = safe_sparse_dot(A, B)
    assert_allclose(actual, expected)

    # sparse / dense ND
    A = rng.random_sample((2, 3))
    B = rng.random_sample((4, 5, 3, 6))
    expected = np.dot(A, B)
    A = csr_container(A)
    actual = safe_sparse_dot(A, B)
    assert_allclose(actual, expected)


@pytest.mark.parametrize(
    "container",
    [np.array, *CSR_CONTAINERS],
    ids=["dense"] + [container.__name__ for container in CSR_CONTAINERS],
)
def test_safe_sparse_dot_2d_1d(container):
    rng = np.random.RandomState(0)
    B = rng.random_sample((10))

    # 2D @ 1D
    A = rng.random_sample((30, 10))
    expected = np.dot(A, B)
    actual = safe_sparse_dot(container(A), B)
    assert_allclose(actual, expected)

    # 1D @ 2D
    A = rng.random_sample((10, 30))
    expected = np.dot(B, A)
    actual = safe_sparse_dot(B, container(A))
    assert_allclose(actual, expected)


@pytest.mark.parametrize("dense_output", [True, False])
def test_safe_sparse_dot_dense_output(dense_output):
    rng = np.random.RandomState(0)

    A = sparse.random(30, 10, density=0.1, random_state=rng)
    B = sparse.random(10, 20, density=0.1, random_state=rng)

    expected = A.dot(B)
    actual = safe_sparse_dot(A, B, dense_output=dense_output)

    assert sparse.issparse(actual) == (not dense_output)

    if dense_output:
        expected = expected.toarray()
    assert_allclose_dense_sparse(actual, expected)