614 lines
20 KiB
Python
614 lines
20 KiB
Python
from itertools import product
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import numpy as np
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import pytest
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from scipy.sparse import issparse
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from sklearn import config_context, datasets
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from sklearn.model_selection import ShuffleSplit
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from sklearn.svm import SVC
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from sklearn.utils._array_api import yield_namespace_device_dtype_combinations
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from sklearn.utils._testing import (
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_array_api_for_tests,
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_convert_container,
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assert_allclose,
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assert_array_almost_equal,
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assert_array_equal,
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)
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from sklearn.utils.estimator_checks import _NotAnArray
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from sklearn.utils.fixes import (
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COO_CONTAINERS,
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CSC_CONTAINERS,
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CSR_CONTAINERS,
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DOK_CONTAINERS,
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LIL_CONTAINERS,
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)
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from sklearn.utils.metaestimators import _safe_split
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from sklearn.utils.multiclass import (
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_ovr_decision_function,
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check_classification_targets,
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class_distribution,
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is_multilabel,
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type_of_target,
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unique_labels,
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)
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multilabel_explicit_zero = np.array([[0, 1], [1, 0]])
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multilabel_explicit_zero[:, 0] = 0
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def _generate_sparse(
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data,
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sparse_containers=tuple(
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COO_CONTAINERS
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+ CSC_CONTAINERS
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+ CSR_CONTAINERS
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+ DOK_CONTAINERS
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+ LIL_CONTAINERS
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),
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dtypes=(bool, int, np.int8, np.uint8, float, np.float32),
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):
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return [
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sparse_container(data, dtype=dtype)
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for sparse_container in sparse_containers
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for dtype in dtypes
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]
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EXAMPLES = {
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"multilabel-indicator": [
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# valid when the data is formatted as sparse or dense, identified
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# by CSR format when the testing takes place
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*_generate_sparse(
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np.random.RandomState(42).randint(2, size=(10, 10)),
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sparse_containers=CSR_CONTAINERS,
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dtypes=(int,),
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),
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[[0, 1], [1, 0]],
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[[0, 1]],
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*_generate_sparse(
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multilabel_explicit_zero, sparse_containers=CSC_CONTAINERS, dtypes=(int,)
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),
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*_generate_sparse([[0, 1], [1, 0]]),
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*_generate_sparse([[0, 0], [0, 0]]),
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*_generate_sparse([[0, 1]]),
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# Only valid when data is dense
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[[-1, 1], [1, -1]],
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np.array([[-1, 1], [1, -1]]),
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np.array([[-3, 3], [3, -3]]),
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_NotAnArray(np.array([[-3, 3], [3, -3]])),
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],
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"multiclass": [
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[1, 0, 2, 2, 1, 4, 2, 4, 4, 4],
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np.array([1, 0, 2]),
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np.array([1, 0, 2], dtype=np.int8),
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np.array([1, 0, 2], dtype=np.uint8),
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np.array([1, 0, 2], dtype=float),
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np.array([1, 0, 2], dtype=np.float32),
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np.array([[1], [0], [2]]),
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_NotAnArray(np.array([1, 0, 2])),
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[0, 1, 2],
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["a", "b", "c"],
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np.array(["a", "b", "c"]),
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np.array(["a", "b", "c"], dtype=object),
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np.array(["a", "b", "c"], dtype=object),
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],
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"multiclass-multioutput": [
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[[1, 0, 2, 2], [1, 4, 2, 4]],
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[["a", "b"], ["c", "d"]],
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np.array([[1, 0, 2, 2], [1, 4, 2, 4]]),
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np.array([[1, 0, 2, 2], [1, 4, 2, 4]], dtype=np.int8),
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np.array([[1, 0, 2, 2], [1, 4, 2, 4]], dtype=np.uint8),
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np.array([[1, 0, 2, 2], [1, 4, 2, 4]], dtype=float),
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np.array([[1, 0, 2, 2], [1, 4, 2, 4]], dtype=np.float32),
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*_generate_sparse(
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[[1, 0, 2, 2], [1, 4, 2, 4]],
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sparse_containers=CSC_CONTAINERS + CSR_CONTAINERS,
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dtypes=(int, np.int8, np.uint8, float, np.float32),
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),
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np.array([["a", "b"], ["c", "d"]]),
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np.array([["a", "b"], ["c", "d"]]),
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np.array([["a", "b"], ["c", "d"]], dtype=object),
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np.array([[1, 0, 2]]),
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_NotAnArray(np.array([[1, 0, 2]])),
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],
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"binary": [
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[0, 1],
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[1, 1],
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[],
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[0],
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np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1]),
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np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=bool),
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np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=np.int8),
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np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=np.uint8),
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np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=float),
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np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=np.float32),
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np.array([[0], [1]]),
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_NotAnArray(np.array([[0], [1]])),
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[1, -1],
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[3, 5],
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["a"],
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["a", "b"],
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["abc", "def"],
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np.array(["abc", "def"]),
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["a", "b"],
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np.array(["abc", "def"], dtype=object),
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],
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"continuous": [
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[1e-5],
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[0, 0.5],
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np.array([[0], [0.5]]),
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np.array([[0], [0.5]], dtype=np.float32),
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],
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"continuous-multioutput": [
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np.array([[0, 0.5], [0.5, 0]]),
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np.array([[0, 0.5], [0.5, 0]], dtype=np.float32),
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np.array([[0, 0.5]]),
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*_generate_sparse(
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[[0, 0.5], [0.5, 0]],
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sparse_containers=CSC_CONTAINERS + CSR_CONTAINERS,
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dtypes=(float, np.float32),
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),
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*_generate_sparse(
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[[0, 0.5]],
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sparse_containers=CSC_CONTAINERS + CSR_CONTAINERS,
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dtypes=(float, np.float32),
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),
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],
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"unknown": [
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[[]],
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np.array([[]], dtype=object),
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[()],
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# sequence of sequences that weren't supported even before deprecation
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np.array([np.array([]), np.array([1, 2, 3])], dtype=object),
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[np.array([]), np.array([1, 2, 3])],
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[{1, 2, 3}, {1, 2}],
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[frozenset([1, 2, 3]), frozenset([1, 2])],
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# and also confusable as sequences of sequences
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[{0: "a", 1: "b"}, {0: "a"}],
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# ndim 0
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np.array(0),
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# empty second dimension
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np.array([[], []]),
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# 3d
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np.array([[[0, 1], [2, 3]], [[4, 5], [6, 7]]]),
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],
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}
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ARRAY_API_EXAMPLES = {
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"multilabel-indicator": [
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np.random.RandomState(42).randint(2, size=(10, 10)),
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[[0, 1], [1, 0]],
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[[0, 1]],
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multilabel_explicit_zero,
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[[0, 0], [0, 0]],
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[[-1, 1], [1, -1]],
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np.array([[-1, 1], [1, -1]]),
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np.array([[-3, 3], [3, -3]]),
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_NotAnArray(np.array([[-3, 3], [3, -3]])),
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],
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"multiclass": [
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[1, 0, 2, 2, 1, 4, 2, 4, 4, 4],
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np.array([1, 0, 2]),
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np.array([1, 0, 2], dtype=np.int8),
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np.array([1, 0, 2], dtype=np.uint8),
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np.array([1, 0, 2], dtype=float),
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np.array([1, 0, 2], dtype=np.float32),
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np.array([[1], [0], [2]]),
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_NotAnArray(np.array([1, 0, 2])),
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[0, 1, 2],
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],
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"multiclass-multioutput": [
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[[1, 0, 2, 2], [1, 4, 2, 4]],
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np.array([[1, 0, 2, 2], [1, 4, 2, 4]]),
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np.array([[1, 0, 2, 2], [1, 4, 2, 4]], dtype=np.int8),
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np.array([[1, 0, 2, 2], [1, 4, 2, 4]], dtype=np.uint8),
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np.array([[1, 0, 2, 2], [1, 4, 2, 4]], dtype=float),
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np.array([[1, 0, 2, 2], [1, 4, 2, 4]], dtype=np.float32),
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np.array([[1, 0, 2]]),
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_NotAnArray(np.array([[1, 0, 2]])),
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],
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"binary": [
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[0, 1],
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[1, 1],
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[],
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[0],
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np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1]),
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np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=bool),
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np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=np.int8),
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np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=np.uint8),
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np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=float),
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np.array([0, 1, 1, 1, 0, 0, 0, 1, 1, 1], dtype=np.float32),
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np.array([[0], [1]]),
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_NotAnArray(np.array([[0], [1]])),
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[1, -1],
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[3, 5],
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],
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"continuous": [
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[1e-5],
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[0, 0.5],
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np.array([[0], [0.5]]),
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np.array([[0], [0.5]], dtype=np.float32),
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],
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"continuous-multioutput": [
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np.array([[0, 0.5], [0.5, 0]]),
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np.array([[0, 0.5], [0.5, 0]], dtype=np.float32),
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np.array([[0, 0.5]]),
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],
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"unknown": [
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[[]],
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[()],
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np.array(0),
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np.array([[[0, 1], [2, 3]], [[4, 5], [6, 7]]]),
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],
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}
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NON_ARRAY_LIKE_EXAMPLES = [
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{1, 2, 3},
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{0: "a", 1: "b"},
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{0: [5], 1: [5]},
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"abc",
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frozenset([1, 2, 3]),
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None,
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]
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MULTILABEL_SEQUENCES = [
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[[1], [2], [0, 1]],
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[(), (2), (0, 1)],
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np.array([[], [1, 2]], dtype="object"),
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_NotAnArray(np.array([[], [1, 2]], dtype="object")),
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]
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def test_unique_labels():
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# Empty iterable
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with pytest.raises(ValueError):
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unique_labels()
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# Multiclass problem
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assert_array_equal(unique_labels(range(10)), np.arange(10))
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assert_array_equal(unique_labels(np.arange(10)), np.arange(10))
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assert_array_equal(unique_labels([4, 0, 2]), np.array([0, 2, 4]))
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# Multilabel indicator
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assert_array_equal(
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unique_labels(np.array([[0, 0, 1], [1, 0, 1], [0, 0, 0]])), np.arange(3)
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)
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assert_array_equal(unique_labels(np.array([[0, 0, 1], [0, 0, 0]])), np.arange(3))
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# Several arrays passed
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assert_array_equal(unique_labels([4, 0, 2], range(5)), np.arange(5))
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assert_array_equal(unique_labels((0, 1, 2), (0,), (2, 1)), np.arange(3))
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# Border line case with binary indicator matrix
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with pytest.raises(ValueError):
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unique_labels([4, 0, 2], np.ones((5, 5)))
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with pytest.raises(ValueError):
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unique_labels(np.ones((5, 4)), np.ones((5, 5)))
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assert_array_equal(unique_labels(np.ones((4, 5)), np.ones((5, 5))), np.arange(5))
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def test_unique_labels_non_specific():
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# Test unique_labels with a variety of collected examples
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# Smoke test for all supported format
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for format in ["binary", "multiclass", "multilabel-indicator"]:
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for y in EXAMPLES[format]:
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unique_labels(y)
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# We don't support those format at the moment
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for example in NON_ARRAY_LIKE_EXAMPLES:
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with pytest.raises(ValueError):
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unique_labels(example)
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for y_type in [
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"unknown",
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"continuous",
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"continuous-multioutput",
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"multiclass-multioutput",
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]:
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for example in EXAMPLES[y_type]:
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with pytest.raises(ValueError):
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unique_labels(example)
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def test_unique_labels_mixed_types():
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# Mix with binary or multiclass and multilabel
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mix_clf_format = product(
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EXAMPLES["multilabel-indicator"], EXAMPLES["multiclass"] + EXAMPLES["binary"]
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)
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for y_multilabel, y_multiclass in mix_clf_format:
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with pytest.raises(ValueError):
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unique_labels(y_multiclass, y_multilabel)
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with pytest.raises(ValueError):
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unique_labels(y_multilabel, y_multiclass)
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with pytest.raises(ValueError):
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unique_labels([[1, 2]], [["a", "d"]])
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with pytest.raises(ValueError):
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unique_labels(["1", 2])
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with pytest.raises(ValueError):
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unique_labels([["1", 2], [1, 3]])
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with pytest.raises(ValueError):
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unique_labels([["1", "2"], [2, 3]])
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def test_is_multilabel():
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for group, group_examples in EXAMPLES.items():
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dense_exp = group == "multilabel-indicator"
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for example in group_examples:
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# Only mark explicitly defined sparse examples as valid sparse
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# multilabel-indicators
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sparse_exp = dense_exp and issparse(example)
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if issparse(example) or (
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hasattr(example, "__array__")
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and np.asarray(example).ndim == 2
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and np.asarray(example).dtype.kind in "biuf"
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and np.asarray(example).shape[1] > 0
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):
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examples_sparse = [
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sparse_container(example)
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for sparse_container in (
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COO_CONTAINERS
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+ CSC_CONTAINERS
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+ CSR_CONTAINERS
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+ DOK_CONTAINERS
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+ LIL_CONTAINERS
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)
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]
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for exmpl_sparse in examples_sparse:
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assert sparse_exp == is_multilabel(
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exmpl_sparse
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), f"is_multilabel({exmpl_sparse!r}) should be {sparse_exp}"
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# Densify sparse examples before testing
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if issparse(example):
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example = example.toarray()
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assert dense_exp == is_multilabel(
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example
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), f"is_multilabel({example!r}) should be {dense_exp}"
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@pytest.mark.parametrize(
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"array_namespace, device, dtype_name",
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yield_namespace_device_dtype_combinations(),
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)
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def test_is_multilabel_array_api_compliance(array_namespace, device, dtype_name):
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xp = _array_api_for_tests(array_namespace, device)
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for group, group_examples in ARRAY_API_EXAMPLES.items():
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dense_exp = group == "multilabel-indicator"
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for example in group_examples:
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if np.asarray(example).dtype.kind == "f":
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example = np.asarray(example, dtype=dtype_name)
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else:
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example = np.asarray(example)
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example = xp.asarray(example, device=device)
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with config_context(array_api_dispatch=True):
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assert dense_exp == is_multilabel(
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example
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), f"is_multilabel({example!r}) should be {dense_exp}"
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def test_check_classification_targets():
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for y_type in EXAMPLES.keys():
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if y_type in ["unknown", "continuous", "continuous-multioutput"]:
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for example in EXAMPLES[y_type]:
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msg = "Unknown label type: "
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with pytest.raises(ValueError, match=msg):
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check_classification_targets(example)
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else:
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for example in EXAMPLES[y_type]:
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check_classification_targets(example)
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# @ignore_warnings
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def test_type_of_target():
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for group, group_examples in EXAMPLES.items():
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for example in group_examples:
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assert (
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type_of_target(example) == group
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), "type_of_target(%r) should be %r, got %r" % (
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example,
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group,
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type_of_target(example),
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)
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for example in NON_ARRAY_LIKE_EXAMPLES:
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msg_regex = r"Expected array-like \(array or non-string sequence\).*"
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with pytest.raises(ValueError, match=msg_regex):
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type_of_target(example)
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for example in MULTILABEL_SEQUENCES:
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msg = (
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"You appear to be using a legacy multi-label data "
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"representation. Sequence of sequences are no longer supported;"
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" use a binary array or sparse matrix instead."
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)
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with pytest.raises(ValueError, match=msg):
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type_of_target(example)
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def test_type_of_target_pandas_sparse():
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pd = pytest.importorskip("pandas")
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y = pd.arrays.SparseArray([1, np.nan, np.nan, 1, np.nan])
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msg = "y cannot be class 'SparseSeries' or 'SparseArray'"
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with pytest.raises(ValueError, match=msg):
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type_of_target(y)
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def test_type_of_target_pandas_nullable():
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"""Check that type_of_target works with pandas nullable dtypes."""
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pd = pytest.importorskip("pandas")
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for dtype in ["Int32", "Float32"]:
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y_true = pd.Series([1, 0, 2, 3, 4], dtype=dtype)
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assert type_of_target(y_true) == "multiclass"
|
|
|
|
y_true = pd.Series([1, 0, 1, 0], dtype=dtype)
|
|
assert type_of_target(y_true) == "binary"
|
|
|
|
y_true = pd.DataFrame([[1.4, 3.1], [3.1, 1.4]], dtype="Float32")
|
|
assert type_of_target(y_true) == "continuous-multioutput"
|
|
|
|
y_true = pd.DataFrame([[0, 1], [1, 1]], dtype="Int32")
|
|
assert type_of_target(y_true) == "multilabel-indicator"
|
|
|
|
y_true = pd.DataFrame([[1, 2], [3, 1]], dtype="Int32")
|
|
assert type_of_target(y_true) == "multiclass-multioutput"
|
|
|
|
|
|
@pytest.mark.parametrize("dtype", ["Int64", "Float64", "boolean"])
|
|
def test_unique_labels_pandas_nullable(dtype):
|
|
"""Checks that unique_labels work with pandas nullable dtypes.
|
|
|
|
Non-regression test for gh-25634.
|
|
"""
|
|
pd = pytest.importorskip("pandas")
|
|
|
|
y_true = pd.Series([1, 0, 0, 1, 0, 1, 1, 0, 1], dtype=dtype)
|
|
y_predicted = pd.Series([0, 0, 1, 1, 0, 1, 1, 1, 1], dtype="int64")
|
|
|
|
labels = unique_labels(y_true, y_predicted)
|
|
assert_array_equal(labels, [0, 1])
|
|
|
|
|
|
@pytest.mark.parametrize("csc_container", CSC_CONTAINERS)
|
|
def test_class_distribution(csc_container):
|
|
y = np.array(
|
|
[
|
|
[1, 0, 0, 1],
|
|
[2, 2, 0, 1],
|
|
[1, 3, 0, 1],
|
|
[4, 2, 0, 1],
|
|
[2, 0, 0, 1],
|
|
[1, 3, 0, 1],
|
|
]
|
|
)
|
|
# Define the sparse matrix with a mix of implicit and explicit zeros
|
|
data = np.array([1, 2, 1, 4, 2, 1, 0, 2, 3, 2, 3, 1, 1, 1, 1, 1, 1])
|
|
indices = np.array([0, 1, 2, 3, 4, 5, 0, 1, 2, 3, 5, 0, 1, 2, 3, 4, 5])
|
|
indptr = np.array([0, 6, 11, 11, 17])
|
|
y_sp = csc_container((data, indices, indptr), shape=(6, 4))
|
|
|
|
classes, n_classes, class_prior = class_distribution(y)
|
|
classes_sp, n_classes_sp, class_prior_sp = class_distribution(y_sp)
|
|
classes_expected = [[1, 2, 4], [0, 2, 3], [0], [1]]
|
|
n_classes_expected = [3, 3, 1, 1]
|
|
class_prior_expected = [[3 / 6, 2 / 6, 1 / 6], [1 / 3, 1 / 3, 1 / 3], [1.0], [1.0]]
|
|
|
|
for k in range(y.shape[1]):
|
|
assert_array_almost_equal(classes[k], classes_expected[k])
|
|
assert_array_almost_equal(n_classes[k], n_classes_expected[k])
|
|
assert_array_almost_equal(class_prior[k], class_prior_expected[k])
|
|
|
|
assert_array_almost_equal(classes_sp[k], classes_expected[k])
|
|
assert_array_almost_equal(n_classes_sp[k], n_classes_expected[k])
|
|
assert_array_almost_equal(class_prior_sp[k], class_prior_expected[k])
|
|
|
|
# Test again with explicit sample weights
|
|
(classes, n_classes, class_prior) = class_distribution(
|
|
y, [1.0, 2.0, 1.0, 2.0, 1.0, 2.0]
|
|
)
|
|
(classes_sp, n_classes_sp, class_prior_sp) = class_distribution(
|
|
y, [1.0, 2.0, 1.0, 2.0, 1.0, 2.0]
|
|
)
|
|
class_prior_expected = [[4 / 9, 3 / 9, 2 / 9], [2 / 9, 4 / 9, 3 / 9], [1.0], [1.0]]
|
|
|
|
for k in range(y.shape[1]):
|
|
assert_array_almost_equal(classes[k], classes_expected[k])
|
|
assert_array_almost_equal(n_classes[k], n_classes_expected[k])
|
|
assert_array_almost_equal(class_prior[k], class_prior_expected[k])
|
|
|
|
assert_array_almost_equal(classes_sp[k], classes_expected[k])
|
|
assert_array_almost_equal(n_classes_sp[k], n_classes_expected[k])
|
|
assert_array_almost_equal(class_prior_sp[k], class_prior_expected[k])
|
|
|
|
|
|
def test_safe_split_with_precomputed_kernel():
|
|
clf = SVC()
|
|
clfp = SVC(kernel="precomputed")
|
|
|
|
iris = datasets.load_iris()
|
|
X, y = iris.data, iris.target
|
|
K = np.dot(X, X.T)
|
|
|
|
cv = ShuffleSplit(test_size=0.25, random_state=0)
|
|
train, test = list(cv.split(X))[0]
|
|
|
|
X_train, y_train = _safe_split(clf, X, y, train)
|
|
K_train, y_train2 = _safe_split(clfp, K, y, train)
|
|
assert_array_almost_equal(K_train, np.dot(X_train, X_train.T))
|
|
assert_array_almost_equal(y_train, y_train2)
|
|
|
|
X_test, y_test = _safe_split(clf, X, y, test, train)
|
|
K_test, y_test2 = _safe_split(clfp, K, y, test, train)
|
|
assert_array_almost_equal(K_test, np.dot(X_test, X_train.T))
|
|
assert_array_almost_equal(y_test, y_test2)
|
|
|
|
|
|
def test_ovr_decision_function():
|
|
# test properties for ovr decision function
|
|
|
|
predictions = np.array([[0, 1, 1], [0, 1, 0], [0, 1, 1], [0, 1, 1]])
|
|
|
|
confidences = np.array(
|
|
[[-1e16, 0, -1e16], [1.0, 2.0, -3.0], [-5.0, 2.0, 5.0], [-0.5, 0.2, 0.5]]
|
|
)
|
|
|
|
n_classes = 3
|
|
|
|
dec_values = _ovr_decision_function(predictions, confidences, n_classes)
|
|
|
|
# check that the decision values are within 0.5 range of the votes
|
|
votes = np.array([[1, 0, 2], [1, 1, 1], [1, 0, 2], [1, 0, 2]])
|
|
|
|
assert_allclose(votes, dec_values, atol=0.5)
|
|
|
|
# check that the prediction are what we expect
|
|
# highest vote or highest confidence if there is a tie.
|
|
# for the second sample we have a tie (should be won by 1)
|
|
expected_prediction = np.array([2, 1, 2, 2])
|
|
assert_array_equal(np.argmax(dec_values, axis=1), expected_prediction)
|
|
|
|
# third and fourth sample have the same vote but third sample
|
|
# has higher confidence, this should reflect on the decision values
|
|
assert dec_values[2, 2] > dec_values[3, 2]
|
|
|
|
# assert subset invariance.
|
|
dec_values_one = [
|
|
_ovr_decision_function(
|
|
np.array([predictions[i]]), np.array([confidences[i]]), n_classes
|
|
)[0]
|
|
for i in range(4)
|
|
]
|
|
|
|
assert_allclose(dec_values, dec_values_one, atol=1e-6)
|
|
|
|
|
|
# TODO(1.7): Change to ValueError when byte labels is deprecated.
|
|
@pytest.mark.parametrize("input_type", ["list", "array"])
|
|
def test_labels_in_bytes_format(input_type):
|
|
# check that we raise an error with bytes encoded labels
|
|
# non-regression test for:
|
|
# https://github.com/scikit-learn/scikit-learn/issues/16980
|
|
target = _convert_container([b"a", b"b"], input_type)
|
|
err_msg = (
|
|
"Support for labels represented as bytes is deprecated in v1.5 and will"
|
|
" error in v1.7. Convert the labels to a string or integer format."
|
|
)
|
|
with pytest.warns(FutureWarning, match=err_msg):
|
|
type_of_target(target)
|