221 lines
7.4 KiB
Python
221 lines
7.4 KiB
Python
import numpy as np
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import pytest
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from sklearn.experimental import enable_iterative_imputer # noqa
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from sklearn.impute import IterativeImputer, KNNImputer, SimpleImputer
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from sklearn.utils._testing import (
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assert_allclose,
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assert_allclose_dense_sparse,
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assert_array_equal,
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)
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from sklearn.utils.fixes import CSR_CONTAINERS
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def imputers():
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return [IterativeImputer(tol=0.1), KNNImputer(), SimpleImputer()]
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def sparse_imputers():
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return [SimpleImputer()]
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# ConvergenceWarning will be raised by the IterativeImputer
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@pytest.mark.filterwarnings("ignore::sklearn.exceptions.ConvergenceWarning")
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@pytest.mark.parametrize("imputer", imputers(), ids=lambda x: x.__class__.__name__)
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def test_imputation_missing_value_in_test_array(imputer):
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# [Non Regression Test for issue #13968] Missing value in test set should
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# not throw an error and return a finite dataset
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train = [[1], [2]]
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test = [[3], [np.nan]]
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imputer.set_params(add_indicator=True)
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imputer.fit(train).transform(test)
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# ConvergenceWarning will be raised by the IterativeImputer
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@pytest.mark.filterwarnings("ignore::sklearn.exceptions.ConvergenceWarning")
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@pytest.mark.parametrize("marker", [np.nan, -1, 0])
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@pytest.mark.parametrize("imputer", imputers(), ids=lambda x: x.__class__.__name__)
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def test_imputers_add_indicator(marker, imputer):
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X = np.array(
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[
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[marker, 1, 5, marker, 1],
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[2, marker, 1, marker, 2],
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[6, 3, marker, marker, 3],
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[1, 2, 9, marker, 4],
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]
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)
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X_true_indicator = np.array(
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[
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[1.0, 0.0, 0.0, 1.0],
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[0.0, 1.0, 0.0, 1.0],
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[0.0, 0.0, 1.0, 1.0],
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[0.0, 0.0, 0.0, 1.0],
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]
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)
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imputer.set_params(missing_values=marker, add_indicator=True)
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X_trans = imputer.fit_transform(X)
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assert_allclose(X_trans[:, -4:], X_true_indicator)
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assert_array_equal(imputer.indicator_.features_, np.array([0, 1, 2, 3]))
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imputer.set_params(add_indicator=False)
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X_trans_no_indicator = imputer.fit_transform(X)
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assert_allclose(X_trans[:, :-4], X_trans_no_indicator)
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# ConvergenceWarning will be raised by the IterativeImputer
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@pytest.mark.filterwarnings("ignore::sklearn.exceptions.ConvergenceWarning")
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@pytest.mark.parametrize("marker", [np.nan, -1])
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@pytest.mark.parametrize(
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"imputer", sparse_imputers(), ids=lambda x: x.__class__.__name__
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)
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@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
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def test_imputers_add_indicator_sparse(imputer, marker, csr_container):
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X = csr_container(
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[
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[marker, 1, 5, marker, 1],
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[2, marker, 1, marker, 2],
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[6, 3, marker, marker, 3],
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[1, 2, 9, marker, 4],
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]
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)
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X_true_indicator = csr_container(
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[
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[1.0, 0.0, 0.0, 1.0],
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[0.0, 1.0, 0.0, 1.0],
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[0.0, 0.0, 1.0, 1.0],
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[0.0, 0.0, 0.0, 1.0],
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]
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)
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imputer.set_params(missing_values=marker, add_indicator=True)
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X_trans = imputer.fit_transform(X)
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assert_allclose_dense_sparse(X_trans[:, -4:], X_true_indicator)
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assert_array_equal(imputer.indicator_.features_, np.array([0, 1, 2, 3]))
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imputer.set_params(add_indicator=False)
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X_trans_no_indicator = imputer.fit_transform(X)
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assert_allclose_dense_sparse(X_trans[:, :-4], X_trans_no_indicator)
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# ConvergenceWarning will be raised by the IterativeImputer
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@pytest.mark.filterwarnings("ignore::sklearn.exceptions.ConvergenceWarning")
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@pytest.mark.parametrize("imputer", imputers(), ids=lambda x: x.__class__.__name__)
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@pytest.mark.parametrize("add_indicator", [True, False])
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def test_imputers_pandas_na_integer_array_support(imputer, add_indicator):
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# Test pandas IntegerArray with pd.NA
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pd = pytest.importorskip("pandas")
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marker = np.nan
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imputer = imputer.set_params(add_indicator=add_indicator, missing_values=marker)
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X = np.array(
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[
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[marker, 1, 5, marker, 1],
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[2, marker, 1, marker, 2],
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[6, 3, marker, marker, 3],
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[1, 2, 9, marker, 4],
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]
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)
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# fit on numpy array
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X_trans_expected = imputer.fit_transform(X)
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# Creates dataframe with IntegerArrays with pd.NA
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X_df = pd.DataFrame(X, dtype="Int16", columns=["a", "b", "c", "d", "e"])
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# fit on pandas dataframe with IntegerArrays
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X_trans = imputer.fit_transform(X_df)
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assert_allclose(X_trans_expected, X_trans)
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@pytest.mark.parametrize("imputer", imputers(), ids=lambda x: x.__class__.__name__)
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@pytest.mark.parametrize("add_indicator", [True, False])
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def test_imputers_feature_names_out_pandas(imputer, add_indicator):
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"""Check feature names out for imputers."""
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pd = pytest.importorskip("pandas")
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marker = np.nan
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imputer = imputer.set_params(add_indicator=add_indicator, missing_values=marker)
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X = np.array(
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[
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[marker, 1, 5, 3, marker, 1],
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[2, marker, 1, 4, marker, 2],
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[6, 3, 7, marker, marker, 3],
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[1, 2, 9, 8, marker, 4],
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]
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)
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X_df = pd.DataFrame(X, columns=["a", "b", "c", "d", "e", "f"])
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imputer.fit(X_df)
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names = imputer.get_feature_names_out()
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if add_indicator:
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expected_names = [
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"a",
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"b",
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"c",
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"d",
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"f",
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"missingindicator_a",
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"missingindicator_b",
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"missingindicator_d",
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"missingindicator_e",
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]
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assert_array_equal(expected_names, names)
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else:
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expected_names = ["a", "b", "c", "d", "f"]
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assert_array_equal(expected_names, names)
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@pytest.mark.parametrize("keep_empty_features", [True, False])
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@pytest.mark.parametrize("imputer", imputers(), ids=lambda x: x.__class__.__name__)
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def test_keep_empty_features(imputer, keep_empty_features):
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"""Check that the imputer keeps features with only missing values."""
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X = np.array([[np.nan, 1], [np.nan, 2], [np.nan, 3]])
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imputer = imputer.set_params(
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add_indicator=False, keep_empty_features=keep_empty_features
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)
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for method in ["fit_transform", "transform"]:
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X_imputed = getattr(imputer, method)(X)
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if keep_empty_features:
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assert X_imputed.shape == X.shape
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else:
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assert X_imputed.shape == (X.shape[0], X.shape[1] - 1)
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@pytest.mark.parametrize("imputer", imputers(), ids=lambda x: x.__class__.__name__)
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@pytest.mark.parametrize("missing_value_test", [np.nan, 1])
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def test_imputation_adds_missing_indicator_if_add_indicator_is_true(
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imputer, missing_value_test
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):
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"""Check that missing indicator always exists when add_indicator=True.
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Non-regression test for gh-26590.
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"""
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X_train = np.array([[0, np.nan], [1, 2]])
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# Test data where missing_value_test variable can be set to np.nan or 1.
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X_test = np.array([[0, missing_value_test], [1, 2]])
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imputer.set_params(add_indicator=True)
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imputer.fit(X_train)
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X_test_imputed_with_indicator = imputer.transform(X_test)
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assert X_test_imputed_with_indicator.shape == (2, 3)
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imputer.set_params(add_indicator=False)
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imputer.fit(X_train)
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X_test_imputed_without_indicator = imputer.transform(X_test)
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assert X_test_imputed_without_indicator.shape == (2, 2)
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assert_allclose(
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X_test_imputed_with_indicator[:, :-1], X_test_imputed_without_indicator
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)
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if np.isnan(missing_value_test):
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expected_missing_indicator = [1, 0]
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else:
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expected_missing_indicator = [0, 0]
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assert_allclose(X_test_imputed_with_indicator[:, -1], expected_missing_indicator)
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