574 lines
17 KiB
Python
574 lines
17 KiB
Python
# Author: Gael Varoquaux
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# License: BSD 3 clause
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import numpy as np
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import scipy.sparse as sp
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import pytest
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import sklearn
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from sklearn.utils._testing import assert_array_equal
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from sklearn.utils._testing import assert_raises
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from sklearn.utils._testing import assert_no_warnings
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from sklearn.utils._testing import assert_warns_message
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from sklearn.utils._testing import ignore_warnings
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from sklearn.base import BaseEstimator, clone, is_classifier, _is_pairwise
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from sklearn.svm import SVC
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from sklearn.pipeline import Pipeline
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from sklearn.model_selection import GridSearchCV
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from sklearn.decomposition import KernelPCA
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from sklearn.tree import DecisionTreeClassifier
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from sklearn.tree import DecisionTreeRegressor
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from sklearn import datasets
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from sklearn.base import TransformerMixin
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from sklearn.utils._mocking import MockDataFrame
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from sklearn import config_context
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import pickle
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#############################################################################
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# A few test classes
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class MyEstimator(BaseEstimator):
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def __init__(self, l1=0, empty=None):
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self.l1 = l1
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self.empty = empty
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class K(BaseEstimator):
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def __init__(self, c=None, d=None):
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self.c = c
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self.d = d
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class T(BaseEstimator):
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def __init__(self, a=None, b=None):
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self.a = a
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self.b = b
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class NaNTag(BaseEstimator):
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def _more_tags(self):
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return {'allow_nan': True}
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class NoNaNTag(BaseEstimator):
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def _more_tags(self):
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return {'allow_nan': False}
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class OverrideTag(NaNTag):
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def _more_tags(self):
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return {'allow_nan': False}
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class DiamondOverwriteTag(NaNTag, NoNaNTag):
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def _more_tags(self):
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return dict()
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class InheritDiamondOverwriteTag(DiamondOverwriteTag):
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pass
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class ModifyInitParams(BaseEstimator):
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"""Deprecated behavior.
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Equal parameters but with a type cast.
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Doesn't fulfill a is a
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"""
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def __init__(self, a=np.array([0])):
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self.a = a.copy()
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class Buggy(BaseEstimator):
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" A buggy estimator that does not set its parameters right. "
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def __init__(self, a=None):
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self.a = 1
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class NoEstimator:
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def __init__(self):
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pass
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def fit(self, X=None, y=None):
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return self
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def predict(self, X=None):
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return None
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class VargEstimator(BaseEstimator):
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"""scikit-learn estimators shouldn't have vargs."""
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def __init__(self, *vargs):
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pass
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#############################################################################
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# The tests
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def test_clone():
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# Tests that clone creates a correct deep copy.
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# We create an estimator, make a copy of its original state
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# (which, in this case, is the current state of the estimator),
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# and check that the obtained copy is a correct deep copy.
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from sklearn.feature_selection import SelectFpr, f_classif
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selector = SelectFpr(f_classif, alpha=0.1)
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new_selector = clone(selector)
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assert selector is not new_selector
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assert selector.get_params() == new_selector.get_params()
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selector = SelectFpr(f_classif, alpha=np.zeros((10, 2)))
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new_selector = clone(selector)
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assert selector is not new_selector
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def test_clone_2():
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# Tests that clone doesn't copy everything.
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# We first create an estimator, give it an own attribute, and
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# make a copy of its original state. Then we check that the copy doesn't
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# have the specific attribute we manually added to the initial estimator.
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from sklearn.feature_selection import SelectFpr, f_classif
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selector = SelectFpr(f_classif, alpha=0.1)
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selector.own_attribute = "test"
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new_selector = clone(selector)
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assert not hasattr(new_selector, "own_attribute")
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def test_clone_buggy():
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# Check that clone raises an error on buggy estimators.
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buggy = Buggy()
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buggy.a = 2
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assert_raises(RuntimeError, clone, buggy)
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no_estimator = NoEstimator()
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assert_raises(TypeError, clone, no_estimator)
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varg_est = VargEstimator()
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assert_raises(RuntimeError, clone, varg_est)
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est = ModifyInitParams()
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assert_raises(RuntimeError, clone, est)
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def test_clone_empty_array():
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# Regression test for cloning estimators with empty arrays
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clf = MyEstimator(empty=np.array([]))
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clf2 = clone(clf)
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assert_array_equal(clf.empty, clf2.empty)
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clf = MyEstimator(empty=sp.csr_matrix(np.array([[0]])))
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clf2 = clone(clf)
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assert_array_equal(clf.empty.data, clf2.empty.data)
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def test_clone_nan():
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# Regression test for cloning estimators with default parameter as np.nan
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clf = MyEstimator(empty=np.nan)
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clf2 = clone(clf)
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assert clf.empty is clf2.empty
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def test_clone_sparse_matrices():
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sparse_matrix_classes = [
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getattr(sp, name)
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for name in dir(sp) if name.endswith('_matrix')]
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for cls in sparse_matrix_classes:
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sparse_matrix = cls(np.eye(5))
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clf = MyEstimator(empty=sparse_matrix)
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clf_cloned = clone(clf)
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assert clf.empty.__class__ is clf_cloned.empty.__class__
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assert_array_equal(clf.empty.toarray(), clf_cloned.empty.toarray())
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def test_clone_estimator_types():
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# Check that clone works for parameters that are types rather than
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# instances
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clf = MyEstimator(empty=MyEstimator)
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clf2 = clone(clf)
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assert clf.empty is clf2.empty
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def test_clone_class_rather_than_instance():
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# Check that clone raises expected error message when
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# cloning class rather than instance
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msg = "You should provide an instance of scikit-learn estimator"
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with pytest.raises(TypeError, match=msg):
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clone(MyEstimator)
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def test_repr():
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# Smoke test the repr of the base estimator.
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my_estimator = MyEstimator()
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repr(my_estimator)
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test = T(K(), K())
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assert (
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repr(test) ==
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"T(a=K(), b=K())")
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some_est = T(a=["long_params"] * 1000)
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assert len(repr(some_est)) == 485
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def test_str():
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# Smoke test the str of the base estimator
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my_estimator = MyEstimator()
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str(my_estimator)
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def test_get_params():
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test = T(K(), K())
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assert 'a__d' in test.get_params(deep=True)
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assert 'a__d' not in test.get_params(deep=False)
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test.set_params(a__d=2)
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assert test.a.d == 2
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assert_raises(ValueError, test.set_params, a__a=2)
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def test_is_classifier():
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svc = SVC()
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assert is_classifier(svc)
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assert is_classifier(GridSearchCV(svc, {'C': [0.1, 1]}))
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assert is_classifier(Pipeline([('svc', svc)]))
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assert is_classifier(Pipeline(
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[('svc_cv', GridSearchCV(svc, {'C': [0.1, 1]}))]))
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def test_set_params():
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# test nested estimator parameter setting
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clf = Pipeline([("svc", SVC())])
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# non-existing parameter in svc
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assert_raises(ValueError, clf.set_params, svc__stupid_param=True)
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# non-existing parameter of pipeline
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assert_raises(ValueError, clf.set_params, svm__stupid_param=True)
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# we don't currently catch if the things in pipeline are estimators
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# bad_pipeline = Pipeline([("bad", NoEstimator())])
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# assert_raises(AttributeError, bad_pipeline.set_params,
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# bad__stupid_param=True)
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def test_set_params_passes_all_parameters():
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# Make sure all parameters are passed together to set_params
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# of nested estimator. Regression test for #9944
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class TestDecisionTree(DecisionTreeClassifier):
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def set_params(self, **kwargs):
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super().set_params(**kwargs)
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# expected_kwargs is in test scope
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assert kwargs == expected_kwargs
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return self
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expected_kwargs = {'max_depth': 5, 'min_samples_leaf': 2}
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for est in [Pipeline([('estimator', TestDecisionTree())]),
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GridSearchCV(TestDecisionTree(), {})]:
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est.set_params(estimator__max_depth=5,
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estimator__min_samples_leaf=2)
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def test_set_params_updates_valid_params():
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# Check that set_params tries to set SVC().C, not
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# DecisionTreeClassifier().C
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gscv = GridSearchCV(DecisionTreeClassifier(), {})
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gscv.set_params(estimator=SVC(), estimator__C=42.0)
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assert gscv.estimator.C == 42.0
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def test_score_sample_weight():
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rng = np.random.RandomState(0)
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# test both ClassifierMixin and RegressorMixin
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estimators = [DecisionTreeClassifier(max_depth=2),
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DecisionTreeRegressor(max_depth=2)]
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sets = [datasets.load_iris(),
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datasets.load_boston()]
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for est, ds in zip(estimators, sets):
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est.fit(ds.data, ds.target)
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# generate random sample weights
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sample_weight = rng.randint(1, 10, size=len(ds.target))
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# check that the score with and without sample weights are different
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assert (est.score(ds.data, ds.target) !=
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est.score(ds.data, ds.target,
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sample_weight=sample_weight)), (
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"Unweighted and weighted scores "
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"are unexpectedly equal")
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def test_clone_pandas_dataframe():
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class DummyEstimator(TransformerMixin, BaseEstimator):
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"""This is a dummy class for generating numerical features
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This feature extractor extracts numerical features from pandas data
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frame.
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Parameters
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----------
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df: pandas data frame
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The pandas data frame parameter.
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Notes
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-----
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"""
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def __init__(self, df=None, scalar_param=1):
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self.df = df
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self.scalar_param = scalar_param
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def fit(self, X, y=None):
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pass
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def transform(self, X):
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pass
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# build and clone estimator
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d = np.arange(10)
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df = MockDataFrame(d)
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e = DummyEstimator(df, scalar_param=1)
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cloned_e = clone(e)
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# the test
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assert (e.df == cloned_e.df).values.all()
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assert e.scalar_param == cloned_e.scalar_param
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def test_pickle_version_warning_is_not_raised_with_matching_version():
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iris = datasets.load_iris()
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tree = DecisionTreeClassifier().fit(iris.data, iris.target)
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tree_pickle = pickle.dumps(tree)
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assert b"version" in tree_pickle
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tree_restored = assert_no_warnings(pickle.loads, tree_pickle)
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# test that we can predict with the restored decision tree classifier
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score_of_original = tree.score(iris.data, iris.target)
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score_of_restored = tree_restored.score(iris.data, iris.target)
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assert score_of_original == score_of_restored
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class TreeBadVersion(DecisionTreeClassifier):
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def __getstate__(self):
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return dict(self.__dict__.items(), _sklearn_version="something")
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pickle_error_message = (
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"Trying to unpickle estimator {estimator} from "
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"version {old_version} when using version "
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"{current_version}. This might "
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"lead to breaking code or invalid results. "
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"Use at your own risk.")
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def test_pickle_version_warning_is_issued_upon_different_version():
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iris = datasets.load_iris()
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tree = TreeBadVersion().fit(iris.data, iris.target)
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tree_pickle_other = pickle.dumps(tree)
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message = pickle_error_message.format(estimator="TreeBadVersion",
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old_version="something",
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current_version=sklearn.__version__)
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assert_warns_message(UserWarning, message, pickle.loads, tree_pickle_other)
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class TreeNoVersion(DecisionTreeClassifier):
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def __getstate__(self):
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return self.__dict__
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def test_pickle_version_warning_is_issued_when_no_version_info_in_pickle():
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iris = datasets.load_iris()
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# TreeNoVersion has no getstate, like pre-0.18
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tree = TreeNoVersion().fit(iris.data, iris.target)
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tree_pickle_noversion = pickle.dumps(tree)
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assert b"version" not in tree_pickle_noversion
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message = pickle_error_message.format(estimator="TreeNoVersion",
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old_version="pre-0.18",
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current_version=sklearn.__version__)
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# check we got the warning about using pre-0.18 pickle
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assert_warns_message(UserWarning, message, pickle.loads,
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tree_pickle_noversion)
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def test_pickle_version_no_warning_is_issued_with_non_sklearn_estimator():
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iris = datasets.load_iris()
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tree = TreeNoVersion().fit(iris.data, iris.target)
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tree_pickle_noversion = pickle.dumps(tree)
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try:
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module_backup = TreeNoVersion.__module__
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TreeNoVersion.__module__ = "notsklearn"
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assert_no_warnings(pickle.loads, tree_pickle_noversion)
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finally:
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TreeNoVersion.__module__ = module_backup
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class DontPickleAttributeMixin:
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def __getstate__(self):
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data = self.__dict__.copy()
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data["_attribute_not_pickled"] = None
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return data
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def __setstate__(self, state):
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state["_restored"] = True
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self.__dict__.update(state)
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class MultiInheritanceEstimator(DontPickleAttributeMixin, BaseEstimator):
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def __init__(self, attribute_pickled=5):
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self.attribute_pickled = attribute_pickled
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self._attribute_not_pickled = None
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def test_pickling_when_getstate_is_overwritten_by_mixin():
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estimator = MultiInheritanceEstimator()
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estimator._attribute_not_pickled = "this attribute should not be pickled"
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serialized = pickle.dumps(estimator)
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estimator_restored = pickle.loads(serialized)
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assert estimator_restored.attribute_pickled == 5
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assert estimator_restored._attribute_not_pickled is None
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assert estimator_restored._restored
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def test_pickling_when_getstate_is_overwritten_by_mixin_outside_of_sklearn():
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try:
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estimator = MultiInheritanceEstimator()
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text = "this attribute should not be pickled"
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estimator._attribute_not_pickled = text
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old_mod = type(estimator).__module__
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type(estimator).__module__ = "notsklearn"
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serialized = estimator.__getstate__()
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assert serialized == {'_attribute_not_pickled': None,
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'attribute_pickled': 5}
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serialized['attribute_pickled'] = 4
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estimator.__setstate__(serialized)
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assert estimator.attribute_pickled == 4
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assert estimator._restored
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finally:
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type(estimator).__module__ = old_mod
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class SingleInheritanceEstimator(BaseEstimator):
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def __init__(self, attribute_pickled=5):
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self.attribute_pickled = attribute_pickled
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self._attribute_not_pickled = None
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def __getstate__(self):
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data = self.__dict__.copy()
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data["_attribute_not_pickled"] = None
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return data
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@ignore_warnings(category=(UserWarning))
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def test_pickling_works_when_getstate_is_overwritten_in_the_child_class():
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estimator = SingleInheritanceEstimator()
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estimator._attribute_not_pickled = "this attribute should not be pickled"
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serialized = pickle.dumps(estimator)
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estimator_restored = pickle.loads(serialized)
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assert estimator_restored.attribute_pickled == 5
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assert estimator_restored._attribute_not_pickled is None
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def test_tag_inheritance():
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# test that changing tags by inheritance is not allowed
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nan_tag_est = NaNTag()
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no_nan_tag_est = NoNaNTag()
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assert nan_tag_est._get_tags()['allow_nan']
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assert not no_nan_tag_est._get_tags()['allow_nan']
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redefine_tags_est = OverrideTag()
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assert not redefine_tags_est._get_tags()['allow_nan']
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diamond_tag_est = DiamondOverwriteTag()
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assert diamond_tag_est._get_tags()['allow_nan']
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inherit_diamond_tag_est = InheritDiamondOverwriteTag()
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assert inherit_diamond_tag_est._get_tags()['allow_nan']
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def test_raises_on_get_params_non_attribute():
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class MyEstimator(BaseEstimator):
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def __init__(self, param=5):
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pass
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def fit(self, X, y=None):
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return self
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est = MyEstimator()
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msg = "'MyEstimator' object has no attribute 'param'"
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with pytest.raises(AttributeError, match=msg):
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est.get_params()
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def test_repr_mimebundle_():
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# Checks the display configuration flag controls the json output
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tree = DecisionTreeClassifier()
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output = tree._repr_mimebundle_()
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assert "text/plain" in output
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assert "text/html" not in output
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with config_context(display='diagram'):
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output = tree._repr_mimebundle_()
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assert "text/plain" in output
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assert "text/html" in output
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def test_repr_html_wraps():
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# Checks the display configuration flag controls the html output
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tree = DecisionTreeClassifier()
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msg = "_repr_html_ is only defined when"
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with pytest.raises(AttributeError, match=msg):
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output = tree._repr_html_()
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|
|
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with config_context(display='diagram'):
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output = tree._repr_html_()
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assert "<style>" in output
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|
|
|
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# TODO: Remove in 1.1 when the _pairwise attribute is removed
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|
def test_is_pairwise():
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|
# simple checks for _is_pairwise
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|
pca = KernelPCA(kernel='precomputed')
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|
with pytest.warns(None) as record:
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|
assert _is_pairwise(pca)
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|
assert not record
|
|
|
|
# pairwise attribute that is not consistent with the pairwise tag
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|
class IncorrectTagPCA(KernelPCA):
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|
_pairwise = False
|
|
|
|
pca = IncorrectTagPCA(kernel='precomputed')
|
|
msg = "_pairwise was deprecated in 0.24 and will be removed in 1.1"
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|
with pytest.warns(FutureWarning, match=msg):
|
|
assert not _is_pairwise(pca)
|
|
|
|
# the _pairwise attribute is present and set to True while pairwise tag is
|
|
# not present
|
|
class TruePairwise(BaseEstimator):
|
|
_pairwise = True
|
|
|
|
true_pairwise = TruePairwise()
|
|
with pytest.warns(FutureWarning, match=msg):
|
|
assert _is_pairwise(true_pairwise)
|
|
|
|
# pairwise attribute is not defined thus tag is used
|
|
est = BaseEstimator()
|
|
with pytest.warns(None) as record:
|
|
assert not _is_pairwise(est)
|
|
assert not record
|