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