from sklearn.linear_model import LogisticRegression, LinearRegression
from sklearn.exceptions import NotFittedError
from sklego.common import flatten
from sklego.meta import Thresholder
from tests.conftest import general_checks, classifier_checks, select_tests
@pytest.mark.parametrize(
"test_fn",
select_tests(flatten([general_checks, classifier_checks]),
exclude=[
"check_sample_weights_invariance",
"check_fit2d_predict1d",
"check_methods_subset_invariance",
"check_dont_overwrite_parameters",
"check_classifiers_classes",
"check_classifiers_train",
"check_supervised_y_2d",
]
# outliers train wont work because we have two thresholds
),
)
def test_standard_checks(test_fn):
trf = Thresholder(LogisticRegression(), threshold=0.5)
test_fn(Thresholder.__name__, trf)
def test_same_threshold():
mod1 = Thresholder(LogisticRegression(), threshold=0.5)
mod2 = LogisticRegression()
X = np.random.normal(0, 1, (100, 3))
import numpy as np
from sklearn.ensemble import IsolationForest
from sklearn.cluster import KMeans
from sklearn.pipeline import Pipeline
from sklego.common import flatten
from sklego.meta import OutlierRemover
from sklego.mixture import GMMOutlierDetector
from tests.conftest import general_checks, select_tests
@pytest.mark.parametrize("test_fn",
select_tests(flatten([general_checks]),
exclude=[
"check_sample_weights_invariance",
"check_methods_subset_invariance"
]))
def test_estimator_checks(test_fn):
gmm_remover = OutlierRemover(outlier_detector=GMMOutlierDetector(),
refit=True)
test_fn(OutlierRemover.__name__, gmm_remover)
isolation_forest_remover = OutlierRemover(
outlier_detector=IsolationForest(), refit=True)
test_fn(OutlierRemover.__name__, isolation_forest_remover)
def test_no_outliers(mocker):
mock_outlier_detector = mocker.Mock()
mock_outlier_detector.fit.return_value = None
import numpy as np
import pytest
from sklego.common import flatten
from sklego.linear_model import ProbWeightRegression
from tests.conftest import nonmeta_checks, regressor_checks, general_checks, select_tests
@pytest.mark.parametrize(
"test_fn",
select_tests(flatten([general_checks, nonmeta_checks, regressor_checks]),
exclude=[
"check_sample_weights_invariance",
]))
@pytest.mark.cvxpy
def test_estimator_checks(test_fn):
regr_min_zero = ProbWeightRegression(non_negative=True)
test_fn(ProbWeightRegression.__name__ + "_min_zero_true", regr_min_zero)
regr_not_min_zero = ProbWeightRegression(non_negative=False)
test_fn(ProbWeightRegression.__name__ + "_min_zero_true_false",
regr_not_min_zero)
@pytest.mark.cvxpy
def test_shape_trained_model(random_xy_dataset_regr):
X, y = random_xy_dataset_regr
mod_no_intercept = ProbWeightRegression()
assert mod_no_intercept.fit(X, y).coefs_.shape == (X.shape[1], )
np.testing.assert_approx_equal(mod_no_intercept.fit(X, y).coefs_.sum(),
1.0,
significant=4)
import numpy as np
import pytest
from sklego.common import flatten
from sklego.linear_model import ProbWeightRegression
from tests.conftest import nonmeta_checks, regressor_checks, general_checks, select_tests
@pytest.mark.parametrize(
"test_fn",
select_tests(
flatten([general_checks, nonmeta_checks, regressor_checks]),
exclude=[
"check_sample_weights_invariance",
"check_sample_weights_list",
"check_sample_weights_pandas_series"
]
)
)
@pytest.mark.cvxpy
def test_estimator_checks(test_fn):
regr_min_zero = ProbWeightRegression(non_negative=True)
test_fn(ProbWeightRegression.__name__ + "_min_zero_true", regr_min_zero)
regr_not_min_zero = ProbWeightRegression(non_negative=False)
test_fn(ProbWeightRegression.__name__ + "_min_zero_true_false", regr_not_min_zero)
@pytest.mark.cvxpy
def test_shape_trained_model(random_xy_dataset_regr):
X, y = random_xy_dataset_regr
mod_no_intercept = ProbWeightRegression()
from sklego.common import flatten
from sklego.meta import ZeroInflatedRegressor
from sklego.testing import check_shape_remains_same_regressor
from tests.conftest import general_checks, select_tests, regressor_checks
@pytest.mark.parametrize("test_fn", [check_shape_remains_same_regressor])
def test_zir(test_fn):
regr = ZeroInflatedRegressor(
classifier=ExtraTreesClassifier(random_state=0),
regressor=ExtraTreesRegressor(random_state=0))
test_fn(ZeroInflatedRegressor.__name__, regr)
@pytest.mark.parametrize("test_fn",
select_tests(
flatten([general_checks, regressor_checks]), ))
def test_estimator_checks(test_fn):
test_fn(
ZeroInflatedRegressor.__name__,
ZeroInflatedRegressor(classifier=ExtraTreesClassifier(random_state=0),
regressor=ExtraTreesRegressor(random_state=0)))
def test_zero_inflated_example():
from sklearn.model_selection import cross_val_score
np.random.seed(0)
X = np.random.randn(10000, 4)
y = ((X[:, 0] > 0) & (X[:, 1] > 0)) * np.abs(
X[:, 2] * X[:, 3]**2) # many zeroes here, in about 75% of the cases.
from sklearn.model_selection import train_test_split
from sklego.common import flatten
from sklego.preprocessing import RandomAdder
from tests.conftest import select_tests, transformer_checks, nonmeta_checks, general_checks
@pytest.mark.parametrize(
"test_fn",
select_tests(
flatten([general_checks, transformer_checks, nonmeta_checks]),
exclude=[
"check_sample_weights_invariance",
"check_methods_subset_invariance",
"check_transformer_data_not_an_array",
"check_transformer_general"
]
)
)
def test_estimator_checks(test_fn):
adder = RandomAdder()
test_fn(RandomAdder.__name__, adder)
def test_dtype_regression(random_xy_dataset_regr):
X, y = random_xy_dataset_regr
assert RandomAdder().fit(X, y).transform(X).dtype == np.float
import numpy as np
import pandas as pd
import pytest
from sklego.common import flatten
from sklego.mixture import GMMOutlierDetector, BayesianGMMOutlierDetector
from tests.conftest import general_checks, nonmeta_checks, select_tests, outlier_checks
@pytest.mark.parametrize(
"test_fn",
select_tests(
flatten([general_checks, nonmeta_checks, outlier_checks]),
exclude=[
"check_sample_weights_invariance",
"check_outliers_train"
]
)
)
def test_estimator_checks(test_fn):
clf_quantile = GMMOutlierDetector(threshold=0.999, method="quantile")
test_fn(GMMOutlierDetector.__name__ + "_quantile", clf_quantile)
clf_stddev = GMMOutlierDetector(threshold=2, method="stddev")
test_fn(GMMOutlierDetector.__name__ + "_stddev", clf_stddev)
bayes_clf_quantile = BayesianGMMOutlierDetector(threshold=0.999, method="quantile")
test_fn(BayesianGMMOutlierDetector.__name__ + "_quantile", bayes_clf_quantile)
bayes_clf_stddev = BayesianGMMOutlierDetector(threshold=2, method="stddev")
test_fn(BayesianGMMOutlierDetector.__name__ + "_stddev", bayes_clf_stddev)
import numpy as np
import pandas as pd
import pytest
from sklego.common import flatten
from sklego.preprocessing import DictMapper
from tests.conftest import select_tests, transformer_checks, general_checks, nonmeta_checks
@pytest.mark.parametrize(
"test_fn",
select_tests(
flatten([general_checks, nonmeta_checks, transformer_checks]),
exclude=["check_sample_weights_invariance", "check_dtype_object"]))
def test_estimator_checks(test_fn):
test_fn(DictMapper.__name__, DictMapper(mapper={"foo": 1}, default=-1))
@pytest.fixture()
def mapper():
return {"foo": 1, "bar": 2, "baz": 3}
@pytest.mark.parametrize(
"input_array,expected_array",
[
(["foo", "bar", "baz"], [1, 2, 3]),
(["foo", "bar", "bar"], [1, 2, 2]),
(["foo", "bar", "monty"], [1, 2, -1]),
(["foo", "bar", np.nan], [1, 2, -1]),
from tests.conftest import (
nonmeta_checks,
general_checks,
transformer_checks,
select_tests,
)
@pytest.mark.parametrize(
"test_fn",
select_tests(
flatten([nonmeta_checks, transformer_checks, general_checks]),
exclude=[
"check_transformer_data_not_an_array",
"check_estimators_nan_inf",
"check_fit2d_predict1d",
"check_sample_weights_invariance",
],
),
)
def test_estimator_checks_binary(test_fn):
random_proj = BinaryRandomProjection(random_seed=42)
test_fn(random_proj, random_proj)
@pytest.mark.parametrize(
"test_fn",
select_tests(
flatten([nonmeta_checks, transformer_checks, general_checks]),
exclude=[
import pytest
import numpy as np
from sklego.common import flatten
from sklego.decomposition import PCAOutlierDetection
from tests.conftest import general_checks, outlier_checks, select_tests, nonmeta_checks
@pytest.mark.parametrize(
"test_fn",
select_tests(flatten([general_checks, nonmeta_checks, outlier_checks]),
exclude=[
"check_sample_weights_invariance",
"check_outliers_fit_predict", "check_outliers_train",
"check_sample_weights_list",
"check_sample_weights_pandas_series"
]))
def test_estimator_checks(test_fn):
outlier_mod = PCAOutlierDetection(n_components=2,
threshold=0.05,
random_state=42,
variant='absolute')
test_fn(PCAOutlierDetection.__name__, outlier_mod)
@pytest.fixture
def dataset():
np.random.seed(42)
return np.concatenate([np.random.normal(0, 1, (2000, 10))])
import pytest
import numpy as np
from sklego.common import flatten
from sklego.decomposition import UMAPOutlierDetection
from tests.conftest import general_checks, outlier_checks, select_tests, nonmeta_checks
@pytest.mark.parametrize(
"test_fn",
select_tests(
flatten([general_checks, nonmeta_checks, outlier_checks]),
exclude=[
"check_sample_weights_invariance", "check_outliers_fit_predict",
"check_outliers_train", "check_fit2d_predict1d",
"check_methods_subset_invariance", "check_fit2d_1sample",
"check_fit2d_1feature", "check_dict_unchanged",
"check_dont_overwrite_parameters",
"check_classifier_data_not_an_array", "check_sample_weights_list",
"check_sample_weights_pandas_series"
]))
def test_estimator_checks(test_fn):
outlier_mod = UMAPOutlierDetection(n_components=2, threshold=0.1)
test_fn(UMAPOutlierDetection.__name__, outlier_mod)
@pytest.fixture
def dataset():
np.random.seed(42)
return np.concatenate([np.random.normal(0, 1, (200, 10))])
import pytest
import numpy as np
import pandas as pd
from sklearn.linear_model import LinearRegression, LogisticRegression
from sklego.common import flatten
from sklego.meta import RegressionOutlierDetector
from tests.conftest import general_checks, select_tests, outlier_checks
@pytest.mark.parametrize(
"test_fn",
select_tests(
flatten([general_checks, outlier_checks]),
exclude=['check_fit2d_predict1d', 'check_fit2d_1feature', 'check_outliers_train']
# outliers train wont work because we have two thresholds
)
)
def test_estimator_checks(test_fn):
mod = RegressionOutlierDetector(LinearRegression(), column=0)
test_fn(RegressionOutlierDetector.__name__, mod)
def test_obvious_example():
# generate random data for illustrative example
np.random.seed(42)
X = np.random.normal(0, 1, (100, 1))
y = 1 + np.sum(X, axis=1).reshape(-1, 1) + np.random.normal(0, 0.2, (100, 1))
for i in [20, 25, 50, 80]:
y[i] += 2
import numpy as np
import pytest
from sklearn.cluster import DBSCAN
from sklearn.ensemble import RandomForestClassifier
from sklearn.linear_model import Ridge, LogisticRegression
from sklego.common import flatten
from sklego.meta import SubjectiveClassifier
from tests.conftest import general_checks, classifier_checks, select_tests
@pytest.mark.parametrize(
"test_fn",
select_tests(
flatten([general_checks, classifier_checks]),
exclude=['check_sample_weights_invariance']
# outliers train wont work because we have two thresholds
)
)
def test_estimator_checks_classification(test_fn):
if test_fn.__name__ == "check_classifiers_classes":
prior = {
"one": 0.1,
"two": 0.1,
"three": 0.1,
-1: 0.1,
1: 0.6,
} # nonsensical prior to make sklearn check pass
else:
prior = {0: 0.7, 1: 0.2, 2: 0.1}
from sklearn.pipeline import Pipeline
from sklearn.linear_model import LinearRegression
from sklearn.model_selection import GridSearchCV
from sklearn.datasets import load_boston
from sklego.common import flatten
from sklego.preprocessing import InformationFilter
from tests.conftest import select_tests, transformer_checks, nonmeta_checks, general_checks
@pytest.mark.parametrize(
"test_fn",
select_tests(flatten([general_checks, transformer_checks, nonmeta_checks]),
exclude=[
"check_sample_weights_invariance",
"check_estimators_empty_data_messages"
]))
def test_estimator_checks(test_fn):
test_fn(InformationFilter.__name__, InformationFilter(columns=[0]))
def test_v_columns_orthogonal():
X, y = load_boston(return_X_y=True)
ifilter = InformationFilter(columns=[11, 12]).fit(X, y)
v_values = ifilter._make_v_vectors(X, [11, 12])
assert v_values.prod(axis=1).sum() == pytest.approx(0, abs=1e-5)
def test_output_orthogonal():
X, y = load_boston(return_X_y=True)
import numpy as np
from sklearn.ensemble import IsolationForest
from sklearn.svm import OneClassSVM
from sklearn.linear_model import LinearRegression
from sklearn.neighbors import LocalOutlierFactor
from sklego.common import flatten
from sklego.mixture import GMMOutlierDetector
from sklego.meta import OutlierClassifier
from tests.conftest import general_checks, select_tests
@pytest.mark.parametrize("test_fn",
select_tests(flatten([general_checks]),
exclude=[
"check_sample_weights_invariance",
]))
def test_estimator_checks(test_fn):
mod_quantile = GMMOutlierDetector(threshold=0.999, method="quantile")
clf_quantile = OutlierClassifier(mod_quantile)
test_fn('OutlierClassifier', clf_quantile)
@pytest.fixture
def dataset():
np.random.seed(42)
return np.random.normal(0, 1, (2000, 2))
@pytest.mark.parametrize(
'outlier_model',
from sklearn.dummy import DummyClassifier
from sklearn.ensemble import StackingClassifier
from sklego.common import flatten
from sklego.meta import Thresholder
from tests.conftest import general_checks, classifier_checks, select_tests
@pytest.mark.parametrize(
"test_fn",
select_tests(
flatten([general_checks, classifier_checks]),
exclude=[
"check_sample_weights_invariance",
"check_fit2d_predict1d",
"check_methods_subset_invariance",
"check_dont_overwrite_parameters",
"check_classifiers_classes",
"check_classifiers_train",
"check_supervised_y_2d",
"check_classifier_data_not_an_array", # https://github.com/koaning/scikit-lego/issues/490
]
# outliers train wont work because we have two thresholds
),
)
def test_standard_checks(test_fn):
trf = Thresholder(LogisticRegression(), threshold=0.5)
test_fn(Thresholder.__name__, trf)
def test_same_threshold():
mod1 = Thresholder(LogisticRegression(), threshold=0.5)
mod2 = LogisticRegression()
return np.array(
[1 if r > 0.0 else 0 for r in np.random.normal(0, 1, len(X))])
@pytest.mark.parametrize(
"test_fn",
select_tests(
include=flatten([general_checks, regressor_checks, nonmeta_checks]),
exclude=[
"check_methods_subset_invariance",
"check_fit2d_1sample",
"check_fit2d_1feature",
"check_regressors_train",
"check_fit2d_predict1d",
"check_fit1d",
"check_regressor_data_not_an_array",
"check_supervised_y_2d",
"check_supervised_y_no_nan",
"check_dtype_object",
"check_complex_data",
"check_estimators_empty_data_messages",
"check_estimators_nan_inf",
"check_estimator_sparse_data",
],
),
)
def test_estimator_checks(test_fn):
clf = FunctionRegressor(func=predict)
test_fn(FunctionRegressor.__name__ + "_fallback", clf)
import numpy as np
import pytest
from sklego.common import flatten
from sklego.dummy import RandomRegressor
from tests.conftest import nonmeta_checks, regressor_checks, general_checks, select_tests
@pytest.mark.parametrize(
"test_fn",
select_tests(flatten([general_checks, nonmeta_checks, regressor_checks]),
exclude=[
"check_sample_weights_invariance",
"check_methods_subset_invariance",
"check_regressors_train"
]))
def test_estimator_checks(test_fn):
# Tests that are skipped:
# 'check_methods_subset_invariance': Since we add noise, the method is not invariant on a subset
# 'check_regressors_train': score is not always greater than 0.5 due to randomness
regr_normal = RandomRegressor(strategy="normal")
test_fn(RandomRegressor.__name__ + "_normal", regr_normal)
regr_uniform = RandomRegressor(strategy="uniform")
test_fn(RandomRegressor.__name__ + "_uniform", regr_uniform)
def test_values_uniform(random_xy_dataset_regr):
X, y = random_xy_dataset_regr
mod = RandomRegressor(strategy="uniform")
predictions = mod.fit(X, y).predict(X)
nonmeta_checks,
)
def double(x, factor=2):
return x * factor
@pytest.mark.parametrize(
"test_fn",
select_tests(
include=flatten([general_checks, transformer_checks, nonmeta_checks]),
exclude=[
"check_estimators_nan_inf",
"check_estimators_empty_data_messages",
"check_transformer_data_not_an_array",
"check_dtype_object",
"check_complex_data",
"check_fit1d",
],
),
)
def test_estimator_checks(test_fn):
clf = PipeTransformer(func=double)
test_fn(PipeTransformer.__name__, clf)
@pytest.mark.parametrize("factor", [1.0, 2.0, 5.0])
def test_basic_example(factor):
np.random.seed(42)
X = np.random.normal(0, 1, (1000, 4))
@pytest.mark.parametrize(
"test_fn",
select_tests(
include=flatten([general_checks, classifier_checks, nonmeta_checks]),
exclude=[
"check_estimators_pickle",
"check_estimator_sparse_data",
"check_estimators_nan_inf",
"check_pipeline_consistency",
"check_complex_data",
"check_fit2d_predict1d",
"check_methods_subset_invariance",
"check_fit1d",
"check_dict_unchanged",
"check_classifier_data_not_an_array",
"check_classifiers_one_label",
"check_classifiers_classes",
"check_classifiers_train",
"check_supervised_y_2d",
"check_supervised_y_no_nan",
"check_estimators_unfitted",
"check_estimators_dtypes",
"check_fit_score_takes_y",
"check_dtype_object",
"check_estimators_empty_data_messages",
"check_sample_weights_list",
"check_sample_weights_pandas_series",
],
),
)
def test_estimator_checks(test_fn):
import pytest
import numpy as np
import pandas as pd
from sklearn.utils.validation import FLOAT_DTYPES
from sklego.common import flatten
from sklego.preprocessing import ColumnCapper
from tests.conftest import select_tests, transformer_checks, general_checks, nonmeta_checks
@pytest.mark.parametrize(
"test_fn",
select_tests(flatten([general_checks, nonmeta_checks, transformer_checks]),
exclude=[
"check_sample_weights_invariance",
"check_estimators_nan_inf", "check_sample_weights_list",
"check_sample_weights_pandas_series"
]))
def test_estimator_checks(test_fn):
test_fn(ColumnCapper.__name__, ColumnCapper())
def test_quantile_range():
def expect_type_error(quantile_range):
with pytest.raises(TypeError):
ColumnCapper(quantile_range)
def expect_value_error(quantile_range):
with pytest.raises(ValueError):
ColumnCapper(quantile_range)
import numpy as np
import pytest
from sklego.common import flatten
from sklego.mixture import GMMClassifier, BayesianGMMClassifier
from tests.conftest import general_checks, nonmeta_checks, select_tests
@pytest.mark.parametrize(
"test_fn",
select_tests(
flatten([general_checks, nonmeta_checks]),
exclude=[
"check_sample_weights_invariance",
"check_non_transformer_estimators_n_iter",
]
)
)
def test_estimator_checks(test_fn):
clf = GMMClassifier()
test_fn(GMMClassifier.__name__, clf)
clf = BayesianGMMClassifier()
test_fn(BayesianGMMClassifier.__name__, clf)
def test_obvious_usecase():
X = np.concatenate(
[np.random.normal(-10, 1, (100, 2)), np.random.normal(10, 1, (100, 2))]
)
y = np.concatenate([np.zeros(100), np.ones(100)])
assert (GMMClassifier().fit(X, y).predict(X) == y).all()
from sklearn.dummy import DummyRegressor
from sklego.common import flatten
from sklego.meta import GroupedPredictor
from sklego.datasets import load_chicken
from tests.conftest import general_checks, select_tests
@pytest.mark.parametrize(
"test_fn",
select_tests(
flatten([general_checks]),
exclude=[
# Nonsense checks because we always need at least two columns (group and value)
"check_fit1d",
"check_fit2d_predict1d",
"check_fit2d_1feature",
"check_transformer_data_not_an_array",
],
),
)
def test_estimator_checks(test_fn):
clf = GroupedPredictor(
estimator=LinearRegression(), groups=0, use_global_model=True
)
test_fn(GroupedPredictor.__name__ + "_fallback", clf)
clf = GroupedPredictor(
estimator=LinearRegression(), groups=0, use_global_model=False
)
test_fn(GroupedPredictor.__name__ + "_nofallback", clf)
general_checks,
nonmeta_checks,
)
@pytest.mark.parametrize(
"test_fn",
select_tests(
include=flatten([general_checks, nonmeta_checks]),
exclude=[
"check_estimators_pickle",
"check_estimators_nan_inf",
"check_estimators_empty_data_messages",
"check_complex_data",
"check_dtype_object",
"check_estimators_dtypes",
"check_dict_unchanged",
"check_fit1d",
"check_methods_subset_invariance",
"check_fit2d_predict1d",
"check_sample_weights_list",
"check_sample_weights_pandas_series",
],
),
)
def test_estimator_checks(test_fn):
"""
We're skipping a lot of tests here mainly because this model is "bespoke"
it is *not* general. Therefore a lot of assumptions are broken.
"""
clf = InteractivePreprocessor.from_json(
def class_based(dataf, sex="male", pclass=1):
predicate = (dataf["sex"] == sex) & (dataf["pclass"] == pclass)
return np.array(predicate).astype(int) * 2 - 1
@pytest.mark.parametrize(
"test_fn",
select_tests(
include=flatten([general_checks, outlier_checks, nonmeta_checks]),
exclude=[
"check_outliers_train",
"check_estimators_nan_inf",
"check_estimators_empty_data_messages",
"check_complex_data",
"check_dtype_object",
"check_classifier_data_not_an_array",
"check_fit1d",
"check_methods_subset_invariance",
"check_fit2d_predict1d",
"check_estimator_sparse_data",
],
),
)
def test_estimator_checks(test_fn):
clf = FunctionOutlierDetector(func=predict)
test_fn(FunctionOutlierDetector.__name__ + "_fallback", clf)
def test_works_with_gridsearch(random_xy_dataset_clf):
X, y = random_xy_dataset_clf
return np.array(predicate).astype(int)
@pytest.mark.parametrize(
"test_fn",
select_tests(
include=flatten([general_checks, classifier_checks, nonmeta_checks]),
exclude=[
"check_methods_subset_invariance",
"check_fit2d_1sample",
"check_fit2d_1feature",
"check_classifier_data_not_an_array",
"check_classifiers_one_label",
"check_classifiers_classes",
"check_classifiers_train",
"check_supervised_y_2d",
"check_estimators_pickle",
"check_pipeline_consistency",
"check_fit2d_predict1d",
"check_fit1d",
"check_dtype_object",
"check_complex_data",
"check_estimators_empty_data_messages",
"check_estimators_nan_inf",
"check_estimator_sparse_data",
],
),
)
def test_estimator_checks(test_fn):
clf = FunctionClassifier(func=predict)
test_fn(FunctionClassifier.__name__ + "_fallback", clf)
