Ease multi-version support for scikit-learn compatible library

sklearn-compat is a small Python package that help developer writing scikit-learn compatible estimators to support multiple scikit-learn versions. Note that we provide a vendorable version of this package in the src/sklearn_compat/_sklearn_compat.py file if you do not want to depend on sklearn-compat as a package. The package is available on PyPI and on conda-forge.

As maintainers of third-party libraries depending on scikit-learn such as imbalanced-learn, skrub, or skops, we usually identified small breaking changes on the "private" developer utilities of scikit-learn. Indeed, each of these third-party libraries code the exact same utilities when it comes to support multiple scikit-learn versions. We therefore decided to factorize these utilities in a dedicated package that we update at each scikit-learn release.

When it comes to support multiple scikit-learn versions, the initial plan as of December 2024 is to follow the SPEC0 recommendations. It means that this utility will support at least the scikit-learn versions up to 2 years or about 4 versions. The current version of sklearn-compat supports scikit-learn >= 1.2.

How to adapt your scikit-learn code

In this section, we describe succinctly the changes you need to do to your code to support multiple scikit-learn versions using sklearn-compat as a package. If you use the vendored version of sklearn-compat, all imports will be changed from:

from sklearn_compat.any_submodule import any_function

to

from path.to._sklearn_compat import any_function

where _sklearn_compat is the vendored version of sklearn-compat in your project.

Upgrading to scikit-learn 1.6

is_clusterer function

The function is_clusterer has been added in scikit-learn 1.6. So we backport it such that you can have access to it in scikit-learn 1.2+. The pattern is the following:

from sklearn.cluster import KMeans
from sklearn_compat.base import is_clusterer

is_clusterer(KMeans())

validate_data function

Your previous code could have looked like this:

class MyEstimator(BaseEstimator):
    def fit(self, X, y=None):
        X = self._validate_data(X, force_all_finite=True)
        return self

There is two major changes in scikit-learn 1.6:

• validate_data has been moved to sklearn.utils.validation.
• force_all_finite is deprecated in favor of the ensure_all_finite parameter.

You can now use the following code for backward compatibility:

from sklearn_compat.utils.validation import validate_data

class MyEstimator(BaseEstimator):
    def fit(self, X, y=None):
        X = validate_data(self, X=X, ensure_all_finite=True)
        return self

check_array and check_X_y functions

The parameter force_all_finite has been deprecated in favor of the ensure_all_finite parameter. You need to modify the call to the function to use the new parameter. So, the change is the same as for validate_data and will look like this:

from sklearn.utils.validation import check_array, check_X_y

check_array(X, force_all_finite=True)
check_X_y(X, y, force_all_finite=True)

to:

from sklearn_compat.utils.validation import check_array, check_X_y

check_array(X, ensure_all_finite=True)
check_X_y(X, y, ensure_all_finite=True)

_check_n_features and _check_feature_names functions

Similarly to validate_data, these two functions have been moved to sklearn.utils.validation instead of being methods of the estimators. So the following code:

class MyEstimator(BaseEstimator):
    def fit(self, X, y=None):
        self._check_n_features(X, reset=True)
        self._check_feature_names(X, reset=True)
        return self

becomes:

from sklearn_compat.utils.validation import _check_n_features, _check_feature_names

class MyEstimator(BaseEstimator):
    def fit(self, X, y=None):
        _check_n_features(self, X, reset=True)
        _check_feature_names(self, X, reset=True)
        return self

Note that it is best to call validate_data with skip_check_array=True instead of calling these private functions. See the section above regarding validate_data.

Tags, __sklearn_tags__ and estimator tags

The estimator tags infrastructure in scikit-learn 1.6 has changed. In order to be compatible with multiple scikit-learn versions, your estimator should implement both _more_tags and __sklearn_tags__:

class MyEstimator(BaseEstimator):
    def _more_tags(self):
        return {"non_deterministic": True, "poor_score": True}

    def __sklearn_tags__(self):
        tags = super().__sklearn_tags__()
        tags.non_deterministic = True
        tags.regressor_tags.poor_score = True
        return tags

In order to get the tags of a given estimator, you can use the get_tags function:

from sklearn_compat.utils import get_tags

tags = get_tags(MyEstimator())

Which uses sklearn.utils.get_tags under the hood from scikit-learn 1.6+.

In case you want to extend the tags, you can inherit from the available tags:

from sklearn_compat.utils._tags import Tags, InputTags

class MyInputTags(InputTags):
    dataframe: bool = False

class MyEstimator(BaseEstimator):
    def __sklearn_tags__(self):
        tags = super().__sklearn_tags__()
        tags.input_tags = MyInputTags(
            one_d_array=tags.input_tags.one_d_array,
            two_d_array=tags.input_tags.two_d_array,
            sparse=tags.input_tags.sparse,
            category=True,
            dataframe=True,
            string=tags.input_tags.string,
            dict=tags.input_tags.dict,
            positive_only=tags.input_tags.positive_only,
            allow_nan=tags.input_tags.allow_nan,
            pairwise=tags.input_tags.pairwise,
        )
        return tags

check_estimator and parametrize_with_checks functions

The new tags don't include a _xfail_checks tags, and instead, the tests which are expected to fail are directly passed to the check_estimator and parametrize_with_checks functions. The two functions available in this package are compatible with the new signature, and patch the estimator in older scikit-learn versions to include the expected failed checks in their tags so that you don't need to include them both in your tests and in your _xfail_checks old tags.

from sklearn_compat.utils.testing import parametrize_with_checks
from mypackage.myestimator import MyEstimator1, MyEstimator2

EXPECTED_FAILED_CHECKS = {
    "MyEstimator1": {"check_name1": "reason1", "check_name2": "reason2"},
    "MyEstimator2": {"check_name3": "reason3"},
}

@parametrize_with_checks([MyEstimator1(), MyEstimator2()],
                        expected_failed_checks=lambda est: EXPECTED_FAILED_CHECKS.get(
                            est.__class__.__name__, {}
                        )
)
def test_my_estimator(estimator, check):
    check(estimator)

Upgrading to scikit-learn 1.5

In scikit-learn 1.5, many developer utilities have been moved to dedicated modules. We provide a compatibility layer such that you don't have to check the version or try to import the utilities from different modules.

In the future, when supporting scikit-learn 1.6+, you will have to change the import from:

from sklearn_compat.utils._indexing import _safe_indexing

to

from sklearn.utils._indexing import _safe_indexing

Thus, the module path will already be correct. Now, we will go into details for each module and function impacted.

extmath module

The function safe_sqr and _approximate_mode have been moved from sklearn.utils to sklearn.utils.extmath.

So some code looking like this:

from sklearn.utils import safe_sqr, _approximate_mode

safe_sqr(np.array([1, 2, 3]))
_approximate_mode(class_counts=np.array([4, 2]), n_draws=3, rng=0)

becomes:

from sklearn_compat.utils.extmath import safe_sqr, _approximate_mode

safe_sqr(np.array([1, 2, 3]))
_approximate_mode(class_counts=np.array([4, 2]), n_draws=3, rng=0)

type_of_target function

The function type_of_target accepts a new parameter raise_unknown. This parameter is available in the sklearn_compat.utils.multiclass.type_of_target function.

from sklearn_compat.utils.multiclass import type_of_target

y = []
# raise an error with unknown target type
type_of_target(y, raise_unknown=True)

fixes module

The functions _in_unstable_openblas_configuration, _IS_32BIT and _IS_WASM have been moved from sklearn.utils to sklearn.utils.fixes.

So the following code:

from sklearn.utils import (
    _in_unstable_openblas_configuration,
    _IS_32BIT,
    _IS_WASM,
)

_in_unstable_openblas_configuration()
print(_IS_32BIT)
print(_IS_WASM)

becomes:

from sklearn_compat.utils.fixes import (
    _in_unstable_openblas_configuration,
    _IS_32BIT,
    _IS_WASM,
)

_in_unstable_openblas_configuration()
print(_IS_32BIT)
print(_IS_WASM)

validation module

The function _to_object_array has been moved from sklearn.utils to sklearn.utils.validation.

So the following code:

from sklearn.utils import _to_object_array

_to_object_array([np.array([0]), np.array([1])])

becomes:

from sklearn_compat.utils.validation import _to_object_array

_to_object_array([np.array([0]), np.array([1])])

_chunking module

The functions gen_batches, gen_even_slices and get_chunk_n_rows have been moved from sklearn.utils to sklearn.utils._chunking. The function chunk_generator has been moved to sklearn.utils._chunking as well but was renamed from _chunk_generator to chunk_generator.

So the following code:

from sklearn.utils import (
    _chunk_generator as chunk_generator,
    gen_batches,
    gen_even_slices,
    get_chunk_n_rows,
)

_chunk_generator(range(10), 3)
gen_batches(7, 3)
gen_even_slices(10, 1)
get_chunk_n_rows(10)

becomes:

from sklearn_compat.utils._chunking import (
    chunk_generator, gen_batches, gen_even_slices, get_chunk_n_rows,
)

chunk_generator(range(10), 3)
gen_batches(7, 3)
gen_even_slices(10, 1)
get_chunk_n_rows(10)

_indexing module

The utility functions _determine_key_type, _safe_indexing, _safe_assign, _get_column_indices, resample and shuffle have been moved from sklearn.utils to sklearn.utils._indexing.

So the following code:

import numpy as np
import pandas as pd
from sklearn.utils import (
    _get_column_indices,
    _safe_indexing,
    _safe_assign,
    resample,
    shuffle,
)

_determine_key_type(np.arange(10))

df = pd.DataFrame({"a": [1, 2, 3], "b": [4, 5, 6]})
_get_column_indices(df, key="b")
_safe_indexing(df, 1, axis=1)
_safe_assign(df, 1, np.array([7, 8, 9]))

array = np.arange(10)
resample(array, n_samples=20, replace=True, random_state=0)
shuffle(array, random_state=0)

becomes:

import numpy as np
import pandas as pd
from sklearn_compat.utils._indexing import (
    _determine_key_type,
    _safe_indexing,
    _safe_assign,
    _get_column_indices,
    resample,
    shuffle,
)

_determine_key_type(np.arange(10))

df = pd.DataFrame({"a": [1, 2, 3], "b": [4, 5, 6]})
_get_column_indices(df, key="b")
_safe_indexing(df, 1, axis=1)
_safe_assign(df, 1, np.array([7, 8, 9]))

array = np.arange(10)
resample(array, n_samples=20, replace=True, random_state=0)
shuffle(array, random_state=0)

_mask module

The functions safe_mask, axis0_safe_slice and indices_to_mask have been moved from sklearn.utils to sklearn.utils._mask.

So the following code:

from sklearn.utils import safe_mask, axis0_safe_slice, indices_to_mask

safe_mask(data, condition)
axis0_safe_slice(X, mask, X.shape[0])
indices_to_mask(indices, 5)

becomes:

from sklearn_compat.utils._mask import safe_mask, axis0_safe_slice, indices_to_mask

safe_mask(data, condition)
axis0_safe_slice(X, mask, X.shape[0])
indices_to_mask(indices, 5)

_missing module

The functions is_scalar_nan have been moved from sklearn.utils to sklearn.utils._missing. The function _is_pandas_na has been moved to sklearn.utils._missing as well and renamed to is_pandas_na.

So the following code:

from sklearn.utils import is_scalar_nan, _is_pandas_na

is_scalar_nan(float("nan"))
_is_pandas_na(float("nan"))

becomes:

from sklearn_compat.utils._missing import is_scalar_nan, is_pandas_na

is_scalar_nan(float("nan"))
is_pandas_na(float("nan"))

_user_interface module

The function _print_elapsed_time has been moved from sklearn.utils to sklearn.utils._user_interface.

So the following code:

from sklearn.utils import _print_elapsed_time

with _print_elapsed_time("sklearn_compat", "testing"):
    time.sleep(0.1)

becomes:

from sklearn_compat.utils._user_interface import _print_elapsed_time

with _print_elapsed_time("sklearn_compat", "testing"):
    time.sleep(0.1)

_optional_dependencies module

The functions check_matplotlib_support and check_pandas_support have been moved from sklearn.utils to sklearn.utils._optional_dependencies.

So the following code:

from sklearn.utils import check_matplotlib_support, check_pandas_support

check_matplotlib_support("sklearn_compat")
check_pandas_support("sklearn_compat")

becomes:

from sklearn_compat.utils._optional_dependencies import (
    check_matplotlib_support, check_pandas_support
)

check_matplotlib_support("sklearn_compat")
check_pandas_support("sklearn_compat")

Upgrading to scikit-learn 1.4

process_routing and _raise_for_params functions

The signature of the process_routing function changed in scikit-learn 1.4. You can import the function from sklearn_compat.utils.metadata_routing. The pattern will change from:

from sklearn.utils.metadata_routing import process_routing

class MetaEstimator(BaseEstimator):
    def fit(self, X, y, sample_weight=None, **fit_params):
        params = process_routing(self, "fit", fit_params, sample_weight=sample_weight)
        return self

becomes:

from sklearn_compat.utils.metadata_routing import process_routing

class MetaEstimator(BaseEstimator):
    def fit(self, X, y, sample_weight=None, **fit_params):
        params = process_routing(self, "fit", sample_weight=sample_weight, **fit_params)
        return self

The _raise_for_params function was also introduced in scikit-learn 1.4. You can import it from sklearn_compat.utils.metadata_routing.

from sklearn_compat.utils.metadata_routing import _raise_for_params

_raise_for_params(params, self, "fit")

Upgrading to scikit-learn 1.2

Parameter validation

scikit-learn introduced a new way to validate parameters at fit time. The recommended way to support this feature in scikit-learn 1.2+ is to inherit from sklearn.base.BaseEstimator and decorate the fit method using the decorator sklearn.base._fit_context. For functions, the decorator to use is sklearn.utils._param_validation.validate_params.

We provide the function sklearn_compat.base._fit_context such that you can always decorate the fit method of your estimator. Equivalently, you can use the function sklearn_compat.utils._param_validation.validate_params to validate the parameters of your function.

Contributing

You can contribute to this package by:

• reporting an incompatibility with a scikit-learn version on the issue tracker. We will do our best to provide a compatibility layer.
• opening a pull-request to add a compatibility layer that you encountered when writing your scikit-learn compatible estimator.

Be aware that to be able to provide sklearn-compat as a vendorable package and a dependency, all the changes are implemented in the src/sklearn_compat/_sklearn_compat.py (indeed not the nicest experience). Then, we need to import the changes made in this file in the submodules to use sklearn-compat as a dependency.