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fix validate_data and force_all_finite warnings #78

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fix validate_data and force_all_finite warnings #78

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9 changes: 8 additions & 1 deletion scikit_mol/applicability/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.utils import check_array
from sklearn.utils._set_output import _SetOutputMixin, _wrap_method_output
from sklearn.utils.validation import check_is_fitted
from sklearn.utils.validation import check_is_fitted, validate_data


class _ADOutputMixin(_SetOutputMixin):
Expand Down Expand Up @@ -254,3 +254,10 @@ def get_feature_names_out(self, input_features=None) -> NDArray[np.str_]:
"""Get feature name for output column."""
# TODO: what is the mechanism around input_features?
return np.array([f"{self.feature_name}"])

def _validate_data(self, X: Any) -> np.ndarray:
"""
Replace deprecated BaseEstimator._validate_data.
Internally calls sklearn.utils.validation.validate_data(_estimator=self, X=X, y=None, reset=True).
"""
return validate_data(self, X=X)
Empty file added scikit_mol/fingerprints/smilestransformer.py
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2 changes: 1 addition & 1 deletion scikit_mol/safeinference.py
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Expand Up @@ -74,7 +74,7 @@ def wrapper(obj, X, y=None, *args, **kwargs):
# TODO, how can we check y in the same way as the estimator?
y = check_array(
y,
force_all_finite=False, # accept_sparse="csr",
ensure_all_finite=False, # accept_sparse="csr",
ensure_2d=False,
dtype=None,
input_name="y",
Expand Down