8000 MAINT Param validation: constraint for numeric missing values by jeremiedbb · Pull Request #26085 · scikit-learn/scikit-learn · GitHub
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MAINT Param validation: constraint for numeric missing values #26085

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Merged
merged 1 commit into from
Apr 4, 2023
Merged

MAINT Param validation: constraint for numeric missing values #26085

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6 changes: 3 additions & 3 deletions sklearn/impute/_base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
from scipy import sparse as sp

from ..base import BaseEstimator, TransformerMixin
from ..utils._param_validation import StrOptions, Hidden
from ..utils._param_validation import StrOptions, Hidden, MissingValues
from ..utils.fixes import _mode
from ..utils.sparsefuncs import _get_median
from ..utils.validation import check_is_fitted
Expand Down Expand Up @@ -78,7 +78,7 @@ class _BaseImputer(TransformerMixin, BaseEstimator):
"""

_parameter_constraints: dict = {
"missing_values": ["missing_values"],
"missing_values": [MissingValues()],
"add_indicator": ["boolean"],
"keep_empty_features": ["boolean"],
}
Expand Down Expand Up @@ -800,7 +800,7 @@ class MissingIndicator(TransformerMixin, BaseEstimator):
"""

_parameter_constraints: dict = {
"missing_values": [numbers.Real, numbers.Integral, str, None],
"missing_values": [MissingValues()],
"features": [StrOptions({"missing-only", "all"})],
"sparse": ["boolean", StrOptions({"auto"})],
"error_on_new": ["boolean"],
Expand Down
19 changes: 17 additions & 2 deletions sklearn/metrics/pairwise.py
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Expand Up @@ -29,7 +29,13 @@
from ..utils._mask import _get_mask
from ..utils.parallel import delayed, Parallel
from ..utils.fixes import sp_base_version, sp_version, parse_version
from ..utils._param_validation import validate_params, Interval, Real, Hidden
from ..utils._param_validation import (
validate_params,
Interval,
Real,
Hidden,
MissingValues,
)

from ._pairwise_distances_reduction import ArgKmin
from ._pairwise_fast import _chi2_kernel_fast, _sparse_manhattan
Expand Down Expand Up @@ -380,6 +386,15 @@ def _euclidean_distances(X, Y, X_norm_squared=None, Y_norm_squared=None, squared
return distances if squared else np.sqrt(distances, out=distances)


@validate_params(
{
"X": ["array-like"],
"Y": ["array-like", None],
"squared": ["boolean"],
"missing_values": [MissingValues(numeric_only=True)],
"copy": ["boolean"],
}
)
def nan_euclidean_distances(
X, Y=None, *, squared=False, missing_values=np.nan, copy=True
):
Expand Down Expand Up @@ -420,7 +435,7 @@ def nan_euclidean_distances(
squared : bool, default=False
Return squared Euclidean distances.

missing_values : np.nan or int, default=np.nan
missing_values : np.nan, float or int, default=np.nan
Representation of missing value.

copy : bool, default=True
Expand Down
1 change: 1 addition & 0 deletions sklearn/tests/test_public_functions.py
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Expand Up @@ -212,6 +212,7 @@ def _check_function_param_validation(
"sklearn.metrics.pairwise.haversine_distances",
"sklearn.metrics.pairwise.laplacian_kernel",
"sklearn.metrics.pairwise.linear_kernel",
"sklearn.metrics.pairwise.nan_euclidean_distances",
"sklearn.metrics.pairwise.paired_cosine_distances",
"sklearn.metrics.pairwise.paired_euclidean_distances",
"sklearn.metrics.pairwise.paired_manhattan_distances",
Expand Down
36 changes: 24 additions & 12 deletions sklearn/utils/_param_validation.py
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Expand Up @@ -48,7 +48,7 @@ def validate_parameter_constraints(parameter_constraints, params, caller_name):
- the string "boolean"
- the string "verbose"
- the string "cv_object"
- the string "missing_values"
- a MissingValues object representing markers for missing values
- a HasMethods object, representing method(s) an object must have
- a Hidden object, representing a constraint not meant to be exposed to the user

Expand Down Expand Up @@ -125,14 +125,14 @@ def make_constraint(constraint):
return _NoneConstraint()
if isinstance(constraint, type):
return _InstancesOf(constraint)
if isinstance(constraint, (Interval, StrOptions, Options, HasMethods)):
if isinstance(
constraint, (Interval, StrOptions, Options, HasMethods, MissingValues)
):
return constraint
if isinstance(constraint, str) and constraint == "boolean":
return _Booleans()
if isinstance(constraint, str) and constraint == "verbose":
return _VerboseHelper()
if isinstance(constraint, str) and constraint == "missing_values":
return _MissingValues()
if isinstance(constraint, str) and constraint == "cv_object":
return _CVObjects()
if isinstance(constraint, Hidden):
Expand Down Expand Up @@ -609,31 +609,40 @@ def __str__(self):
)


class _MissingValues(_Constraint):
class MissingValues(_Constraint):
"""Helper constraint for the `missing_values` parameters.

Convenience for
[
Integral,
Interval(Real, None, None, closed="both"),
str,
None,
str, # when numeric_only is False
None, # when numeric_only is False
_NanConstraint(),
_PandasNAConstraint(),
]

Parameters
----------
numeric_only : bool, default=False
Whether to consider only numeric missing value markers.

"""

def __init__(self):
def __init__(self, numeric_only=False):
super().__init__()

self.numeric_only = numeric_only

self._constraints = [
_InstancesOf(Integral),
# we use an interval of Real to ignore np.nan that has its own constraint
Interval(Real, None, None, closed="both"),
_InstancesOf(str),
_NoneConstraint(),
_NanConstraint(),
_PandasNAConstraint(),
]
if not self.numeric_only:
self._constraints.extend([_InstancesOf(str), _NoneConstraint()])

def is_satisfied_by(self, val):
return any(c.is_satisfied_by(val) for c in self._constraints)
Expand Down Expand Up @@ -752,7 +761,7 @@ def generate_invalid_param_val(constraint):
if isinstance(constraint, StrOptions):
return f"not {' or '.join(constraint.options)}"

if isinstance(constraint, _MissingValues):
if isinstance(constraint, MissingValues):
return np.array([1, 2, 3])

if isinstance(constraint, _VerboseHelper):
Expand Down Expand Up @@ -841,9 +850,12 @@ def generate_valid_param(constraint):
if isinstance(constraint, _VerboseHelper):
return 1

if isinstance(constraint, _MissingValues):
if isinstance(constraint, MissingValues) and constraint.numeric_only:
return np.nan

if isinstance(constraint, MissingValues) and not constraint.numeric_only:
return "missing"

if isinstance(constraint, HasMethods):
return type(
"ValidHasMethods", (), {m: lambda self: None for m in constraint.methods}
Expand Down
22 changes: 12 additions & 10 deletions sklearn/utils/tests/test_param_validation.py
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Expand Up @@ -16,7 +16,7 @@
from sklearn.utils._param_validation import _Callables
from sklearn.utils._param_validation import _CVObjects
from sklearn.utils._param_validation import _InstancesOf
from sklearn.utils._param_validation import _MissingValues
from sklearn.utils._param_validation import MissingValues
from sklearn.utils._param_validation import _PandasNAConstraint
from sklearn.utils._param_validation import _IterablesNotString
from sklearn.utils._param_validation import _NoneConstraint
Expand Down Expand Up @@ -202,7 +202,8 @@ def a(self):
Interval(Real, 0, None, closed="left"),
Interval(Real, None, None, closed="neither"),
StrOptions({"a", "b", "c"}),
_MissingValues(),
MissingValues(),
MissingValues(numeric_only=True),
_VerboseHelper(),
HasMethods("fit"),
_IterablesNotString(),
Expand Down Expand Up @@ -337,7 +338,8 @@ def test_generate_invalid_param_val_all_valid(constraint):
_SparseMatrices(),
_Booleans(),
_VerboseHelper(),
_MissingValues(),
MissingValues(),
MissingValues(numeric_only=True),
StrOptions({"a", "b", "c"}),
Options(Integral, {1, 2, 3}),
Interval(Integral, None, None, closed="neither"),
Expand Down Expand Up @@ -378,12 +380,12 @@ def test_generate_valid_param(constraint):
(Real, 0.5),
("boolean", False),
("verbose", 1),
("missing_values", -1),
("missing_values", -1.0),
("missing_values", None),
("missing_values", float("nan")),
("missing_values", np.nan),
("missing_values", "missing"),
(MissingValues(), -1),
(MissingValues(), -1.0),
(MissingValues(), None),
(MissingValues(), float("nan")),
(MissingValues(), np.nan),
(MissingValues(), "missing"),
(HasMethods("fit"), _Estimator(a=0)),
("cv_object", 5),
],
Expand All @@ -408,7 +410,7 @@ def test_is_satisfied_by(constraint_declaration, value):
(int, _InstancesOf),
("boolean", _Booleans),
("verbose", _VerboseHelper),
("missing_values", _MissingValues),
(MissingValues(numeric_only=True), MissingValues),
(HasMethods("fit"), HasMethods),
("cv_object", _CVObjects),
],
Expand Down
0