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MAINT Deprecate utils.extmath.safe_min #14554

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Merged
merged 5 commits into from
Aug 2, 2019
Merged

MAINT Deprecate utils.extmath.safe_min #14554

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e14d3b0
Deprecate safe_min
rth Aug 2, 2019
7b441dd
Add deprecation notice
rth Aug 2, 2019
2fb61c3
Update sklearn/utils/extmath.py
rth Aug 2, 2019
a8e02cc
Update sklearn/utils/extmath.py
rth Aug 2, 2019
71c1921
Update sklearn/utils/tests/test_extmath.py
rth Aug 2, 2019
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3 changes: 1 addition & 2 deletions sklearn/decomposition/nmf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,6 @@
from ..base import BaseEstimator, TransformerMixin
from ..utils import check_random_state, check_array
from ..utils.extmath import randomized_svd, safe_sparse_dot, squared_norm
from ..utils.extmath import safe_min
from ..utils.validation import check_is_fitted, check_non_negative
from ..exceptions import ConvergenceWarning
from .cdnmf_fast import _update_cdnmf_fast
Expand Down Expand Up @@ -1000,7 +999,7 @@ def non_negative_factorization(X, W=None, H=None, n_components=None,
check_non_negative(X, "NMF (input X)")
beta_loss = _check_string_param(solver, regularization, beta_loss, init)

if safe_min(X) == 0 and beta_loss <= 0:
if X.min() == 0 and beta_loss <= 0:
raise ValueError("When beta_loss <= 0 and X contains zeros, "
"the solver may diverge. Please add small values to "
"X, or use a positive beta_loss.")
Expand Down
7 changes: 6 additions & 1 deletion sklearn/utils/extmath.py
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Expand Up @@ -20,6 +20,7 @@
from ._logistic_sigmoid import _log_logistic_sigmoid
from .sparsefuncs_fast import csr_row_norms
from .validation import check_array
from .deprecation import deprecated


def squared_norm(x):
Expand Down Expand Up @@ -602,11 +603,15 @@ def softmax(X, copy=True):
return X


@deprecated("safe_min is deprecated in version 0.22 and will be removed "
"in version 0.24.")
def safe_min(X):
"""Returns the minimum value of a dense or a CSR/CSC matrix.

Adapated from https://stackoverflow.com/q/13426580

.. deprecated:: 0.22.0

Parameters
----------
X : array_like
Expand Down Expand Up @@ -646,7 +651,7 @@ def make_nonnegative(X, min_value=0):
ValueError
When X is sparse
"""
min_ = safe_min(X)
min_ = X.min()
if min_ < min_value:
if sparse.issparse(X):
raise ValueError("Cannot make the data matrix"
Expand Down
8 changes: 8 additions & 0 deletions sklearn/utils/tests/test_extmath.py
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Expand Up @@ -31,6 +31,7 @@
from sklearn.utils.extmath import _deterministic_vector_sign_flip
from sklearn.utils.extmath import softmax
from sklearn.utils.extmath import stable_cumsum
from sklearn.utils.extmath import safe_min
from sklearn.datasets.samples_generator import make_low_rank_matrix


Expand Down Expand Up @@ -640,3 +641,10 @@ def test_stable_cumsum():
assert_array_equal(stable_cumsum(A, axis=0), np.cumsum(A, axis=0))
assert_array_equal(stable_cumsum(A, axis=1), np.cumsum(A, axis=1))
assert_array_equal(stable_cumsum(A, axis=2), np.cumsum(A, axis=2))


def test_safe_min():
msg = ("safe_min is deprecated in version 0.22 and will be removed "
"in version 0.24.")
with pytest.warns(DeprecationWarning, match=msg):
safe_min(np.ones(10))