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Jun 28, 2021
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FIX Uses code literals in deprecated to prevent linking #20410

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f842c97
FIX Uses code literals in deprecated to prevent linking
thomasjpfan Jun 27, 2021
7445d9e
TST Adjusts tests
thomasjpfan Jun 27, 2021
9b71bf7
TST Fixes a few more test cases
thomasjpfan Jun 27, 2021
fd0b75d
TST Fixes a few more test cases
thomasjpfan Jun 28, 2021
31f3362
Avoid FutureWarning in test_pls.py
ogrisel Jun 28, 2021
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6 changes: 3 additions & 3 deletions doc/developers/contributing.rst
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Expand Up @@ -222,7 +222,7 @@ latest up-to-date workflow.
`Video <https://youtu.be/dyxS9KKCNzA>`__,
`Transcript
<https://github.com/data-umbrella/event-transcripts/blob/main/2021/27-thomas-pr.md>`__

.. note::
In January 2021, the default branch name changed from ``master`` to ``main``
for the scikit-learn GitHub repository to use more inclusive terms.
Expand Down Expand Up @@ -1115,8 +1115,8 @@ use the decorator ``deprecated`` on a property. Please note that the
decorator for the docstrings to be rendered properly.
E.g., renaming an attribute ``labels_`` to ``classes_`` can be done as::

@deprecated("Attribute labels_ was deprecated in version 0.13 and "
"will be removed in 0.15. Use 'classes_' instead")
@deprecated("Attribute `labels_` was deprecated in version 0.13 and "
"will be removed in 0.15. Use `classes_` instead")
@property
def labels_(self):
return self.classes_
Expand Down
4 changes: 2 additions & 2 deletions sklearn/calibration.py
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Expand Up @@ -652,8 +652,8 @@ def __init__(self, base_estimator, calibrators, *, classes, method="sigmoid"):
# TODO: Remove in 1.1
# mypy error: Decorated property not supported
@deprecated( # type: ignore
"calibrators_ is deprecated in 0.24 and will be removed in 1.1"
"(renaming of 0.26). Use calibrators instead."
"`calibrators_` is deprecated in 0.24 and will be removed in 1.1"
"(renaming of 0.26). Use `calibrators` instead."
)
@property
def calibrators_(self):
Expand Down
2 changes: 1 addition & 1 deletion sklearn/cluster/_affinity_propagation.py
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Expand Up @@ -400,7 +400,7 @@ def __init__(
# TODO: Remove in 1.1
# mypy error: Decorated property not supported
@deprecated( # type: ignore
"Attribute _pairwise was deprecated in "
"Attribute `_pairwise` was deprecated in "
"version 0.24 and will be removed in 1.1 (renaming of 0.26)."
)
@property
Expand Down
6 changes: 4 additions & 2 deletions sklearn/cluster/_birch.py
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Expand Up @@ -473,15 +473,17 @@ def __init__(

# TODO: Remove in 1.2
# mypy error: Decorated property not supported
@deprecated("fit_ is deprecated in 1.0 and will be removed in 1.2") # type: ignore
@deprecated( # type: ignore
"`fit_` is deprecated in 1.0 and will be removed in 1.2"
)
@property
def fit_(self):
return self._deprecated_fit

# TODO: Remove in 1.2
# mypy error: Decorated property not supported
@deprecated( # type: ignore
"partial_fit_ is deprecated in 1.0 and will be removed in 1.2"
"`partial_fit_` is deprecated in 1.0 and will be removed in 1.2"
)
@property
def partial_fit_(self):
Expand Down
6 changes: 3 additions & 3 deletions sklearn/cluster/_kmeans.py
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Expand Up @@ -1697,23 +1697,23 @@ def __init__(
self.reassignment_ratio = reassignment_ratio

@deprecated( # type: ignore
"The attribute 'counts_' is deprecated in 0.24"
"The attribute `counts_` is deprecated in 0.24"
" and will be removed in 1.1 (renaming of 0.26)."
)
@property
def counts_(self):
return self._counts

@deprecated( # type: ignore
"The attribute 'init_size_' is deprecated in "
"The attribute `init_size_` is deprecated in "
"0.24 and will be removed in 1.1 (renaming of 0.26)."
)
@property
def init_size_(self):
return self._init_size

@deprecated( # type: ignore
"The attribute 'random_state_' is deprecated "
"The attribute `random_state_` is deprecated "
"in 0.24 and will be removed in 1.1 (renaming of 0.26)."
)
@property
Expand Down
2 changes: 1 addition & 1 deletion sklearn/cluster/_spectral.py
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Expand Up @@ -637,7 +637,7 @@ def _more_tags(self):
# TODO: Remove in 1.1
# mypy error: Decorated property not supported
@deprecated( # type: ignore
"Attribute _pairwise was deprecated in "
"Attribute `_pairwise` was deprecated in "
"version 0.24 and will be removed in 1.1 (renaming of 0.26)."
)
@property
Expand Down
2 changes: 1 addition & 1 deletion sklearn/cluster/tests/test_affinity_propagation.py
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Expand Up @@ -260,6 +260,6 @@ def test_sparse_input_for_fit_predict():
# TODO: Remove in 1.1
def test_affinity_propagation_pairwise_is_deprecated():
afp = AffinityPropagation(affinity="precomputed")
msg = r"Attribute _pairwise was deprecated in version 0\.24"
msg = r"Attribute `_pairwise` was deprecated in version 0\.24"
with pytest.warns(FutureWarning, match=msg):
afp._pairwise
2 changes: 1 addition & 1 deletion sklearn/cluster/tests/test_birch.py
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Expand Up @@ -181,7 +181,7 @@ def test_birch_n_clusters_long_int():
@pytest.mark.parametrize("attribute", ["fit_", "partial_fit_"])
def test_birch_fit_attributes_deprecated(attribute):
"""Test that fit_ and partial_fit_ attributes are deprecated."""
msg = f"{attribute} is deprecated in 1.0 and will be removed in 1.2"
msg = f"`{attribute}` is deprecated in 1.0 and will be removed in 1.2"
X, y = make_blobs(n_samples=10)
brc = Birch().fit(X, y)

Expand Down
2 changes: 1 addition & 1 deletion sklearn/cluster/tests/test_k_means.py
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Expand Up @@ -986,7 +986,7 @@ def test_minibatch_kmeans_deprecated_attributes(attr):
# check that we raise a deprecation warning when accessing `init_size_`
# FIXME: remove in 1.1
depr_msg = (
f"The attribute '{attr}' is deprecated in 0.24 and will be " f"removed in 1.1"
f"The attribute `{attr}` is deprecated in 0.24 and will be " f"removed in 1.1"
)
km = MiniBatchKMeans(n_clusters=2, n_init=1, init="random", random_state=0)
km.fit(X)
Expand Down
2 changes: 1 addition & 1 deletion sklearn/cluster/tests/test_spectral.py
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Expand Up @@ -305,6 +305,6 @@ def test_verbose(assign_labels, capsys):
@pytest.mark.parametrize("affinity", ["precomputed", "precomputed_nearest_neighbors"])
def test_pairwise_is_deprecated(affinity):
sp = SpectralClustering(affinity=affinity)
msg = r"Attribute _pairwise was deprecated in version 0\.24"
msg = r"Attribute `_pairwise` was deprecated in version 0\.24"
with pytest.warns(FutureWarning, match=msg):
sp._pairwise
9 changes: 5 additions & 4 deletions sklearn/covariance/_graph_lasso.py
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Expand Up @@ -931,8 +931,9 @@ def fit(self, X, y=None):
# TODO: Remove in 1.1 when grid_scores_ is deprecated
# mypy error: Decorated property not supported
@deprecated( # type: ignore
"The grid_scores_ attribute is deprecated in version 0.24 in favor "
"of cv_results_ and will be removed in version 1.1 (renaming of 0.26)."
"The `grid_scores_` attribute is deprecated in version 0.24 in favor "
"of `cv_results_` and will be removed in version 1.1 "
"(renaming of 0.26)."
)
@property
def grid_scores_(self):
Expand All @@ -945,8 +946,8 @@ def grid_scores_(self):
# TODO: Remove in 1.1 when cv_alphas_ is deprecated
# mypy error: Decorated property not supported
@deprecated( # type: ignore
"The cv_alphas_ attribute is deprecated in version 0.24 in favor "
"of cv_results_['alpha'] and will be removed in version 1.1 "
"The `cv_alphas_` attribute is deprecated in version 0.24 in favor "
"of `cv_results_['alpha']` and will be removed in version 1.1 "
"(renaming of 0.26)."
)
@property
Expand Down
8 changes: 4 additions & 4 deletions sklearn/covariance/tests/test_graphical_lasso.py
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Expand Up @@ -180,16 +180,16 @@ def test_graphical_lasso_cv_grid_scores_and_cv_alphas_deprecated():

total_alphas = n_refinements * n_alphas + 1
msg = (
r"The grid_scores_ attribute is deprecated in version 0\.24 in "
r"favor of cv_results_ and will be removed in version 1\.1 "
r"The `grid_scores_` attribute is deprecated in version 0\.24 in "
r"favor of `cv_results_` and will be removed in version 1\.1 "
r"\(renaming of 0\.26\)."
)
with pytest.warns(FutureWarning, match=msg):
assert cov.grid_scores_.shape == (total_alphas, splits)

msg = (
r"The cv_alphas_ attribute is deprecated in version 0\.24 in "
r"favor of cv_results_\['alpha'\] and will be removed in version "
r"The `cv_alphas_` attribute is deprecated in version 0\.24 in "
r"favor of `cv_results_\['alpha'\]` and will be removed in version "
r"1\.1 \(renaming of 0\.26\)"
)
with pytest.warns(FutureWarning, match=msg):
Expand Down
26 changes: 13 additions & 13 deletions sklearn/cross_decomposition/_pls.py
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Expand Up @@ -465,39 +465,39 @@ def fit_transform(self, X, y=None):

# mypy error: Decorated property not supported
@deprecated( # type: ignore
"Attribute norm_y_weights was deprecated in version 0.24 and "
"Attribute `norm_y_weights` was deprecated in version 0.24 and "
"will be removed in 1.1 (renaming of 0.26)."
)
@property
def norm_y_weights(self):
return self._norm_y_weights

@deprecated( # type: ignore
"Attribute x_mean_ was deprecated in version 0.24 and "
"Attribute `x_mean_` was deprecated in version 0.24 and "
"will be removed in 1.1 (renaming of 0.26)."
)
@property
def x_mean_(self):
return self._x_mean

@deprecated( # type: ignore
"Attribute y_mean_ was deprecated in version 0.24 and "
"Attribute `y_mean_` was deprecated in version 0.24 and "
"will be removed in 1.1 (renaming of 0.26)."
)
@property
def y_mean_(self):
return self._y_mean

@deprecated( # type: ignore
"Attribute x_std_ was deprecated in version 0.24 and "
"Attribute `x_std_` was deprecated in version 0.24 and "
"will be removed in 1.1 (renaming of 0.26)."
)
@property
def x_std_(self):
return self._x_std

@deprecated( # type: ignore
"Attribute y_std_ was deprecated in version 0.24 and "
"Attribute `y_std_` was deprecated in version 0.24 and "
"will be removed in 1.1 (renaming of 0.26)."
)
@property
Expand All @@ -510,7 +510,7 @@ def x_scores_(self):
if not isinstance(self, PLSRegression):
pass
warnings.warn(
"Attribute x_scores_ was deprecated in version 0.24 and "
"Attribute `x_scores_` was deprecated in version 0.24 and "
"will be removed in 1.1 (renaming of 0.26). Use "
"est.transform(X) on the training data instead.",
FutureWarning,
Expand All @@ -522,7 +522,7 @@ def y_scores_(self):
# TODO: raise error in 1.1 instead
if not isinstance(self, PLSRegression):
warnings.warn(
"Attribute y_scores_ was deprecated in version 0.24 and "
"Attribute `y_scores_` was deprecated in version 0.24 and "
"will be removed in 1.1 (renaming of 0.26). Use "
"est.transform(X) on the training data instead.",
FutureWarning,
Expand Down Expand Up @@ -1013,7 +1013,7 @@ def fit(self, X, Y):

# mypy error: Decorated property not supported
@deprecated( # type: ignore
"Attribute x_scores_ was deprecated in version 0.24 and "
"Attribute `x_scores_` was deprecated in version 0.24 and "
"will be removed in 1.1 (renaming of 0.26). Use est.transform(X) on "
"the training data instead."
)
Expand All @@ -1023,7 +1023,7 @@ def x_scores_(self):

# mypy error: Decorated property not supported
@deprecated( # type: ignore
"Attribute y_scores_ was deprecated in version 0.24 and "
"Attribute `y_scores_` was deprecated in version 0.24 and "
"will be removed in 1.1 (renaming of 0.26). Use est.transform(X, Y) "
"on the training data instead."
)
Expand All @@ -1032,31 +1032,31 @@ def y_scores_(self):
return self._y_scores

@deprecated( # type: ignore
"Attribute x_mean_ was deprecated in version 0.24 and "
"Attribute `x_mean_` was deprecated in version 0.24 and "
"will be removed in 1.1 (renaming of 0.26)."
)
@property
def x_mean_(self):
return self._x_mean

@deprecated( # type: ignore
"Attribute y_mean_ was deprecated in version 0.24 and "
"Attribute `y_mean_` was deprecated in version 0.24 and "
"will be removed in 1.1 (renaming of 0.26)."
)
@property
def y_mean_(self):
return self._y_mean

@deprecated( # type: ignore
"Attribute x_std_ was deprecated in version 0.24 and "
"Attribute `x_std_` was deprecated in version 0.24 and "
"will be removed in 1.1 (renaming of 0.26)."
)
@property
def x_std_(self):
return self._x_std

@deprecated( # type: ignore
"Attribute y_std_ was deprecated in version 0.24 and "
"Attribute `y_std_` was deprecated in version 0.24 and "
"will be removed in 1.1 (renaming of 0.26)."
)
@property
Expand Down
19 changes: 12 additions & 7 deletions sklearn/cross_decomposition/tests/test_pls.py
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Expand Up @@ -15,6 +15,7 @@
from sklearn.utils import check_random_state
from sklearn.utils.extmath import svd_flip
from sklearn.exceptions import ConvergenceWarning
from sklearn.utils._testing import ignore_warnings


def assert_matrix_orthogonal(M):
Expand Down Expand Up @@ -344,7 +345,7 @@ def test_convergence_fail():
pls_nipals.fit(X, Y)


@pytest.mark.filterwarnings("ignore:.*scores_ was deprecated") # 1.1
@pytest.mark.filterwarnings("ignore:.*`scores_` was deprecated") # 1.1
@pytest.mark.parametrize("Est", (PLSSVD, PLSRegression, PLSCanonical))
def test_attibutes_shapes(Est):
# Make sure attributes are of the correct shape depending on n_components
Expand All @@ -355,9 +356,13 @@ def test_attibutes_shapes(Est):
pls = Est(n_components=n_components)
pls.fit(X, Y)
assert all(
attr.shape[1] == n_components
for attr in (pls.x_scores_, pls.y_scores_, pls.x_weights_, pls.y_weights_)
attr.shape[1] == n_components for attr in (pls.x_weights_, pls.y_weights_)
)
# TODO: remove in 1.1
with ignore_warnings(category=FutureWarning):
assert all(
attr.shape[1] == n_components for attr in (pls.x_scores_, pls.y_scores_)
)


@pytest.mark.parametrize("Est", (PLSRegression, PLSCanonical, CCA))
Expand Down Expand Up @@ -500,9 +505,9 @@ def test_scores_deprecations(Est):
X = rng.randn(10, 5)
Y = rng.randn(10, 3)
est = Est().fit(X, Y)
with pytest.warns(FutureWarning, match="x_scores_ was deprecated"):
with pytest.warns(FutureWarning, match="`x_scores_` was deprecated"):
assert_allclose(est.x_scores_, est.transform(X))
with pytest.warns(FutureWarning, match="y_scores_ was deprecated"):
with pytest.warns(FutureWarning, match="`y_scores_` was deprecated"):
assert_allclose(est.y_scores_, est.transform(X, Y)[1])


Expand All @@ -512,7 +517,7 @@ def test_norm_y_weights_deprecation(Est):
X = rng.randn(10, 5)
Y = rng.randn(10, 3)
est = Est().fit(X, Y)
with pytest.warns(FutureWarning, match="norm_y_weights was deprecated"):
with pytest.warns(FutureWarning, match="`norm_y_weights` was deprecated"):
est.norm_y_weights


Expand All @@ -524,7 +529,7 @@ def test_mean_and_std_deprecation(Estimator, attribute):
X = rng.randn(10, 5)
Y = rng.randn(10, 3)
estimator = Estimator().fit(X, Y)
with pytest.warns(FutureWarning, match=f"{attribute} was deprecated"):
with pytest.warns(FutureWarning, match=f"`{attribute}` was deprecated"):
getattr(estimator, attribute)


Expand Down
4 changes: 2 additions & 2 deletions sklearn/decomposition/_dict_learning.py
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Expand Up @@ -1262,9 +1262,9 @@ def fit(self, X, y=None):
return self

@deprecated( # type: ignore
"The attribute 'components_' is deprecated "
"The attribute `components_` is deprecated "
"in 0.24 and will be removed in 1.1 (renaming of 0.26). Use the "
"'dictionary' instead."
"`dictionary` instead."
)
@property
def components_(self):
Expand Down
2 changes: 1 addition & 1 deletion sklearn/decomposition/_kernel_pca.py
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Expand Up @@ -239,7 +239,7 @@ def __init__(
# TODO: Remove in 1.1
# mypy error: Decorated property not supported
@deprecated( # type: ignore
"Attribute _pairwise was deprecated in "
"Attribute `_pairwise` was deprecated in "
"version 0.24 and will be removed in 1.1 (renaming of 0.26)."
)
@property
Expand Down
2 changes: 1 addition & 1 deletion sklearn/decomposition/tests/test_dict_learning.py
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Expand Up @@ -626,7 +626,7 @@ def test_sparse_coder_deprecation():
init_dict = rng.rand(n_components, n_features)
sc = SparseCoder(init_dict)

with pytest.warns(FutureWarning, match="'components_' is deprecated"):
with pytest.warns(FutureWarning, match="`components_` is deprecated"):
sc.components_


Expand Down
2 changes: 1 addition & 1 deletion sklearn/decomposition/tests/test_kernel_pca.py
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Expand Up @@ -530,6 +530,6 @@ def test_kernel_pcc_pairwise_is_deprecated():
Tests that a `FutureWarning` is issued when `_pairwise` is accessed.
"""
kp = KernelPCA(kernel="precomputed")
msg = r"Attribute _pairwise was deprecated in version 0\.24"
msg = r"Attribute `_pairwise` was deprecated in version 0\.24"
with pytest.warns(FutureWarning, match=msg):
kp._pairwise
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