MNT Deprecate metrics.pairwise.paired_*_distances and paired_distances public functions #27129

Shreesha3112 · 2023-08-22T09:50:46Z

Reference Issues/PRs

Fixes #26982

What does this implement/fix? Explain your changes.

Deprecates metrics.pairwise.paired_*_distance functions and metrics.pairwise.paired_distance

metrics.pairwise.paired_euclidean_distances
metrics.pairwise.paired_manhattan_distances
metrics.pairwise.paired_cosine_distances
metrics.pairwise.paired_distances

Any other comments?

…distance_public_funcs

github-actions · 2023-08-22T09:52:39Z

✔️ Linting Passed

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…distance_public_funcs

Shreesha3112 · 2023-08-22T10:24:20Z

I've noticed that the changes to metrics.pairwise.paired_distance could impact cluster.AgglomerativeClustering. Specifically, the linkage_tree function relies on metrics.pairwise.paired_distances when the affinity isn't precomputed. Given this, should I go ahead and make the required changes to both metrics.pairwise.paired_distances and the linkage_tree function within this PR, or would it be preferred to handle them separately?

ogrisel · 2023-08-22T12:18:38Z

Maybe we could put the code in private functions (with a _ prefix and without redundant input parameter and data checks) and make the deprecated public functions call their private counterparts.

The AgglomerativeClustering estimator could then directly call the private functions.

…distance_public_funcs

glemaitre · 2023-10-31T16:03:31Z

I resolved the conflicts with main. I will give a round of review.

glemaitre

I am fine with the deprecation. I only commented to add some info that we use when we grep the files seeking for deprecated function/variables.

sklearn/metrics/pairwise.py

sklearn/metrics/tests/test_pairwise.py

glemaitre · 2023-10-31T16:18:39Z

sklearn/tests/test_public_functions.py

@@ -275,10 +275,6 @@ def _check_function_param_validation(
    "sklearn.metrics.pairwise.linear_kernel",
    "sklearn.metrics.pairwise.manhattan_distances",
    "sklearn.metrics.pairwise.nan_euclidean_distances",
-    "sklearn.metrics.pairwise.paired_cosine_distances",


I would still test them but add a comment above to remove them.

I think this still needs to be reverted.

glemaitre

I am fine with the deprecation. I only commented to add some info that we use when we grep the files seeking for deprecated function/variables. Thanks @Shreesha3112

glemaitre

I am fine with the deprecation. I only commented to add some info that we use when we grep the files seeking for deprecated function/variables. Thanks @Shreesha3112

Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>

amueller

Looks good but I'd add a note to the deprecation message that tells users what function to use instead (pairwise_distances I assume).

thomasjpfan

Looks good but I'd add a note to the deprecation message that tells users what function to use instead (pairwise_distances I assume).

@amueller If the paired_*_distances are removed, there is no direct replacement.

thomasjpfan · 2024-02-23T00:06:08Z

doc/modules/classes.rst

-   metrics.pairwise.paired_euclidean_distances
-   metrics.pairwise.paired_manhattan_distances
-   metrics.pairwise.paired_cosine_distances
-   metrics.pairwise.paired_distances


Can these be moved to

scikit-learn/doc/modules/classes.rst

Lines 1903 to 1904 in 93f6ce9

Recently deprecated

===================

?

thomasjpfan · 2024-02-23T00:06:40Z

doc/whats_new/v1.4.rst

+  :func:`~metrics.pairwise.paired_euclidean_distances`,
+  :func:`~metrics.pairwise.paired_manhattan_distances` and
+  :func:`~metrics.pairwise.paired_cosine_distances` are now deprecated and
+  will be removed in 1.6.


Since 1.4 is released, this changelog entry needs to be moved to v1.5.rst and:

Suggested change

will be removed in 1.6.

will be removed in 1.7.

thomasjpfan · 2024-02-23T00:06:49Z

sklearn/metrics/pairwise.py

@@ -1129,6 +1130,11 @@ def cosine_distances(X, Y=None):
    return S


+# TODO(1.6): Remove in 1.6


Suggested change

# TODO(1.6): Remove in 1.6

# TODO(1.7): Remove in 1.7

thomasjpfan · 2024-02-23T00:06:57Z

sklearn/metrics/pairwise.py

+# TODO(1.6): Remove in 1.6
+@deprecated(
+    "The public function `sklearn.pairwise.paired_euclidean_distances` has been "
+    "deprecated in 1.4 and will be removed in 1.6."


Suggested change

"deprecated in 1.4 and will be removed in 1.6."

"deprecated in 1.5 and will be removed in 1.7."

thomasjpfan · 2024-02-23T00:07:14Z

sklearn/metrics/pairwise.py

@@ -1157,6 +1186,11 @@ def paired_euclidean_distances(X, Y):
    return row_norms(X - Y)


+# TODO(1.6): Remove in 1.6


Suggested change

# TODO(1.6): Remove in 1.6

# TODO(1.7): Remove in 1.7

thomasjpfan · 2024-02-23T00:07:30Z

sklearn/metrics/pairwise.py

+# TODO*1.6: Remove in 1.6
+@deprecated(
+    "The public function `sklearn.pairwise.paired_cosine_distances` has been "
+    "deprecated in 1.4 and will be removed in 1.6."


Suggested change

"deprecated in 1.4 and will be removed in 1.6."

"deprecated in 1.5 and will be removed in 1.7."

thomasjpfan · 2024-02-23T00:07:38Z

sklearn/metrics/pairwise.py

@@ -1201,6 +1260,11 @@ def paired_manhattan_distances(X, Y):
        return np.abs(diff).sum(axis=-1)


+# TODO*1.6: Remove in 1.6


Suggested change

# TODO*1.6: Remove in 1.6

# TODO(1.7): Remove in 1.7

thomasjpfan · 2024-02-23T00:07:45Z

sklearn/metrics/pairwise.py


+# TODO(1.6): Remove in 1.6


Suggested change

# TODO(1.6): Remove in 1.6

# TODO(1.7): Remove in 1.7

thomasjpfan · 2024-02-23T00:07:52Z

sklearn/metrics/pairwise.py

+# TODO(1.6): Remove in 1.6
+@deprecated(
+    "The public function `sklearn.pairwise.paired_distances` has been "
+    "deprecated in 1.4 and will be removed in 1.6."


Suggested change

"deprecated in 1.4 and will be removed in 1.6."

"deprecated in 1.5 and will be removed in 1.7."

thomasjpfan · 2024-02-23T00:08:39Z

sklearn/tests/test_public_functions.py

@@ -275,10 +275,6 @@ def _check_function_param_validation(
    "sklearn.metrics.pairwise.linear_kernel",
    "sklearn.metrics.pairwise.manhattan_distances",
    "sklearn.metrics.pairwise.nan_euclidean_distances",
-    "sklearn.metrics.pairwise.paired_cosine_distances",


I think this still needs to be reverted.

shreesha3112 added 2 commits August 22, 2023 12:42

deprecate metrics.pairwise.paired_*_distances public functions

6cb4c44

Merge remote-tracking branch 'upstream/main' into deprecate_pairwise_…

1f91db3

…distance_public_funcs

github-actions bot added the module:metrics label Aug 22, 2023

Shreesha3112 changed the title ~~API Deprecate metrics.pairwise.paired_*_distance public functions~~ MNT Deprecate metrics.pairwise.paired_*_distance public functions Aug 22, 2023

shreesha3112 added 2 commits August 22, 2023 15:34

update PR number in changelog

270ec8e

Merge remote-tracking branch 'upstream/main' into deprecate_pairwise_…

5b84071

…distance_public_funcs

Shreesha3112 marked this pull request as ready for review August 22, 2023 10:25

shreesha3112 added 3 commits August 24, 2023 17:21

added private paired_functons and updated agglometrative clustering

aff52bf

resolve merge conflict

d7821b3

Removed paired_distance from public classes

bac00ac

Shreesha3112 changed the title ~~MNT Deprecate metrics.pairwise.paired_*_distance public functions~~ MNT Deprecate metrics.pairwise.paired_*_distances and paired_distances public functions Aug 24, 2023

shreesha3112 added 4 commits August 24, 2023 20:57

add deprecation for paired_distances

58f92b6

Merge remote-tracking branch 'upstream/main' into deprecate_pairwise_…

74fb1f6

…distance_public_funcs

remove paired_distance public functions from param_validation_list

708b696

Merge remote-tracking branch 'upstream/main' into deprecate_pairwise_…

0e2629c

…distance_public_funcs

glemaitre self-requested a review October 31, 2023 15:59

Merge remote-tracking branch 'origin/main' into pr/Shreesha3112/27129

928c6f4

glemaitre approved these changes Oct 31, 2023

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glemaitre added the Waiting for Second Reviewer First reviewer is done, need a second one! label Oct 31, 2023

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Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>

amueller approved these changes Feb 9, 2024

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thomasjpfan reviewed Feb 23, 2024

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MNT Deprecate metrics.pairwise.paired_*_distances and paired_distances public functions #27129

MNT Deprecate metrics.pairwise.paired_*_distances and paired_distances public functions #27129

Shreesha3112 commented Aug 22, 2023 •

edited

github-actions bot commented Aug 22, 2023 •

edited

Shreesha3112 commented Aug 22, 2023

ogrisel commented Aug 22, 2023

glemaitre commented Oct 31, 2023

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thomasjpfan Feb 23, 2024

		@@ -1129,6 +1130,11 @@ def cosine_distances(X, Y=None):
		return S


		# TODO(1.6): Remove in 1.6

	"deprecated in 1.4 and will be removed in 1.6."
	"deprecated in 1.5 and will be removed in 1.7."

		@@ -1157,6 +1186,11 @@ def paired_euclidean_distances(X, Y):
		return row_norms(X - Y)


		# TODO(1.6): Remove in 1.6

		@@ -1201,6 +1260,11 @@ def paired_manhattan_distances(X, Y):
		return np.abs(diff).sum(axis=-1)


		# TODO*1.6: Remove in 1.6

MNT Deprecate metrics.pairwise.paired_*_distances and paired_distances public functions #27129

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MNT Deprecate metrics.pairwise.paired_*_distances and paired_distances public functions #27129

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Shreesha3112 commented Aug 22, 2023 • edited

Reference Issues/PRs

What does this implement/fix? Explain your changes.

Any other comments?

github-actions bot commented Aug 22, 2023 • edited

✔️ Linting Passed

Shreesha3112 commented Aug 22, 2023

ogrisel commented Aug 22, 2023

glemaitre commented Oct 31, 2023

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Shreesha3112 commented Aug 22, 2023 •

edited

github-actions bot commented Aug 22, 2023 •

edited