MAINT dynamically expose kulsinski and remove support in BallTree #25417

glemaitre · 2023-01-17T11:28:40Z

closes #25212
addresses some of issues in #25202

Remove support for kulsinski by dynamically importing it depending on SciPy and removing it from the BallTree.

jjerphan

LGTM.

doc/whats_new/v1.3.rst

sklearn/metrics/pairwise.py

lesteve · 2023-01-17T15:34:47Z

Looks like you have a docstring issue

GL09: Deprecation warning should precede extended summary

glemaitre · 2023-01-17T15:36:16Z

I will use a note then :)

sklearn/cluster/_optics.py

sklearn/metrics/pairwise.py

ogrisel · 2023-01-18T16:49:52Z

There still seems to be related failures in the scipy-dev build on this PR, see build log

For example, NearestNeighbors(algorithm='brute', metric='kulsinski', metric_params={}) fails with ValueError: Unknown Distance Metric: kulsinski in test_neighbors.py.

glemaitre · 2023-01-19T10:21:22Z

The condition for the dynamic support is not right when testing against SciPy current development version.

I don't think this is right to make conditions on unreleased, alpha, or beta versions.

jjerphan · 2023-01-19T10:31:16Z

Alternatively, we can change the condition to use "1.10.999" instead of "1.11.dev".

FYI, this is what has been used in #25393.

glemaitre · 2023-01-19T11:10:13Z

I think that I prefer introducing sp_base_version = parse_version(sp_version.base_version) and using it since this is really what we seek. It looks cleaner to me.

jjerphan · 2023-01-19T11:20:08Z

Ah yes, that's even clearer.

glemaitre · 2023-01-19T11:37:55Z

Kulsinski fix will not be for today: we stumped into numpy/numpy#23033 / scipy/scipy#17811 now

glemaitre · 2023-01-24T10:02:09Z

Triggering the scipy-dev build. Let's see if we get closer to a working CI.

glemaitre · 2023-01-24T11:06:37Z

The remaining error is not linked with the current PR. So the tests are passing with scipy-dev.

jjerphan

LGTM, thank you @glemaitre.

I just have one comment regarding preserving lexicographic orders.

sklearn/neighbors/_base.py

sklearn/metrics/pairwise.py

sklearn/metrics/_dist_metrics.pyx.tp

sklearn/metrics/pairwise.py

glemaitre · 2023-01-24T14:08:32Z

Same comment here regarding lexicographic order.

Do we care about the order? Is there anything relying on it or do we have somewhere where we use list indexing?

jjerphan · 2023-01-24T17:36:18Z

I think it's possible that something depends on an order. I think a canonical sorted representation might prevent problems.

glemaitre · 2023-01-24T19:10:40Z

I think it's possible that something depends on an order. I think a canonical sorted representation might prevent problems.

Then, it will fail with SciPy 1.11 because the order is different since an entry is missing.
Also, the lexicographic ordering is not imposed in all lists (e.g. BOOL_METRICS).
I can add a sorted but I really think that this is unnecessary and that we should have been using set as a data structure.

thomasjpfan

I'm okay with not using lexical ordering. Overall looks good.

thomasjpfan · 2023-01-24T19:59:37Z

sklearn/utils/fixes.py

@@ -25,6 +25,7 @@

 np_version = parse_version(np.__version__)
 sp_version = parse_version(scipy.__version__)
+sp_base_version = parse_version(sp_version.base_version)


For our purposes, I think we should always use the base version. What do you think of setting np_version and sp_version to their base versions?

Yep almost convinced as well. I will check that we don't have corner cases relying on bugfix versions in our codebase.

Do you want to do that as part of this PR? I think it should be done a follow PR to keep things focused on fixing one problem at a time.

I think we should keep all 4:

np_version = parse_version(np.__version__) sp_version = parse_version(scipy.__version__) np_base_version = parse_version(np_version.base_version) sp_base_version = parse_version(sp_version.base_version)

and progressively migrate to use np_base_version and sp_base_version in the scikit-learn code-base.

But I would still keep np_version and sp_version unchanged for backward compat because those attributes are not explicitly private and furthermore I prefer the descriptive names.

I'm okay with having another sp_base_version. I was concerned with adding another public *_version variable that could confuse our contributors or third party developers that depend on utils.fixes.sp_version. (They need to decide which one to use)

ogrisel

+1 on my side once the merge conflict on the version imports is solved and without sorting the metrics lists for the sake of simplicity. I don't think we are likely to make assumptions on the order of those lists.

jjerphan · 2023-01-26T09:56:53Z

I think this PR is mergeable.

@thomasjpfan: do you agree with what @ogrisel has proposed in #25417? Do you think this can be merged?

lesteve · 2023-01-26T11:48:52Z

All CIs were red (likely an issue with resolving the conflicts in the merge commit), I pushed a fix, let's see what happens ...

I put this on auto-merge, I think using base_version as suggested in #25417 (comment) can be done in another PR.

jjerphan · 2023-01-26T12:10:01Z

Thanks, I was the culprit that rushed to have this PR merged and the issue resolved.

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Fan <thomasjpfan@gmail.com> Co-authored-by: Jérémie du Boisberranger <34657725+jeremiedbb@users.noreply.github.com> * MAINT Update pyparsing.py to use bool instead of double negation (scikit-learn#25724) * API Deprecates values in partial_dependence in favor of pdp_values (scikit-learn#21809) Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com> Co-authored-by: Jérémie du Boisberranger <34657725+jeremiedbb@users.noreply.github.com> * API Use grid_values instead of pdp_values in partial_dependence (scikit-learn#25732) * MAINT remove np.product and inf/nan aliases in favor of canonical names (scikit-learn#25741) * MAINT Parameters validation for metrics.label_ranking_loss (scikit-learn#25742) Co-authored-by: Jérémie du Boisberranger <34657725+jeremiedbb@users.noreply.github.com> * MAINT Parameters validation for metrics.coverage_error (scikit-learn#25748) * MAINT Parameters validation for metrics.dcg_score (scikit-learn#25749) * MAINT replace cnp.ndarray with memory views in _fast_dict (scikit-learn#25754) * MAINT Parameter Validation for feature_selection.f_regression (scikit-learn#25736) Co-authored-by: Jérémie du Boisberranger <34657725+jeremiedbb@users.noreply.github.com> * MAINT Parameters validation for feature_selection.r_regression (scikit-learn#25734) Co-authored-by: Jérémie du Boisberranger <34657725+jeremiedbb@users.noreply.github.com> * MAINT Parameter Validation for metrics.get_scorer (scikit-learn#25738) Co-authored-by: Jérémie du Boisberranger <34657725+jeremiedbb@users.noreply.github.com> * DOC Move allowing pandas nullable dtypes to 1.2.2 (scikit-learn#25692) * MAINT replace cnp.ndarray with memory views in sparsefuncs_fast (scikit-learn#25764) * MAINT parameter validation for sklearn.datasets.fetch_covtype (scikit-learn#25759) Co-authored-by: Jérémie du Boisberranger <34657725+jeremiedbb@users.noreply.github.com> * MAINT Define centralized generic, but with explicit precision, types (scikit-learn#25739) * CI Disable network when SciPy requires it (scikit-learn#25743) * CI Open issue when arm wheel fails on CirrusCI (scikit-learn#25620) * ENH Speed-up expected mutual information (scikit-learn#25713) Co-authored-by: Kshitij Mathur <k.mathur68@gmail.com> Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com> Co-authored-by: Omar Salman <omar.salman@arbisoft.com> * FIX add retry mechanism to handle quotechar in read_csv (scikit-learn#25511) * Merge Population Creation (#1) --------- Co-authored-by: Alex Buzenet <94121450+albuzenet@users.noreply.github.com> Co-authored-by: Alex <alex.buzenet.fr@gmail.com> Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com> Co-authored-by: Julien Jerphanion <git@jjerphan.xyz> Co-authored-by: Adam Kania <48769688+remilvus@users.noreply.github.com> Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org> Co-authored-by: Jérémie du Boisberranger <jeremiedbb@users.noreply.github.com> Co-authored-by: Shady el Gewily <90049412+shadyelgewily-slimstock@users.noreply.github.com> Co-authored-by: John Pangas <swiftyxswaggy@outlook.com> Co-authored-by: Felipe Siola <fsiola@gmail.com> Co-authored-by: Felipe Breve Siola <felipe.breve-siola@klarna.com> Co-authored-by: Tim Head <betatim@gmail.com> Co-authored-by: Christian Lorentzen <lorentzen.ch@gmail.com> Co-authored-by: Loïc Estève <loic.esteve@ymail.com> Co-authored-by: Anthony22-dev <122220081+Anthony22-dev@users.noreply.github.com> Co-authored-by: adossantosalfam <anthony.dos_santos_alfama@insa-rouen.fr> Co-authored-by: Xiao Yuan <yuanx749@gmail.com> Co-authored-by: Thomas J. Fan <thomasjpfan@gmail.com> Co-authored-by: Omar Salman <omar.salman@arbisoft.com> Co-authored-by: Rahil Parikh <75483881+rprkh@users.noreply.github.com> Co-authored-by: Gael Varoquaux <gael.varoquaux@normalesup.org> Co-authored-by: Arturo Amor <86408019+ArturoAmorQ@users.noreply.github.com> Co-authored-by: Jérémie du Boisberranger <34657725+jeremiedbb@users.noreply.github.com> Co-authored-by: Meekail Zain <34613774+Micky774@users.noreply.github.com> Co-authored-by: davidblnc <40642621+davidblnc@users.noreply.github.com> Co-authored-by: Changyao Chen <changyao.chen@gmail.com> Co-authored-by: Nicola Fanelli <48762613+nicolafan@users.noreply.github.com> Co-authored-by: Vincent M <maladiere.vincent@yahoo.fr> Co-authored-by: partev <petrosyan@gmail.com> Co-authored-by: ouss1508 <121971998+ouss1508@users.noreply.github.com> Co-authored-by: ashah002 <97778401+ashah002@users.noreply.github.com> Co-authored-by: Ahmedbgh <83551938+Ahmedbgh@users.noreply.github.com> Co-authored-by: Pooja M <90301980+pm155@users.noreply.github.com> Co-authored-by: Ian Thompson <ianiat11@gmail.com> Co-authored-by: Ian Thompson <ian.thompson@hrblock.com> Co-authored-by: SANJAI_3 <86285670+sanjail3@users.noreply.github.com> Co-authored-by: Kaushik Amar Das <cozek@users.noreply.github.com> Co-authored-by: Kaushik Amar Das <kaushik.amar.das@accenture.com> Co-authored-by: Nawazish Alam <nawazishmail@gmail.com> Co-authored-by: William M <64324808+Akbeeh@users.noreply.github.com> Co-authored-by: Jérémie du Boisberranger <jeremiedbb@yahoo.fr> Co-authored-by: JanFidor <66260538+JanFidor@users.noreply.github.com> Co-authored-by: Adam Li <adam2392@gmail.com> Co-authored-by: Logan Thomas <logan.thomas005@gmail.com> Co-authored-by: Vyom Pathak <angerstick3@gmail.com> Co-authored-by: as-90 <88336957+as-90@users.noreply.github.com> Co-authored-by: Marvin Krawutschke <101656586+Marvvxi@users.noreply.github.com> Co-authored-by: Haesun Park <haesunrpark@gmail.com> Co-authored-by: Christine P. 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glemaitre added 15 commits December 19, 2022 10:34

MAINT introduce kulczynski1 in place of kulsinski

8e94171

[scipy-dev] trigger scipy-dev

72bf8b4

FIX add alias for DistanceMetric

ae64e3e

[scipy-dev] trigger scipy-dev

83d5728

Merge remote-tracking branch 'origin/main' into is/25202

ebfa51a

Implement Kulczynski1Distance

1ebe6a0

add more details

a24c415

[scipy-dev] trigger scipy-dev

f5d993c

iter

1025f7a

iter

aba5a12

iter

3cc450a

remove support in BallTree

8f90880

Merge remote-tracking branch 'origin/main' into is/25202

d9a8077

doc glitch whats new

44b4cbe

MAINT dynamically expose kulsinski and remove support in BallTree

62bca89

github-actions bot added cython module:cluster module:metrics module:neighbors labels Jan 17, 2023

glemaitre added 3 commits January 17, 2023 12:29

update pr number

5077b4d

Merge remote-tracking branch 'origin/main' into remove_kulskinski

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less diff

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jjerphan previously approved these changes Jan 17, 2023

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fixes

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glemaitre commented Jan 17, 2023

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glemaitre and others added 2 commits January 17, 2023 16:37

Apply suggestions from code review

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jjerphan added the Waiting for Second Reviewer First reviewer is done, need a second one! label Jan 18, 2023

[scipy-dev] use base version to handle dev version

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glemaitre removed the Waiting for Second Reviewer First reviewer is done, need a second one! label Jan 19, 2023

glemaitre added 3 commits January 23, 2023 19:56

Merge branch 'main' into remove_kulskinski

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Merge branch 'main' into remove_kulskinski

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ogrisel approved these changes Jan 25, 2023

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Merge branch 'main' into remove_kulskinski

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Fix

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lesteve enabled auto-merge (squash) January 26, 2023 11:49

lesteve merged commit 8640ed7 into scikit-learn:main Jan 26, 2023

jjerphan mentioned this pull request Jan 26, 2023

FIX Conditionally resolve metric deprecated by SciPy #25285

Closed

jjerphan mentioned this pull request Feb 9, 2023

pairwise_distances is inconsistent with scipy.spatial.distance when using metric="matching" #25532

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magnusbarata mentioned this pull request Apr 23, 2023

MAINT Deprecate matching as metric #26264

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MAINT dynamically expose kulsinski and remove support in BallTree #25417

MAINT dynamically expose kulsinski and remove support in BallTree #25417

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MAINT dynamically expose kulsinski and remove support in BallTree #25417

MAINT dynamically expose kulsinski and remove support in BallTree #25417

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