8000 MAINT Sync `hdbscan` branch with `main` by Micky774 · Pull Request #25124 · scikit-learn/scikit-learn · GitHub
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MAINT Sync hdbscan branch with main #25124

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@Micky774 Micky774 commented Dec 6, 2022

Reference Issues/PRs

Towards #24686

What does this implement/fix? Explain your changes.

Syncs with main and moves setup/build configuration to setup.py.

Any other comments?

jeremiedbb and others added 30 commits October 13, 2022 14:54
@jeremiedbb
MAINT clean deprecation for 1.2: leftovers (scikit-learn#24647)
8648cf9
@thatgeeman
DOC Ensure that gen_batches passes numpydoc validation (scikit-learn#…
0003ee0 
…24609)
@jjerphan @thomasjpfan @ogrisel
MAINT PairwiseDistancesReduction: Update comments and remove unused…
d524875 
… symbols (scikit-learn#24625)

Co-authored-by: Thomas J. Fan <thomasjpfan@gmail.com>
Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org>
@lesteve
MAINT Fix full doc build by avoiding plot_set_output.py side-effect (s…
29d89f0 
…cikit-learn#24654)
@jeremiedbb
MAINT Clean deprecation for 1.2: load_boston follow-up (scikit-learn#…
6818c9b 
…24653)

* remove load_boston references from the docs

* iter

* update poor_score
@ArturoAmorQ
MAINT set plotly min to 5.10 (scikit-learn#24629)
6c00e94
@ogrisel @jjerphan
OPTIM use pairwise_distances_argmin in NearestCentroid.predict (sciki…
e01035d 
…t-learn#24645)



Co-authored-by: Julien Jerphanion <git@jjerphan.xyz>
@glemaitre @betatim
@ogrisel @lesteve
MAINT use nanmin to replace nan by finite values in ranking of Search…
c0b3385 
…CV (scikit-learn#24543)


Co-authored-by: Tim Head <betatim@gmail.com>
Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org>
Co-authored-by: Loïc Estève <loic.esteve@ymail.com>
@jjerphan @ogrisel @thomasjpfan
MAINT PairwiseDistancesReduction: Rename some symbols and files (sc…
5b45d1f 
…ikit-learn#24623)

Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org>
Co-authored-by: Thomas J. Fan <thomasjpfan@gmail.com>
@awinml @glemaitre
DOC Ensures that sklearn.utils.extmath.randomized_svd passes numpyd…
aa7fd7a 
…oc validation (scikit-learn#24607)

Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
@michpara @glemaitre @thomasjpfan
DOC Ensures that if_delegate_has_method passes numpydoc validation (s…
0c8820b 
…cikit-learn#24633)

Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
Co-authored-by: Thomas J. Fan <thomasjpfan@gmail.com>
@cmarmo
Add msvcp140.dll to Windows 64 bit wheels (scikit-learn#24631)
5c897f1
@awinml @jeremiedbb
DOC Ensures that sklearn.utils.extmath.fast_logdet passes numpydoc va…
9a697e4 
…lidation (scikit-learn#24605)

Co-authored-by: jeremie du boisberranger <jeremiedbb@yahoo.fr>
@thomasjpfan @ogrisel
MNT Do not update docs with deprecated decorator (scikit-learn#24410)
eb5f340 
Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org>
@jeremiedbb
MAINT Clean deprecation for 1.2: default random_state in randomized_s…
96f0a01 
…vd (scikit-learn#24661)
@jeremiedbb
MAINT Clean deprecation for 1.2: feature names exact match (scikit-le…
04d0e4a 
…arn#24660)
@jeremiedbb @jjerphan
MAINT Bump min dependencies for 1.2 (scikit-learn#24650)
6697de3 
Co-authored-by: Julien Jerphanion <git@jjerphan.xyz>
@rusdes
API Remove sklearn.metrics.manhattan_distances option `sum_over_fea…
7cf938c 
…tures` (scikit-learn#24630)
@jeremiedbb
EFF avoid computing inertia in KMeans' predict (scikit-learn#24666)
8610e14
@rprkh
DOC make plot_agglomerative_clustering_metrics.py colorblind friend…
935f7e6 
…ly (scikit-learn#24655)
@x110 @glemaitre @ArturoAmorQ
DOC use KBinsDiscretizer in lieu of KMeans in vector quantization exa…
5af75b9 
…mple (scikit-learn#24374)

Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
Co-authored-by: Arturo Amor <86408019+ArturoAmorQ@users.noreply.github.com>
@OmarManzoor
TST use global_random_seed in sklearn/cluster/tests/test_dbscan.py (s…
625650f 
…cikit-learn#24598)
@lesteve
HOTFIX Temporarily disable py38_conda_defaults_openblas build (scikit…
69ca8d5 
…-learn#24693)
@betatim @glemaitre
DOC Fix typo and adjust wording in set_output example (scikit-learn…
98a3fdf 
…#24689)

Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
@thomasjpfan
DOC Improve docstring around set_output (scikit-learn#24672)
d4306ba 
* DOC Improve docstring around set_output

* DOC Improve docs around set_output

* DOC Address comments

* DOC Better grammar

* DOC Improve wording

* DOC Improves docstring in set_config
@thomasjpfan @glemaitre
ENH Makes OneToOneFeatureMixin and ClassNamePrefixFeaturesOutMixin pu…
1dc23d7 
…blic (scikit-learn#24688)

Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
@AlessandroMiola
DOC Fix typo in plot_set_output.py example (scikit-learn#24704)
6eb4633
@lesteve @glemaitre
MAINT Fix build when SKLEARN_OPENMP_PARALLELISM_ENABLED=False (scikit…
d7af20c 
…-learn#24682)

Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
@glemaitre
MAINT renable Linux + Python 3.8 build with OpenBLAS (scikit-learn#24705
3e6a39a 
)
@cmarmo @jjerphan @thomasjpfan
CI Add wheel builds for Python 3.11 (scikit-learn#24446)
38c34af 
Co-authored-by: Julien Jerphanion <git@jjerphan.xyz>
Co-authored-by: Thomas J. Fan <thomasjpfan@gmail.com>
gu1show and others added 22 commits December 1, 2022 07:57
@gu1show @lesteve
DOC: add link to linkcheck_ignore (scikit-learn#25082)
05eed66 
Co-authored-by: Loïc Estève <loic.esteve@ymail.com>
@thomasjpfan
DOC Clarify fill_value behavior in SimpleImputer (scikit-learn#25081)
ba5f9e0 
Fixes scikit-learn#12306
@adam2392 @jshinm
MAINT Handle Criterion.samples using a memoryview (scikit-learn#25005)
599e03c 
Co-authored-by: Jong Shin <jshin.m@gmail.com>
@scottgigante-immunai
DOC Improve docs of BaseLabelPropagation.transduction_ (scikit-learn#…
2b34dfd 
…24985)
@lesteve
DOC fix typo in cross_validate docstring (scikit-learn#25090)
04f3298
@thomasjpfan
CI Fixes CI for windows (scikit-learn#25091)
7af5297
@ArturoAmorQ @glemaitre
FIX Array validation for DecisionBoundaryDisplay (scikit-learn#25077)
c047241 
Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
@thomasjpfan
FIX Fixes check_array for pd.NA in a series (scikit-learn#25080)
54d91d3
@jeremiedbb
MAINT Make param validation more lenient towards downstream dependenc…
5e25f8e 
…ies (scikit-learn#25088)
@ogrisel @jeremiedbb
ENH better error message in HGBRT with feature names (scikit-learn#25092
c557080 
)

Co-authored-by: jeremie du boisberranger <jeremiedbb@yahoo.fr>
@ogrisel
MAINT adjust tolerance in test_balance_property (scikit-learn#25098)
caefdd4
@jjerphan
MAINT Remove warnings in vendored lib{linear,svm} C++ code (scikit-…
4dde64d 
…learn#24998)
@glemaitre
DOC fix missing return line in docstring (scikit-learn#25099)
07958e6
@thomasjpfan
MNT Require matplotlib in test_input_data_dimension test (scikit-lear…
d52e946 
…n#25104)
@ArturoAmorQ @betatim
@jeremiedbb @glemaitre
DOC Rework k-means assumptions example (scikit-learn#24970)
cbfb6ab 
Co-authored-by: Tim Head <betatim@gmail.com>
Co-authored-by: Jérémie du Boisberranger <34657725+jeremiedbb@users.noreply.github.com>
Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
@glemaitre @jeremiedbb
FIX ignore *args and **kwargs in parameter validation of public funct…
b01f018 
…ions (scikit-learn#25114)

Co-authored-by: Jérémie du Boisberranger <34657725+jeremiedbb@users.noreply.github.com>
closes scikit-learn#25113
@glemaitre @betatim @jjerphan
FIX always expose best_loss_, validation_scores_, and best_validation…
1f9dc71 
…_score (scikit-learn#24683)

Co-authored-by: Tim Head <betatim@gmail.com>
Co-authored-by: Julien Jerphanion <git@jjerphan.xyz>
@thomasjpfan @Micky774
FEA Adds FeatureUnion.__getitem__ to access transformers (scikit-lear…
f7e6977 
…n#25093)

Co-authored-by: Meekail Zain <34613774+Micky774@users.noreply.github.com>
@jeremiedbb
MAINT Allow partial param validation for functions (scikit-learn#25087)
14130f4
@jeremiedbb
update release checklist regarding SECURITY.md (scikit-learn#25122)
981e728
@ramvikrams
DOC add more details for n_jobs in MeanShift docstring (scikit-lear…
9a98487 
…n#25083)

* Doc changed n_init to n_jobs in mean_shift.py
@Micky774
Merge branch 'main' into sync_hdbscan
8fca502
@Micky774 Micky774 added the Quick Review For PRs that are quick to review label Dec 6, 2022
@github-actions github-actions bot added the cython label Dec 6, 2022
@thomasjpfan
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I think sklearn/cluster/_hdbscan/setup.py still needs to be removed. For the future, with big syncs like this, it's nice to have the change you made be in it's own commit so it's easier to review. In this case, it's the migration to the root setup.py.

I checked locally that squashing and merging this into hdbscan does not make it too hard to merge the feature branch, hdbscan, into main.

@Micky774 Micky774 closed this Dec 7, 2022
@Micky774 Micky774 mentioned this pull request Dec 7, 2022
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@Micky774 Micky774 deleted the sync_hdbscan branch December 7, 2022 18:01
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