MAINT Sync `hdbscan` branch with `main` #25124

Micky774 · 2022-12-06T22:46:11Z

Reference Issues/PRs

What does this implement/fix? Explain your changes.

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

Any other comments?

… symbols (scikit-learn#24625) Co-authored-by: Thomas J. Fan <[email protected]> Co-authored-by: Olivier Grisel <[email protected]>

…cikit-learn#24654)

…24653) * remove load_boston references from the docs * iter * update poor_score

…t-learn#24645) Co-authored-by: Julien Jerphanion <[email protected]>

…CV (scikit-learn#24543) Co-authored-by: Tim Head <[email protected]> Co-authored-by: Olivier Grisel <[email protected]> Co-authored-by: Loïc Estève <[email protected]>

…ikit-learn#24623) Co-authored-by: Olivier Grisel <[email protected]> Co-authored-by: Thomas J. Fan <[email protected]>

…oc validation (scikit-learn#24607) Co-authored-by: Guillaume Lemaitre <[email protected]>

…cikit-learn#24633) Co-authored-by: Guillaume Lemaitre <[email protected]> Co-authored-by: Thomas J. Fan <[email protected]>

…lidation (scikit-learn#24605) Co-authored-by: jeremie du boisberranger <[email protected]>

Co-authored-by: Olivier Grisel <[email protected]>

…vd (scikit-learn#24661)

…arn#24660)

Co-authored-by: Julien Jerphanion <[email protected]>

…tures` (scikit-learn#24630)

…ly (scikit-learn#24655)

…mple (scikit-learn#24374) Co-authored-by: Guillaume Lemaitre <[email protected]> Co-authored-by: Arturo Amor <[email protected]>

…cikit-learn#24598)

…-learn#24693)

…#24689) Co-authored-by: Guillaume Lemaitre <[email protected]>

* 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

…blic (scikit-learn#24688) Co-authored-by: Guillaume Lemaitre <[email protected]>

…-learn#24682) Co-authored-by: Guillaume Lemaitre <[email protected]>

)

Co-authored-by: Julien Jerphanion <[email protected]> Co-authored-by: Thomas J. Fan <[email protected]>

Co-authored-by: Loïc Estève <[email protected]>

Fixes scikit-learn#12306

Co-authored-by: Jong Shin <[email protected]>

…24985)

Co-authored-by: Guillaume Lemaitre <[email protected]>

…ies (scikit-learn#25088)

) Co-authored-by: jeremie du boisberranger <[email protected]>

…learn#24998)

…n#25104)

Co-authored-by: Tim Head <[email protected]> Co-authored-by: Jérémie du Boisberranger <[email protected]> Co-authored-by: Guillaume Lemaitre <[email protected]>

…ions (scikit-learn#25114) Co-authored-by: Jérémie du Boisberranger <[email protected]> closes scikit-learn#25113

…_score (scikit-learn#24683) Co-authored-by: Tim Head <[email protected]> Co-authored-by: Julien Jerphanion <[email protected]>

…n#25093) Co-authored-by: Meekail Zain <[email protected]>

…n#25083) * Doc changed n_init to n_jobs in mean_shift.py

thomasjpfan · 2022-12-07T16:58:40Z

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.

jeremiedbb and others added 30 commits October 13, 2022 14:54

MAINT clean deprecation for 1.2: leftovers (scikit-learn#24647)

8648cf9

DOC Ensure that gen_batches passes numpydoc validation (scikit-learn#…

0003ee0

…24609)

MAINT PairwiseDistancesReduction: Update comments and remove unused…

d524875

… symbols (scikit-learn#24625) Co-authored-by: Thomas J. Fan <[email protected]> Co-authored-by: Olivier Grisel <[email protected]>

MAINT Fix full doc build by avoiding plot_set_output.py side-effect (s…

29d89f0

…cikit-learn#24654)

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

MAINT set plotly min to 5.10 (scikit-learn#24629)

6c00e94

OPTIM use pairwise_distances_argmin in NearestCentroid.predict (sciki…

e01035d

…t-learn#24645) Co-authored-by: Julien Jerphanion <[email protected]>

MAINT use nanmin to replace nan by finite values in ranking of Search…

c0b3385

…CV (scikit-learn#24543) Co-authored-by: Tim Head <[email protected]> Co-authored-by: Olivier Grisel <[email protected]> Co-authored-by: Loïc Estève <[email protected]>

MAINT PairwiseDistancesReduction: Rename some symbols and files (sc…

5b45d1f

…ikit-learn#24623) Co-authored-by: Olivier Grisel <[email protected]> Co-authored-by: Thomas J. Fan <[email protected]>

DOC Ensures that sklearn.utils.extmath.randomized_svd passes numpyd…

aa7fd7a

…oc validation (scikit-learn#24607) Co-authored-by: Guillaume Lemaitre <[email protected]>

DOC Ensures that if_delegate_has_method passes numpydoc validation (s…

0c8820b

…cikit-learn#24633) Co-authored-by: Guillaume Lemaitre <[email protected]> Co-authored-by: Thomas J. Fan <[email protected]>

Add msvcp140.dll to Windows 64 bit wheels (scikit-learn#24631)

5c897f1

DOC Ensures that sklearn.utils.extmath.fast_logdet passes numpydoc va…

9a697e4

…lidation (scikit-learn#24605) Co-authored-by: jeremie du boisberranger <[email protected]>

MNT Do not update docs with deprecated decorator (scikit-learn#24410)

eb5f340

Co-authored-by: Olivier Grisel <[email protected]>

MAINT Clean deprecation for 1.2: default random_state in randomized_s…

96f0a01

…vd (scikit-learn#24661)

MAINT Clean deprecation for 1.2: feature names exact match (scikit-le…

04d0e4a

…arn#24660)

MAINT Bump min dependencies for 1.2 (scikit-learn#24650)

6697de3

Co-authored-by: Julien Jerphanion <[email protected]>

API Remove sklearn.metrics.manhattan_distances option `sum_over_fea…

7cf938c

…tures` (scikit-learn#24630)

EFF avoid computing inertia in KMeans' predict (scikit-learn#24666)

8610e14

DOC make plot_agglomerative_clustering_metrics.py colorblind friend…

935f7e6

…ly (scikit-learn#24655)

DOC use KBinsDiscretizer in lieu of KMeans in vector quantization exa…

5af75b9

…mple (scikit-learn#24374) Co-authored-by: Guillaume Lemaitre <[email protected]> Co-authored-by: Arturo Amor <[email protected]>

TST use global_random_seed in sklearn/cluster/tests/test_dbscan.py (s…

625650f

…cikit-learn#24598)

HOTFIX Temporarily disable py38_conda_defaults_openblas build (scikit…

69ca8d5

…-learn#24693)

DOC Fix typo and adjust wording in set_output example (scikit-learn…

98a3fdf

…#24689) Co-authored-by: Guillaume Lemaitre <[email protected]>

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

ENH Makes OneToOneFeatureMixin and ClassNamePrefixFeaturesOutMixin pu…

1dc23d7

…blic (scikit-learn#24688) Co-authored-by: Guillaume Lemaitre <[email protected]>

DOC Fix typo in plot_set_output.py example (scikit-learn#24704)

6eb4633

MAINT Fix build when SKLEARN_OPENMP_PARALLELISM_ENABLED=False (scikit…

d7af20c

…-learn#24682) Co-authored-by: Guillaume Lemaitre <[email protected]>

MAINT renable Linux + Python 3.8 build with OpenBLAS (scikit-learn#24705

3e6a39a

)

CI Add wheel builds for Python 3.11 (scikit-learn#24446)

38c34af

Co-authored-by: Julien Jerphanion <[email protected]> Co-authored-by: Thomas J. Fan <[email protected]>

gu1show and others added 22 commits December 1, 2022 07:57

DOC: add link to linkcheck_ignore (scikit-learn#25082)

05eed66

Co-authored-by: Loïc Estève <[email protected]>

DOC Clarify fill_value behavior in SimpleImputer (scikit-learn#25081)

ba5f9e0

Fixes scikit-learn#12306

MAINT Handle Criterion.samples using a memoryview (scikit-learn#25005)

599e03c

Co-authored-by: Jong Shin <[email protected]>

DOC Improve docs of BaseLabelPropagation.transduction_ (scikit-learn#…

2b34dfd

…24985)

DOC fix typo in cross_validate docstring (scikit-learn#25090)

04f3298

CI Fixes CI for windows (scikit-learn#25091)

7af5297

FIX Array validation for DecisionBoundaryDisplay (scikit-learn#25077)

c047241

Co-authored-by: Guillaume Lemaitre <[email protected]>

FIX Fixes check_array for pd.NA in a series (scikit-learn#25080)

54d91d3

MAINT Make param validation more lenient towards downstream dependenc…

5e25f8e

…ies (scikit-learn#25088)

ENH better error message in HGBRT with feature names (scikit-learn#25092

c557080

) Co-authored-by: jeremie du boisberranger <[email protected]>

MAINT adjust tolerance in test_balance_property (scikit-learn#25098)

caefdd4

MAINT Remove warnings in vendored lib{linear,svm} C++ code (scikit-…

4dde64d

…learn#24998)

DOC fix missing return line in docstring (scikit-learn#25099)

07958e6

MNT Require matplotlib in test_input_data_dimension test (scikit-lear…

d52e946

…n#25104)

DOC Rework k-means assumptions example (scikit-learn#24970)

cbfb6ab

Co-authored-by: Tim Head <[email protected]> Co-authored-by: Jérémie du Boisberranger <[email protected]> Co-authored-by: Guillaume Lemaitre <[email protected]>

FIX ignore *args and **kwargs in parameter validation of public funct…

b01f018

…ions (scikit-learn#25114) Co-authored-by: Jérémie du Boisberranger <[email protected]> closes scikit-learn#25113

FIX always expose best_loss_, validation_scores_, and best_validation…

1f9dc71

…_score (scikit-learn#24683) Co-authored-by: Tim Head <[email protected]> Co-authored-by: Julien Jerphanion <[email protected]>

FEA Adds FeatureUnion.__getitem__ to access transformers (scikit-lear…

f7e6977

…n#25093) Co-authored-by: Meekail Zain <[email protected]>

MAINT Allow partial param validation for functions (scikit-learn#25087)

14130f4

update release checklist regarding SECURITY.md (scikit-learn#25122)

981e728

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

Merge branch 'main' into sync_hdbscan

8fca502

Micky774 added the Quick Review For PRs that are quick to review label Dec 6, 2022

github-actions bot added the cython label Dec 6, 2022

Micky774 added the No Changelog Needed label Dec 6, 2022

Removed unnecessary setup.py

782834d

Micky774 closed this Dec 7, 2022

Micky774 mentioned this pull request Dec 7, 2022

MAINT Sync hdbscan branch with main #25134

Merged

Micky774 deleted the sync_hdbscan branch December 7, 2022 18:01

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MAINT Sync `hdbscan` branch with `main` #25124

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Micky774 commented Dec 6, 2022

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thomasjpfan commented Dec 7, 2022

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MAINT Sync hdbscan branch with main #25124

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Micky774 commented Dec 6, 2022

Reference Issues/PRs

What does this implement/fix? Explain your changes.

Any other comments?

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thomasjpfan commented Dec 7, 2022

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MAINT Sync `hdbscan` branch with `main` #25124

MAINT Sync `hdbscan` branch with `main` #25124