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Release 1.2.1 #25442

Merged
merged 93 commits into from Jan 24, 2023
Merged

Release 1.2.1 #25442

merged 93 commits into from Jan 24, 2023

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jjerphan
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@jjerphan jjerphan commented Jan 20, 2023

Release checklist as indicated in the docs:

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Following #25436 (comment), #25114 and #25131 aren't part of this release.

Original commits at the start of the rebase
cat git-rebase-todo-before
pick 5014d02b39 DOC correct link for image in the PDP documentation (#25054)
pick 02d45e580a DOC Update docs for making a release (#25047)
pick f9453d5765 MAINT Remove -Wcpp warnings when compiling sklearn.cluster._hierarchical_fast (#24914)
pick 18741d0b2a MAINT Bump version number to 1.3 (#25046)
pick 981fb3be07 DOC make interaction constraints a MajorFeature in whatsnew (#25055)
pick b2ee09535f MAINT Update what's new 1.2 (#25057)
pick 2ee1c0d5c6 MAINT Parameters validation for sklearn.metrics.zero_one_loss (#25025)
pick 35b826a49c TST use global_dtype in sklearn/manifold/tests/test_isomap.py (#22673)
pick 86080bbd5f ENH cartesian accepts mixed dtypes arrays (#25067)
pick 808c32df07 MAINT Remove -Wcpp warnings when compiling sklearn.linear_model._sag_fast (#24975)
pick f7239bf1a1 BLD Reduce binary size of wheels (#25063)
pick 31909634cf MAINT Parameters validation for `sklearn.metrics.mean_absolute_error` (#24943)
pick 7e0ed1ec00 MAINT Parameters validation for sklearn.metrics.auc (#25008)
pick 2d475c0d36 MAINT Parameters validation for cluster.estimate_bandwidth (#24869)
pick 8d9d6793a9 MAINT Parameters validation for `sklearn.feature_extraction.grid_to_graph` (#24887)
pick 167b2980b9 MAINT Parameters validation for `sklearn.feature_extraction.image.img_to_graph` (#24886)
pick f2f3b3cef0 MAINT Remove `-Wcpp` warnings when compiling `sklearn.manifold._utils` (#24925)
pick 4501959493 DOC adding PDP for categorical features in highlights (#25065)
pick 599e03cb07 MAINT Handle `Criterion.samples` using a memoryview (#25005)
pick 2b34dfde24 DOC Improve docs of BaseLabelPropagation.transduction_ (#24985)
pick 04f3298727 DOC fix typo in cross_validate docstring (#25090)
pick 7af5297c9f CI Fixes CI for windows (#25091)
pick c04724114a FIX Array validation for DecisionBoundaryDisplay (#25077)
pick 54d91d3cbe FIX Fixes check_array for pd.NA in a series (#25080)
pick 5e25f8e06d MAINT Make param validation more lenient towards downstream dependencies (#25088)
pick c557080d39 ENH better error message in HGBRT with feature names (#25092)
pick caefdd4790 MAINT adjust tolerance in test_balance_property (#25098)
pick 4dde64d61e MAINT Remove warnings in vendored `lib{linear,svm}` C++ code (#24998)
pick d52e946fa4 MNT Require matplotlib in test_input_data_dimension test (#25104)
pick b01f018c9b FIX ignore *args and **kwargs in parameter validation of public functions (#25114)
pick 1f9dc717f4 FIX always expose best_loss_, validation_scores_, and best_validation_score (#24683)
pick f7e6977a08 FEA Adds FeatureUnion.__getitem__ to access transformers (#25093)
pick 14130f44eb MAINT Allow partial param validation for functions (#25087)
pick 981e728b81 update release checklist regarding SECURITY.md (#25122)
pick 6643c2ceae MAINT Parameters validation for `metrics.roc_curve` (#25108)
pick 929b3dc188 FIX pos_label constraint in roc_curve (param validation) (#25131)
pick e99cd11eb5 FIX Remove spurious `UserWarning` (#25129)
pick 9527920c3d BLD Reduces size of wheels by stripping symbols (#25123)
pick 556454121e MAINT Remove -Wcpp warnings when compiling `_kd_tree` and `_ball_tree` (#24965)
pick 29b4cca3c0 CI Fixes Azure atlas CI job (#25136)
pick 0057118016 MAINT update SECURITY.md (#25138)
pick 0266481aeb DOC Add missing step to the "making a release" checklist (#25139)
pick 17b8278342 MNT parameter validation for covariance.empirical_covariance (#25146)
pick 754bd5245a MAINT validate parameters of Pipeline (#25133)
pick a576bcc22f FIX Convert boolean pd.Series to boolean ndarrays (#25147)
pick 743fe8e5a2 CI Introduces macOS arm64 wheel building with Cirrus CI [cd build cirrus] (#25048)
pick 530fb72856 MAINT exclude cirrus.star from MANIFEST (#25185)
pick f2c78fe8c5 MAINT handle deprecations from `importlib.resources` (#25157)
pick e1ec3f99a3 CI Adds quicker CI failure to reduce resource usage (#21497)
pick c0eb3d3724 DOC improve inline comments in SAGA (#25100)
pick 1f3c1be77a ENH add support for sample_weight in KBinsDiscretizer with strategy="quantile" (#24935)
pick 53a16094d2 MAINT sync lobpcg with SciPy main (#25176)
pick bd3ab49781 ENH improve error messages for invalid categorical variables in HGBDT (#25173)
pick 6367597810 MAINT Remove -Wcpp warnings when compiling sklearn.ensemble._gradient_boosting (#25033)
pick 205f3b76ef MAINT Remove `_arr` suffixes from `_binary_tree` (#25106)
pick a0829ac893 Use `check_array` to validate `y` (#25089)
pick b0bf2315a7 MAINT fix deprecation raised in scipy-dev build (#25175)
pick 9017c70183 FIX fix pickling for empty object with Python 3.11+ (#25188)
pick 708b810742 DOC fix rendering of versionadded (#25211)
pick 2bb0340b9d MAINT parameters validation for sklearn.metrics.r2_score (#25155)
pick ce89a4ff15 MAINT use parameter validation framework for ColumnTransformer (#25137)
pick 6235bce4ea DOC add link to Korean documentation translation (#25205)
pick fba66ded6c FIX Allow tuple for ColumnTransformer 'transformers' parameter (#25222)
pick 0b202caf56 ENH Add option to pass custom scorer for RandomForest OOB calculation (#25177)
pick c78a422edc DOC consistency fixes in multiclass estimators docstring (#25226)
pick ecb9a70e82 FIX Ensure dtype of categories is `object` for strings in `OneHotEncoder` (#25174)
pick efddd9afeb MAINT Parameters validation for metrics.cohen_kappa_score (#25233)
pick f9c454d6b7 MAINT Parameters validation for make_sparse_coded_signal (#25152)
pick 209c132786 MAINT add parameter validation for SearchCV (#25151)
pick 0ab47124fc MAINT Parameters validation for decomposition.sparse_encode (#25061)
pick 8a9635f588 MAINT Parameters validation for classification.confusion_matrix (#25141)
pick 15327787c1 MAINT Parameters validation for `sklearn.metrics.mean_tweedie_deviance` (#25234)
pick 9a90af5151 MAINT Parameters validation for covariance.ledoit_wolf (#24870)
pick a4d470838f MAINT Parameters validation for `covariance.oas` (#24904)
pick ec95edc810 MAINT validate parameter for affinity_propagation (#25026)
pick a7e513c62b MAINT Parameters validation for sklearn.feature_extraction.image.extract_patches_2d (#25149)
pick 1280e099a4 TST check error consistency when calling get_feature_names_out on unfitted estimator (#25223)
pick 3a30538113 MAINT Parameters validation for `fastica` (#24924)
pick 8256a48519 MAINT Parameters validation for metrics.mutual_info_score (#25243)
pick de16d93969 MAINT Refactors __reduce__ to parent splitter (#25199)
pick 6227ee1de7 MNT Remove unneeded computation (#25194)
pick 6261579c1f MAINT Parameters validation for cluster.cluster_optics_dbscan (#25007)
pick d17d0f9f72 FIX `cross_validate` with multimetric scoring returns the non-failed scorers results even if some fail (#23101)
pick 5aa9b99114 MAINT Parameters validation for decomposition.dict_learning (#24871)
pick affaa62b1d ENH added original version of pickled estimator in state dict (#22094)
pick f86aae2ccc MAINT Parameters validation for sklearn.metrics.multilabel_confusion_matrix (#25248)
pick d00d983279 MAINT Parameters validation for cluster.compute_optics_graph (#25245)
pick 2cce02414d TST Add common tests for single class fitting induced by sample weights (#24140)
pick 190c214341 MAINT Parameter validation for sklearn.metrics.mean_squared_error (#25260)
pick ebfaf8e9ff MAINT Parameter validation for sklearn.metrics.det_curve (#25256)
pick a7728f6036 DOC fix typo in logistic regression (#25263)
pick 96a0bc861a ENH remove redundant expr in min_max_dist (#25262)
pick 8679db47e1 FIX regression due to memoryview in SGD when using verbose (#25250)
pick bd555228f7 FIX deprecate sample_weight in predict method of BaseKMeans (#25251)
pick 53123d0cc5 MAINT Parameters validation for sklearn.covariance.shrunk_covariance (#25269)
pick ce00ba817e MAINT Parameters validation for sklearn.datasets.fetch_california_housing (#25265)
pick 1c6e182f92 MAINT Remove -Wcpp warnings when compiling sklearn.svm._libsvm (#25064)
pick e0041bc44a DOC include kernel_approx ref in svm (#25266)
pick f30d35befd Revert "ENH added original version of pickled estimator in state dict" (#25279)
pick 8d74f16582 FIX Handles all numerical DataFrames with check_inverse=True in FunctionTransformer (#25274)
pick 375df8f715 TST use global_random_seed in sklearn/covariance/tests/test_elliptic_envelope.py (#25272)
pick 29317601c3 FIX Raises informative error in FeatureHasher when a sample is a single string (#25094)
pick cde6d65794 ENH KBinsDiscretizer sample_weight support for kmeans strategy (#25257)
pick e411c29625 MNT Enable O3 optimization for trees (#25277)
pick 97fe999f47 FIX Allow input validation by pass in MLPClassifier (#24873)
pick 906faa5574 DOC Minor refinements of lars_path docstring (#25235)
pick 62a017efa0 MAINT use ArgKmin in OutputCodeClassifier (#25196)
pick 0fe2b2c8ca MAINT Remove -Wcpp warnings when compiling sklearn.neighbors._quad_tree (#25225)
pick e0a29df428 MAINT remove -Wsign-compare when compiling `sklearn.utils.sparsefuncs_fast` (#25244)
pick 35b5ee6577 ENH Raise NotFittedError in get_feature_names_out for estimators that use OnetoOneFeatureMixin  (#25294)
pick 9e61f7895b MAINT update sklearn-ci email to ci@scikit-learn.org (#25302)
pick 3efdc8965f Document config_context and transform output (#25289)
pick ba1d23d13e TST Remove ConvergenceWarnings in test_logistic (#25062)
pick 38d7fba586 MAINT Parameters validation for sklearn.random_projection.johnson_lindenstrauss_min_dim (#25278)
pick 37bd51d935 ENH Raise NotFittedError in get_feature_names_out for AdditiveChi2Sampler (#25291)
pick 9e08ed2279 DOC fix formatting changelog (#25315)
pick 0a36bd8892 MAINT Remove -Wcpp warnings when compiling sklearn.svm._liblinear (#25112)
pick f7e5f412dd CI fix test in scipy-dev build following deprecation of array elementwise comparison with string (#25316)
pick fb9c549689 FIX Add stride to `y` in `_ger_memview` (#25323)
pick 860b34c5b3 DOC fix typo in euclidean_distances (#25331)
pick bc00bdce93 DOC document how to generate a valid CIRCLE_CI_TOKEN (#25338)
pick 44bf2abffc DOC fix typo in doc/developers/contributing.rst (#25343) (#25344)
pick a0a6ea744f FIX Fixes transform wrappig in _SetOutputMixin (#25295)
pick 2c7d1ef84b TST Fixes set random seed for test_multinomial_binary_probabilities (#25352)
pick d3c365e2d4 CI Only run cirrus on the scikit-learn repo (#25349)
pick 5a3c057c0d MNT Fixes convergence issue in test_logistic.py (#25345)
pick c892ade837 DOC Improve documentation regarding some pitfalls in interpretation (#20451)
pick 93533ddaff MNT Refactor tree to share splitters between dense and sparse data (#25306)
pick 5b23a2d77b MAINT always seed make_classification in tests (#25353)
pick 26aaa8698b MNT minor clean-up of sklearn/conftests.py (#25358)
pick fdbe4413b7 CI Remove unused env var (#25359)
pick 7d47190cef MNT [scipy-dev] [pypy] [azure parallel] update lock files (#25361)
pick 6ce482c127 TST use global_random_seed in sklearn/cluster/tests/test_hierarchical.py (#25281)
pick f5ae73dcb4 CI Use latest Cython sources in scipy-dev build (#25300)
pick 52e89a4e17 MAINT Clean deprecations in MiniBatchDictionaryLearning (#25357)
pick c676917697 FEA Store the  GradientBoosting OOB Scores in the `oob_score(s)_` fitted attributes (#24882)
pick 70c690ebdd ENH Adds InconsistentVersionWarning when unpickling version doesn't match (#25297)
pick 3bc36e000d ENH Add feature_name_combiner to OneHotEncoder (#22506)
pick 55f024f489 DOC replace markdown by rst (#25368)
pick 8b06f6a979 DOC update the documentation of fit of stateless transformers (#25191)
pick ee1f6048ad DOC Includes jquery to fix website (#25371)
pick c3fca81536 FIX Support read-only sparse datasets for `Tree`-based estimators (#25341)
pick 464922b4ac DOC only use chi2 on binary and counts features (#24684)
pick 2fd6e34f2b DOC Adds sklearn-evaluation to related_projects (#25375)
pick dc7ef61d0d CI Migrate Linux ARM job to CirrusCI (#25366)
pick f45a9071e1 FIX skip space after delimiter in fetch_openml when using pandas parser (#25312)
pick 5af8c6b080 CI Adds arm wheel build in cirrus CI (#25362)
pick fbd95f1764 FIX Set TSNE's internal PCA to always use numpy as output (#25370)
pick 0867da5954 DOC Adds logo back to navbar (#25382)
pick 6823e20e10 CI Make no-OpenMP build fail with unprotected `cimport openmp` (#25391)
pick dec902a7a5 MAINT Parameters validation for sklearn.metrics.cluster.contingency_matrix (#25309)
pick 769ae439f0 MAINT fix typo in comments of t-SNE code base (#25394)
pick bf40b5b622 CI sanitize commit message for Azure (#25376)
pick f34994003e MAINT Parameters validation for cluster.ward_tree (#25388)
pick 2ee3418339 MAINT Parameters validation for metrics.balanced_accuracy_score (#25335)
pick f7eea97809 MAINT Parameters validation for sklearn.metrics.average_precision_score (#25318)
pick 1a4cc0bb85 Fix color maps of contour and scatter plots. (#25329)
pick d61efb6363 DOC fix typo in docstring of RandomizedSearchCV (#25396)
pick 475ee60ad1 DOC cross-reference the term metaestimator in SelfTrainingClassifier (#25325)
pick d3811dcaa2 MAINT Remove -Wsign-compare warnings when compiling sklearn.neighbors._quad_tree (#25271)
pick 9b536c1db9 DOC Add ledoit_wolf_shrinkage reference to the public api (#25255)
pick bf03a63546 ENH add feature_names_in_ in FeatureUnion (#25220)
pick 550fa9c28c MAINT Remove -Wcpp warnings when compiling sklearn.svm._libsvm_sparse (#25337)
pick 71ca9258d3 CI Update conda-lock from 1.2.1 to 1.3.0 (#25404)
pick d5fcb20b39 DOC fix name of estimator used when referring to code example (#25408)
pick 2e63d2e41a ENH Raise NotFittedError in get_feature_names_out for Stacking and Voting - Classifier and Regressor (#25324)
pick 71a647f8bc FIX expose fill_value in IterativeImputer (#25232)
pick d60af3de41 MNT fix test following scipy dev change (#25393)
pick f1340c73ab CI Adapt handling of discarded fused typed memoryview (#25425)
pick 8ce4a67ef5 MAINT Parameters validation for sklearn.metrics.hamming_loss (#25347)
pick a18a1edfea MAINT Parameters validation for metrics.median_absolute_error (#25410)
pick 7c91462fdb ENH Raise NotFittedError in get_feature_names_out for Imputers and Isotonic Regression (#25367)
pick 1e9829ae1c DOC Fix typo in LogisticRegressionCV (#25428)
pick 5f70c4468c BLD Update Cython minimum version to `0.29.33` (#25342)
pick eb8d45e666 MNT Reduces the number of runs for circleci redirector job (#25426)
pick 134c492bf0 CI Enable native osx-arm64 wheels on Python 3.8 (#25427)
pick e010e4f007 MAINT make `AdditiveChi2Sampler` stateless and check that stateless `Transformers` don't raise `NotFittedError` (#25190)
pick 55eaa4ba5c FIX SplineTransformer.get_feature_names_out returns correct names for extrapolations=periodic (#25296)
pick 0260283326 DOC Add detail about dataframe passthrough columns (#25423)
pick d431d7e911 FIX Better support large or read-only datasets in `decomposition.DictionaryLearning` (#25172)
pick cfd428afc5 FIX online updates in MiniBatchDictionaryLearning (#25354)
pick 4b55dee764 DOC Rework Importance of Feature Scaling example (#25012)
pick 3f82f84059 ENH Introduces the __sklearn_clone__ protocol (#24568)
pick 2248b4a078 DOC Update "About Us" (#25435)
pick c3340c029b DOC Improve visibility of warning message on example "Pitfalls in the interpretation of coefficients of linear models" (#25441)
pick 4162ade89a DOC Update changelog before the 1.2.1 release (#25436)
pick de084fc3f0 CI Update nogil lock file (#25437)
pick a7cd0ca44d FIX propagate configuration to workers in parallel (#25363)
pick b3bd78a275 CI Update nogil lock file (#25455)

# Rebase 98cf537f5c..b3bd78a275 onto 98cf537f5c (189 commands)
#
# Commands:
# p, pick <commit> = use commit
# r, reword <commit> = use commit, but edit the commit message
# e, edit <commit> = use commit, but stop for amending
# s, squash <commit> = use commit, but meld into previous commit
# f, fixup [-C | -c] <commit> = like "squash" but keep only the previous
#                    commit's log message, unless -C is used, in which case
#                    keep only this commit's message; -c is same as -C but
#                    opens the editor
# x, exec <command> = run command (the rest of the line) using shell
# b, break = stop here (continue rebase later with 'git rebase --continue')
# d, drop <commit> = remove commit
# l, label <label> = label current HEAD with a name
# t, reset <label> = reset HEAD to a label
# m, merge [-C <commit> | -c <commit>] <label> [# <oneline>]
#         create a merge commit using the original merge commit's
#         message (or the oneline, if no original merge commit was
#         specified); use -c <commit> to reword the commit message
# u, update-ref <ref> = track a placeholder for the <ref> to be updated
#                       to this position in the new commits. The <ref> is
#                       updated at the end of the rebase
#
# These lines can be re-ordered; they are executed from top to bottom.
#
# If you remove a line here THAT COMMIT WILL BE LOST.
#
# However, if you remove everything, the rebase will be aborted.
#
Chosen commit for the rebase
cat git-rebase-todo-after
pick 5014d02b39 DOC correct link for image in the PDP documentation (#25054)
pick 02d45e580a DOC Update docs for making a release (#25047)
pick 981fb3be07 DOC make interaction constraints a MajorFeature in whatsnew (#25055)
pick b2ee09535f MAINT Update what's new 1.2 (#25057)
pick 35b826a49c TST use global_dtype in sklearn/manifold/tests/test_isomap.py (#22673)
pick f7239bf1a1 BLD Reduce binary size of wheels (#25063)
pick 4501959493 DOC adding PDP for categorical features in highlights (#25065)
pick 2b34dfde24 DOC Improve docs of BaseLabelPropagation.transduction_ (#24985)
pick 04f3298727 DOC fix typo in cross_validate docstring (#25090)
pick 7af5297c9f CI Fixes CI for windows (#25091)
pick c04724114a FIX Array validation for DecisionBoundaryDisplay (#25077)
pick 54d91d3cbe FIX Fixes check_array for pd.NA in a series (#25080)
pick 5e25f8e06d MAINT Make param validation more lenient towards downstream dependencies (#25088)
pick caefdd4790 MAINT adjust tolerance in test_balance_property (#25098)
pick d52e946fa4 MNT Require matplotlib in test_input_data_dimension test (#25104)
pick 1f9dc717f4 FIX always expose best_loss_, validation_scores_, and best_validation_score (#24683)
pick 14130f44eb MAINT Allow partial param validation for functions (#25087)
pick 981e728b81 update release checklist regarding SECURITY.md (#25122)
pick e99cd11eb5 FIX Remove spurious `UserWarning` (#25129)
pick 9527920c3d BLD Reduces size of wheels by stripping symbols (#25123)
pick 29b4cca3c0 CI Fixes Azure atlas CI job (#25136)
pick 0057118016 MAINT update SECURITY.md (#25138)
pick 0266481aeb DOC Add missing step to the "making a release" checklist (#25139)
pick a576bcc22f FIX Convert boolean pd.Series to boolean ndarrays (#25147)
pick 743fe8e5a2 CI Introduces macOS arm64 wheel building with Cirrus CI [cd build cirrus] (#25048)
pick 530fb72856 MAINT exclude cirrus.star from MANIFEST (#25185)
pick f2c78fe8c5 MAINT handle deprecations from `importlib.resources` (#25157)
pick e1ec3f99a3 CI Adds quicker CI failure to reduce resource usage (#21497)
pick c0eb3d3724 DOC improve inline comments in SAGA (#25100)
pick 53a16094d2 MAINT sync lobpcg with SciPy main (#25176)
pick a0829ac893 Use `check_array` to validate `y` (#25089)
pick b0bf2315a7 MAINT fix deprecation raised in scipy-dev build (#25175)
pick 9017c70183 FIX fix pickling for empty object with Python 3.11+ (#25188)
pick 708b810742 DOC fix rendering of versionadded (#25211)
pick 6235bce4ea DOC add link to Korean documentation translation (#25205)
pick c78a422edc DOC consistency fixes in multiclass estimators docstring (#25226)
pick ecb9a70e82 FIX Ensure dtype of categories is `object` for strings in `OneHotEncoder` (#25174)
pick 1280e099a4 TST check error consistency when calling get_feature_names_out on unfitted estimator (#25223)
pick d17d0f9f72 FIX `cross_validate` with multimetric scoring returns the non-failed scorers results even if some fail (#23101)
pick 2cce02414d TST Add common tests for single class fitting induced by sample weights (#24140)
pick a7728f6036 DOC fix typo in logistic regression (#25263)
pick 8679db47e1 FIX regression due to memoryview in SGD when using verbose (#25250)
pick e0041bc44a DOC include kernel_approx ref in svm (#25266)
pick 8d74f16582 FIX Handles all numerical DataFrames with check_inverse=True in FunctionTransformer (#25274)
pick 375df8f715 TST use global_random_seed in sklearn/covariance/tests/test_elliptic_envelope.py (#25272)
pick 29317601c3 FIX Raises informative error in FeatureHasher when a sample is a single string (#25094)
pick e411c29625 MNT Enable O3 optimization for trees (#25277)
pick 97fe999f47 FIX Allow input validation by pass in MLPClassifier (#24873)
pick 906faa5574 DOC Minor refinements of lars_path docstring (#25235)
pick 9e61f7895b MAINT update sklearn-ci email to ci@scikit-learn.org (#25302)
pick 3efdc8965f Document config_context and transform output (#25289)
pick ba1d23d13e TST Remove ConvergenceWarnings in test_logistic (#25062)
pick 9e08ed2279 DOC fix formatting changelog (#25315)
pick f7e5f412dd CI fix test in scipy-dev build following deprecation of array elementwise comparison with string (#25316)
pick 860b34c5b3 DOC fix typo in euclidean_distances (#25331)
pick bc00bdce93 DOC document how to generate a valid CIRCLE_CI_TOKEN (#25338)
pick 44bf2abffc DOC fix typo in doc/developers/contributing.rst (#25343) (#25344)
pick a0a6ea744f FIX Fixes transform wrappig in _SetOutputMixin (#25295)
pick 2c7d1ef84b TST Fixes set random seed for test_multinomial_binary_probabilities (#25352)
pick d3c365e2d4 CI Only run cirrus on the scikit-learn repo (#25349)
pick 5a3c057c0d MNT Fixes convergence issue in test_logistic.py (#25345)
pick c892ade837 DOC Improve documentation regarding some pitfalls in interpretation (#20451)
pick 5b23a2d77b MAINT always seed make_classification in tests (#25353)
pick 26aaa8698b MNT minor clean-up of sklearn/conftests.py (#25358)
pick fdbe4413b7 CI Remove unused env var (#25359)
pick 7d47190cef MNT [scipy-dev] [pypy] [azure parallel] update lock files (#25361)
pick 6ce482c127 TST use global_random_seed in sklearn/cluster/tests/test_hierarchical.py (#25281)
pick f5ae73dcb4 CI Use latest Cython sources in scipy-dev build (#25300)
pick 55f024f489 DOC replace markdown by rst (#25368)
pick 8b06f6a979 DOC update the documentation of fit of stateless transformers (#25191)
pick ee1f6048ad DOC Includes jquery to fix website (#25371)
pick c3fca81536 FIX Support read-only sparse datasets for `Tree`-based estimators (#25341)
pick 464922b4ac DOC only use chi2 on binary and counts features (#24684)
pick 2fd6e34f2b DOC Adds sklearn-evaluation to related_projects (#25375)
pick dc7ef61d0d CI Migrate Linux ARM job to CirrusCI (#25366)
pick f45a9071e1 FIX skip space after delimiter in fetch_openml when using pandas parser (#25312)
pick 5af8c6b080 CI Adds arm wheel build in cirrus CI (#25362)
pick fbd95f1764 FIX Set TSNE's internal PCA to always use numpy as output (#25370)
pick 0867da5954 DOC Adds logo back to navbar (#25382)
pick 6823e20e10 CI Make no-OpenMP build fail with unprotected `cimport openmp` (#25391)
pick 769ae439f0 MAINT fix typo in comments of t-SNE code base (#25394)
pick bf40b5b622 CI sanitize commit message for Azure (#25376)
pick 1a4cc0bb85 Fix color maps of contour and scatter plots. (#25329)
pick d61efb6363 DOC fix typo in docstring of RandomizedSearchCV (#25396)
pick 475ee60ad1 DOC cross-reference the term metaestimator in SelfTrainingClassifier (#25325)
pick 71ca9258d3 CI Update conda-lock from 1.2.1 to 1.3.0 (#25404)
pick d5fcb20b39 DOC fix name of estimator used when referring to code example (#25408)
pick d60af3de41 MNT fix test following scipy dev change (#25393)
pick f1340c73ab CI Adapt handling of discarded fused typed memoryview (#25425)
pick 1e9829ae1c DOC Fix typo in LogisticRegressionCV (#25428)
pick eb8d45e666 MNT Reduces the number of runs for circleci redirector job (#25426)
pick 134c492bf0 CI Enable native osx-arm64 wheels on Python 3.8 (#25427)
pick 55eaa4ba5c FIX SplineTransformer.get_feature_names_out returns correct names for extrapolations=periodic (#25296)
pick 0260283326 DOC Add detail about dataframe passthrough columns (#25423)
pick d431d7e911 FIX Better support large or read-only datasets in `decomposition.DictionaryLearning` (#25172)
pick cfd428afc5 FIX online updates in MiniBatchDictionaryLearning (#25354)
pick 4b55dee764 DOC Rework Importance of Feature Scaling example (#25012)
pick 2248b4a078 DOC Update "About Us" (#25435)
pick c3340c029b DOC Improve visibility of warning message on example "Pitfalls in the interpretation of coefficients of linear models" (#25441)
pick 4162ade89a DOC Update changelog before the 1.2.1 release (#25436)
pick a7cd0ca44d FIX propagate configuration to workers in parallel (#25363)

# Rebase 98cf537f5c..b3bd78a275 onto 98cf537f5c (189 commands)
#
# Commands:
# p, pick <commit> = use commit
# r, reword <commit> = use commit, but edit the commit message
# e, edit <commit> = use commit, but stop for amending
# s, squash <commit> = use commit, but meld into previous commit
# f, fixup [-C | -c] <commit> = like "squash" but keep only the previous
#                    commit's log message, unless -C is used, in which case
#                    keep only this commit's message; -c is same as -C but
#                    opens the editor
# x, exec <command> = run command (the rest of the line) using shell
# b, break = stop here (continue rebase later with 'git rebase --continue')
# d, drop <commit> = remove commit
# l, label <label> = label current HEAD with a name
# t, reset <label> = reset HEAD to a label
# m, merge [-C <commit> | -c <commit>] <label> [# <oneline>]
#         create a merge commit using the original merge commit's
#         message (or the oneline, if no original merge commit was
#         specified); use -c <commit> to reword the commit message
# u, update-ref <ref> = track a placeholder for the <ref> to be updated
#                       to this position in the new commits. The <ref> is
#                       updated at the end of the rebase
#
# These lines can be re-ordered; they are executed from top to bottom.
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# If you remove a line here THAT COMMIT WILL BE LOST.
#
# However, if you remove everything, the rebase will be aborted.
#
Excluded commit
diff git-rebase-todo-before git-rebase-todo-after
3,4d2
< pick f9453d5765 MAINT Remove -Wcpp warnings when compiling sklearn.cluster._hierarchical_fast (#24914)
< pick 18741d0b2a MAINT Bump version number to 1.3 (#25046)
7d4
< pick 2ee1c0d5c6 MAINT Parameters validation for sklearn.metrics.zero_one_loss (#25025)
9,10d5
< pick 86080bbd5f ENH cartesian accepts mixed dtypes arrays (#25067)
< pick 808c32df07 MAINT Remove -Wcpp warnings when compiling sklearn.linear_model._sag_fast (#24975)
12,17d6
< pick 31909634cf MAINT Parameters validation for `sklearn.metrics.mean_absolute_error` (#24943)
< pick 7e0ed1ec00 MAINT Parameters validation for sklearn.metrics.auc (#25008)
< pick 2d475c0d36 MAINT Parameters validation for cluster.estimate_bandwidth (#24869)
< pick 8d9d6793a9 MAINT Parameters validation for `sklearn.feature_extraction.grid_to_graph` (#24887)
< pick 167b2980b9 MAINT Parameters validation for `sklearn.feature_extraction.image.img_to_graph` (#24886)
< pick f2f3b3cef0 MAINT Remove `-Wcpp` warnings when compiling `sklearn.manifold._utils` (#24925)
19d7
< pick 599e03cb07 MAINT Handle `Criterion.samples` using a memoryview (#25005)
26d13
< pick c557080d39 ENH better error message in HGBRT with feature names (#25092)
28d14
< pick 4dde64d61e MAINT Remove warnings in vendored `lib{linear,svm}` C++ code (#24998)
30d15
< pick b01f018c9b FIX ignore *args and **kwargs in parameter validation of public functions (#25114)
32d16
< pick f7e6977a08 FEA Adds FeatureUnion.__getitem__ to access transformers (#25093)
35,36d18
< pick 6643c2ceae MAINT Parameters validation for `metrics.roc_curve` (#25108)
< pick 929b3dc188 FIX pos_label constraint in roc_curve (param validation) (#25131)
39d20
< pick 556454121e MAINT Remove -Wcpp warnings when compiling `_kd_tree` and `_ball_tree` (#24965)
43,44d23
< pick 17b8278342 MNT parameter validation for covariance.empirical_covariance (#25146)
< pick 754bd5245a MAINT validate parameters of Pipeline (#25133)
51d29
< pick 1f3c1be77a ENH add support for sample_weight in KBinsDiscretizer with strategy="quantile" (#24935)
53,55d30
< pick bd3ab49781 ENH improve error messages for invalid categorical variables in HGBDT (#25173)
< pick 6367597810 MAINT Remove -Wcpp warnings when compiling sklearn.ensemble._gradient_boosting (#25033)
< pick 205f3b76ef MAINT Remove `_arr` suffixes from `_binary_tree` (#25106)
60,61d34
< pick 2bb0340b9d MAINT parameters validation for sklearn.metrics.r2_score (#25155)
< pick ce89a4ff15 MAINT use parameter validation framework for ColumnTransformer (#25137)
63,64d35
< pick fba66ded6c FIX Allow tuple for ColumnTransformer 'transformers' parameter (#25222)
< pick 0b202caf56 ENH Add option to pass custom scorer for RandomForest OOB calculation (#25177)
67,76d37
< pick efddd9afeb MAINT Parameters validation for metrics.cohen_kappa_score (#25233)
< pick f9c454d6b7 MAINT Parameters validation for make_sparse_coded_signal (#25152)
< pick 209c132786 MAINT add parameter validation for SearchCV (#25151)
< pick 0ab47124fc MAINT Parameters validation for decomposition.sparse_encode (#25061)
< pick 8a9635f588 MAINT Parameters validation for classification.confusion_matrix (#25141)
< pick 15327787c1 MAINT Parameters validation for `sklearn.metrics.mean_tweedie_deviance` (#25234)
< pick 9a90af5151 MAINT Parameters validation for covariance.ledoit_wolf (#24870)
< pick a4d470838f MAINT Parameters validation for `covariance.oas` (#24904)
< pick ec95edc810 MAINT validate parameter for affinity_propagation (#25026)
< pick a7e513c62b MAINT Parameters validation for sklearn.feature_extraction.image.extract_patches_2d (#25149)
78,82d38
< pick 3a30538113 MAINT Parameters validation for `fastica` (#24924)
< pick 8256a48519 MAINT Parameters validation for metrics.mutual_info_score (#25243)
< pick de16d93969 MAINT Refactors __reduce__ to parent splitter (#25199)
< pick 6227ee1de7 MNT Remove unneeded computation (#25194)
< pick 6261579c1f MAINT Parameters validation for cluster.cluster_optics_dbscan (#25007)
84,87d39
< pick 5aa9b99114 MAINT Parameters validation for decomposition.dict_learning (#24871)
< pick affaa62b1d ENH added original version of pickled estimator in state dict (#22094)
< pick f86aae2ccc MAINT Parameters validation for sklearn.metrics.multilabel_confusion_matrix (#25248)
< pick d00d983279 MAINT Parameters validation for cluster.compute_optics_graph (#25245)
89,90d40
< pick 190c214341 MAINT Parameter validation for sklearn.metrics.mean_squared_error (#25260)
< pick ebfaf8e9ff MAINT Parameter validation for sklearn.metrics.det_curve (#25256)
92d41
< pick 96a0bc861a ENH remove redundant expr in min_max_dist (#25262)
94,97d42
< pick bd555228f7 FIX deprecate sample_weight in predict method of BaseKMeans (#25251)
< pick 53123d0cc5 MAINT Parameters validation for sklearn.covariance.shrunk_covariance (#25269)
< pick ce00ba817e MAINT Parameters validation for sklearn.datasets.fetch_california_housing (#25265)
< pick 1c6e182f92 MAINT Remove -Wcpp warnings when compiling sklearn.svm._libsvm (#25064)
99d43
< pick f30d35befd Revert "ENH added original version of pickled estimator in state dict" (#25279)
103d46
< pick cde6d65794 ENH KBinsDiscretizer sample_weight support for kmeans strategy (#25257)
107,110d49
< pick 62a017efa0 MAINT use ArgKmin in OutputCodeClassifier (#25196)
< pick 0fe2b2c8ca MAINT Remove -Wcpp warnings when compiling sklearn.neighbors._quad_tree (#25225)
< pick e0a29df428 MAINT remove -Wsign-compare when compiling `sklearn.utils.sparsefuncs_fast` (#25244)
< pick 35b5ee6577 ENH Raise NotFittedError in get_feature_names_out for estimators that use OnetoOneFeatureMixin  (#25294)
114,115d52
< pick 38d7fba586 MAINT Parameters validation for sklearn.random_projection.johnson_lindenstrauss_min_dim (#25278)
< pick 37bd51d935 ENH Raise NotFittedError in get_feature_names_out for AdditiveChi2Sampler (#25291)
117d53
< pick 0a36bd8892 MAINT Remove -Wcpp warnings when compiling sklearn.svm._liblinear (#25112)
119d54
< pick fb9c549689 FIX Add stride to `y` in `_ger_memview` (#25323)
128d62
< pick 93533ddaff MNT Refactor tree to share splitters between dense and sparse data (#25306)
135,138d68
< pick 52e89a4e17 MAINT Clean deprecations in MiniBatchDictionaryLearning (#25357)
< pick c676917697 FEA Store the  GradientBoosting OOB Scores in the `oob_score(s)_` fitted attributes (#24882)
< pick 70c690ebdd ENH Adds InconsistentVersionWarning when unpickling version doesn't match (#25297)
< pick 3bc36e000d ENH Add feature_name_combiner to OneHotEncoder (#22506)
151d80
< pick dec902a7a5 MAINT Parameters validation for sklearn.metrics.cluster.contingency_matrix (#25309)
154,156d82
< pick f34994003e MAINT Parameters validation for cluster.ward_tree (#25388)
< pick 2ee3418339 MAINT Parameters validation for metrics.balanced_accuracy_score (#25335)
< pick f7eea97809 MAINT Parameters validation for sklearn.metrics.average_precision_score (#25318)
160,163d85
< pick d3811dcaa2 MAINT Remove -Wsign-compare warnings when compiling sklearn.neighbors._quad_tree (#25271)
< pick 9b536c1db9 DOC Add ledoit_wolf_shrinkage reference to the public api (#25255)
< pick bf03a63546 ENH add feature_names_in_ in FeatureUnion (#25220)
< pick 550fa9c28c MAINT Remove -Wcpp warnings when compiling sklearn.svm._libsvm_sparse (#25337)
166,167d87
< pick 2e63d2e41a ENH Raise NotFittedError in get_feature_names_out for Stacking and Voting - Classifier and Regressor (#25324)
< pick 71a647f8bc FIX expose fill_value in IterativeImputer (#25232)
170,172d89
< pick 8ce4a67ef5 MAINT Parameters validation for sklearn.metrics.hamming_loss (#25347)
< pick a18a1edfea MAINT Parameters validation for metrics.median_absolute_error (#25410)
< pick 7c91462fdb ENH Raise NotFittedError in get_feature_names_out for Imputers and Isotonic Regression (#25367)
174d90
< pick 5f70c4468c BLD Update Cython minimum version to `0.29.33` (#25342)
177d92
< pick e010e4f007 MAINT make `AdditiveChi2Sampler` stateless and check that stateless `Transformers` don't raise `NotFittedError` (#25190)
183d97
< pick 3f82f84059 ENH Introduces the __sklearn_clone__ protocol (#24568)
187d100
< pick de084fc3f0 CI Update nogil lock file (#25437)
189d101
< pick b3bd78a275 CI Update nogil lock file (#25455)

jeremiedbb and others added 25 commits January 23, 2023 16:13
…-learn#22673)

Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
Co-authored-by: Jérémie du Boisberranger <jeremiedbb@users.noreply.github.com>
)



Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org>
Co-authored-by: Julien Jerphanion <git@jjerphan.xyz>
Co-authored-by: Julien Jerphanion <git@jjerphan.xyz>
Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org>
Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org>
Co-authored-by: Loïc Estève <loic.esteve@ymail.com>
Co-authored-by: Julien Jerphanion <git@jjerphan.xyz>
closes scikit-learn#25073
Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org>
Co-authored-by: Loïc Estève <loic.esteve@ymail.com>
Co-authored-by: Adrin Jalali <adrin.jalali@gmail.com>
Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>

Python 3.11 introduces `__getstate__` on the `object` level, which breaks our existing `__getstate__` code for objects w/o any attributes. This fixes the issue.
…der` (scikit-learn#25174)

Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
Co-authored-by: Thomas J. Fan <thomasjpfan@gmail.com>
…scorers results even if some fail (scikit-learn#23101)

Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
ScottMGustafson and others added 8 commits January 23, 2023 16:54
…ionaryLearning` (scikit-learn#25172)

Co-authored-by: Loïc Esteve <loic.esteve@ymail.com>
Co-authored-by: Thomas J. Fan <thomasjpfan@gmail.com>
Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org>
Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
Co-authored-by: Christian Lorentzen <lorentzen.ch@gmail.com>
Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org>
Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org>
Co-authored-by: Thomas J. Fan <thomasjpfan@gmail.com>
@jjerphan jjerphan marked this pull request as ready for review January 23, 2023 16:56
@jeremiedbb
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Before merging, I just noticed that there are 2 sections changes impacting all modules in the what's new (in main and in this branch). I think we should fix the what's in main and backport here first.

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ogrisel commented Jan 23, 2023

The 8e28c6a backport to 1.2.X (SECURITY.md) is not really needed for a bugfix release. Only the SECURITY.md file in main is meaningful.

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ogrisel commented Jan 23, 2023

From a quick glance at th included and excluded commit lists, everything looks good to me besides the comments above. The [cd build] CI looks good as well.

@jjerphan
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8e28c6a has been reverted to remove the changes made to SECURITY.md

#25461 opened to fix the change log.

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Everything builds correctly.

I am waiting for this PR to be merged before proceeding with the next steps.

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+1 once #25461 has been backported here.

Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org>
Co-authored-by: Jérémie du Boisberranger <jeremiedbb@users.noreply.github.com>
@adrinjalali adrinjalali merged commit 3a69ddb into scikit-learn:1.2.X Jan 24, 2023
adrinjalali pushed a commit that referenced this pull request Jan 24, 2023
@jjerphan jjerphan deleted the release-1.2.1 branch January 24, 2023 13:33
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