Mailman 3 August 2019 - Scikit-learn-commits

[scikit-learn/scikit-learn] bb208d: FIX pls y_score initialization with a constant col...
by camilaagw Aug. 22, 2019

Aug. 22, 2019

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: bb208d3bf6e77a4408c00b5fb6a6b7ce674b8912 https://github.com/scikit-learn/scikit-learn/commit/bb208d3bf6e77a4408c00b5… Author: camilaagw <camilaagw(a)gmail.com> Date: 2019-08-22 (Thu, 22 Aug 2019) Changed paths: M doc/whats_new/v0.22.rst M sklearn/cross_decomposition/pls_.py M sklearn/cross_decomposition/tests/test_pls.py Log Message: ----------- FIX pls y_score initialization with a constant column (#14450) Fixes #13609

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[scikit-learn/scikit-learn] 17786a: don't overwrite precompute=True in lassocv (#14591)
by Andreas Mueller Aug. 22, 2019

Aug. 22, 2019

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: 17786ae933c95fbe422297ebecdc25d2b0ebc4d1 https://github.com/scikit-learn/scikit-learn/commit/17786ae933c95fbe422297e… Author: Andreas Mueller <andreas.mueller(a)columbia.edu> Date: 2019-08-22 (Thu, 22 Aug 2019) Changed paths: M doc/whats_new/v0.22.rst M sklearn/linear_model/coordinate_descent.py M sklearn/linear_model/tests/test_coordinate_descent.py Log Message: ----------- don't overwrite precompute=True in lassocv (#14591) * don't overwrite precompute=True * ENH Adds test to precompute * check that mock was called * whatsnew

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[scikit-learn/scikit-learn] 68044b: BLD/CI Fix pypy build (#14708)
by Thomas J Fan Aug. 21, 2019

Aug. 21, 2019

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: 68044b061d7abc0c16f632890939438033306161 https://github.com/scikit-learn/scikit-learn/commit/68044b061d7abc0c16f6328… Author: Thomas J Fan <thomasjpfan(a)gmail.com> Date: 2019-08-21 (Wed, 21 Aug 2019) Changed paths: M build_tools/circle/build_test_pypy.sh Log Message: ----------- BLD/CI Fix pypy build (#14708)

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[scikit-learn/scikit-learn] 4b6273: ENH Native support for missing values in GBDTs (#1...
by Nicolas Hug Aug. 21, 2019

Aug. 21, 2019

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: 4b6273b87442a4437d8b3873ea3022ae163f4fdf https://github.com/scikit-learn/scikit-learn/commit/4b6273b87442a4437d8b387… Author: Nicolas Hug <contact(a)nicolas-hug.com> Date: 2019-08-21 (Wed, 21 Aug 2019) Changed paths: M benchmarks/bench_hist_gradient_boosting.py M doc/modules/ensemble.rst M doc/whats_new/v0.22.rst M sklearn/ensemble/_hist_gradient_boosting/_binning.pyx M sklearn/ensemble/_hist_gradient_boosting/_gradient_boosting.pyx M sklearn/ensemble/_hist_gradient_boosting/_loss.pyx M sklearn/ensemble/_hist_gradient_boosting/_predictor.pyx M sklearn/ensemble/_hist_gradient_boosting/binning.py A sklearn/ensemble/_hist_gradient_boosting/common.pxd A sklearn/ensemble/_hist_gradient_boosting/common.pyx M sklearn/ensemble/_hist_gradient_boosting/gradient_boosting.py M sklearn/ensemble/_hist_gradient_boosting/grower.py M sklearn/ensemble/_hist_gradient_boosting/histogram.pyx M sklearn/ensemble/_hist_gradient_boosting/loss.py M sklearn/ensemble/_hist_gradient_boosting/predictor.py M sklearn/ensemble/_hist_gradient_boosting/splitting.pyx M sklearn/ensemble/_hist_gradient_boosting/tests/test_binning.py M sklearn/ensemble/_hist_gradient_boosting/tests/test_compare_lightgbm.py M sklearn/ensemble/_hist_gradient_boosting/tests/test_gradient_boosting.py M sklearn/ensemble/_hist_gradient_boosting/tests/test_grower.py M sklearn/ensemble/_hist_gradient_boosting/tests/test_histogram.py M sklearn/ensemble/_hist_gradient_boosting/tests/test_loss.py M sklearn/ensemble/_hist_gradient_boosting/tests/test_predictor.py M sklearn/ensemble/_hist_gradient_boosting/tests/test_splitting.py R sklearn/ensemble/_hist_gradient_boosting/types.pxd R sklearn/ensemble/_hist_gradient_boosting/types.pyx M sklearn/ensemble/_hist_gradient_boosting/utils.pyx M sklearn/ensemble/setup.py Log Message: ----------- ENH Native support for missing values in GBDTs (#13911) * Added NaN support in mapper * pep * WIP * some more * WIP * WIP * bug fix * basic tests * some doc * avoid some interactions * Added tag * better test * decent test + fix bug * add missing_fraction param to benchmark * bin training and validation data separately * shorter test * Map missing values to first bin instead of last * pep8 * Added whats new entry * avoid some python interactions * make predict_binned work * fixed bug due to offset in bin_thresholds_ attribute * more sensible binning strat * typo * user name * Add small test * convert to fortran array in tests * some doc * Added function test * pep8 * Bin validation data using binmaper of training data * Allocate first bin for missing entries based on the whole data, not just training data. * Addressed Thomas' comments * Update sklearn/ensemble/_hist_gradient_boosting/tests/test_grower.py * Addressed Guillaume's comments * always allocate first bin for missing values * reduce diff * minor more consistent test * typo * WIP * some doc * reduce diff * pep8 * minor * remove prints * towards nan only splits * don't check right to left on split_on_nan * cleaups * format and comment * Fixed bug + added more tests * refactor tests * put back n_threads to max value * minor changes * minor cleaning * Add (failing) test that checks equivalence with min max imputation * Decrease the likelihood of ties when training the trees * More robust test * Fix pytest parametrization * Check bin thresholds in test * Try to make the test even easier to see if the Linux 32bit build would pass in this case * Don't check last non-missing bin if there's no nan * Improve min-max imputation test * FIX: _find_best_bin_to_split_right_to_left is still required even when left to right wants to split on nans * comments * remove split_on_nan * ooops deleted useless files * Got rid of individual checks in predictor code +inf thresholds are only allowed in a split on nan situation. Thresholds that are computed as +inf are capped to a very high constant value * can also remove special case in binning code * minor typos + more consistent test * renamed types -> common * 1e300 -> almost inf * added user guide section on missing values * Addressed Olivier's comment + updated whatsnew * addressed comments * Fix doctest formatting * Fix nan predictive doctest

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[scikit-learn/scikit-learn] a05c8d: MNT Fix assert raises in sklearn/feature_extractio...
by Samesh Lakhotia Aug. 21, 2019

Aug. 21, 2019

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: a05c8d89d977a7b4df768a83657eeded561160ad https://github.com/scikit-learn/scikit-learn/commit/a05c8d89d977a7b4df768a8… Author: Samesh Lakhotia <43701530+sameshl(a)users.noreply.github.com> Date: 2019-08-21 (Wed, 21 Aug 2019) Changed paths: M sklearn/feature_extraction/tests/test_feature_hasher.py M sklearn/feature_extraction/tests/test_image.py M sklearn/feature_extraction/tests/test_text.py Log Message: ----------- MNT Fix assert raises in sklearn/feature_extraction/tests/ (#14694)

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[scikit-learn/scikit-learn] a2968c: MNT Fix assert raises in sklearn/feature_selection...
by Samesh Lakhotia Aug. 21, 2019

Aug. 21, 2019

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: a2968c2e4f0cbd5e957b0ba1d63ce2cb16d8008f https://github.com/scikit-learn/scikit-learn/commit/a2968c2e4f0cbd5e957b0ba… Author: Samesh Lakhotia <43701530+sameshl(a)users.noreply.github.com> Date: 2019-08-21 (Wed, 21 Aug 2019) Changed paths: M sklearn/feature_selection/tests/test_base.py M sklearn/feature_selection/tests/test_chi2.py M sklearn/feature_selection/tests/test_feature_select.py M sklearn/feature_selection/tests/test_from_model.py M sklearn/feature_selection/tests/test_mutual_info.py M sklearn/feature_selection/tests/test_variance_threshold.py Log Message: ----------- MNT Fix assert raises in sklearn/feature_selection/tests/ (#14697)

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[scikit-learn/scikit-learn] e912fe: MNT Fix assert raises in sklearn/manifold/tests/ (...
by Samesh Lakhotia Aug. 21, 2019

Aug. 21, 2019

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: e912fe7984127a5ca9dd35ffe316b69aa33d8cc9 https://github.com/scikit-learn/scikit-learn/commit/e912fe7984127a5ca9dd35f… Author: Samesh Lakhotia <43701530+sameshl(a)users.noreply.github.com> Date: 2019-08-21 (Wed, 21 Aug 2019) Changed paths: M sklearn/manifold/tests/test_locally_linear.py M sklearn/manifold/tests/test_mds.py M sklearn/manifold/tests/test_spectral_embedding.py M sklearn/manifold/tests/test_t_sne.py Log Message: ----------- MNT Fix assert raises in sklearn/manifold/tests/ (#14699)

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[scikit-learn/scikit-learn] 9e3216: FIX Passes sample_weight to roc_auc_curve in plot_...
by Thomas J Fan Aug. 21, 2019

Aug. 21, 2019

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: 9e3216ecf99612b8b733e13a154a6c92e9856798 https://github.com/scikit-learn/scikit-learn/commit/9e3216ecf99612b8b733e13… Author: Thomas J Fan <thomasjpfan(a)gmail.com> Date: 2019-08-21 (Wed, 21 Aug 2019) Changed paths: M sklearn/metrics/_plot/roc_curve.py M sklearn/metrics/_plot/tests/test_plot_roc_curve.py Log Message: ----------- FIX Passes sample_weight to roc_auc_curve in plot_roc_auc_curve (#14701)

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[scikit-learn/scikit-learn] 951c50: API Use tag requires_positive_X for NMF + LDA + Mu...
by Alexandre Gramfort Aug. 20, 2019

Aug. 20, 2019

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: 951c5019ac104cd271eed28cac147dbc1b261685 https://github.com/scikit-learn/scikit-learn/commit/951c5019ac104cd271eed28… Author: Alexandre Gramfort <alexandre.gramfort(a)m4x.org> Date: 2019-08-20 (Tue, 20 Aug 2019) Changed paths: M doc/developers/contributing.rst M doc/whats_new/v0.22.rst M sklearn/decomposition/nmf.py M sklearn/decomposition/online_lda.py M sklearn/naive_bayes.py M sklearn/utils/estimator_checks.py Log Message: ----------- API Use tag requires_positive_X for NMF + LDA + MultinomialNB/ComplementNB (#14680)

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[scikit-learn/scikit-learn] 67c94c: Add Minimal Cost-Complexity Pruning to Decision Tr...
by Thomas J Fan Aug. 20, 2019

Aug. 20, 2019

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: 67c94c7e2a24bf5848ff8dc068849b3d83e3c96a https://github.com/scikit-learn/scikit-learn/commit/67c94c7e2a24bf5848ff8dc… Author: Thomas J Fan <thomasjpfan(a)gmail.com> Date: 2019-08-20 (Tue, 20 Aug 2019) Changed paths: M doc/modules/tree.rst M doc/whats_new/v0.22.rst A examples/tree/plot_cost_complexity_pruning.py M sklearn/ensemble/forest.py M sklearn/ensemble/gradient_boosting.py M sklearn/tree/_tree.pyx M sklearn/tree/tests/test_tree.py M sklearn/tree/tree.py Log Message: ----------- Add Minimal Cost-Complexity Pruning to Decision Trees (#12887)

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