Mailman 3 October 2018 - Scikit-learn-commits

[scikit-learn/scikit-learn] 029691: FIX (0.21) OPTICS processing order (#12357)
by GitHub Oct. 13, 2018

Oct. 13, 2018

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: 0296916d7d61036eceafa1739599368a9aaf075b https://github.com/scikit-learn/scikit-learn/commit/0296916d7d61036eceafa17… Author: Erich Schubert <kno10(a)users.noreply.github.com> Date: 2018-10-14 (Sun, 14 Oct 2018) Changed paths: M doc/whats_new/v0.21.rst R sklearn/cluster/_optics_inner.pyx M sklearn/cluster/optics_.py M sklearn/cluster/setup.py M sklearn/cluster/tests/test_optics.py Log Message: ----------- FIX (0.21) OPTICS processing order (#12357) * Add a test case for OPTICS bug (closes #12134) * ENH Fix processing order in OPTICS. See #12090 The current code may expand the wrong point, because it only considers the neighbors of the current point, not all currently unprocessed points (which may have a better reachability). Using the distance from the latest point as tiebreaker then does not work anymore, because it might not yet be computed for all unprocessed points when using an index. If we choose the first on ties, we get the same result same as R and ELKI. But the order of points in "unproc" is also unstable, so we cannot rely on the first smallest to have the smallest index. Instead of the cython quick_scan, we now use numpy masked arrays. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[scikit-learn/scikit-learn] 76b107: TST Fix missing assert and parametrize k-means tes...
by GitHub Oct. 13, 2018

Oct. 13, 2018

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: 76b10782a953ba355abd2717ed871284399091ed https://github.com/scikit-learn/scikit-learn/commit/76b10782a953ba355abd271… Author: jeremiedbb <34657725+jeremiedbb(a)users.noreply.github.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: M sklearn/cluster/tests/test_k_means.py Log Message: ----------- TST Fix missing assert and parametrize k-means tests (#12368) **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[scikit-learn/scikit-learn] 1e7cd7: BUG Fix OrdinalEncoder with manually specified cat...
by GitHub Oct. 13, 2018

Oct. 13, 2018

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: 1e7cd7df9dee31d035ddb789f8e5138201da0ebc https://github.com/scikit-learn/scikit-learn/commit/1e7cd7df9dee31d035ddb78… Author: Joris Van den Bossche <jorisvandenbossche(a)gmail.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: M doc/whats_new/v0.20.rst M sklearn/preprocessing/_encoders.py M sklearn/preprocessing/tests/test_encoders.py Log Message: ----------- BUG Fix OrdinalEncoder with manually specified categories (#12367) **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[scikit-learn/scikit-learn] c76dc0: EXA Fix labels overlap in Out-of-core classificati...
by GitHub Oct. 13, 2018

Oct. 13, 2018

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: c76dc05881cdb1c2d5ad180f2c56a9af0c00e54c https://github.com/scikit-learn/scikit-learn/commit/c76dc05881cdb1c2d5ad180… Author: Xing Han Lu <xhlperso(a)gmail.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: M examples/applications/plot_out_of_core_classification.py Log Message: ----------- EXA Fix labels overlap in Out-of-core classification of text documents example (#12359) **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[scikit-learn/scikit-learn] c13ba2: [MRG] Matplotlib tree plotting (#9251)
by GitHub Oct. 11, 2018

Oct. 11, 2018

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: c13ba26c4780d6088c40db3cc0f8367df4e27f1f https://github.com/scikit-learn/scikit-learn/commit/c13ba26c4780d6088c40db3… Author: Andreas Mueller <t3kcit(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/Makefile M doc/modules/tree.rst M doc/whats_new/v0.21.rst M examples/tree/plot_iris.py M sklearn/tree/__init__.py A sklearn/tree/_reingold_tilford.py M sklearn/tree/export.py M sklearn/tree/tests/test_export.py A sklearn/tree/tests/test_reingold_tilford.py Log Message: ----------- [MRG] Matplotlib tree plotting (#9251) * add reingold tillford tree layout algorithm * add first silly implementation of matplotlib based plotting for trees * object oriented design for export_graphviz so it can be extended * add class for mlp export * add colors * separately scale x and y, add arrowheads, fix strings * implement max_depth * don't use alpha for coloring because it makes boxes transparent * remove unused variables * vertical center of boxes * fix/simplify newline trimming * somewhere in the middle of stuff trying to get rid of scalex, scaley * remove "find_longest_child" for now, fix tests * make scalex and scaley internal, and ax local. render everything once to get the bbox sizes, then again to actually plot it with known extents. * add some margin to the max bbox width * add _BaseTreeExporter baseclass * add docstring to plot_tree * use data coordinates so we can put the plot in a subplot, remove some hacks. * remove scalex, scaley, add automatic font size * use rendered stuff for setting limits (well nearly there) * import plot_tree into tree module * set limits before font size adjustment? * add tree plotting via matplotlib to iris example and to docs * pep8 fix * skip doctest on plot_tree because matplotlib is not installed on all CI machines * redo everything in axis pixel coordinates re-introduce scalex, scaley add max_extents to tree to get tree size before plotting * fix max-depth parent node positioning and don't consider deep nodes in layouting * consider height in fontsize computation in case someone gave us a very flat figure * fix error when max_depth is None * add docstring for tree plotting fontsize * starting on jnothman's review * renaming fixes * whatsnew for tree plotting * clear axes prior to doing anything. * fix doctests * skip matplotlib doctest * trying to debug circle failure * trying to show full traceback * more print debugging * remove debugging crud * hack around matplotlib <1.5 issues * copy bbox args because old matplotlib is weird. * pep8 fixes * add explicit boxstyle * more pep8 * even more pep8 * add comment about matplotlib version requirement * remove redundant file * add whatsnew entry that the merge lost * fix merge issue * more merge issues * whitespace ... * remove doctest skip to see what's happening * added some simple invariance tests buchheim function * refactor ___init__ into superclass * added some tests of plot_tree * put skip back in, fix typo, fix versionadded number * remove unused parameters special_characters and parallel_leaves from mpl plotting * rename tests to test_reingold_tilford * added license header from pymag-trees repo * remove duplicate test file. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[scikit-learn/scikit-learn] 0f94f2: MNT simple deprecations and removals for 0.21 (#12...
by GitHub Oct. 11, 2018

Oct. 11, 2018

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: 0f94f2962b5b0573144dfd4a67803aea0bab99bd https://github.com/scikit-learn/scikit-learn/commit/0f94f2962b5b0573144dfd4… Author: Andreas Mueller <t3kcit(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/modules/classes.rst M sklearn/cluster/hierarchical.py M sklearn/cluster/tests/test_hierarchical.py M sklearn/covariance/graph_lasso_.py M sklearn/covariance/tests/test_graph_lasso.py M sklearn/covariance/tests/test_graphical_lasso.py M sklearn/datasets/__init__.py R sklearn/datasets/mlcomp.py M sklearn/decomposition/fastica_.py M sklearn/decomposition/online_lda.py M sklearn/decomposition/sparse_pca.py M sklearn/decomposition/tests/test_kernel_pca.py M sklearn/decomposition/tests/test_online_lda.py M sklearn/decomposition/tests/test_pca.py M sklearn/decomposition/tests/test_sparse_pca.py M sklearn/discriminant_analysis.py M sklearn/gaussian_process/gpr.py M sklearn/kernel_approximation.py M sklearn/linear_model/__init__.py M sklearn/linear_model/least_angle.py R sklearn/linear_model/randomized_l1.py M sklearn/linear_model/tests/test_huber.py R sklearn/linear_model/tests/test_randomized_l1.py M sklearn/manifold/t_sne.py M sklearn/metrics/pairwise.py M sklearn/metrics/tests/test_classification.py M sklearn/metrics/tests/test_pairwise.py M sklearn/model_selection/tests/test_split.py M sklearn/neighbors/__init__.py R sklearn/neighbors/approximate.py R sklearn/neighbors/tests/test_approximate.py M sklearn/neighbors/tests/test_kd_tree.py M sklearn/neighbors/tests/test_lof.py M sklearn/preprocessing/__init__.py M sklearn/preprocessing/_function_transformer.py M sklearn/preprocessing/data.py M sklearn/preprocessing/tests/test_data.py M sklearn/preprocessing/tests/test_encoders.py M sklearn/preprocessing/tests/test_function_transformer.py M sklearn/semi_supervised/label_propagation.py M sklearn/semi_supervised/tests/test_label_propagation.py M sklearn/tests/test_calibration.py M sklearn/tests/test_discriminant_analysis.py M sklearn/tests/test_kernel_approximation.py R sklearn/utils/arpack.py M sklearn/utils/extmath.py M sklearn/utils/graph.py M sklearn/utils/random.py M sklearn/utils/setup.py R sklearn/utils/sparsetools/__init__.py R sklearn/utils/sparsetools/setup.py R sklearn/utils/sparsetools/tests/__init__.py M sklearn/utils/stats.py M sklearn/utils/tests/test_extmath.py R sklearn/utils/tests/test_graph.py R sklearn/utils/tests/test_stats.py M sklearn/utils/tests/test_utils.py Log Message: ----------- MNT simple deprecations and removals for 0.21 (#12238) Part of #11992. These were all the things that seemed pretty straight-forward. It's actually a bit bulky but should still be easy to review, hopefully. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[scikit-learn/scikit-learn] 8985a6: DOC Update v0.20.rst with power_transform API chan...
by GitHub Oct. 11, 2018

Oct. 11, 2018

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: 8985a6309d31b7e756338238c04aea5ad5603ab0 https://github.com/scikit-learn/scikit-learn/commit/8985a6309d31b7e75633823… Author: Eric Chang <ericchang2017(a)u.northwestern.edu> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/whats_new/v0.20.rst Log Message: ----------- DOC Update v0.20.rst with power_transform API change (#12351) **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[scikit-learn/scikit-learn] 831c76: ENH (0.21) Add max_error to the existing set of me...
by GitHub Oct. 11, 2018

Oct. 11, 2018

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: 831c760ccf7711fe95477b172da1f0a1616ac575 https://github.com/scikit-learn/scikit-learn/commit/831c760ccf7711fe95477b1… Author: Krishna Sangeeth <kskrishnasangeeth(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/modules/classes.rst M doc/modules/model_evaluation.rst M doc/whats_new/v0.21.rst M sklearn/metrics/__init__.py M sklearn/metrics/regression.py M sklearn/metrics/scorer.py M sklearn/metrics/tests/test_common.py M sklearn/metrics/tests/test_regression.py M sklearn/metrics/tests/test_score_objects.py Log Message: ----------- ENH (0.21) Add max_error to the existing set of metrics for regression (#12232) **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[scikit-learn/scikit-learn] 39bd73: [MRG] Move RandomTreesEmbedding criterion & max_fe...
by GitHub Oct. 10, 2018

Oct. 10, 2018

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: 39bd736e595470840460b15ef0eaec398421c061 https://github.com/scikit-learn/scikit-learn/commit/39bd736e595470840460b15… Author: Rohan Varma <rvarm1(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M sklearn/ensemble/forest.py Log Message: ----------- [MRG] Move RandomTreesEmbedding criterion & max_features to be class attributes (#12324) * rm criterion and max_features from __init__ and store them as class attrs instead * make sure that the docstring comes first **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[scikit-learn/scikit-learn] 00c2f4: DOC fix logistic regression.fit docstring on y (#1...
by GitHub Oct. 10, 2018

Oct. 10, 2018

Branch: refs/heads/master Home: https://github.com/scikit-learn/scikit-learn Commit: 00c2f411cf87c83abdf6ad59fa522ad16a2a18cb https://github.com/scikit-learn/scikit-learn/commit/00c2f411cf87c83abdf6ad5… Author: Adrin Jalali <adrin.jalali(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M sklearn/linear_model/logistic.py Log Message: ----------- DOC fix logistic regression.fit docstring on y (#12343) **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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