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Merged
merged 32 commits into from
Nov 28, 2019
Merged

Release 0.22rc3 #15715

merged 32 commits into from
Nov 28, 2019

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adrinjalali
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I've included the doc changes, and the ones which were suggested to be included.

The only one I was a bit surprised about is #11514 which I've included since it touches the whats_new, but it's not a very minor change.

It'd be also nice to have #15626 here.

drop 947f37e3a1 MNT bump version to 0.23.dev0 and add new whats_new (#15631)
pick 9dcdb8789a DOC Adds confusion matrix to whats new (#15656)
pick f7ed72aa44 ENH reduce memory consumption in nan_euclidean_distances (#15615)
pick 60248946bd EXA Adds example for tree.ExtraTreeRegressor (#15213)
pick e254b30b6e MAINT run latest CI on Python 3.8 (#15637)
drop b6f124c848 MAINT Improve variable order in BaseDecisionTree (#15664)
pick a723bea9c9 [MRG] Enables CircleCI to fail when sphinx warns (#15633)
pick 663d052d3c [MRG] documentation for random_state in forest.py (#15516)
pick 43d8dee07b MNT improve the convergence warning message for LogisticRegression (#15665)
pick 6231d5ae51 MAINT Add _distributor_init.py (#15570)
drop 12196dab9b MNT replaced check_consistent_length, etc with _check_sample_weight in BaseGradientBoosting (#15478)
pick e81884f919 TST Fix leak in tmp folders in LFW test when pillow is missing (#15676)
pick ce1b171e39 MNT pin pytest in failing job on azure (#15677)
pick 0831dfbe95 [MRG] BUG Fixes test_scale_and_stability in windows (#15661)
drop 641b863188 MNT fix filtering of examples file to run by sphinx (#15680)
pick 10b8bf7c54 [MRG] Improve error message with implicit pos_label in _binary_clf_curve (#15562)
pick cc9066f964 DOC add transform y section to faq.rst (#15484)
pick ccac637855 FIX Clip distances below 0 (#15683)
drop 1c546cd9b1 CLN Move gradient and hessian closer to for loop in hist GBDT (#15686)
pick 6b8e545293 MNT bump the version of numpydoc and sphinx gallery (#15681)
pick 2151b79a91 FIX Releases memory in liblinear (#15687)
pick e06cc9e3fe MNT Better error message for MinMaxScaler and sparse data (#15695)
pick 0c2da0cb48 DOC Fix various sphinx warnings. (#15692)
pick db59dd74df [MRG] Fast, low memory, single linkage implementation (#11514)
pick 308a54e3ae CI Use new conda syntax to select blas (#15705)
pick c1ba7bfe43 DOC versionadded labels for NearestNeighbors, KNeighborsRegressor and RadiusNeighborsRegressor (#15688)
pick 9f5b97119b CLN Removes ccp_alpha from RandomTreesEmbedding (#15708)
pick fc46a13d57 DOC Wrong statement in release highlight (#15704)
pick 4f97facc3a DOC Further 0.22 whats_new cleanup (#15675)

thomasjpfan and others added 24 commits November 25, 2019 12:50
* documentation for random_state in forests

* move note to parameter

* same for RandomForestRegressor

* add doc for ExtraTreesRegressor and ExtraTreesClassifier

* skip line

* lint

* move note back to where it was

* add Glossary in RandomForestRegressor

* adding description for RandomTreesEmbedding

* small fix

* correct description for RandomTreesEmbedding
…1514)

* First cut at basic single linkage internals

* Refer to correct dist_metrics package

* Add csgraph sparse implementation for single linkage

* Add fast labelling/conversion from MST to single linkage tree; remove uneeded single_linkage.pyx file.

* Ensure existing tests cover single linkage

* Name cingle linkage labelling correctly.

* Iterating toward correct solution. Still have to get n_clusters, compute_full_tree=False working

* Get n_components correct.

* Update docstrings.

* Fix the parents array when we don't get the "full tree"

* Add single linkage to agglomerative clustering example.

* Add single linkage to digits agglomerative clustering example.

* Update documentation to reflect the addition of single linkage.

* Update documentation to reflect the addition of single linkage.

* Pep8 fix for class declaration in cython

* Fix heading in clustering docs

* Update the digits clustering text to reflect the new reality.

* Provide a more complete comparison of the different linkage methods, highlighting the relative strengths and weaknesses.

* We don't need connectivity here, and we can ignore issues with warnings for spectral clustering.

* Add an explicit test that single linkage successfully works on examples it should perform well on.

* Update docs with a more complete comparison on linkage methods (scale to be determined?)

* List formatting in example linkage comparison.

* Flake8 fixes.

* Flake8 fixes.

* More Flake8 fixes.

* Fix agglomerative plot example with correct subplot spec

* Explicitly test linkages (including single) produce results identical to scipy.cluster.hierarchical

* Fix comment on why we sort (consistency)

* Make dense single linkage faster

* Add docstring to new mst-linkage-core computations.

* Add a test that new single linkage code matches scipy

* Ensure we only attemtp this for metrics Jake implemented.

* Per amueller; it's a long paper, ref the figure.

* Clean up a few things.

* Too many blank lines for flake8

* Bad scipy slink input

* Flake8 fixes

* Clean up cython a little; fix typo/carryover

* Convert memoryview to numpy array on return

* Just convert to the correct dtype

* Update sklearn/cluster/_hierarchical.pyx

Co-Authored-By: Nicolas Hug <contact@nicolas-hug.com>

* Update sklearn/cluster/_hierarchical.pyx

Co-Authored-By: Nicolas Hug <contact@nicolas-hug.com>

* Update sklearn/cluster/_hierarchical.pyx

Co-Authored-By: Nicolas Hug <contact@nicolas-hug.com>

* Update sklearn/cluster/tests/test_hierarchical.py

Co-Authored-By: Nicolas Hug <contact@nicolas-hug.com>

* Fixes as per @NicolasHug suggestions.

* Update renaming of params in test_hierarchical

* Relative import?

* Ah, it got renamed in master...

* A bad merge on my part.

* In principle this is in sklearn.neighbors now...

* No; not that way...

* Declare dim before use.

* Update sklearn/cluster/tests/test_hierarchical.py

Co-Authored-By: Nicolas Hug <contact@nicolas-hug.com>

* Remaining fixes per Nicolas Hug.

* Update sklearn/cluster/tests/test_hierarchical.py

Co-Authored-By: Nicolas Hug <contact@nicolas-hug.com>

* Fix flake8 issues.

* Switch from stable to mergesort per jnotham

* Update sklearn/cluster/_hierarchical.py

Co-Authored-By: Nicolas Hug <contact@nicolas-hug.com>

* Skip checks that are already validated.

* Update docstring per Gael's suggestion

* Add a benchmark script for agglomerative clustering

* Fix some flake8 issues

* No flake8 on the one line

* Update parameters and output for benchmark hierarchical

* Switch to 2D plotting for hierarchical benchmark

* Wrong colormap name

* Formatting fpr bench hierarchical

* Add an item to WhatsNew
* whats_new cleanup

* fix indent

* reorder hgbt ones

* add Guillaume to contributors and remove unnecessary entry
@adrinjalali adrinjalali added this to the 0.22 milestone Nov 25, 2019
@jnothman
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I'd usually exclude something like #11514 after a feature freeze unless it was very clear that consensus was to release it in a hurry.

@ogrisel
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ogrisel commented Nov 25, 2019

I'd usually exclude something like #11514 after a feature freeze unless it was very clear that consensus was to release it in a hurry.

If we do that, (I am +0 for not including it to respect our agreed upon process), we need to change the what's new entry to move it to 0.23 in master.

@jnothman
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The pick list looks good, thanks

#15711 should also be considered before release. And yes, #15626 should be resolved if we want it to be useful any time soon

@adrinjalali
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I don't think #15711 is a blocker, but happy to have more opinions there.

Also, I'm going to remove #11514 then.

@adrinjalali
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I think we can ignore the circleci failures since they seem to be absent if we do a [doc build], which is what happens on the 0.22.X branch anyway. WDYT @cmarmo ?

Although it does make me think if we should fix our script. These seem false positives to me.

@thomasjpfan
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Yea the script needs to be adjusted to either not error on images from the api docs or run the examples for them.

* include all pxd files in package

* _libsvm _liblinear to pxi + add a test

* simplify stuff + use pathlib

* cln

* more cln
@jnothman
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jnothman commented Nov 26, 2019 via email

@cmarmo
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cmarmo commented Nov 26, 2019

@adrinjalali , @thomasjpfan , yes this is clearly a false positive but the script merged in #15680 should work for all the failing cases in this PR.
I've checked the build log on circleCI and the executed command is

 sed -e 's/_([[:digit:]][[:digit:]][[:digit:]]|thumb).png/.py/'

not

 sed -E 's/_([[:digit:]][[:digit:]][[:digit:]]|thumb).png/.py/'

as expected.
Something to do with the release freezing?

@thomasjpfan
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This was dropped, so it is using the old -e:

drop 641b863188 MNT fix filtering of examples file to run by sphinx (#15680)

@adrinjalali
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All green. Shall we merge for me to tag and make the wheels?

@jnothman
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Do we expect any further changes before final?

@qinhanmin2014
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Perhaps add c4733f4 and 63cd600.
And I prefer to merge #15412 to correct the doc.
Regarding other 0.22 issues, I think we can solve the HGBDT issues and the encoder issues in 0.23. For LR preconditioning, we've updated the doc.
One remaing issue is #15573 by @amueller (I saw it just now o(╥﹏╥)o), I guess we can leave it to 0.23.

@qinhanmin2014
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Maybe we can skip the rc3 and release directly?

@NicolasHug
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What are the HGBDT issues @qinhanmin2014 ?

@qinhanmin2014
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What are the HGBDT issues @qinhanmin2014 ?

#14696
#14516

@jnothman
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jnothman commented Nov 27, 2019 via email

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I don't think this pull request updates the version!

@jnothman jnothman mentioned this pull request Nov 28, 2019
@jnothman
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Ready to merge, tag and proceed with release as far as I'm concerned

@jnothman jnothman merged commit 0a56df6 into scikit-learn:0.22.X Nov 28, 2019
@adrinjalali adrinjalali deleted the release-0.22rc3 branch November 28, 2019 10:00
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