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[MRG + 1] Removed deprecated stuff in 0.18#5451

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amueller merged 2 commits intoscikit-learn:masterfrom
zermelozf:deprecated-stuff
Oct 21, 2015
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[MRG + 1] Removed deprecated stuff in 0.18#5451
amueller merged 2 commits intoscikit-learn:masterfrom
zermelozf:deprecated-stuff

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@zermelozf
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Contributes to #5434.

Removes the following deprecated code:

  • pooling_func in transform of AgglomerationTransform in file cluster/_feature_agglomeration.py
  • random_state parameter in cluster/dbscan_.py
  • n_components in cluster/hierarchical.py
  • max_iterations in cluster/mean_shift_.py
  • support for class_weight="subsample" in utils/class_weight.py
  • allow_lists and allow_nd/ insklearn/cross_validation.py`.
  • estimator_params in sklearn/feature_selection/rfe.py
  • threshold_ in 'OutlierDetectionMixinat filesklearn/covariance/outlier_detection.py`
  • precompute="auto" in sklearn/linear_models/coordinate_descent.py and sklearn/utils/class_weight.py
  • thresh in sklearn/mixture/dpgmm.py and sklearn/mixture/gmm.py.
  • deprecation warnings in sklearn/multiclass.py.
  • deprecation warnings in sklearn/neighbors.
  • deprecation warnings in sklearn/preprocessing.
  • deprecation warnings in sklearn/utils/classs_weight.py

@zermelozf zermelozf force-pushed the deprecated-stuff branch 3 times, most recently from fe39f7e to e584345 Compare October 19, 2015 14:54
@ogrisel
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ogrisel commented Oct 19, 2015

Ignore the circle CI report, this is unrelated to this PR.

@amueller
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travis fails though, because of some test of the deprecation in enet.

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This cleanup makes me unreasonably happy!

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@zermelozf zermelozf force-pushed the deprecated-stuff branch 2 times, most recently from cdba563 to 07ca31f Compare October 20, 2015 08:22
@zermelozf zermelozf changed the title Removed deprecation warnings. Removed deprecated stuff in 0.18 Oct 20, 2015
@raghavrv
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-500 lines 🍻

@raghavrv
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@amueller @GaelVaroquaux Could you take a look at this since travis seems to be happy?

@zermelozf zermelozf changed the title Removed deprecated stuff in 0.18 [MRG] Removed deprecated stuff in 0.18 Oct 20, 2015
@glouppe
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glouppe commented Oct 20, 2015

Looks good to me, but we should wait for CircleCI to be back up, to be sure examples are still fine.

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this part needs to be undone. It should be 0.19. Please change the error accordingly. Why is auto in this list twice?

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Ok, I added it back without the duplicate.

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Would fit on one line maybe?

@ogrisel
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ogrisel commented Oct 20, 2015

circleci should no longer be triggered on PRs. It's supposed to be triggered only after merge to master:

https://github.com/scikit-learn/scikit-learn/blob/master/circle.yml#L31

If it does not, it might be that I don't understand how to interpret the documentation of this feature.

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yeah this should also be 0.19 I guess.

@amueller
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looks great apart from my two comments. sorry for the confusion, I think that was me. I'm bad at counting.

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this needs to go back in, too.

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It's back now.

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I cannot see this: the tests need to be restored to check that the class_weight='subsample' option is still supported (despite being deprecated).

@zermelozf zermelozf force-pushed the deprecated-stuff branch 4 times, most recently from 8aa4a7f to d63b33f Compare October 20, 2015 15:57
@amueller
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LGTM

@amueller amueller changed the title [MRG] Removed deprecated stuff in 0.18 [MRG + 1] Removed deprecated stuff in 0.18 Oct 20, 2015
@ogrisel
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ogrisel commented Oct 20, 2015

This comment #5451 (diff) was not addressed.

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"... is deprecated in 0.17 and will be removed in 0.19..."

It's important to be explicit with the version number when it was deprecated to make it easier to detect violations to our deprecation policy.

@ogrisel ogrisel added this to the 0.17 milestone Oct 21, 2015
@ogrisel
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ogrisel commented Oct 21, 2015

Added the 0.17 milestone because we need to backport the fix for the incorrect deprecation warning messages to the 0.17.0 release.

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ogrisel commented Oct 21, 2015

@zermelozf once my last comments are addressed, +1 for merge as well. You don't need to wait for appveyor. I am afraid it won't catch up this week...

@zermelozf
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@ogrisel @amueller, It should be good now. Tests for deprecated keyword 'auto' should be back and I have added the '0.17' thing in the warning messages.

amueller added a commit that referenced this pull request Oct 21, 2015
[MRG + 1] Removed deprecated stuff in 0.18
@amueller amueller merged commit bad3dd6 into scikit-learn:master Oct 21, 2015
@amueller
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@ogrisel you wanna backport?

@amueller
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did the backport myself

@amueller
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@zermelozf is your handle refering to https://en.wikipedia.org/wiki/Zermelo%E2%80%93Fraenkel_set_theory ? I guess there is an extra Z.

amueller pushed a commit that referenced this pull request Oct 21, 2015
glouppe pushed a commit to glouppe/scikit-learn that referenced this pull request Oct 26, 2015
yarikoptic added a commit to yarikoptic/scikit-learn that referenced this pull request Oct 27, 2015
* commit '0.17b1-14-g4e6829c':
  Corrected macro ROC in example plot_roc
  BF: FIX OvR decision_function_shape in SVC
  Fix fit_transform, stability issue and scale issue in PLS
  FIX class_weight in LogisticRegression and LogisticRegressionCV
  FIX MaxAbsScaler on sparse matrices with 1 row
  Deprecate residues_ in LinearRegression
  Addressed comments on PR scikit-learn#5451
  MAINT Removed deprecated stuff.
  MAINT disable circle ci on 0.17.X
  MAINT: deprecation warns from StandardScaler std_
  FIX: remove shuffling in LabelKFold
  FIX skip LDA deprecation test on python3.3 that has no reload.
  Fix broken examples using RandomTreeEmbeddings
  MAINT Use the full listing of the rackspace wheelhouse for appveyor

Conflicts:
    sklearn/externals/joblib/format_stack.py -- removed
yarikoptic added a commit to yarikoptic/scikit-learn that referenced this pull request Oct 27, 2015
* dfsg:
  Corrected macro ROC in example plot_roc
  BF: FIX OvR decision_function_shape in SVC
  Fix fit_transform, stability issue and scale issue in PLS
  FIX class_weight in LogisticRegression and LogisticRegressionCV
  FIX MaxAbsScaler on sparse matrices with 1 row
  Deprecate residues_ in LinearRegression
  Addressed comments on PR scikit-learn#5451
  MAINT Removed deprecated stuff.
  MAINT disable circle ci on 0.17.X
  MAINT: deprecation warns from StandardScaler std_
  FIX: remove shuffling in LabelKFold
  FIX skip LDA deprecation test on python3.3 that has no reload.
  Fix broken examples using RandomTreeEmbeddings
  MAINT Use the full listing of the rackspace wheelhouse for appveyor
amueller pushed a commit to amueller/scikit-learn that referenced this pull request Oct 30, 2015
yarikoptic added a commit to yarikoptic/scikit-learn that referenced this pull request Nov 14, 2015
* commit '0.17b1-14-g4e6829c':
  Corrected macro ROC in example plot_roc
  BF: FIX OvR decision_function_shape in SVC
  Fix fit_transform, stability issue and scale issue in PLS
  FIX class_weight in LogisticRegression and LogisticRegressionCV
  FIX MaxAbsScaler on sparse matrices with 1 row
  Deprecate residues_ in LinearRegression
  Addressed comments on PR scikit-learn#5451
  MAINT Removed deprecated stuff.
  MAINT disable circle ci on 0.17.X
  MAINT: deprecation warns from StandardScaler std_
  FIX: remove shuffling in LabelKFold
  FIX skip LDA deprecation test on python3.3 that has no reload.
  Fix broken examples using RandomTreeEmbeddings
  MAINT Use the full listing of the rackspace wheelhouse for appveyor
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6 participants