Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Remove abstractmethod that silently brake downstream packages #15996

Merged

Conversation

@bsipocz
Copy link
Contributor

bsipocz commented Dec 31, 2019

This PR removes the abstractmethod _check_X that has been added silently in #12569, to be included in the next bugfix release 0.22.1

As the BaseNB class is going away anyway and downstream is not suppose to subclass private base classes, I suppose this can be a patch only for the bugfix, but not the next feature release.

cc @jnothman

@bsipocz bsipocz mentioned this pull request Dec 31, 2019
4 of 4 tasks complete
@jnothman jnothman added this to the 0.22.1 milestone Dec 31, 2019
@rth
rth approved these changes Dec 31, 2019
Copy link
Member

rth left a comment

Thanks @bsipocz ! LGTM.

As the BaseNB class is going away anyway and downstream is not suppose to subclass private base classes, I suppose this can be a patch only for the bugfix, but not the next feature release.

True, but I think it's also fine to keep in master since BaseNB is only going to be removed in 0.24.

Copy link
Member

ogrisel left a comment

LGTM as well.

@ogrisel

This comment has been minimized.

Copy link
Member

ogrisel commented Dec 31, 2019

I will add a what's new entry and merge.

@ogrisel ogrisel merged commit 70d8b70 into scikit-learn:master Dec 31, 2019
19 checks passed
19 checks passed
LGTM analysis: C/C++ No code changes detected
Details
LGTM analysis: JavaScript No code changes detected
Details
LGTM analysis: Python No new or fixed alerts
Details
ci/circleci: deploy Your tests passed on CircleCI!
Details
ci/circleci: doc Your tests passed on CircleCI!
Details
ci/circleci: doc artifact Link to 0/doc/_changed.html
Details
ci/circleci: doc-min-dependencies Your tests passed on CircleCI!
Details
ci/circleci: lint Your tests passed on CircleCI!
Details
scikit-learn.scikit-learn Build #20191231.12 succeeded
Details
scikit-learn.scikit-learn (Linting) Linting succeeded
Details
scikit-learn.scikit-learn (Linux py35_conda_openblas) Linux py35_conda_openblas succeeded
Details
scikit-learn.scikit-learn (Linux py35_ubuntu_atlas) Linux py35_ubuntu_atlas succeeded
Details
scikit-learn.scikit-learn (Linux pylatest_pip_openblas_pandas) Linux pylatest_pip_openblas_pandas succeeded
Details
scikit-learn.scikit-learn (Linux32 py35_ubuntu_atlas_32bit) Linux32 py35_ubuntu_atlas_32bit succeeded
Details
scikit-learn.scikit-learn (Linux_Runs pylatest_conda_mkl) Linux_Runs pylatest_conda_mkl succeeded
Details
scikit-learn.scikit-learn (Windows py35_pip_openblas_32bit) Windows py35_pip_openblas_32bit succeeded
Details
scikit-learn.scikit-learn (Windows py37_conda_mkl) Windows py37_conda_mkl succeeded
Details
scikit-learn.scikit-learn (macOS pylatest_conda_mkl) macOS pylatest_conda_mkl succeeded
Details
scikit-learn.scikit-learn (macOS pylatest_conda_mkl_no_openmp) macOS pylatest_conda_mkl_no_openmp succeeded
Details
@ogrisel

This comment has been minimized.

Copy link
Member

ogrisel commented Dec 31, 2019

Thanks @bsipocz!

@qinhanmin2014

This comment has been minimized.

Copy link
Member

qinhanmin2014 commented Dec 31, 2019

I'm afraid that this is not correct, because we use self._check_X in BaseNB
(will post more details tomorrow)
ping @ogrisel @rth

@ogrisel

This comment has been minimized.

Copy link
Member

ogrisel commented Dec 31, 2019

Indeed you are right. Let me fix this in another PR.

ogrisel added a commit to ogrisel/scikit-learn that referenced this pull request Dec 31, 2019
@bsipocz

This comment has been minimized.

Copy link
Contributor Author

bsipocz commented Dec 31, 2019

I'm afraid that this is not correct, because we use self._check_X in BaseNB

of course, I'm sorry not spotting it, shouldn't have opened a PR in the middle of the night. (But then it may also that there is no sufficient test coverage for the BaseNB to pick that up?)

@qinhanmin2014

This comment has been minimized.

Copy link
Member

qinhanmin2014 commented Jan 1, 2020

of course, I'm sorry not spotting it, shouldn't have opened a PR in the middle of the night. (But then it may also that there is no sufficient test coverage for the BaseNB to pick that up?)

We usually don't test the base class.

You're welcomed to contribute at any time, sorry if my comments make you unhappy.

@bsipocz

This comment has been minimized.

Copy link
Contributor Author

bsipocz commented Jan 1, 2020

Oh, not at all, there is not a single trace of unhappiness.

ogrisel added a commit to ogrisel/scikit-learn that referenced this pull request Jan 2, 2020
@ogrisel

This comment has been minimized.

Copy link
Member

ogrisel commented Jan 2, 2020

Well we do not have tests for the BaseNB class itself but It was never intended to be part of the public API. It's just that in the past we did not make the base classes explicitly private.

The implementation classes are properly tested, so I think this is fine as it is.

ogrisel added a commit that referenced this pull request Jan 2, 2020
* DOC fixed default values in dbscan (#15753)

* DOC fix incorrect branch reference in contributing doc (#15779)

* DOC relabel Feature -> Efficiency in change log (#15770)

* DOC fixed Birch default value (#15780)

* STY Minior change on code padding in website theme (#15768)

* DOC Fix yticklabels order in permutation importances example (#15799)

* Fix yticklabels order in permutation importances example

* STY Update wrapper width (#15793)

* DOC Long sentence was hard to parse and ambiguous in _classification.py (#15769)

* DOC Removed duplicate 'classes_' attribute in Naive Bayes classifiers (#15811)

* BUG Fixes pandas dataframe bug with boolean dtypes (#15797)

* BUG Returns only public estimators in all_estimators (#15380)

* DOC improve doc for multiclass and types_of_target (#15333)

* TST Increases tol for check_pca_float_dtype_preservation assertion (#15775)

* update _alpha_grid class in _coordinate_descent.py (#15835)

* FIX Explicit conversion of ndarray to object dtype. (#15832)

* BLD Parallelize sphinx builds on circle ci (#15745)

* DOC correct url for preprocessing (#15853)

* MNT avoid generating too many cross links in examples (#15844)

* DOC Correct wrong doc in precision_recall_fscore_support (#15833)

* DOC add comment in check_pca_float_dtype_preservation (#15819)

Documenting the changes in #15775

* DOC correct indents in docstring _split.py (#15843)

* DOC fix docstring of KMeans based on sklearn guideline (#15754)

* DOC fix docstring of AgglomerativeClustering based on sklearn guideline (#15764)

* DOC fix docstring of AffinityPropagation based on sklearn guideline (#15777)

* DOC fixed SpectralCoclustering and SpectralBiclustering docstrings following sklearn guideline (#15778)

* DOC fix FeatureAgglomeration and MiniBatchKMeans docstring following sklearn guideline (#15809)

* TST Specify random_state in test_cv_iterable_wrapper (#15829)

* DOC Include LinearSV{C, R} in models that support sample_weights (#15871)

* DOC correct some indents (#15875)

* DOC Fix documentation of default values in tree classes (#15870)

* DOC fix typo in docstring (#15887)

* DOC FIX default value for xticks_rotation in plot_confusion_matrix (#15890)

* Fix imports in pip3 ubuntu by suffixing affected files (#15891)

* MNT Raise erorr when normalize is invalid in confusion_matrix (#15888)

* [MRG] DOC Increases search results for API object results (#15574)

* MNT Ignores warning in pyamg for deprecated scipy.random (#15914)

* DOC Instructions to troubleshoot Windows path length limit (#15916)

* DOC add versionadded directive to some estimators (#15849)

* DOC clarify doc-string of roc_auc_score and add references (#15293)

* MNT Adds skip lint to azure pipeline CI (#15904)

* BLD Fixes bug when building with NO_MATHJAX=1 (#15892)

* [MRG] BUG Checks to number of axes in passed in ax more generically (#15760)

* EXA Minor fixes in plot_sparse_logistic_regression_20newsgroups.py (#15925)

* BUG Do not shadow public functions with deprecated modules (#15846)

* Import sklearn._distributor_init first (#15929)

* DOC Fix typos, via a Levenshtein-style corrector (#15923)

* DOC in canned comment, mention that PR title becomes commit me… (#15935)

* DOC/EXA Correct spelling of "Classification" (#15938)

* BUG fix pip3 ubuntu update by suffixing file (#15928)

* [MRG] Ways to compute center_shift_total were different in "full" and "elkan" algorithms. (#15930)

* TST Fixes integer test for train and test indices (#15941)

* BUG ensure that parallel/sequential give the same permutation importances (#15933)

* Formatting fixes in changelog (#15944)

* MRG FIX: order of values of self.quantiles_ in QuantileTransformer (#15751)

* [MRG] BUG Fixes constrast in plot_confusion_matrix (#15936)

* BUG use zero_division argument in classification_report (#15879)

* DOC change logreg solver in plot_logistic_path (#15927)

* DOC fix whats new ordering (#15961)

* COSMIT use np.iinfo to define the max int32 (#15960)

* DOC Apply numpydoc validation to VotingRegressor methods (#15969)

Co-authored-by: Tiffany R. Williams <Tiffany8@users.noreply.github.com>

* DOC improve naive_bayes.py documentation (#15943)

Co-authored-by: Jigna Panchal <40188288+jigna-panchal@users.noreply.github.com>

* DOC Fix default values in Perceptron documentation (#15965)

* DOC Improve default values in logistic documentation (#15966)

Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>

* DOC Improve documentation of default values for imputers (#15964)

* EXA/MAINT Simplify code in manifold learning example (#15949)

* DOC Improve default values in SGD documentation (#15967)

* DOC Improve defaults in neural network documentation (#15968)

* FIX use safe_sparse_dot for callable kernel in LabelSpreading (#15868)

* BUG Adds attributes back to check_is_fitted (#15947)

Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org>

* DOC update check_is_fitted what's new

* DOC change python-devel to python3-devel for yum. (#15986)

* DOC Correct the default value of values_format in plot_confusion_matrix (#15981)

* [MRG] MNT Updates pypy to use 7.2.0 (#15954)

* FIX Add missing 'values_format' param to disp.plot() in plot_confusion_matrix (#15937)

* FIX support scalar values in fit_params in SearchCV (#15863)

* support a scalar fit param

* pep8

* TST add test for desired behavior

* FIX introduce _check_fit_params to validate parameters

* DOC update whats new

* TST tests both grid-search and randomize-search

* PEP8

* DOC revert unecessary change

* TST add test for _check_fit_params

* olivier comments

* TST fixes

* DOC whats new

* DOC whats new

* TST revert type of error

* add olivier suggestions

* address olivier comments

* address thomas comments

* PEP8

* comments olivier

* TST fix test by passing X

* avoid to call twice tocsr

* add case column/row sparse in check_fit_param

* provide optional indices

* TST check content when indexing params

* PEP8

* TST update tests to check identity

* stupid fix

* use a distribution in RandomizedSearchCV

* MNT add lightgbm to one of the CI build

* move to another build

* do not install dependencies lightgbm

* MNT comments on the CI setup

* address some comments

* Test fit_params compat without dependency on lightgbm

Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
Co-authored-by: Olivier Grisel <olivier.grisel@ensta.org>

* Remove abstractmethod that silently brake downstream packages (#15996)

* FIX restore BaseNB._check_X without abstractmethod decoration (#15997)

* Update v0.22 changelog for 0.22.1 (#16002)

- set the date
- move entry for quantile transformer to the 0.22.1 section
- fix alphabetical ordering of modules

* STY Removes hidden scroll bar (#15999)

* Flake8 fixes

* Fix: remove left-over lines that should have been deleted during conflict resolution when rebasing

* Fix missing imports

* Update version

* Fix test_check_is_fitted

* Make test_sag_regressor_computed_correctly deterministic (#16003)

Fix #15818.

Co-authored-by: cgsavard <claire.savard@colorado.edu>
Co-authored-by: Joel Nothman <joel.nothman@gmail.com>
Co-authored-by: Thomas J Fan <thomasjpfan@gmail.com>
Co-authored-by: Matt Hall <matt@agilegeoscience.com>
Co-authored-by: Kathryn Poole <kathryn.poole2@gmail.com>
Co-authored-by: lucyleeow <jliu176@gmail.com>
Co-authored-by: JJmistry <jayminm22@gmail.com>
Co-authored-by: Juan Carlos Alfaro Jiménez <JuanCarlos.Alfaro@uclm.es>
Co-authored-by: SylvainLan <sylvain.s.lannuzel@gmail.com>
Co-authored-by: Nicolas Hug <contact@nicolas-hug.com>
Co-authored-by: Hanmin Qin <qinhanmin2005@sina.com>
Co-authored-by: Adrin Jalali <adrin.jalali@gmail.com>
Co-authored-by: Vachan D A <vachanda@users.noreply.github.com>
Co-authored-by: Sambhav Kothari <sambhavs.email@gmail.com>
Co-authored-by: wenliwyan <12013376+wenliwyan@users.noreply.github.com>
Co-authored-by: shivamgargsya <shivam.gargshya@gmail.com>
Co-authored-by: Reshama Shaikh <rs2715@stern.nyu.edu>
Co-authored-by: Oliver Urs Lenz <oulenz@users.noreply.github.com>
Co-authored-by: Loïc Estève <loic.esteve@ymail.com>
Co-authored-by: Brian Wignall <BrianWignall@gmail.com>
Co-authored-by: Ritchie Ng <ritchieng@u.nus.edu>
Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
Co-authored-by: inderjeet <43402782+inder128@users.noreply.github.com>
Co-authored-by: scibol <scibol@users.noreply.github.com>
Co-authored-by: Tirth Patel <tirthasheshpatel@gmail.com>
Co-authored-by: Bibhash Chandra Mitra <bibhashm220896@gmail.com>
Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
Co-authored-by: Tiffany R. Williams <Tiffany8@users.noreply.github.com>
Co-authored-by: Jigna Panchal <40188288+jigna-panchal@users.noreply.github.com>
Co-authored-by: @nkish <19225359+ankishb@users.noreply.github.com>
Co-authored-by: Pulkit Mehta <pulkit_mehta_work@yahoo.com>
Co-authored-by: David Breuer <DavidBreuer@users.noreply.github.com>
Co-authored-by: Niklas <niklas.sm+github@gmail.com>
Co-authored-by: Windber <guolipengyeah@126.com>
Co-authored-by: Stephen Blystone <29995339+blynotes@users.noreply.github.com>
Co-authored-by: Brigitta Sipőcz <b.sipocz@gmail.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
5 participants
You can’t perform that action at this time.