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

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Merged
merged 5 commits into from
Dec 31, 2019
Merged

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

merged 5 commits into from
Dec 31, 2019

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blynotes
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I added the missing 'values_format' parameter to the "disp.plot()" call in "plot_confusion_matrix".

Reference Issues/PRs

No related issues found.

What does this implement/fix? Explain your changes.

Problem Description

  • The class ConfusionMatrixDisplay's plot() function already has the values_format parameter.
  • "plot_confusion_matrix" function also has the values_format parameter.
  • However, "plot_confusion_matrix" was not passing it's values_format value when calling the ConfusionMatrixDisplay's plot().
  • This resulted in being unable to change the format of the values in the confusion matrix when calling plot_confusion_matrix(), even when you passed a value for "values_format". The confusion matrix always displayed in scientific notation.

My Solution

  • I fixed this by adding the missing parameter to the plot() call in "plot_confusion_matrix".

Simplified example of the code, for further clarification:

   class ConfusionMatrixDisplay:
       ...__init__ function goes here...
       def plot(self, ..., values_format=None, ...):  # <-- values_format is already there.
           ...

   def plot_confusion_matrix(...,
                             values_format=None,  # <-- values_format is already there.
                             ...):
       ...
       disp = ConfusionMatrixDisplay(...)
       return disp.plot(...)  # <-- values_format is missing from here and NOT passed to plot.

Any other comments?

None. Thank you!

thomasjpfan
thomasjpfan reviewed Dec 20, 2019
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This needs a test to make sure that plot_confusion_matrix passes through values_format and changes the text in the plot.

@blynotes
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Hi Thomas, I have updated test_plot_confusion_matrix.py with a new test to verify plot_confusion_matrix passes through values_format and changes the text in the plot.

qinhanmin2014
qinhanmin2014 approved these changes Dec 28, 2019
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thanks
Please add an entry to the change log at doc/whats_new/v*.rst. Like the other entries there, please reference this pull request with :pr: and credit yourself (and other contributors if applicable) with :user:.
this should be included in 0.22.1

@qinhanmin2014 qinhanmin2014 added this to the 0.22.1 milestone Dec 28, 2019
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ping the reviewers in plot_confusion_matrix PR
@thomasjpfan @NicolasHug @glemaitre @jnothman @amueller

thomasjpfan
thomasjpfan approved these changes Dec 28, 2019
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LGTM! Please add an BUG entry to the whats new in 0.22.1.

qinhanmin2014
qinhanmin2014 reviewed Dec 29, 2019
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sklearn/metrics/_plot/tests/test_plot_confusion_matrix.py Outdated
assert disp.text_.shape == (n_classes, n_classes)

expected_text = np.array([format(v, values_format)
for v in cm.ravel(order="C")])
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And another small comment, order="C" can be removed here and below.

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Removed 'order="C"' in both places in the latest commit. Thanks!

@blynotes
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Hi Thomas and Hanmin, I have updated the v0.22.rst with a |Fix| entry in 0.22.1, and removed order="C" per Hanmin's suggestion.

Let me know if there is anything else I need to do. Thank you!

@qinhanmin2014
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Please check the diff @blynotes

@blynotes
I added the missing "values_format" parameter to "disp.plot()" call i…
76d285e 
…n "plot_confusion_matrix".

"disp" is an object of class ConfusionMatrixDisplay.
ConfusionMatrixDisplay's plot() function already has the values_format parameter.
And the "plot_confusion_matrix" function also has the values_format parameter, but it was not passed when calling plot().
@blynotes
Added test coverage to verify 'plot_confusion_matrix' passes through …
aa75f93 
…'values_format' and changes the text in the plot.
@blynotes
Merge remote-tracking branch 'upstream/master' into update-plot_confu…
ddbabf2 
…sion_matrix
@blynotes
Updated Release Notes and removed 'order="C"' from the cm.ravel() cal…
dd4fc16 
…l in test_plot_confusion_matrix.py's test_confusion_matrix_text_format() call.
@blynotes
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Sorry, I'm new to the git commands and still learning. Please check it now.

qinhanmin2014
qinhanmin2014 approved these changes Dec 31, 2019
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thanks

@qinhanmin2014 qinhanmin2014 merged commit eb3ad2d into scikit-learn:master Dec 31, 2019
ogrisel pushed a commit to ogrisel/scikit-learn that referenced this pull request Dec 31, 2019
@blynotes @ogrisel
FIX Add missing 'values_format' param to disp.plot() in plot_confusio…
1a46a72 
…n_matrix (scikit-learn#15937)
@blynotes blynotes deleted the update-plot_confusion_matrix branch December 31, 2019 19:47
ogrisel pushed a commit to ogrisel/scikit-learn that referenced this pull request Jan 2, 2020
@blynotes @ogrisel
FIX Add missing 'values_format' param to disp.plot() in plot_confusio…
cbe29e0 
…n_matrix (scikit-learn#15937)
ogrisel added a commit that referenced this pull request Jan 2, 2020
@ogrisel @cgsavard
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0.22.1 release (#15998)
e5698bd 
* 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>
panpiort8 pushed a commit to panpiort8/scikit-learn that referenced this pull request Mar 3, 2020
@blynotes
FIX Add missing 'values_format' param to disp.plot() in plot_confusio…
b945f04 
…n_matrix (scikit-learn#15937)
Pseudomanifold pushed a commit to BorgwardtLab/scikit-learn that referenced this pull request Apr 24, 2020
@ogrisel @cgsavard
@jnothman @thomasjpfan @kwinkunks @kp1302 @lucyleeow @JJmistry @alfaro96 @SylvainLan @NicolasHug @qinhanmin2014 @adrinjalali @vachanda @sambhav @wenliwyan @shivamgargsya @oulenz @lesteve @bwignall @ritchieng @glemaitre @inder128 @scibol @tirthasheshpatel @Bibyutatsu @agramfort @Tiffany8 @jigna-panchal @ankishb @pulkitmehtawork @DavidBreuer @nik-sm @Windber @blynotes @bsipocz @Pseudomanifold
0.22.1 release (scikit-learn#15998)
2e162b2 
* DOC fixed default values in dbscan (scikit-learn#15753)

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

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

* DOC fixed Birch default value (scikit-learn#15780)

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

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

* Fix yticklabels order in permutation importances example

* STY Update wrapper width (scikit-learn#15793)

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

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

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

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

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

* TST Increases tol for check_pca_float_dtype_preservation assertion (scikit-learn#15775)

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

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

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

* DOC correct url for preprocessing (scikit-learn#15853)

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

* DOC Correct wrong doc in precision_recall_fscore_support (scikit-learn#15833)

* DOC add comment in check_pca_float_dtype_preservation (scikit-learn#15819)

Documenting the changes in scikit-learn#15775

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

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

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

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

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

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

* TST Specify random_state in test_cv_iterable_wrapper (scikit-learn#15829)

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

* DOC correct some indents (scikit-learn#15875)

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

* DOC fix typo in docstring (scikit-learn#15887)

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

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

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

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

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

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

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

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

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

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

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

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

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

* Import sklearn._distributor_init first (scikit-learn#15929)

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

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

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

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

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

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

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

* Formatting fixes in changelog (scikit-learn#15944)

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

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

* BUG use zero_division argument in classification_report (scikit-learn#15879)

* DOC change logreg solver in plot_logistic_path (scikit-learn#15927)

* DOC fix whats new ordering (scikit-learn#15961)

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

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

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

* DOC improve naive_bayes.py documentation (scikit-learn#15943)

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

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

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

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

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

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

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

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

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

* BUG Adds attributes back to check_is_fitted (scikit-learn#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. (scikit-learn#15986)

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

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

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

* FIX support scalar values in fit_params in SearchCV (scikit-learn#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 (scikit-learn#15996)

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

* Update v0.22 changelog for 0.22.1 (scikit-learn#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 (scikit-learn#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 (scikit-learn#16003)

Fix scikit-learn#15818.

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@thomasjpfan thomasjpfan thomasjpfan approved these changes

@qinhanmin2014 qinhanmin2014 qinhanmin2014 approved these changes

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