MNT Fix pre-commit issues (scikit-learn#31013)

DimitriPapadopoulos · web-flow · commit 4cd9d78579cf · 2025-03-22T10:49:53.000+01:00
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,7 @@
+exclude: '^(.git/|sklearn/externals/|asv_benchmarks/env/)'
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v5.0.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -13,4 +13,3 @@ all priceless contributions.
 
 We abide by the principles of openness, respect, and consideration of others of
 the Python Software Foundation: https://www.python.org/psf/codeofconduct/
-
diff --git a/asv_benchmarks/benchmarks/config.json b/asv_benchmarks/benchmarks/config.json
@@ -9,7 +9,7 @@
     // Can be overridden by environment variable SKLBENCH_PROFILE.
     "profile": "regular",
 
-    // List of values of n_jobs to use for estimators which accept this 
+    // List of values of n_jobs to use for estimators which accept this
     // parameter (-1 means all cores). An empty list means all values from 1 to
     // the maximum number of available cores.
     // Can be overridden by environment variable SKLBENCH_NJOBS.
diff --git a/doc/developers/maintainer.rst.template b/doc/developers/maintainer.rst.template
@@ -136,7 +136,7 @@ Reference Steps
         {%- if key != "rc" %}
         * [ ] Publish to https://github.com/scikit-learn/scikit-learn/releases
         {%- endif %}
-        * [ ] Announce on mailing list and on social media platforms (LinkedIn, Bluesky, etc.) 
+        * [ ] Announce on mailing list and on social media platforms (LinkedIn, Bluesky, etc.)
         {%- if key != "rc" %}
         * [ ] Update SECURITY.md in main branch
         {%- endif %}
diff --git a/doc/logos/README.md b/doc/logos/README.md
@@ -36,10 +36,10 @@ You may highlight or reference your work with scikit-learn by using one of the l
 
 | | |
 | - | - |
-|  <img src="1280px-scikit-learn-logo.png" height="100px"> | __Logo 1__ <br> File type: PNG <br> File size: 49 KB (1280 x 689 px) <br> File name: [1280px-scikit-learn-logo.png](https://github.com/scikit-learn/scikit-learn/blob/main/doc/logos/1280px-scikit-learn-logo.png) | 
+|  <img src="1280px-scikit-learn-logo.png" height="100px"> | __Logo 1__ <br> File type: PNG <br> File size: 49 KB (1280 x 689 px) <br> File name: [1280px-scikit-learn-logo.png](https://github.com/scikit-learn/scikit-learn/blob/main/doc/logos/1280px-scikit-learn-logo.png) |
 |  <img src="favicon.ico" height="100px"> | __Logo 2__ <br> File type: ICO <br> File size:  2 KB (32 x 32 px) <br> File name: [favicon.ico](https://github.com/scikit-learn/scikit-learn/blob/main/doc/logos/favicon.ico) |
-|  <img src="scikit-learn-logo-without-subtitle.svg" height="100px"> | __Logo 3__ <br> File type: SVG <br> File size: 5 KB <br> File name: [scikit-learn-logo-without-subtitle.svg](https://github.com/scikit-learn/scikit-learn/blob/main/doc/logos/scikit-learn-logo-without-subtitle.svg) | 
-|  <img src="scikit-learn-logo.svg" height="200px"> | __Logo 4__ <br> File type: SVG <br> File size: 4.59 KB <br> File name: [scikit-learn-logo.svg](https://github.com/scikit-learn/scikit-learn/blob/main/doc/logos/scikit-learn-logo.svg) | 
+|  <img src="scikit-learn-logo-without-subtitle.svg" height="100px"> | __Logo 3__ <br> File type: SVG <br> File size: 5 KB <br> File name: [scikit-learn-logo-without-subtitle.svg](https://github.com/scikit-learn/scikit-learn/blob/main/doc/logos/scikit-learn-logo-without-subtitle.svg) |
+|  <img src="scikit-learn-logo.svg" height="200px"> | __Logo 4__ <br> File type: SVG <br> File size: 4.59 KB <br> File name: [scikit-learn-logo.svg](https://github.com/scikit-learn/scikit-learn/blob/main/doc/logos/scikit-learn-logo.svg) |
 
 <br>
 
@@ -51,8 +51,8 @@ You may highlight or reference your work with scikit-learn by using one of the l
 
 - __Clear Space:__ To ensure the logo is clearly visible in all uses, surround it with a sufficient amount of clear space that is free of type, graphics, and other elements that might cause visual clutter. Do not overlap or obscure the logo with text, images, or other elements. The image below demonstrates the suggested amount of clear space margins to use around the logo. <br> <center><img src="brand_guidelines/scikitlearn_logo_clearspace_updated.png" width="250px"></center>
 
-- __Colors:__ Only use logos in the approved color palette defined above. Do not recolor the logo. 
-- __Typeface:__ Do not change the typeface used in the logo. 
+- __Colors:__ Only use logos in the approved color palette defined above. Do not recolor the logo.
+- __Typeface:__ Do not change the typeface used in the logo.
 - __No Modification:__ Do not attempt recreate or otherwise modify the scikit-learn logo.
 
 
diff --git a/doc/modules/biclustering.rst b/doc/modules/biclustering.rst
@@ -288,7 +288,7 @@ available:
 
 2. Assign biclusters from one set to another in a one-to-one fashion
    to maximize the sum of their similarities. This step is performed
-   using :func:`scipy.optimize.linear_sum_assignment`, which uses a 
+   using :func:`scipy.optimize.linear_sum_assignment`, which uses a
    modified Jonker-Volgenant algorithm.
 
 3. The final sum of similarities is divided by the size of the larger
@@ -303,4 +303,4 @@ are identical.
 
 * Hochreiter, Bodenhofer, et. al., 2010. `FABIA: factor analysis
   for bicluster acquisition
-  <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881408/>`__.
+  <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881408/>`__.
diff --git a/doc/modules/feature_selection.rst b/doc/modules/feature_selection.rst
@@ -224,8 +224,8 @@ alpha parameter, the fewer features selected.
   noise, the smallest absolute value of non-zero coefficients, and the
   structure of the design matrix X. In addition, the design matrix must
   display certain specific properties, such as not being too correlated.
-  On the use of Lasso for sparse signal recovery, see this example on 
-  compressive sensing: 
+  On the use of Lasso for sparse signal recovery, see this example on
+  compressive sensing:
   :ref:`sphx_glr_auto_examples_applications_plot_tomography_l1_reconstruction.py`.
 
   There is no general rule to select an alpha parameter for recovery of
diff --git a/doc/modules/svm.rst b/doc/modules/svm.rst
@@ -809,7 +809,7 @@ used, please refer to their respective papers.
   Volume 14 Issue 3, August 2004, p. 199-222.
 
 .. [#7] Schölkopf et. al `New Support Vector Algorithms
-  <https://www.stat.purdue.edu/~yuzhu/stat598m3/Papers/NewSVM.pdf>`_, 
+  <https://www.stat.purdue.edu/~yuzhu/stat598m3/Papers/NewSVM.pdf>`_,
   Neural Computation 12, 1207-1245 (2000).
 
 .. [#8] Crammer and Singer `On the Algorithmic Implementation of Multiclass
diff --git a/doc/testimonials/README.txt b/doc/testimonials/README.txt
@@ -5,4 +5,3 @@ https://docs.google.com/spreadsheet/ccc?key=0AhGnAxuBDhjmdDYwNzlZVE5SMkFsMjNBbGl
 
 To obtain access to this file, send an email to:
 nelle dot varoquaux at gmail dot com
-
diff --git a/doc/whats_new/upcoming_changes/sklearn.inspection/26202.enhancement.rst b/doc/whats_new/upcoming_changes/sklearn.inspection/26202.enhancement.rst
@@ -2,4 +2,4 @@
   users to pass their own grid of values at which the partial dependence should be
   calculated.
   By :user:`Freddy A. Boulton <freddyaboulton>` and :user:`Stephen Pardy
-  <stephenpardy>`
+  <stephenpardy>`
diff --git a/doc/whats_new/upcoming_changes/sklearn.inspection/29797.enhancement.rst b/doc/whats_new/upcoming_changes/sklearn.inspection/29797.enhancement.rst
@@ -1,4 +1,4 @@
 - :class:`inspection.DecisionBoundaryDisplay` now supports
   plotting all classes for multi-class problems when `response_method` is
   'decision_function', 'predict_proba' or 'auto'.
-  By :user:`Lucy Liu <lucyleeow>`
+  By :user:`Lucy Liu <lucyleeow>`
diff --git a/doc/whats_new/v1.6.rst b/doc/whats_new/v1.6.rst
@@ -748,38 +748,38 @@ Python and CPython ecosystem, for example :user:`Nathan Goldbaum <ngoldbaum>`,
 Thanks to everyone who has contributed to the maintenance and improvement of
 the project since version 1.5, including:
 
-Aaron Schumacher, Abdulaziz Aloqeely, abhi-jha, Acciaro Gennaro Daniele, Adam 
-J. Stewart, Adam Li, Adeel Hassan, Adeyemi Biola, Aditi Juneja, Adrin Jalali, 
-Aisha, Akanksha Mhadolkar, Akihiro Kuno, Alberto Torres, alexqiao, Alihan 
-Zihna, Aniruddha Saha, antoinebaker, Antony Lee, Anurag Varma, Arif Qodari, 
-Arthur Courselle, ArthurDbrn, Arturo Amor, Aswathavicky, Audrey Flanders, 
-aurelienmorgan, Austin, awwwyan, AyGeeEm, a.zy.lee, baggiponte, BlazeStorm001, 
-bme-git, Boney Patel, brdav, Brigitta Sipőcz, Cailean Carter, Camille 
-Troillard, Carlo Lemos, Christian Lorentzen, Christian Veenhuis, Christine P. 
-Chai, claudio, Conrad Stevens, datarollhexasphericon, Davide Chicco, David 
-Matthew Cherney, Dea María Léon, Deepak Saldanha, Deepyaman Datta, 
-dependabot[bot], dinga92, Dmitry Kobak, Domenico, Drew Craeton, dymil, Edoardo 
-Abati, EmilyXinyi, Eric Larson, Evelyn, fabianhenning, Farid "Freddie" Taba, 
-Gael Varoquaux, Giorgio Angelotti, Gleb Levitski, Guillaume Lemaitre, Guntitat 
-Sawadwuthikul, Haesun Park, Hanjun Kim, Henrique Caroço, hhchen1105, Hugo 
-Boulenger, Ilya Komarov, Inessa Pawson, Ivan Pan, Ivan Wiryadi, Jaimin Chauhan, 
-Jakob Bull, James Lamb, Janez Demšar, Jérémie du Boisberranger, Jérôme 
-Dockès, Jirair Aroyan, João Morais, Joe Cainey, Joel Nothman, John Enblom, 
-JorgeCardenas, Joseph Barbier, jpienaar-tuks, Julian Chan, K.Bharat Reddy, 
-Kevin Doshi, Lars, Loic Esteve, Lucas Colley, Lucy Liu, lunovian, Marc Bresson, 
-Marco Edward Gorelli, Marco Maggi, Marco Wolsza, Maren Westermann, 
-MarieS-WiMLDS, Martin Helm, Mathew Shen, mathurinm, Matthew Feickert, Maxwell 
-Liu, Meekail Zain, Michael Dawson, Miguel Cárdenas, m-maggi, mrastgoo, Natalia 
-Mokeeva, Nathan Goldbaum, Nathan Orgera, nbrown-ScottLogic, Nikita Chistyakov, 
-Nithish Bolleddula, Noam Keidar, NoPenguinsLand, Norbert Preining, notPlancha, 
-Olivier Grisel, Omar Salman, ParsifalXu, Piotr, Priyank Shroff, Priyansh Gupta, 
-Quentin Barthélemy, Rachit23110261, Rahil Parikh, raisadz, Rajath, 
-renaissance0ne, Reshama Shaikh, Roberto Rosati, Robert Pollak, rwelsch427, 
-Santiago Castro, Santiago M. Mola, scikit-learn-bot, sean moiselle, SHREEKANT 
-VITTHAL NANDIYAWAR, Shruti Nath, Søren Bredlund Caspersen, Stefanie Senger, 
-Stefano Gaspari, Steffen Schneider, Štěpán Sršeň, Sylvain Combettes, 
-Tamara, Thomas, Thomas Gessey-Jones, Thomas J. Fan, Thomas Li, ThorbenMaa, 
-Tialo, Tim Head, Tuhin Sharma, Tushar Parimi, Umberto Fasci, UV, vedpawar2254, 
-Velislav Babatchev, Victoria Shevchenko, viktor765, Vince Carey, Virgil Chan, 
-Wang Jiayi, Xiao Yuan, Xuefeng Xu, Yao Xiao, yareyaredesuyo, Zachary Vealey, 
+Aaron Schumacher, Abdulaziz Aloqeely, abhi-jha, Acciaro Gennaro Daniele, Adam
+J. Stewart, Adam Li, Adeel Hassan, Adeyemi Biola, Aditi Juneja, Adrin Jalali,
+Aisha, Akanksha Mhadolkar, Akihiro Kuno, Alberto Torres, alexqiao, Alihan
+Zihna, Aniruddha Saha, antoinebaker, Antony Lee, Anurag Varma, Arif Qodari,
+Arthur Courselle, ArthurDbrn, Arturo Amor, Aswathavicky, Audrey Flanders,
+aurelienmorgan, Austin, awwwyan, AyGeeEm, a.zy.lee, baggiponte, BlazeStorm001,
+bme-git, Boney Patel, brdav, Brigitta Sipőcz, Cailean Carter, Camille
+Troillard, Carlo Lemos, Christian Lorentzen, Christian Veenhuis, Christine P.
+Chai, claudio, Conrad Stevens, datarollhexasphericon, Davide Chicco, David
+Matthew Cherney, Dea María Léon, Deepak Saldanha, Deepyaman Datta,
+dependabot[bot], dinga92, Dmitry Kobak, Domenico, Drew Craeton, dymil, Edoardo
+Abati, EmilyXinyi, Eric Larson, Evelyn, fabianhenning, Farid "Freddie" Taba,
+Gael Varoquaux, Giorgio Angelotti, Gleb Levitski, Guillaume Lemaitre, Guntitat
+Sawadwuthikul, Haesun Park, Hanjun Kim, Henrique Caroço, hhchen1105, Hugo
+Boulenger, Ilya Komarov, Inessa Pawson, Ivan Pan, Ivan Wiryadi, Jaimin Chauhan,
+Jakob Bull, James Lamb, Janez Demšar, Jérémie du Boisberranger, Jérôme
+Dockès, Jirair Aroyan, João Morais, Joe Cainey, Joel Nothman, John Enblom,
+JorgeCardenas, Joseph Barbier, jpienaar-tuks, Julian Chan, K.Bharat Reddy,
+Kevin Doshi, Lars, Loic Esteve, Lucas Colley, Lucy Liu, lunovian, Marc Bresson,
+Marco Edward Gorelli, Marco Maggi, Marco Wolsza, Maren Westermann,
+MarieS-WiMLDS, Martin Helm, Mathew Shen, mathurinm, Matthew Feickert, Maxwell
+Liu, Meekail Zain, Michael Dawson, Miguel Cárdenas, m-maggi, mrastgoo, Natalia
+Mokeeva, Nathan Goldbaum, Nathan Orgera, nbrown-ScottLogic, Nikita Chistyakov,
+Nithish Bolleddula, Noam Keidar, NoPenguinsLand, Norbert Preining, notPlancha,
+Olivier Grisel, Omar Salman, ParsifalXu, Piotr, Priyank Shroff, Priyansh Gupta,
+Quentin Barthélemy, Rachit23110261, Rahil Parikh, raisadz, Rajath,
+renaissance0ne, Reshama Shaikh, Roberto Rosati, Robert Pollak, rwelsch427,
+Santiago Castro, Santiago M. Mola, scikit-learn-bot, sean moiselle, SHREEKANT
+VITTHAL NANDIYAWAR, Shruti Nath, Søren Bredlund Caspersen, Stefanie Senger,
+Stefano Gaspari, Steffen Schneider, Štěpán Sršeň, Sylvain Combettes,
+Tamara, Thomas, Thomas Gessey-Jones, Thomas J. Fan, Thomas Li, ThorbenMaa,
+Tialo, Tim Head, Tuhin Sharma, Tushar Parimi, Umberto Fasci, UV, vedpawar2254,
+Velislav Babatchev, Victoria Shevchenko, viktor765, Vince Carey, Virgil Chan,
+Wang Jiayi, Xiao Yuan, Xuefeng Xu, Yao Xiao, yareyaredesuyo, Zachary Vealey,
 Ziad Amerr
diff --git a/examples/cross_decomposition/README.txt b/examples/cross_decomposition/README.txt
@@ -4,4 +4,3 @@ Cross decomposition
 -------------------
 
 Examples concerning the :mod:`sklearn.cross_decomposition` module.
-
diff --git a/examples/decomposition/README.txt b/examples/decomposition/README.txt
@@ -4,4 +4,3 @@ Decomposition
 -------------
 
 Examples concerning the :mod:`sklearn.decomposition` module.
-
diff --git a/examples/developing_estimators/README.txt b/examples/developing_estimators/README.txt
@@ -3,4 +3,4 @@
 Developing Estimators
 ---------------------
 
-Examples concerning the development of Custom Estimator.
+Examples concerning the development of Custom Estimator.
diff --git a/examples/frozen/README.txt b/examples/frozen/README.txt
@@ -4,4 +4,3 @@ Frozen Estimators
 -----------------
 
 Examples concerning the :mod:`sklearn.frozen` module.
-
diff --git a/examples/gaussian_process/README.txt b/examples/gaussian_process/README.txt
@@ -4,4 +4,3 @@ Gaussian Process for Machine Learning
 -------------------------------------
 
 Examples concerning the :mod:`sklearn.gaussian_process` module.
-
diff --git a/examples/inspection/README.txt b/examples/inspection/README.txt
@@ -4,4 +4,3 @@ Inspection
 ----------
 
 Examples related to the :mod:`sklearn.inspection` module.
-
diff --git a/examples/manifold/README.txt b/examples/manifold/README.txt
@@ -4,4 +4,3 @@ Manifold learning
 -----------------------
 
 Examples concerning the :mod:`sklearn.manifold` module.
-
diff --git a/examples/miscellaneous/README.txt b/examples/miscellaneous/README.txt
@@ -4,4 +4,3 @@ Miscellaneous
 -------------
 
 Miscellaneous and introductory examples for scikit-learn.
-
diff --git a/sklearn/datasets/images/README.txt b/sklearn/datasets/images/README.txt
@@ -16,6 +16,3 @@ Retrieved 21st August, 2011 from [3] by Robert Layton
 [1] https://creativecommons.org/licenses/by/2.0/
 [2] https://www.flickr.com/photos/vultilion/
 [3] https://www.flickr.com/photos/vultilion/6056698931/sizes/z/in/photostream/
-
-
-
diff --git a/sklearn/datasets/tests/data/svmlight_classification.txt b/sklearn/datasets/tests/data/svmlight_classification.txt
@@ -1,7 +1,7 @@
 # comment
 # note: the next line contains a tab
 1.0 3:2.5 	   11:-5.2 16:1.5 # and an inline comment
-2.0 6:1.0 13:-3 
+2.0 6:1.0 13:-3
 # another comment
 3.0 21:27
 4.0 2:1.234567890123456e10 # double precision value
diff --git a/sklearn/datasets/tests/data/svmlight_multilabel.txt b/sklearn/datasets/tests/data/svmlight_multilabel.txt
@@ -1,5 +1,5 @@
 # multilabel dataset in SVMlight format
 1,0 2:2.5   10:-5.2 15:1.5
-2 5:1.0 12:-3 
+2 5:1.0 12:-3
  2:3.5 11:26
 1,2 20:27
diff --git a/sklearn/svm/src/liblinear/linear.h b/sklearn/svm/src/liblinear/linear.h
@@ -84,4 +84,3 @@ void set_print_string_function(void (*print_func) (const char*));
 #endif
 
 #endif /* _LIBLINEAR_H */
-
diff --git a/sklearn/utils/src/MurmurHash3.cpp b/sklearn/utils/src/MurmurHash3.cpp
@@ -343,4 +343,3 @@ void MurmurHash3_x64_128 ( const void * key, const int len,
 }
 
 //-----------------------------------------------------------------------------
-

Original file line number	Diff line number	Diff line change
`@@ -13,4 +13,3 @@ all priceless contributions.`
`13`	`13`
`14`	`14`	`We abide by the principles of openness, respect, and consideration of others of`
`15`	`15`	`the Python Software Foundation: https://www.python.org/psf/codeofconduct/`
`16`		`-`
Original file line number	Diff line number	Diff line change
`@@ -5,4 +5,3 @@ https://docs.google.com/spreadsheet/ccc?key=0AhGnAxuBDhjmdDYwNzlZVE5SMkFsMjNBbGl`
`5`	`5`
`6`	`6`	`To obtain access to this file, send an email to:`
`7`	`7`	`nelle dot varoquaux at gmail dot com`
`8`		`-`