Lots of new untracked files after merging with master?

TLDR: run git clean -xi and remove all files that you didn’t create yourself, then re-install, or use snippet below.

If you’re contributing a PR and you recently merged upstream/master, you should see a lot untracked files when running git status.

This is normal: these files were previously automatically generated and added to the .gitignore. They have now been taken out of the gitignore (https://github.com/scikit-learn/scikit-learn/pull/17132) and can be safely removed.

To remove them, you can use git clean -xi. This will also remove installation files like .so, dll or .c files, so you’ll finally need to re-install scikit-learn by running e.g. pip install -e . or make in.

[NicolasHug]

Alternatively you can also copy/paste this if you’re on a unix system:

rm sklearn/cluster/affinity_propagation_.py sklearn/cluster/bicluster.py sklearn/cluster/birch.py sklearn/cluster/dbscan_.py sklearn/cluster/hierarchical.py sklearn/cluster/k_means_.py sklearn/cluster/mean_shift_.py sklearn/cluster/optics_.py sklearn/cluster/spectral.py sklearn/covariance/elliptic_envelope.py sklearn/covariance/empirical_covariance_.py sklearn/covariance/graph_lasso_.py sklearn/covariance/robust_covariance.py sklearn/covariance/shrunk_covariance_.py sklearn/cross_decomposition/cca_.py sklearn/cross_decomposition/pls_.py sklearn/datasets/base.py sklearn/datasets/california_housing.py sklearn/datasets/covtype.py sklearn/datasets/kddcup99.py sklearn/datasets/lfw.py sklearn/datasets/olivetti_faces.py sklearn/datasets/openml.py sklearn/datasets/rcv1.py sklearn/datasets/samples_generator.py sklearn/datasets/species_distributions.py sklearn/datasets/svmlight_format.py sklearn/datasets/twenty_newsgroups.py sklearn/decomposition/base.py sklearn/decomposition/cdnmf_fast.py sklearn/decomposition/dict_learning.py sklearn/decomposition/factor_analysis.py sklearn/decomposition/fastica_.py sklearn/decomposition/incremental_pca.py sklearn/decomposition/kernel_pca.py sklearn/decomposition/nmf.py sklearn/decomposition/online_lda.py sklearn/decomposition/online_lda_fast.py sklearn/decomposition/pca.py sklearn/decomposition/sparse_pca.py sklearn/decomposition/truncated_svd.py sklearn/ensemble/bagging.py sklearn/ensemble/base.py sklearn/ensemble/forest.py sklearn/ensemble/gradient_boosting.py sklearn/ensemble/iforest.py sklearn/ensemble/voting.py sklearn/ensemble/weight_boosting.py sklearn/feature_extraction/dict_vectorizer.py sklearn/feature_extraction/hashing.py sklearn/feature_extraction/stop_words.py sklearn/feature_selection/base.py sklearn/feature_selection/from_model.py sklearn/feature_selection/mutual_info.py sklearn/feature_selection/rfe.py sklearn/feature_selection/univariate_selection.py sklearn/feature_selection/variance_threshold.py sklearn/gaussian_process/gpc.py sklearn/gaussian_process/gpr.py sklearn/inspection/partial_dependence.py sklearn/linear_model/base.py sklearn/linear_model/bayes.py sklearn/linear_model/cd_fast.py sklearn/linear_model/coordinate_descent.py sklearn/linear_model/huber.py sklearn/linear_model/least_angle.py sklearn/linear_model/logistic.py sklearn/linear_model/omp.py sklearn/linear_model/passive_aggressive.py sklearn/linear_model/perceptron.py sklearn/linear_model/ransac.py sklearn/linear_model/ridge.py sklearn/linear_model/sag.py sklearn/linear_model/sag_fast.py sklearn/linear_model/sgd_fast.py sklearn/linear_model/stochastic_gradient.py sklearn/linear_model/theil_sen.py sklearn/manifold/isomap.py sklearn/manifold/locally_linear.py sklearn/manifold/mds.py sklearn/manifold/spectral_embedding_.py sklearn/manifold/t_sne.py sklearn/metrics/base.py sklearn/metrics/classification.py sklearn/metrics/cluster/bicluster.py sklearn/metrics/cluster/expected_mutual_info_fast.py sklearn/metrics/cluster/supervised.py sklearn/metrics/cluster/unsupervised.py sklearn/metrics/pairwise_fast.py sklearn/metrics/ranking.py sklearn/metrics/regression.py sklearn/metrics/scorer.py sklearn/mixture/base.py sklearn/mixture/bayesian_mixture.py sklearn/mixture/gaussian_mixture.py sklearn/neighbors/ball_tree.py sklearn/neighbors/base.py sklearn/neighbors/classification.py sklearn/neighbors/dist_metrics.py sklearn/neighbors/graph.py sklearn/neighbors/kd_tree.py sklearn/neighbors/kde.py sklearn/neighbors/lof.py sklearn/neighbors/nca.py sklearn/neighbors/nearest_centroid.py sklearn/neighbors/quad_tree.py sklearn/neighbors/regression.py sklearn/neighbors/typedefs.py sklearn/neighbors/unsupervised.py sklearn/neural_network/multilayer_perceptron.py sklearn/neural_network/rbm.py sklearn/preprocessing/data.py sklearn/preprocessing/label.py sklearn/semi_supervised/label_propagation.py sklearn/svm/base.py sklearn/svm/bounds.py sklearn/svm/classes.py sklearn/svm/liblinear.py sklearn/svm/libsvm.py sklearn/svm/libsvm_sparse.py sklearn/tree/export.py sklearn/tree/tree.py sklearn/utils/fast_dict.py sklearn/utils/mocking.py sklearn/utils/seq_dataset.py sklearn/utils/weight_vector.py 

You shouldn’t need to re-install

[NicolasHug]

It’s been a while, this is probably not relevant anymore so I’ll close and unpin the issue