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RFC On the relative harm of cosmetic changes #11336

@jnothman

Description

@jnothman

I can't remember where, but there was a recent PR offering cosmetic (e.g. PEP8) fixes, and we usually reject these PRs as causing merge conflicts with existing open PRs. @amueller wanted to know exactly how many PRs were affected by each change.

If we knew it would affect no or few open/active PRs, we might be keen to fix flake8 issues, or to modernise tests (pytest style).

Thus, using https://gist.github.com/jnothman/41a5e05c82c4508afa7bee3b493752dd, I have determined which lines are modified (or adjacent to modified lines) by which open PRs.

https://www.dropbox.com/s/jsf07i40npq5o5g/lines-modified-by-open-prs.zip?dl=0 shows the results with a file of results for PRs that can currently be merged into master, and a file of results for PRs that cannot currently be merged into master. Each file has three columns: PR#, file name, line#.

Looking at just the file names, the following files in master are never modified by open PRs:

diff <(git ls-tree -r master --name-only | sort) <(cat lines-modified-merge* | cut -f2 | sort -u) | grep '<'
.coveragerc
.landscape.yml
AUTHORS.rst
MANIFEST.in
benchmarks/bench_20newsgroups.py
benchmarks/bench_glm.py
benchmarks/bench_glmnet.py
benchmarks/bench_isotonic.py
benchmarks/bench_multilabel_metrics.py
benchmarks/bench_plot_neighbors.py
benchmarks/bench_plot_parallel_pairwise.py
benchmarks/bench_random_projections.py
benchmarks/bench_tree.py
build_tools/appveyor/install.ps1
build_tools/appveyor/run_with_env.cmd
doc/images/cds-logo.png
doc/images/dysco.png
doc/images/inria-logo.jpg
doc/images/iris.pdf
doc/images/iris.svg
doc/images/last_digit.png
doc/images/lda_model_graph.png
doc/images/ml_map.png
doc/images/multilayerperceptron_network.png
doc/images/no_image.png
doc/images/nyu_short_color.png
doc/images/plot_digits_classification.png
doc/images/plot_face_recognition_1.png
doc/images/plot_face_recognition_2.png
doc/images/rbm_graph.png
doc/images/scikit-learn-logo-notext.png
doc/images/sloan_banner.png
doc/includes/big_toc_css.rst
doc/includes/bigger_toc_css.rst
doc/logos/favicon.ico
doc/logos/identity.pdf
doc/logos/scikit-learn-logo-notext.png
doc/logos/scikit-learn-logo-small.png
doc/logos/scikit-learn-logo-thumb.png
doc/logos/scikit-learn-logo.bmp
doc/logos/scikit-learn-logo.png
doc/logos/scikit-learn-logo.svg
doc/model_selection.rst
doc/modules/glm_data/lasso_enet_coordinate_descent.png
doc/modules/isotonic.rst
doc/preface.rst
doc/sphinxext/MANIFEST.in
doc/sphinxext/github_link.py
doc/templates/class.rst
doc/templates/class_with_call.rst
doc/templates/class_without_init.rst
doc/templates/deprecated_class.rst
doc/templates/deprecated_class_with_call.rst
doc/templates/deprecated_class_without_init.rst
doc/templates/deprecated_function.rst
doc/templates/function.rst
doc/templates/generate_deprecated.sh
doc/testimonials/README.txt
doc/testimonials/images/Makefile
doc/testimonials/images/aweber.png
doc/testimonials/images/bestofmedia-logo.png
doc/testimonials/images/betaworks.png
doc/testimonials/images/birchbox.jpg
doc/testimonials/images/booking.png
doc/testimonials/images/change-logo.png
doc/testimonials/images/dataiku_logo.png
doc/testimonials/images/datapublica.png
doc/testimonials/images/datarobot.png
doc/testimonials/images/evernote.png
doc/testimonials/images/howaboutwe.png
doc/testimonials/images/huggingface.png
doc/testimonials/images/infonea.jpg
doc/testimonials/images/inria.png
doc/testimonials/images/lovely.png
doc/testimonials/images/machinalis.png
doc/testimonials/images/okcupid.png
doc/testimonials/images/ottogroup_logo.png
doc/testimonials/images/peerindex.png
doc/testimonials/images/phimeca.png
doc/testimonials/images/rangespan.png
doc/testimonials/images/solido_logo.png
doc/testimonials/images/spotify.png
doc/testimonials/images/telecomparistech.jpg
doc/testimonials/images/yhat.png
doc/testimonials/images/zopa.png
doc/themes/scikit-learn/static/css/bootstrap-responsive.css
doc/themes/scikit-learn/static/css/bootstrap-responsive.min.css
doc/themes/scikit-learn/static/css/bootstrap.css
doc/themes/scikit-learn/static/css/bootstrap.min.css
doc/themes/scikit-learn/static/css/examples.css
doc/themes/scikit-learn/static/img/FNRS-logo.png
doc/themes/scikit-learn/static/img/columbia.png
doc/themes/scikit-learn/static/img/forkme.png
doc/themes/scikit-learn/static/img/glyphicons-halflings-white.png
doc/themes/scikit-learn/static/img/glyphicons-halflings.png
doc/themes/scikit-learn/static/img/google.png
doc/themes/scikit-learn/static/img/inria-small.jpg
doc/themes/scikit-learn/static/img/inria-small.png
doc/themes/scikit-learn/static/img/nyu_short_color.png
doc/themes/scikit-learn/static/img/plot_classifier_comparison_1.png
doc/themes/scikit-learn/static/img/plot_manifold_sphere_1.png
doc/themes/scikit-learn/static/img/scikit-learn-logo-notext.png
doc/themes/scikit-learn/static/img/scikit-learn-logo-small.png
doc/themes/scikit-learn/static/img/scikit-learn-logo.png
doc/themes/scikit-learn/static/img/scikit-learn-logo.svg
doc/themes/scikit-learn/static/img/sloan_logo.jpg
doc/themes/scikit-learn/static/img/sydney-primary.jpeg
doc/themes/scikit-learn/static/img/sydney-stacked.jpeg
doc/themes/scikit-learn/static/img/telecom.png
doc/themes/scikit-learn/static/jquery.maphilight.js
doc/themes/scikit-learn/static/jquery.maphilight.min.js
doc/themes/scikit-learn/static/js/bootstrap.js
doc/themes/scikit-learn/static/js/bootstrap.min.js
doc/themes/scikit-learn/static/js/copybutton.js
doc/themes/scikit-learn/theme.conf
doc/tune_toc.rst
doc/tutorial/common_includes/info.txt
doc/tutorial/statistical_inference/finding_help.rst
doc/tutorial/statistical_inference/index.rst
doc/tutorial/text_analytics/.gitignore
doc/tutorial/text_analytics/data/movie_reviews/fetch_data.py
doc/tutorial/text_analytics/data/twenty_newsgroups/fetch_data.py
doc/tutorial/text_analytics/solutions/exercise_02_sentiment.py
doc/tutorial/text_analytics/solutions/generate_skeletons.py
doc/unsupervised_learning.rst
examples/applications/README.txt
examples/applications/svm_gui.py
examples/bicluster/README.txt
examples/bicluster/plot_spectral_biclustering.py
examples/bicluster/plot_spectral_coclustering.py
examples/classification/README.txt
examples/classification/plot_classification_probability.py
examples/classification/plot_lda.py
examples/cluster/README.txt
examples/covariance/README.txt
examples/covariance/plot_lw_vs_oas.py
examples/cross_decomposition/README.txt
examples/datasets/README.txt
examples/datasets/plot_random_multilabel_dataset.py
examples/decomposition/README.txt
examples/decomposition/plot_beta_divergence.py
examples/decomposition/plot_incremental_pca.py
examples/decomposition/plot_pca_vs_lda.py
examples/ensemble/README.txt
examples/ensemble/plot_forest_importances.py
examples/ensemble/plot_forest_importances_faces.py
examples/ensemble/plot_gradient_boosting_oob.py
examples/ensemble/plot_gradient_boosting_quantile.py
examples/exercises/README.txt
examples/exercises/plot_cv_digits.py
examples/feature_selection/README.txt
examples/feature_selection/plot_rfe_digits.py
examples/feature_selection/plot_rfe_with_cross_validation.py
examples/feature_selection/plot_select_from_model_boston.py
examples/gaussian_process/README.txt
examples/gaussian_process/plot_compare_gpr_krr.py
examples/gaussian_process/plot_gpr_co2.py
examples/linear_model/README.txt
examples/linear_model/plot_huber_vs_ridge.py
examples/linear_model/plot_iris_logistic.py
examples/linear_model/plot_logistic.py
examples/linear_model/plot_ols_ridge_variance.py
examples/linear_model/plot_omp.py
examples/linear_model/plot_polynomial_interpolation.py
examples/linear_model/plot_ridge_coeffs.py
examples/linear_model/plot_robust_fit.py
examples/manifold/README.txt
examples/manifold/plot_mds.py
examples/mixture/README.txt
examples/mixture/plot_gmm.py
examples/mixture/plot_gmm_covariances.py
examples/mixture/plot_gmm_pdf.py
examples/mixture/plot_gmm_selection.py
examples/mixture/plot_gmm_sin.py
examples/model_selection/README.txt
examples/neighbors/README.txt
examples/neural_networks/README.txt
examples/neural_networks/plot_mnist_filters.py
examples/preprocessing/README.txt
examples/preprocessing/plot_function_transformer.py
examples/semi_supervised/README.txt
examples/svm/README.txt
examples/text/README.txt
examples/tree/README.txt
site.cfg
sklearn/__check_build/_check_build.pyx
sklearn/__check_build/setup.py
sklearn/cluster/tests/__init__.py
sklearn/cluster/tests/common.py
sklearn/compose/tests/__init__.py
sklearn/covariance/tests/__init__.py
sklearn/cross_decomposition/tests/__init__.py
sklearn/datasets/data/diabetes_data.csv.gz
sklearn/datasets/data/diabetes_target.csv.gz
sklearn/datasets/data/digits.csv.gz
sklearn/datasets/data/linnerud_exercise.csv
sklearn/datasets/data/linnerud_physiological.csv
sklearn/datasets/images/README.txt
sklearn/datasets/images/china.jpg
sklearn/datasets/images/flower.jpg
sklearn/datasets/tests/__init__.py
sklearn/datasets/tests/data/svmlight_classification.txt
sklearn/datasets/tests/data/svmlight_invalid.txt
sklearn/datasets/tests/data/svmlight_invalid_order.txt
sklearn/datasets/tests/data/svmlight_multilabel.txt
sklearn/decomposition/_online_lda.pyx
sklearn/decomposition/tests/__init__.py
sklearn/ensemble/setup.py
sklearn/ensemble/tests/__init__.py
sklearn/externals/__init__.py
sklearn/externals/joblib/_multiprocessing_helpers.py
sklearn/externals/six.py
sklearn/feature_extraction/__init__.py
sklearn/feature_extraction/tests/__init__.py
sklearn/feature_selection/tests/__init__.py
sklearn/feature_selection/tests/test_variance_threshold.py
sklearn/feature_selection/variance_threshold.py
sklearn/gaussian_process/tests/__init__.py
sklearn/linear_model/tests/__init__.py
sklearn/manifold/tests/__init__.py
sklearn/metrics/cluster/tests/__init__.py
sklearn/metrics/pairwise_fast.pyx
sklearn/metrics/tests/__init__.py
sklearn/mixture/tests/__init__.py
sklearn/model_selection/tests/__init__.py
sklearn/model_selection/tests/common.py
sklearn/neighbors/tests/__init__.py
sklearn/neural_network/_stochastic_optimizers.py
sklearn/neural_network/tests/__init__.py
sklearn/neural_network/tests/test_stochastic_optimizers.py
sklearn/preprocessing/tests/__init__.py
sklearn/semi_supervised/tests/__init__.py
sklearn/src/cblas/ATL_drefasum.c
sklearn/src/cblas/ATL_drefcopy.c
sklearn/src/cblas/ATL_drefgemv.c
sklearn/src/cblas/ATL_drefgemvN.c
sklearn/src/cblas/ATL_drefgemvT.c
sklearn/src/cblas/ATL_drefger.c
sklearn/src/cblas/ATL_drefrot.c
sklearn/src/cblas/ATL_drefrotg.c
sklearn/src/cblas/ATL_dsrefdot.c
sklearn/src/cblas/ATL_srefasum.c
sklearn/src/cblas/ATL_srefcopy.c
sklearn/src/cblas/ATL_srefgemv.c
sklearn/src/cblas/ATL_srefgemvN.c
sklearn/src/cblas/ATL_srefgemvT.c
sklearn/src/cblas/ATL_srefger.c
sklearn/src/cblas/ATL_srefnrm2.c
sklearn/src/cblas/ATL_srefrot.c
sklearn/src/cblas/ATL_srefrotg.c
sklearn/src/cblas/README.txt
sklearn/src/cblas/atlas_aux.h
sklearn/src/cblas/atlas_dsysinfo.h
sklearn/src/cblas/atlas_enum.h
sklearn/src/cblas/atlas_level1.h
sklearn/src/cblas/atlas_level2.h
sklearn/src/cblas/atlas_ptalias1.h
sklearn/src/cblas/atlas_ptalias2.h
sklearn/src/cblas/atlas_refalias1.h
sklearn/src/cblas/atlas_refalias2.h
sklearn/src/cblas/atlas_reflevel2.h
sklearn/src/cblas/atlas_reflvl2.h
sklearn/src/cblas/atlas_refmisc.h
sklearn/src/cblas/atlas_ssysinfo.h
sklearn/src/cblas/atlas_type.h
sklearn/src/cblas/cblas_dasum.c
sklearn/src/cblas/cblas_daxpy.c
sklearn/src/cblas/cblas_ddot.c
sklearn/src/cblas/cblas_dgemv.c
sklearn/src/cblas/cblas_dger.c
sklearn/src/cblas/cblas_dnrm2.c
sklearn/src/cblas/cblas_drot.c
sklearn/src/cblas/cblas_drotg.c
sklearn/src/cblas/cblas_dscal.c
sklearn/src/cblas/cblas_errprn.c
sklearn/src/cblas/cblas_sasum.c
sklearn/src/cblas/cblas_saxpy.c
sklearn/src/cblas/cblas_sdot.c
sklearn/src/cblas/cblas_sgemv.c
sklearn/src/cblas/cblas_sger.c
sklearn/src/cblas/cblas_snrm2.c
sklearn/src/cblas/cblas_srot.c
sklearn/src/cblas/cblas_srotg.c
sklearn/src/cblas/cblas_sscal.c
sklearn/svm/src/liblinear/COPYRIGHT
sklearn/svm/src/liblinear/tron.cpp
sklearn/svm/src/liblinear/tron.h
sklearn/svm/src/libsvm/LIBSVM_CHANGES
sklearn/svm/src/libsvm/libsvm_template.cpp
sklearn/svm/tests/__init__.py
sklearn/tests/__init__.py
sklearn/tests/test_check_build.py
sklearn/tree/tests/__init__.py
sklearn/utils/_logistic_sigmoid.pyx
sklearn/utils/_scipy_sparse_lsqr_backport.py
sklearn/utils/arrayfuncs.pyx
sklearn/utils/fast_dict.pyx
sklearn/utils/lgamma.pxd
sklearn/utils/lgamma.pyx
sklearn/utils/murmurhash.pxd
sklearn/utils/murmurhash.pyx
sklearn/utils/optimize.py
sklearn/utils/sparsetools/tests/__init__.py
sklearn/utils/src/MurmurHash3.cpp
sklearn/utils/src/MurmurHash3.h
sklearn/utils/src/cholesky_delete.h
sklearn/utils/src/gamma.c
sklearn/utils/src/gamma.h
sklearn/utils/tests/__init__.py
sklearn/utils/tests/test_bench.py
sklearn/utils/tests/test_fast_dict.py
sklearn/utils/tests/test_linear_assignment.py
sklearn/utils/tests/test_murmurhash.py
sklearn/utils/tests/test_optimize.py
sklearn/utils/tests/test_shortest_path.py

with the following flake8 errors:

benchmarks/bench_plot_neighbors.py:39:5: E265 block comment should start with '# '
benchmarks/bench_plot_neighbors.py:62:5: E265 block comment should start with '# '
benchmarks/bench_plot_neighbors.py:85:5: E265 block comment should start with '# '
benchmarks/bench_plot_parallel_pairwise.py:11:1: E302 expected 2 blank lines, found 1
benchmarks/bench_random_projections.py:77:9: E128 continuation line under-indented for visual indent
benchmarks/bench_random_projections.py:85:28: E128 continuation line under-indented for visual indent
benchmarks/bench_random_projections.py:86:28: E128 continuation line under-indented for visual indent
benchmarks/bench_random_projections.py:96:80: E501 line too long (80 > 79 characters)
benchmarks/bench_random_projections.py:218:15: E128 continuation line under-indented for visual indent
examples/applications/svm_gui.py:24:1: E402 module level import not at top of file
examples/applications/svm_gui.py:27:1: E402 module level import not at top of file
examples/applications/svm_gui.py:28:1: E402 module level import not at top of file
examples/applications/svm_gui.py:29:1: E402 module level import not at top of file
examples/applications/svm_gui.py:30:1: E402 module level import not at top of file
examples/applications/svm_gui.py:38:1: E402 module level import not at top of file
examples/applications/svm_gui.py:39:1: E402 module level import not at top of file
examples/applications/svm_gui.py:41:1: E402 module level import not at top of file
examples/applications/svm_gui.py:42:1: E402 module level import not at top of file
examples/applications/svm_gui.py:43:1: E402 module level import not at top of file
examples/bicluster/plot_spectral_biclustering.py:23:1: E402 module level import not at top of file
examples/bicluster/plot_spectral_biclustering.py:24:1: E402 module level import not at top of file
examples/bicluster/plot_spectral_biclustering.py:26:1: E402 module level import not at top of file
examples/bicluster/plot_spectral_biclustering.py:27:1: E402 module level import not at top of file
examples/bicluster/plot_spectral_biclustering.py:28:1: E402 module level import not at top of file
examples/bicluster/plot_spectral_biclustering.py:29:1: E402 module level import not at top of file
examples/bicluster/plot_spectral_coclustering.py:22:1: E402 module level import not at top of file
examples/bicluster/plot_spectral_coclustering.py:23:1: E402 module level import not at top of file
examples/bicluster/plot_spectral_coclustering.py:25:1: E402 module level import not at top of file
examples/bicluster/plot_spectral_coclustering.py:26:1: E402 module level import not at top of file
examples/bicluster/plot_spectral_coclustering.py:27:1: E402 module level import not at top of file
examples/bicluster/plot_spectral_coclustering.py:28:1: E402 module level import not at top of file
examples/classification/plot_classification_probability.py:19:1: E402 module level import not at top of file
examples/classification/plot_classification_probability.py:20:1: E402 module level import not at top of file
examples/classification/plot_classification_probability.py:22:1: E402 module level import not at top of file
examples/classification/plot_classification_probability.py:23:1: E402 module level import not at top of file
examples/classification/plot_classification_probability.py:24:1: E402 module level import not at top of file
examples/classification/plot_classification_probability.py:25:1: E402 module level import not at top of file
examples/classification/plot_classification_probability.py:26:1: E402 module level import not at top of file
examples/classification/plot_lda.py:48:80: E501 line too long (84 > 79 characters)
examples/classification/plot_lda.py:49:80: E501 line too long (82 > 79 characters)
examples/covariance/plot_lw_vs_oas.py:25:1: E402 module level import not at top of file
examples/covariance/plot_lw_vs_oas.py:26:1: E402 module level import not at top of file
examples/covariance/plot_lw_vs_oas.py:27:1: E402 module level import not at top of file
examples/covariance/plot_lw_vs_oas.py:29:1: E402 module level import not at top of file
examples/decomposition/plot_incremental_pca.py:26:1: E402 module level import not at top of file
examples/decomposition/plot_incremental_pca.py:27:1: E402 module level import not at top of file
examples/decomposition/plot_incremental_pca.py:29:1: E402 module level import not at top of file
examples/decomposition/plot_incremental_pca.py:30:1: E402 module level import not at top of file
examples/decomposition/plot_pca_vs_lda.py:21:1: E402 module level import not at top of file
examples/decomposition/plot_pca_vs_lda.py:23:1: E402 module level import not at top of file
examples/decomposition/plot_pca_vs_lda.py:24:1: E402 module level import not at top of file
examples/decomposition/plot_pca_vs_lda.py:25:1: E402 module level import not at top of file
examples/ensemble/plot_forest_importances.py:15:1: E402 module level import not at top of file
examples/ensemble/plot_forest_importances.py:16:1: E402 module level import not at top of file
examples/ensemble/plot_forest_importances.py:18:1: E402 module level import not at top of file
examples/ensemble/plot_forest_importances.py:19:1: E402 module level import not at top of file
examples/ensemble/plot_forest_importances.py:51:8: E128 continuation line under-indented for visual indent
examples/ensemble/plot_forest_importances_faces.py:15:1: E402 module level import not at top of file
examples/ensemble/plot_forest_importances_faces.py:16:1: E402 module level import not at top of file
examples/ensemble/plot_forest_importances_faces.py:18:1: E402 module level import not at top of file
examples/ensemble/plot_forest_importances_faces.py:19:1: E402 module level import not at top of file
examples/ensemble/plot_gradient_boosting_oob.py:32:1: E402 module level import not at top of file
examples/ensemble/plot_gradient_boosting_oob.py:33:1: E402 module level import not at top of file
examples/ensemble/plot_gradient_boosting_oob.py:35:1: E402 module level import not at top of file
examples/ensemble/plot_gradient_boosting_oob.py:36:1: E402 module level import not at top of file
examples/ensemble/plot_gradient_boosting_oob.py:37:1: E402 module level import not at top of file
examples/ensemble/plot_gradient_boosting_quantile.py:22:1: E265 block comment should start with '# '
examples/exercises/plot_cv_digits.py:14:1: E402 module level import not at top of file
examples/exercises/plot_cv_digits.py:15:1: E402 module level import not at top of file
examples/exercises/plot_cv_digits.py:16:1: E402 module level import not at top of file
examples/exercises/plot_cv_digits.py:34:1: E402 module level import not at top of file
examples/feature_selection/plot_rfe_digits.py:11:80: E501 line too long (94 > 79 characters)
examples/feature_selection/plot_rfe_digits.py:16:1: E402 module level import not at top of file
examples/feature_selection/plot_rfe_digits.py:17:1: E402 module level import not at top of file
examples/feature_selection/plot_rfe_digits.py:18:1: E402 module level import not at top of file
examples/feature_selection/plot_rfe_digits.py:19:1: E402 module level import not at top of file
examples/feature_selection/plot_rfe_with_cross_validation.py:11:1: E402 module level import not at top of file
examples/feature_selection/plot_rfe_with_cross_validation.py:12:1: E402 module level import not at top of file
examples/feature_selection/plot_rfe_with_cross_validation.py:13:1: E402 module level import not at top of file
examples/feature_selection/plot_rfe_with_cross_validation.py:14:1: E402 module level import not at top of file
examples/feature_selection/plot_rfe_with_cross_validation.py:15:1: E402 module level import not at top of file
examples/feature_selection/plot_select_from_model_boston.py:14:1: E402 module level import not at top of file
examples/feature_selection/plot_select_from_model_boston.py:15:1: E402 module level import not at top of file
examples/feature_selection/plot_select_from_model_boston.py:17:1: E402 module level import not at top of file
examples/feature_selection/plot_select_from_model_boston.py:18:1: E402 module level import not at top of file
examples/feature_selection/plot_select_from_model_boston.py:19:1: E402 module level import not at top of file
examples/feature_selection/plot_select_from_model_boston.py:25:80: E501 line too long (84 > 79 characters)
examples/feature_selection/plot_select_from_model_boston.py:46:29: W291 trailing whitespace
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The following files are modified by a single open PR:

cat lines-modified-merge* | cut -f1-2 | sort -u | cut -f2 | sort | uniq -c | sort -n | awk '$1 == 2 {print $2}'
.codecov.yml
COPYING
ISSUE_TEMPLATE.md
PULL_REQUEST_TEMPLATE.md
benchmarks/.gitignore
benchmarks/bench_isolation_forest.py
benchmarks/bench_lof.py
benchmarks/bench_plot_fastkmeans.py
benchmarks/bench_plot_incremental_pca.py
benchmarks/bench_plot_omp_lars.py
benchmarks/bench_plot_svd.py
benchmarks/bench_plot_ward.py
benchmarks/bench_rcv1_logreg_convergence.py
benchmarks/bench_sample_without_replacement.py
benchmarks/bench_sparsify.py
benchmarks/bench_text_vectorizers.py
benchmarks/bench_tsne_mnist.py
benchmarks/plot_tsne_mnist.py
build_tools/appveyor/requirements.txt
build_tools/circle/checkout_merge_commit.sh
build_tools/travis/after_success.sh
build_tools/windows/windows_testing_downloader.ps1
doc/datasets/labeled_faces.rst
doc/datasets/olivetti_faces.rst
doc/datasets/rcv1.rst
doc/datasets/twenty_newsgroups.rst
doc/developers/index.rst
doc/make.bat
doc/modules/cross_decomposition.rst
doc/modules/density.rst
doc/modules/kernel_ridge.rst
doc/modules/label_propagation.rst
doc/modules/lda_qda.rst
doc/modules/random_projection.rst
doc/presentations.rst
doc/templates/numpydoc_docstring.rst
doc/themes/scikit-learn/static/ML_MAPS_README.rst
doc/themes/scikit-learn/static/jquery.js
doc/themes/scikit-learn/static/js/extra.js
doc/tutorial/index.rst
doc/tutorial/machine_learning_map/ML_MAPS_README.txt
doc/tutorial/machine_learning_map/index.rst
doc/tutorial/machine_learning_map/pyparsing.py
doc/tutorial/machine_learning_map/svg2imagemap.py
doc/tutorial/statistical_inference/putting_together.rst
doc/tutorial/statistical_inference/settings.rst
doc/tutorial/text_analytics/data/languages/fetch_data.py
doc/tutorial/text_analytics/skeletons/exercise_01_language_train_model.py
doc/tutorial/text_analytics/skeletons/exercise_02_sentiment.py
doc/tutorial/text_analytics/solutions/exercise_01_language_train_model.py
doc/whats_new/v0.13.rst
doc/whats_new/v0.14.rst
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doc/whats_new/v0.16.rst
doc/whats_new/v0.17.rst
doc/whats_new/v0.18.rst
doc/whats_new/v0.19.rst
examples/.flake8
examples/applications/plot_face_recognition.py
examples/applications/plot_model_complexity_influence.py
examples/applications/plot_out_of_core_classification.py
examples/applications/plot_outlier_detection_housing.py
examples/applications/plot_prediction_latency.py
examples/applications/plot_species_distribution_modeling.py
examples/calibration/README.txt
examples/calibration/plot_calibration_multiclass.py
examples/classification/plot_digits_classification.py
examples/cluster/plot_agglomerative_clustering.py
examples/cluster/plot_agglomerative_clustering_metrics.py
examples/cluster/plot_birch_vs_minibatchkmeans.py
examples/cluster/plot_cluster_iris.py
examples/cluster/plot_coin_segmentation.py
examples/cluster/plot_coin_ward_segmentation.py
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examples/cluster/plot_dict_face_patches.py
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examples/cluster/plot_kmeans_assumptions.py
examples/cluster/plot_kmeans_digits.py
examples/cluster/plot_kmeans_silhouette_analysis.py
examples/cluster/plot_linkage_comparison.py
examples/cluster/plot_mini_batch_kmeans.py
examples/cluster/plot_segmentation_toy.py
examples/cluster/plot_ward_structured_vs_unstructured.py
examples/compose/README.txt
examples/compose/plot_column_transformer.py
examples/compose/plot_column_transformer_mixed_types.py
examples/compose/plot_compare_reduction.py
examples/compose/plot_digits_pipe.py
examples/compose/plot_feature_union.py
examples/compose/plot_transformed_target.py
examples/covariance/plot_covariance_estimation.py
examples/covariance/plot_mahalanobis_distances.py
examples/covariance/plot_robust_vs_empirical_covariance.py
examples/covariance/plot_sparse_cov.py
examples/cross_decomposition/plot_compare_cross_decomposition.py
examples/datasets/plot_digits_last_image.py
examples/datasets/plot_iris_dataset.py
examples/datasets/plot_random_dataset.py
examples/decomposition/plot_ica_blind_source_separation.py
examples/decomposition/plot_ica_vs_pca.py
examples/decomposition/plot_kernel_pca.py
examples/decomposition/plot_pca_3d.py
examples/decomposition/plot_pca_vs_fa_model_selection.py
examples/decomposition/plot_sparse_coding.py
examples/ensemble/plot_adaboost_hastie_10_2.py
examples/ensemble/plot_adaboost_multiclass.py
examples/ensemble/plot_adaboost_regression.py
examples/ensemble/plot_adaboost_twoclass.py
examples/ensemble/plot_bias_variance.py
examples/ensemble/plot_forest_iris.py
examples/ensemble/plot_gradient_boosting_regression.py
examples/ensemble/plot_gradient_boosting_regularization.py
examples/ensemble/plot_partial_dependence.py
examples/ensemble/plot_random_forest_regression_multioutput.py
examples/ensemble/plot_voting_decision_regions.py
examples/ensemble/plot_voting_probas.py
examples/exercises/plot_cv_diabetes.py
examples/exercises/plot_digits_classification_exercise.py
examples/exercises/plot_iris_exercise.py
examples/feature_selection/plot_f_test_vs_mi.py
examples/feature_selection/plot_feature_selection.py
examples/feature_selection/plot_permutation_test_for_classification.py
examples/gaussian_process/plot_gpc.py
examples/gaussian_process/plot_gpc_iris.py
examples/gaussian_process/plot_gpc_isoprobability.py
examples/gaussian_process/plot_gpc_xor.py
examples/gaussian_process/plot_gpr_noisy.py
examples/gaussian_process/plot_gpr_noisy_targets.py
examples/gaussian_process/plot_gpr_prior_posterior.py
examples/linear_model/plot_ard.py
examples/linear_model/plot_bayesian_ridge.py
examples/linear_model/plot_lasso_dense_vs_sparse_data.py
examples/linear_model/plot_lasso_lars.py
examples/linear_model/plot_lasso_model_selection.py
examples/linear_model/plot_logistic_l1_l2_sparsity.py
examples/linear_model/plot_logistic_multinomial.py
examples/linear_model/plot_logistic_path.py
examples/linear_model/plot_multi_task_lasso_support.py
examples/linear_model/plot_ols.py
examples/linear_model/plot_ols_3d.py
examples/linear_model/plot_ransac.py
examples/linear_model/plot_ridge_path.py
examples/linear_model/plot_sgd_comparison.py
examples/linear_model/plot_sgd_iris.py
examples/linear_model/plot_sgd_loss_functions.py
examples/linear_model/plot_sgd_penalties.py
examples/linear_model/plot_sgd_separating_hyperplane.py
examples/linear_model/plot_sgd_weighted_samples.py
examples/linear_model/plot_sparse_logistic_regression_20newsgroups.py
examples/linear_model/plot_sparse_logistic_regression_mnist.py
examples/linear_model/plot_theilsen.py
examples/manifold/plot_swissroll.py
examples/manifold/plot_t_sne_perplexity.py
examples/mixture/plot_concentration_prior.py
examples/model_selection/grid_search_text_feature_extraction.py
examples/model_selection/plot_cv_predict.py
examples/model_selection/plot_grid_search_digits.py
examples/model_selection/plot_learning_curve.py
examples/model_selection/plot_multi_metric_evaluation.py
examples/model_selection/plot_roc.py
examples/model_selection/plot_roc_crossval.py
examples/model_selection/plot_train_error_vs_test_error.py
examples/model_selection/plot_underfitting_overfitting.py
examples/model_selection/plot_validation_curve.py
examples/multioutput/README.txt
examples/multioutput/plot_classifier_chain_yeast.py
examples/neighbors/plot_digits_kde_sampling.py
examples/neighbors/plot_species_kde.py
examples/neural_networks/plot_mlp_alpha.py
examples/neural_networks/plot_mlp_training_curves.py
examples/plot_isotonic_regression.py
examples/plot_johnson_lindenstrauss_bound.py
examples/plot_kernel_ridge_regression.py
examples/plot_multilabel.py
examples/plot_multioutput_face_completion.py
examples/preprocessing/plot_all_scaling.py
examples/semi_supervised/plot_label_propagation_digits.py
examples/semi_supervised/plot_label_propagation_digits_active_learning.py
examples/semi_supervised/plot_label_propagation_versus_svm_iris.py
examples/svm/plot_custom_kernel.py
examples/svm/plot_separating_hyperplane.py
examples/svm/plot_svm_anova.py
examples/svm/plot_svm_kernels.py
examples/svm/plot_svm_margin.py
examples/svm/plot_svm_nonlinear.py
examples/svm/plot_svm_scale_c.py
examples/svm/plot_weighted_samples.py
examples/text/plot_hashing_vs_dict_vectorizer.py
examples/tree/plot_tree_regression.py
examples/tree/plot_tree_regression_multioutput.py
examples/tree/plot_unveil_tree_structure.py
sklearn/__check_build/__init__.py
sklearn/_config.py
sklearn/cluster/_dbscan_inner.pyx
sklearn/cluster/_hierarchical.pyx
sklearn/cluster/_k_means_elkan.pyx
sklearn/cluster/setup.py
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sklearn/covariance/__init__.py
sklearn/covariance/robust_covariance.py
sklearn/covariance/shrunk_covariance_.py
sklearn/covariance/tests/test_covariance.py
sklearn/covariance/tests/test_elliptic_envelope.py
sklearn/datasets/_svmlight_format.pyx
sklearn/datasets/data/boston_house_prices.csv
sklearn/datasets/data/breast_cancer.csv
sklearn/datasets/data/iris.csv
sklearn/datasets/data/wine_data.csv
sklearn/datasets/descr/boston_house_prices.rst
sklearn/datasets/descr/diabetes.rst
sklearn/datasets/descr/iris.rst
sklearn/datasets/descr/linnerud.rst
sklearn/datasets/descr/wine_data.rst
sklearn/datasets/setup.py
sklearn/datasets/tests/test_california_housing.py
sklearn/datasets/tests/test_common.py
sklearn/datasets/tests/test_covtype.py
sklearn/datasets/tests/test_kddcup99.py
sklearn/datasets/tests/test_lfw.py
sklearn/datasets/tests/test_mldata.py
sklearn/datasets/tests/test_rcv1.py
sklearn/decomposition/cdnmf_fast.pyx
sklearn/decomposition/tests/test_factor_analysis.py
sklearn/externals/README
sklearn/externals/conftest.py
sklearn/externals/joblib/disk.py
sklearn/feature_extraction/setup.py
sklearn/feature_selection/mutual_info_.py
sklearn/feature_selection/tests/test_base.py
sklearn/feature_selection/tests/test_chi2.py
sklearn/gaussian_process/__init__.py
sklearn/gaussian_process/correlation_models.py
sklearn/gaussian_process/regression_models.py
sklearn/linear_model/sgd_fast.pxd
sklearn/linear_model/sgd_fast_helpers.h
sklearn/linear_model/tests/test_omp.py
sklearn/manifold/setup.py
sklearn/manifold/tests/test_locally_linear.py
sklearn/metrics/cluster/expected_mutual_info_fast.pyx
sklearn/metrics/cluster/setup.py
sklearn/mixture/__init__.py
sklearn/neighbors/nearest_centroid.py
sklearn/neighbors/quad_tree.pxd
sklearn/neighbors/quad_tree.pyx
sklearn/neighbors/tests/test_quad_tree.py
sklearn/neighbors/typedefs.pyx
sklearn/preprocessing/_encoders.py
sklearn/preprocessing/tests/test_encoders.py
sklearn/semi_supervised/__init__.py
sklearn/src/cblas/atlas_misc.h
sklearn/src/cblas/atlas_reflevel1.h
sklearn/src/cblas/cblas.h
sklearn/src/cblas/cblas_dcopy.c
sklearn/src/cblas/cblas_scopy.c
sklearn/src/cblas/cblas_xerbla.c
sklearn/svm/bounds.py
sklearn/svm/liblinear.pxd
sklearn/svm/liblinear.pyx
sklearn/svm/libsvm.pxd
sklearn/svm/setup.py
sklearn/svm/src/liblinear/linear.h
sklearn/svm/src/libsvm/libsvm_sparse_helper.c
sklearn/tests/test_init.py
sklearn/tests/test_random_projection.py
sklearn/tree/setup.py
sklearn/utils/bench.py
sklearn/utils/fast_dict.pxd
sklearn/utils/graph_shortest_path.pyx
sklearn/utils/sparsetools/__init__.py
sklearn/utils/tests/test_deprecation.py
sklearn/utils/tests/test_metaestimators.py
sklearn/utils/tests/test_stats.py
sklearn/utils/weight_vector.pxd

The following are modified by 2 open PRs:

.circleci/config.yml
.mailmap
CONTRIBUTING.md
benchmarks/bench_covertype.py
benchmarks/bench_mnist.py
benchmarks/bench_plot_lasso_path.py
benchmarks/bench_plot_randomized_svd.py
benchmarks/bench_saga.py
benchmarks/bench_sgd_regression.py
build_tools/circle/list_versions.py
build_tools/travis/flake8_diff.sh
conftest.py
doc/README.md
doc/conftest.py
doc/data_transforms.rst
doc/datasets/covtype.rst
doc/datasets/kddcup99.rst
doc/developers/maintainer.rst
doc/modules/computational_performance.rst
doc/modules/covariance.rst
doc/modules/learning_curve.rst
doc/modules/unsupervised_reduction.rst
doc/sphinxext/sphinx_issues.py
doc/supervised_learning.rst
doc/tutorial/machine_learning_map/parse_path.py
doc/user_guide.rst
doc/whats_new/older_versions.rst
examples/README.txt
examples/applications/plot_tomography_l1_reconstruction.py
examples/applications/wikipedia_principal_eigenvector.py
examples/classification/plot_classifier_comparison.py
examples/classification/plot_lda_qda.py
examples/cluster/plot_adjusted_for_chance_measures.py
examples/cluster/plot_dbscan.py
examples/cluster/plot_face_compress.py
examples/cluster/plot_kmeans_stability_low_dim_dense.py
examples/decomposition/plot_pca_iris.py
examples/ensemble/plot_ensemble_oob.py
examples/ensemble/plot_feature_transformation.py
examples/ensemble/plot_gradient_boosting_early_stopping.py
examples/ensemble/plot_isolation_forest.py
examples/ensemble/plot_random_forest_embedding.py
examples/feature_selection/plot_feature_selection_pipeline.py
examples/linear_model/plot_lasso_and_elasticnet.py
examples/manifold/plot_compare_methods.py
examples/manifold/plot_lle_digits.py
examples/manifold/plot_manifold_sphere.py
examples/model_selection/plot_confusion_matrix.py
examples/model_selection/plot_randomized_search.py
examples/neighbors/plot_kde_1d.py
examples/neighbors/plot_lof.py
examples/neighbors/plot_nearest_centroid.py
examples/neural_networks/plot_rbm_logistic_classification.py
examples/preprocessing/plot_power_transformer.py
examples/preprocessing/plot_scaling_importance.py
examples/semi_supervised/plot_label_propagation_structure.py
examples/svm/plot_iris.py
examples/svm/plot_oneclass.py
examples/svm/plot_rbf_parameters.py
examples/svm/plot_separating_hyperplane_unbalanced.py
examples/svm/plot_svm_regression.py
examples/tree/plot_iris.py
sklearn/_build_utils/__init__.py
sklearn/_isotonic.pyx
sklearn/cluster/_feature_agglomeration.py
sklearn/cluster/bicluster.py
sklearn/cluster/tests/test_affinity_propagation.py
sklearn/cluster/tests/test_feature_agglomeration.py
sklearn/compose/__init__.py
sklearn/covariance/elliptic_envelope.py
sklearn/covariance/empirical_covariance_.py
sklearn/covariance/tests/test_graphical_lasso.py
sklearn/covariance/tests/test_robust_covariance.py
sklearn/cross_decomposition/__init__.py
sklearn/datasets/descr/breast_cancer.rst
sklearn/datasets/descr/digits.rst
sklearn/datasets/mlcomp.py
sklearn/datasets/mldata.py
sklearn/datasets/tests/test_20news.py
sklearn/decomposition/base.py
sklearn/decomposition/tests/test_incremental_pca.py
sklearn/externals/_pilutil.py
sklearn/externals/copy_joblib.sh
sklearn/externals/funcsigs.py
sklearn/externals/joblib/_compat.py
sklearn/externals/joblib/_memory_helpers.py
sklearn/externals/joblib/_parallel_backends.py
sklearn/externals/joblib/backports.py
sklearn/externals/joblib/format_stack.py
sklearn/externals/joblib/logger.py
sklearn/externals/joblib/memory.py
sklearn/externals/joblib/numpy_pickle_compat.py
sklearn/externals/joblib/numpy_pickle_utils.py
sklearn/externals/setup.py
sklearn/feature_extraction/stop_words.py
sklearn/feature_extraction/tests/test_dict_vectorizer.py
sklearn/feature_selection/tests/test_mutual_info.py
sklearn/gaussian_process/tests/test_gaussian_process.py
sklearn/gaussian_process/tests/test_gpc.py
sklearn/linear_model/randomized_l1.py
sklearn/linear_model/sag_fast.pyx
sklearn/linear_model/tests/test_passive_aggressive.py
sklearn/linear_model/tests/test_perceptron.py
sklearn/linear_model/tests/test_theil_sen.py
sklearn/linear_model/theil_sen.py
sklearn/manifold/_barnes_hut_tsne.pyx
sklearn/manifold/_utils.pyx
sklearn/metrics/cluster/bicluster.py
sklearn/metrics/cluster/tests/test_bicluster.py
sklearn/metrics/cluster/tests/test_common.py
sklearn/metrics/setup.py
sklearn/mixture/dpgmm.py
sklearn/mixture/tests/test_bayesian_mixture.py
sklearn/mixture/tests/test_dpgmm.py
sklearn/mixture/tests/test_mixture.py
sklearn/neighbors/graph.py
sklearn/neighbors/tests/test_nearest_centroid.py
sklearn/neighbors/typedefs.pxd
sklearn/neural_network/_base.py
sklearn/svm/__init__.py
sklearn/svm/libsvm_sparse.pyx
sklearn/svm/src/liblinear/liblinear_helper.c
sklearn/svm/src/liblinear/linear.cpp
sklearn/svm/src/libsvm/libsvm_helper.c
sklearn/tests/test_config.py
sklearn/tests/test_docstring_parameters.py
sklearn/tests/test_isotonic.py
sklearn/tree/_criterion.pxd
sklearn/utils/_random.pxd
sklearn/utils/_unittest_backport.py
sklearn/utils/arpack.py
sklearn/utils/deprecation.py
sklearn/utils/linear_assignment_.py
sklearn/utils/sparsetools/setup.py
sklearn/utils/tests/test_graph.py
sklearn/utils/tests/test_random.py
sklearn/utils/tests/test_seq_dataset.py
sklearn/utils/tests/test_utils.py
sklearn/utils/weight_vector.pyx

What do we think of offering contributors to do cleanups of flake8 or removing assert_{true,false,equal,dict_equal} in these files?

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