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‎.codecov.yml

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@@ -12,11 +12,8 @@ coverage:
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default:
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# Be tolerant on slight code coverage diff on PRs to limit
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# noisy red coverage status on github PRs.
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# Note The coverage stats are still uploaded
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# Note: The coverage stats are still uploaded
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# to codecov so that PR reviewers can see uncovered lines
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# in the github diff if they install the codecov browser
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# extension:
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# https://github.com/codecov/browser-extension
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target: auto
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threshold: 1%
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‎.github/workflows/labeler.yml

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@@ -8,6 +8,7 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- uses: thomasjpfan/labeler@v2.4.6
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continue-on-error: true
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if: github.repository == 'scikit-learn/scikit-learn'
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with:
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repo-token: "${{ secrets.GITHUB_TOKEN }}"

‎.gitignore

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@@ -77,157 +77,3 @@ _configtest.o.d
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sklearn/utils/_seq_dataset.pyx
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sklearn/utils/_seq_dataset.pxd
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sklearn/linear_model/_sag_fast.pyx
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# deprecated paths
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# TODO: Remove in 0.24
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# All of these files should have a match in _build_utils/deprecated_modules.py
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sklearn/utils/mocking.py
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sklearn/ensemble/bagging.py
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sklearn/ensemble/base.py
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sklearn/ensemble/forest.py
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sklearn/ensemble/gradient_boosting.py
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sklearn/ensemble/iforest.py
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sklearn/ensemble/stacking.py
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sklearn/ensemble/voting.py
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sklearn/ensemble/weight_boosting.py
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sklearn/tree/export.py
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sklearn/tree/tree.py
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sklearn/neural_network/rbm.py
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sklearn/neural_network/multilayer_perceptron.py
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sklearn/utils/weight_vector.py
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sklearn/utils/seq_dataset.py
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sklearn/utils/fast_dict.py
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sklearn/utils/testing.py
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sklearn/cluster/affinity_propagation_.py
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sklearn/cluster/bicluster.py
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sklearn/cluster/birch.py
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sklearn/cluster/dbscan_.py
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sklearn/cluster/hierarchical.py
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sklearn/cluster/k_means_.py
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sklearn/cluster/mean_shift_.py
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sklearn/cluster/optics_.py
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sklearn/cluster/spectral.py
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sklearn/mixture/base.py
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sklearn/mixture/gaussian_mixture.py
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sklearn/mixture/bayesian_mixture.py
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sklearn/covariance/elliptic_envelope.py
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sklearn/covariance/empirical_covariance_.py
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sklearn/covariance/graph_lasso_.py
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sklearn/covariance/robust_covariance.py
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sklearn/covariance/shrunk_covariance_.py
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sklearn/cross_decomposition/cca_.py
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sklearn/cross_decomposition/pls_.py
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sklearn/svm/base.py
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sklearn/svm/classes.py
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sklearn/svm/bounds.py
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sklearn/svm/libsvm.py
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sklearn/svm/libsvm_sparse.py
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sklearn/svm/liblinear.py
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sklearn/decomposition/base.py
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sklearn/decomposition/dict_learning.py
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sklearn/decomposition/cdnmf_fast.py
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sklearn/decomposition/factor_analysis.py
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sklearn/decomposition/fastica_.py
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sklearn/decomposition/incremental_pca.py
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sklearn/decomposition/kernel_pca.py
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sklearn/decomposition/nmf.py
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sklearn/decomposition/online_lda.py
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sklearn/decomposition/online_lda_fast.py
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sklearn/decomposition/pca.py
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sklearn/decomposition/sparse_pca.py
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sklearn/decomposition/truncated_svd.py
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sklearn/gaussian_process/gpr.py
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sklearn/gaussian_process/gpc.py
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sklearn/datasets/base.py
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sklearn/datasets/california_housing.py
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sklearn/datasets/covtype.py
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sklearn/datasets/kddcup99.py
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sklearn/datasets/lfw.py
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sklearn/datasets/olivetti_faces.py
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sklearn/datasets/openml.py
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sklearn/datasets/rcv1.py
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sklearn/datasets/samples_generator.py
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sklearn/datasets/species_distributions.py
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sklearn/datasets/svmlight_format.py
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sklearn/datasets/twenty_newsgroups.py
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sklearn/feature_extraction/dict_vectorizer.py
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sklearn/feature_extraction/hashing.py
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sklearn/feature_extraction/stop_words.py
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sklearn/linear_model/base.py
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sklearn/linear_model/bayes.py
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sklearn/linear_model/cd_fast.py
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sklearn/linear_model/coordinate_descent.py
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sklearn/linear_model/huber.py
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sklearn/linear_model/least_angle.py
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sklearn/linear_model/logistic.py
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sklearn/linear_model/omp.py
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sklearn/linear_model/passive_aggressive.py
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sklearn/linear_model/perceptron.py
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sklearn/linear_model/ransac.py
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sklearn/linear_model/ridge.py
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sklearn/linear_model/sag.py
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sklearn/linear_model/sag_fast.py
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sklearn/linear_model/sgd_fast.py
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sklearn/linear_model/stochastic_gradient.py
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sklearn/linear_model/theil_sen.py
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sklearn/metrics/cluster/bicluster.py
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sklearn/metrics/cluster/supervised.py
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sklearn/metrics/cluster/unsupervised.py
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sklearn/metrics/cluster/expected_mutual_info_fast.py
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sklearn/metrics/base.py
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sklearn/metrics/classification.py
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sklearn/metrics/regression.py
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sklearn/metrics/ranking.py
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sklearn/metrics/pairwise_fast.py
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sklearn/metrics/scorer.py
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sklearn/inspection/partial_dependence.py
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sklearn/inspection/permutation_importance.py
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sklearn/neighbors/ball_tree.py
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sklearn/neighbors/base.py
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sklearn/neighbors/classification.py
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sklearn/neighbors/dist_metrics.py
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sklearn/neighbors/graph.py
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sklearn/neighbors/kd_tree.py
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sklearn/neighbors/kde.py
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sklearn/neighbors/lof.py
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sklearn/neighbors/nca.py
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sklearn/neighbors/nearest_centroid.py
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sklearn/neighbors/quad_tree.py
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sklearn/neighbors/regression.py
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sklearn/neighbors/typedefs.py
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sklearn/neighbors/unsupervised.py
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sklearn/manifold/isomap.py
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sklearn/manifold/locally_linear.py
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sklearn/manifold/mds.py
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sklearn/manifold/spectral_embedding_.py
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sklearn/manifold/t_sne.py
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sklearn/semi_supervised/label_propagation.py
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sklearn/preprocessing/data.py
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sklearn/preprocessing/label.py
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sklearn/feature_selection/base.py
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sklearn/feature_selection/from_model.py
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sklearn/feature_selection/mutual_info.py
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sklearn/feature_selection/rfe.py
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sklearn/feature_selection/univariate_selection.py
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sklearn/feature_selection/variance_threshold.py

‎Makefile

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clean: clean-ctags
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$(PYTHON) setup.py clean
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rm -rf dist
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# TODO: Remove in when all modules are removed.
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$(PYTHON) sklearn/_build_utils/deprecated_modules.py
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in: inplace # just a shortcut
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inplace:

‎azure-pipelines.yml

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pool:
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vmImage: ubuntu-18.04
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steps:
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- bash: echo "##vso[task.prependpath]$CONDA/bin"
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displayName: Add conda to PATH
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- bash: sudo chown -R $USER $CONDA
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displayName: Take ownership of conda installation
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- task: UsePythonVersion@0
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inputs:
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versionSpec: '3.8'
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- bash: |
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set -ex
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conda create --name flake8_env --yes python=3.8
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source activate flake8_env
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pip install flake8 mypy==0.770
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displayName: Install flake8
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displayName: Install linters
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- bash: |
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set -ex
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if [[ $BUILD_SOURCEVERSIONMESSAGE =~ \[lint\ skip\] ]]; then
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# skip linting
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echo "Skipping linting"
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echo "Skipping flake8 linting"
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exit 0
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else
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source activate flake8_env
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./build_tools/circle/linting.sh
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fi
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displayName: Run linting
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- bash: |
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set -ex
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if [[ $BUILD_SOURCEVERSIONMESSAGE =~ \[lint\ skip\] ]]; then
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# skip linting
41-
echo "Skipping linting"
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echo "Skipping mypy linting"
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exit 0
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else
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source activate flake8_env
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mypy sklearn/ --ignore-missing-imports
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fi
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displayName: Run mypy

‎build_tools/generate_authors_table.py

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print("user:", file=sys.stderr)
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user = input()
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passwd = getpass.getpass("Password or access token:\n")
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auth = (user, passwd)
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token = getpass.getpass("access token:\n")
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auth = (user, token)
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LOGO_URL = 'https://avatars2.githubusercontent.com/u/365630?v=4'
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REPO_FOLDER = Path(path.abspath(__file__)).parent.parent
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3939
def get_contributors():
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"""Get the list of contributor profiles. Require admin rights."""
41-
# get members of scikit-learn core-dev on GitHub
41+
# get core devs and triage team
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core_devs = []
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team = 11523
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for page in [1, 2]: # 30 per page
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reply = get("https://api.github.com/teams/%d/members?page=%d" %
46-
(team, page))
47-
core_devs.extend(reply.json())
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triage_team = []
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for team_id, lst in zip((11523, 3593183), (core_devs, triage_team)):
45+
for page in [1, 2]: # 30 per page
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reply = get(
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f"https://api.github.com/teams/{team_id}/members?page={page}"
48+
)
49+
lst.extend(reply.json())
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4951
# get members of scikit-learn on GitHub
5052
members = []
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5557
members.extend(reply.json())
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5759
# keep only the logins
58-
core_devs = [c['login'] for c in core_devs]
59-
members = [c['login'] for c in members]
60+
core_devs = set(c['login'] for c in core_devs)
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triage_team = set(c['login'] for c in triage_team)
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members = set(c['login'] for c in members)
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6164
# add missing contributors with GitHub accounts
62-
members.extend(['dubourg', 'mbrucher', 'thouis', 'jarrodmillman'])
65+
members |= {'dubourg', 'mbrucher', 'thouis', 'jarrodmillman'}
6366
# add missing contributors without GitHub accounts
64-
members.extend(['Angel Soler Gollonet'])
67+
members |= {'Angel Soler Gollonet'}
6568
# remove CI bots
66-
members.remove('sklearn-ci')
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members.remove('sklearn-lgtm')
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members.remove('sklearn-wheels')
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members -= {'sklearn-ci', 'sklearn-lgtm', 'sklearn-wheels'}
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triage_team -= core_devs # remove ogrisel from triage_team
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# remove duplicate, and get the difference of the two sets
71-
core_devs = set(core_devs)
72-
members = set(members)
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emeritus = members.difference(core_devs)
72+
emeritus = members - core_devs - triage_team
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7574
# get profiles from GitHub
7675
core_devs = [get_profile(login) for login in core_devs]
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emeritus = [get_profile(login) for login in emeritus]
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triage_team = [get_profile(login) for login in triage_team]
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# sort by last name
8080
core_devs = sorted(core_devs, key=key)
8181
emeritus = sorted(emeritus, key=key)
82+
triage_team = sorted(triage_team, key=key)
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83-
return core_devs, emeritus
84+
return core_devs, emeritus, triage_team
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8687
def get_profile(login):
@@ -143,10 +144,13 @@ def g 57AE enerate_list(contributors):
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144145
if __name__ == "__main__":
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core_devs, emeritus = get_contributors()
147+
core_devs, emeritus, triage_team = get_contributors()
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148149
with open(REPO_FOLDER / "doc" / "authors.rst", "w+") as rst_file:
149150
rst_file.write(generate_table(core_devs))
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151152
with open(REPO_FOLDER / "doc" / "authors_emeritus.rst", "w+") as rst_file:
152153
rst_file.write(generate_list(emeritus))
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with open(REPO_FOLDER / "doc" / "triage_team.rst", "w+") as rst_file:
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rst_file.write(generate_table(triage_team))

‎conftest.py

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import pytest
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from _pytest.doctest import DoctestItem
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from sklearn import set_config
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from sklearn.utils import _IS_32BIT
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from sklearn.externals import _pilutil
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from sklearn._build_utils.deprecated_modules import _DEPRECATED_MODULES
2018

2119
PYTEST_MIN_VERSION = '3.3.0'
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9795
def pytest_unconfigure(config):
9896
import sys
9997
del sys._is_pytest_session
100-
101-
102-
# TODO: Remove when modules are deprecated in 0.24
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# Configures pytest to ignore deprecated modules.
104-
collect_ignore_glob = [
105-
os.path.join(*deprecated_path.split(".")) + ".py"
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for _, deprecated_path, _, _ in _DEPRECATED_MODULES]

‎doc/about.rst

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:ref:`How you can contribute to the project <contributing>`
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Triage Team
42+
-----------
43+
The following people are active contributors who also help with triaging
44+
issues, PRs, and general maintenance:
45+
46+
.. include:: triage_team.rst
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Emeritus Core Developers
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------------------------
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The following people have been active contributors in the past, but are no

‎doc/authors.rst

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</div>
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<div>
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<a href='https://github.com/thomasjpfan'><img src='https://avatars2.githubusercontent.com/u/5402633?v=4' class='avatar' /></a> <br />
22-
<p>Thomas J Fan</p>
22+
<p>Thomas J. Fan</p>
2323
</div>
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<div>
2525
<a href='https://github.com/agramfort'><img src='https://avatars2.githubusercontent.com/u/161052?v=4' class='avatar' /></a> <br />

‎doc/governance.rst

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approval of all the current TC members. TC members who do not actively engage
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with the TC duties are expected to resign.
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74-
The initial Technical Committee of scikit-learn consists of :user:`Alexandre Gramfort <agramfort>`,
75-
:user:`Olivier Grisel <ogrisel>`, :user:`Andreas Müller <amueller>`, :user:`Joel Nothman <jnothman>`,
76-
:user:`Hanmin Qin <qinhanmin2014>`, :user:`Gaël Varoquaux <GaelVaroquaux>`, and
77-
:user:`Roman Yurchak <rth>`.
74+
The Technical Committee of scikit-learn consists of :user:`Alexandre
75+
Gramfort <agramfort>`, :user:`Olivier Grisel <ogrisel>`, :user:`Adrin Jalali
76+
<adrinjalali>`, :user:`Andreas Müller <amueller>`, :user:`Joel Nothman
77+
<jnothman>`, :user:`Hanmin Qin <qinhanmin2014>`, :user:`Gaël Varoquaux
78+
<GaelVaroquaux>`, and :user:`Roman Yurchak <rth>`.
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Decision Making Process
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=======================

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