Merge pull request scikit-learn#2 from ericpre/varimax

Varimax PR: address review comments

.binder/requirements.txt

@@ -1,4 +1,4 @@
---find-links https://sklearn-nightly.scdn8.secure.raxcdn.com scikit-learn
+--extra-index https://pypi.anaconda.org/scipy-wheels-nightly/simple scikit-learn
 --pre
 matplotlib
 scikit-image

.circleci/config.yml

@@ -9,17 +9,17 @@ jobs:
       - MKL_NUM_THREADS: 2
       - MINICONDA_PATH: ~/miniconda
       - CONDA_ENV_NAME: testenv
-      - PYTHON_VERSION: 3.5
-      - NUMPY_VERSION: 1.11.0
-      - SCIPY_VERSION: 0.17.0
-      - MATPLOTLIB_VERSION: 1.5.1
+      - PYTHON_VERSION: 3.6
+      - NUMPY_VERSION: 1.13.3
+      - SCIPY_VERSION: 0.19.1
+      - MATPLOTLIB_VERSION: 2.1.1
       # on conda, this is the latest for python 3.5
       # The following places need to be in sync with regard to Cython version:
       # - .circleci config file
       # - sklearn/_build_utils/__init__.py
       # - advanced installation guide
       - CYTHON_VERSION: 0.28.5
-      - SCIKIT_IMAGE_VERSION: 0.12.3
+      - SCIKIT_IMAGE_VERSION: 0.13
     steps:
       - checkout
       - run: ./build_tools/circle/checkout_merge_commit.sh

.github/ISSUE_TEMPLATE/bug_report.md

@@ -2,13 +2,15 @@
 name: Bug report
 about: Create a report to help us reproduce and correct the bug
 title: ''
-labels: Bug
+labels: 'Bug: triage'
 assignees: ''
 
 ---
 
+<!--
 Before submitting a bug, please make sure the issue hasn't been already
 addressed by searching through the past issues.
+-->
 
 #### Describe the bug
 <!--

.github/labeler.yml

@@ -0,0 +1,80 @@
+module:cluster:
+- sklearn/cluster/**/*
+
+module:common:
+- sklearn/common/**/*
+
+module:compose:
+- sklearn/compose/**/*
+
+module:covariance:
+- sklearn/covariance/**/*
+
+module:cross_decomposition:
+- sklearn/cross_decomposition/**/*
+
+module:datasets:
+- sklearn/datasets/**/*
+
+module:decomposition:
+- sklearn/decomposition/**/*
+
+module:ensemble:
+- sklearn/ensemble/**/*
+
+module:feature_extraction:
+- sklearn/feature_extraction/**/*
+
+module:feature_selection:
+- sklearn/feature_selection/**/*
+
+module:gaussian_process:
+- sklearn/gaussian_process/**/*
+
+module:impute:
+- sklearn/impute/**/*
+
+module:inspection:
+- sklearn/inspection/**/*
+
+module:linear_model:
+- sklearn/linear_model/**/*
+
+module:manifold:
+- sklearn/manifold/**/*
+
+module:metrics:
+- sklearn/metrics/**/*
+
+module:mixture:
+- sklearn/mixture/**/*
+
+module:model_selection:
+- sklearn/model_selection/**/*
+
+module:naive_bayes:
+- sklearn/naive_bayes.py
+
+module:neighbors:
+- sklearn/neighbors/**/*
+
+module:neural_network:
+- sklearn/neural_network/**/*
+
+module:pipeline:
+- sklearn/pipeline.py
+
+module:preprocessing:
+- sklearn/preprocessing/**/*
+
+module:semi_supervised:
+- sklearn/semi_supervised/**/*
+
+module:svm:
+- sklearn/svm/**/*
+
+module:tree:
+- sklearn/tree/**/*
+
+module:utils:
+- sklearn/utils/**/*

.github/workflows/assign.yml

@@ -0,0 +1,16 @@
+
+name: Assign
+on:
+  issue_comment:
+    types: created
+
+jobs:
+  one:
+    runs-on: ubuntu-latest
+    steps:
+    - if: github.event.comment.body == 'take'
+      name:
+      run: |
+        echo "Assigning issue ${{ github.event.issue.number }} to ${{ github.event.comment.user.login }}"
+        curl -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" -d '{"assignees": ["${{ github.event.comment.user.login }}"]}' https://api.github.com/repos/${{ github.repository }}/issues/${{ github.event.issue.number }}/assignees
+        curl -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" -X "DELETE" https://api.github.com/repos/${{ github.repository }}/issues/${{ github.event.issue.number }}/labels/help%20wanted

.github/workflows/labeler.yml

@@ -0,0 +1,14 @@
+name: "Pull Request Labeler"
+on:
+  schedule:
+    - cron: "*/10 * * * *"
+
+jobs:
+  triage:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: thomasjpfan/labeler@v2.4.6
+      if: github.repository == 'scikit-learn/scikit-learn'
+      with:
+        repo-token: "${{ secrets.GITHUB_TOKEN }}"
+        max-labels: "3"

.github/workflows/unassign.yml

@@ -0,0 +1,14 @@
+name: Unassign
+#Runs when a contributor has unassigned themselves from the issue and adds 'help wanted' and 'stalled' tags
+on:
+  issues:
+    types: unassigned
+
+jobs:
+  one:
+    runs-on: ubuntu-latest
+    steps:
+      - name:
+        run: |
+          echo "Marking issue ${{ github.event.issue.number }} as stalled"
+          curl -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" -d '{"labels": ["help wanted","Stalled"]}' https://api.github.com/repos/${{ github.repository }}/issues/${{ github.event.issue.number }}/labels

.gitignore

@@ -39,6 +39,7 @@ doc/samples
 *.prof
 .tox/
 .coverage
+pip-wheel-metadata
 
 lfw_preprocessed/
 nips2010_pdf/

.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+-   repo: https://gitlab.com/pycqa/flake8
+    rev: 3.7.8
+    hooks:
+    -   id: flake8
+        types: [file, python]
+        # only check for unused imports for now, as long as
+        # the code is not fully PEP8 compatible
+        args: [--select=F401]
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.730
+    hooks:
+     -  id: mypy
+        args:
+          - --ignore-missing-imports
+        files: sklearn/

CODE_OF_CONDUCT.md

@@ -0,0 +1,16 @@
+# Code of Conduct
+
+We are a community based on openness and friendly, didactic, discussions.
+
+We aspire to treat everybody equally, and value their contributions.
+
+Decisions are made based on technical merit and consensus.
+
+Code is not the only way to help the project. Reviewing pull requests,
+answering questions to help others on mailing lists or issues, organizing and
+teaching tutorials, working on the website, improving the documentation, are
+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/
+

COPYING

@@ -1,6 +1,6 @@
 New BSD License
 
-Copyright (c) 2007–2019 The scikit-learn developers.
+Copyright (c) 2007–2020 The scikit-learn developers.
 All rights reserved.
 
 

MANIFEST.in

@@ -5,3 +5,4 @@ recursive-include sklearn *.c *.h *.pyx *.pxd *.pxi *.tp
 recursive-include sklearn/datasets *.csv *.csv.gz *.rst *.jpg *.txt *.arff.gz *.json.gz
 include COPYING
 include README.rst
+include pyproject.toml

Makefile

@@ -67,4 +67,4 @@ code-analysis:
 	pylint -E -i y sklearn/ -d E1103,E0611,E1101
 
 flake8-diff:
-	./build_tools/circle/linting.sh
+	git diff upstream/master -u -- "*.py" | flake8 --diff

README.rst

@@ -14,8 +14,8 @@
 .. |CircleCI| image:: https://circleci.com/gh/scikit-learn/scikit-learn/tree/master.svg?style=shield&circle-token=:circle-token
 .. _CircleCI: https://circleci.com/gh/scikit-learn/scikit-learn
 
-.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/scikit-learn.svg
-.. _PythonVersion: https://img.shields.io/pypi/pyversions/scikit-learn.svg
+.. |PythonVersion| image:: https://img.shields.io/badge/python-3.6%20%7C%203.7%20%7C%203.8-blue
+.. _PythonVersion: https://img.shields.io/badge/python-3.6%20%7C%203.7%20%7C%203.8-blue
 
 .. |PyPi| image:: https://badge.fury.io/py/scikit-learn.svg
 .. _PyPi: https://badge.fury.io/py/scikit-learn
@@ -31,12 +31,12 @@ SciPy and is distributed under the 3-Clause BSD license.
 
 The project was started in 2007 by David Cournapeau as a Google Summer
 of Code project, and since then many volunteers have contributed. See
-the `About us <http://scikit-learn.org/dev/about.html#authors>`__ page
+the `About us <https://scikit-learn.org/dev/about.html#authors>`__ page
 for a list of core contributors.
 
 It is currently maintained by a team of volunteers.
 
-Website: http://scikit-learn.org
+Website: https://scikit-learn.org
 
 
 Installation
@@ -47,18 +47,19 @@ Dependencies
 
 scikit-learn requires:
 
-- Python (>= 3.5)
-- NumPy (>= 1.11.0)
-- SciPy (>= 0.17.0)
+- Python (>= 3.6)
+- NumPy (>= 1.13.3)
+- SciPy (>= 0.19.1)
 - joblib (>= 0.11)
 
 **Scikit-learn 0.20 was the last version to support Python 2.7 and Python 3.4.**
-scikit-learn 0.21 and later require Python 3.5 or newer.
+scikit-learn 0.23 and later require Python 3.6 or newer.
 
 Scikit-learn plotting capabilities (i.e., functions start with ``plot_``
-and classes end with "Display") require Matplotlib (>= 1.5.1). For running the
-examples Matplotlib >= 1.5.1 is required. A few examples require
-scikit-image >= 0.12.3, a few examples require pandas >= 0.18.0.
+and classes end with "Display") require Matplotlib (>= 2.1.1). For running the
+examples Matplotlib >= 2.1.1 is required. A few examples require
+scikit-image >= 0.13, a few examples require pandas >= 0.18.0, some examples
+require seaborn >= 0.9.0.
 
 User installation
 ~~~~~~~~~~~~~~~~~
@@ -72,21 +73,21 @@ or ``conda``::
 
     conda install scikit-learn
 
-The documentation includes more detailed `installation instructions <http://scikit-learn.org/stable/install.html>`_.
+The documentation includes more detailed `installation instructions <https://scikit-learn.org/stable/install.html>`_.
 
 
 Changelog
 ---------
 
-See the `changelog <http://scikit-learn.org/dev/whats_new.html>`__
+See the `changelog <https://scikit-learn.org/dev/whats_new.html>`__
 for a history of notable changes to scikit-learn.
 
 Development
 -----------
 
 We welcome new contributors of all experience levels. The scikit-learn
 community goals are to be helpful, welcoming, and effective. The
-`Development Guide <http://scikit-learn.org/stable/developers/index.html>`_
+`Development Guide <https://scikit-learn.org/stable/developers/index.html>`_
 has detailed information about contributing code, documentation, tests, and
 more. We've included some basic information in this README.
 
@@ -119,7 +120,7 @@ source directory (you will need to have ``pytest`` >= 3.3.0 installed)::
 
     pytest sklearn
 
-See the web page http://scikit-learn.org/dev/developers/advanced_installation.html#testing
+See the web page https://scikit-learn.org/dev/developers/advanced_installation.html#testing
 for more information.
 
     Random number generation can be controlled during testing by setting
@@ -130,15 +131,15 @@ Submitting a Pull Request
 
 Before opening a Pull Request, have a look at the
 full Contributing page to make sure your code complies
-with our guidelines: http://scikit-learn.org/stable/developers/index.html
+with our guidelines: https://scikit-learn.org/stable/developers/index.html
 
 
 Project History
 ---------------
 
 The project was started in 2007 by David Cournapeau as a Google Summer
 of Code project, and since then many volunteers have contributed. See
-the `About us <http://scikit-learn.org/dev/about.html#authors>`__ page
+the `About us <https://scikit-learn.org/dev/about.html#authors>`__ page
 for a list of core contributors.
 
 The project is currently maintained by a team of volunteers.
@@ -152,19 +153,19 @@ Help and Support
 Documentation
 ~~~~~~~~~~~~~
 
-- HTML documentation (stable release): http://scikit-learn.org
-- HTML documentation (development version): http://scikit-learn.org/dev/
-- FAQ: http://scikit-learn.org/stable/faq.html
+- HTML documentation (stable release): https://scikit-learn.org
+- HTML documentation (development version): https://scikit-learn.org/dev/
+- FAQ: https://scikit-learn.org/stable/faq.html
 
 Communication
 ~~~~~~~~~~~~~
 
 - Mailing list: https://mail.python.org/mailman/listinfo/scikit-learn
 - IRC channel: ``#scikit-learn`` at ``webchat.freenode.net``
 - Stack Overflow: https://stackoverflow.com/questions/tagged/scikit-learn
-- Website: http://scikit-learn.org
+- Website: https://scikit-learn.org
 
 Citation
 ~~~~~~~~
 
-If you use scikit-learn in a scientific publication, we would appreciate citations: http://scikit-learn.org/stable/about.html#citing-scikit-learn
+If you use scikit-learn in a scientific publication, we would appreciate citations: https://scikit-learn.org/stable/about.html#citing-scikit-learn