scikit-learn · RianneSchouten · Jun 27, 2018 · Jun 27, 2018 · Jun 28, 2018 · Jun 28, 2018
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -41,13 +41,12 @@ jobs:
       # Test examples run with minimal dependencies
       - MINICONDA_PATH: ~/miniconda
       - CONDA_ENV_NAME: testenv
-      - PYTHON_VERSION: 2
-      - NUMPY_VERSION: 1.8.2
-      # XXX: plot_gpc_xor.py fails with scipy 0.13.3
-      - SCIPY_VERSION: 0.14
-      - MATPLOTLIB_VERSION: 1.3
-      - SCIKIT_IMAGE_VERSION: 0.9.3
-      - PANDAS_VERSION: 0.13.1
+      - PYTHON_VERSION: "2"
+      - NUMPY_VERSION: "1.10"
+      - SCIPY_VERSION: "0.16"
+      - MATPLOTLIB_VERSION: "1.4"
+      - SCIKIT_IMAGE_VERSION: "0.11"
+      - PANDAS_VERSION: "0.17.1"
     steps:
       - checkout
       - run: ./build_tools/circle/checkout_merge_commit.sh
@@ -65,6 +64,21 @@ jobs:
           path: ~/log.txt
           destination: log.txt
 
+  pypy3:
+    docker:
+      - image: pypy:3-6.0.0
+    steps:
+      - restore_cache:
+          keys:
+            - pypy3-ccache-{{ .Branch }}
+            - pypy3-ccache
+      - checkout
+      - run: ./build_tools/circle/build_test_pypy.sh
+      - save_cache:
+          key: pypy3-ccache-{{ .Branch }}-{{ .BuildNum }}
+          paths:
+            - ~/.ccache
+            - ~/.cache/pip
 
   deploy:
     docker:
@@ -89,6 +103,21 @@ workflows:
     jobs:
       - python3
       - python2
+      - pypy3:
+          filters:
+            branches:
+              only:
+                - 0.20.X
       - deploy:
           requires:
             - python3
+  pypy:
+    triggers:
+      - schedule:
+          cron: "0 0 * * *"
+          filters:
+            branches:
+              only:
+                - master
+    jobs:
+      - pypy3
diff --git a/.travis.yml b/.travis.yml
@@ -46,7 +46,7 @@ matrix:
            CYTHON_VERSION="*" PYAMG_VERSION="*" PILLOW_VERSION="*"
            JOBLIB_VERSION="*" COVERAGE=true
            CHECK_PYTEST_SOFT_DEPENDENCY="true" TEST_DOCSTRINGS="true"
-           SKLEARN_SITE_JOBLIB=1
+           SKLEARN_SITE_JOBLIB=1 CHECK_WARNINGS="true"
       if: type != cron
     # flake8 linting on diff wrt common ancestor with upstream/master
     - env: RUN_FLAKE8="true" SKIP_TESTS="true"
@@ -58,11 +58,14 @@ matrix:
     # installed from their CI wheels in a virtualenv with the Python
     # interpreter provided by travis.
     -  python: 3.6
-       env: DISTRIB="scipy-dev"
+       env: DISTRIB="scipy-dev" CHECK_WARNINGS="true"
        if: type = cron OR commit_message =~ /\[scipy-dev\]/
 
 install: source build_tools/travis/install.sh
-script: bash build_tools/travis/test_script.sh
+script: 
+  - bash build_tools/travis/test_script.sh
+  - bash build_tools/travis/test_docs.sh
+  - bash build_tools/travis/test_pytest_soft_dependency.sh
 after_success: source build_tools/travis/after_success.sh
 notifications:
   webhooks:

diff --git a/AUTHORS.rst b/AUTHORS.rst
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -178,17 +178,25 @@ following rules before submitting:
    as your Python, scikit-learn, numpy, and scipy versions. This information
    can be found by running the following code snippet:
 
-  ```python
-  import platform; print(platform.platform())
-  import sys; print("Python", sys.version)
-  import numpy; print("NumPy", numpy.__version__)
-  import scipy; print("SciPy", scipy.__version__)
-  import sklearn; print("Scikit-Learn", sklearn.__version__)
-  ```
+   For scikit-learn >= 0.20:
+
+   ```python
+   import sklearn; sklearn.show_versions()
+   ```
+
+   For scikit-learn < 0.20:
+
+   ```python
+   import platform; print(platform.platform())
+   import sys; print("Python", sys.version)
+   import numpy; print("NumPy", numpy.__version__)
+   import scipy; print("SciPy", scipy.__version__)
+   import sklearn; print("Scikit-Learn", sklearn.__version__)
+   ```
 
 -  Please be specific about what estimators and/or functions are involved
    and the shape of the data, as appropriate; please include a
-   [reproducible](http://stackoverflow.com/help/mcve) code snippet
+   [reproducible](https://stackoverflow.com/help/mcve) code snippet
    or link to a [gist](https://gist.github.com). If an exception is raised,
    please provide the traceback.
 
@@ -222,8 +230,8 @@ be placed in ``_build/html/stable`` and are viewable in a web browser. See the
 
 For building the documentation, you will need
 [sphinx](http://sphinx.pocoo.org/),
-[matplotlib](http://matplotlib.org/), and
-[pillow](http://pillow.readthedocs.io/en/latest/).
+[matplotlib](https://matplotlib.org/), and
+[pillow](https://pillow.readthedocs.io/en/latest/).
 
 When you are writing documentation, it is important to keep a good
 compromise between mathematical and algorithmic details, and give

diff --git a/ISSUE_TEMPLATE.md b/ISSUE_TEMPLATE.md
@@ -1,6 +1,6 @@
 <!--
 If your issue is a usage question, submit it here instead:
-- StackOverflow with the scikit-learn tag: http://stackoverflow.com/questions/tagged/scikit-learn
+- StackOverflow with the scikit-learn tag: https://stackoverflow.com/questions/tagged/scikit-learn
 - Mailing List: https://mail.python.org/mailman/listinfo/scikit-learn
 For more information, see User Questions: http://scikit-learn.org/stable/support.html#user-questions
 -->
@@ -43,6 +43,9 @@ it in the issue: https://gist.github.com
 #### Versions
 <!--
 Please run the following snippet and paste the output below.
+For scikit-learn >= 0.20:
+import sklearn; sklearn.show_versions()
+For scikit-learn < 0.20:
 import platform; print(platform.platform())
 import sys; print("Python", sys.version)
 import numpy; print("NumPy", numpy.__version__)

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -4,6 +4,5 @@ recursive-include examples *
 recursive-include sklearn *.c *.h *.pyx *.pxd *.pxi
 recursive-include sklearn/datasets *.csv *.csv.gz *.rst *.jpg *.txt *.arff.gz *.json.gz
 include COPYING
-include AUTHORS.rst
 include README.rst
 
diff --git a/README.rst b/README.rst
@@ -34,7 +34,8 @@ SciPy and 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 `AUTHORS.rst <AUTHORS.rst>`_ file for a complete list of contributors.
+the `About us <http://scikit-learn.org/dev/about.html#authors>`_ page
+for a list of core contributors.
 
 It is currently maintained by a team of volunteers.
 
@@ -56,8 +57,8 @@ scikit-learn requires:
 **Scikit-learn 0.20 is the last version to support Python2.7.**
 Scikit-learn 0.21 and later will require Python 3.5 or newer.
 
-For running the examples Matplotlib >= 1.3.1 is required. A few examples
-require scikit-image >= 0.9.3 and a few examples require pandas >= 0.13.1.
+For running the examples Matplotlib >= 1.4 is required. A few examples
+require scikit-image >= 0.11.3 and a few examples require pandas >= 0.17.1.
 
 scikit-learn also uses CBLAS, the C interface to the Basic Linear Algebra
 Subprograms library. scikit-learn comes with a reference implementation, but
@@ -100,7 +101,7 @@ Important links
 ~~~~~~~~~~~~~~~
 
 - Official source code repo: https://github.com/scikit-learn/scikit-learn
-- Download releases: https://pypi.python.org/pypi/scikit-learn
+- Download releases: https://pypi.org/project/scikit-learn/
 - Issue tracker: https://github.com/scikit-learn/scikit-learn/issues
 
 Source code
@@ -120,7 +121,7 @@ Testing
 ~~~~~~~
 
 After installation, you can launch the test suite from outside the
-source directory (you will need to have the ``pytest`` package installed)::
+source directory (you will need to have ``pytest`` >= 3.3.0 installed)::
 
     pytest sklearn
 
@@ -143,7 +144,8 @@ 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  `AUTHORS.rst <AUTHORS.rst>`_ file for a complete list of contributors.
+the  `About us <http://scikit-learn.org/dev/about.html#authors>`_ page
+for a list of core contributors.
 
 The project is currently maintained by a team of volunteers.
 
@@ -165,7 +167,7 @@ Communication
 
 - Mailing list: https://mail.python.org/mailman/listinfo/scikit-learn
 - IRC channel: ``#scikit-learn`` at ``webchat.freenode.net``
-- Stack Overflow: http://stackoverflow.com/questions/tagged/scikit-learn
+- Stack Overflow: https://stackoverflow.com/questions/tagged/scikit-learn
 - Website: http://scikit-learn.org
 
 Citation

diff --git a/appveyor.yml b/appveyor.yml
@@ -6,7 +6,7 @@ environment:
   global:
     # SDK v7.0 MSVC Express 2008's SetEnv.cmd script will fail if the
     # /E:ON and /V:ON options are not enabled in the batch script interpreter
-    # See: http://stackoverflow.com/a/13751649/163740
+    # See: https://stackoverflow.com/a/13751649/163740
     CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\build_tools\\appveyor\\run_with_env.cmd"
     WHEELHOUSE_UPLOADER_USERNAME: sklearn-appveyor
     WHEELHOUSE_UPLOADER_SECRET:
@@ -20,6 +20,7 @@ environment:
     - PYTHON: "C:\\Python37-x64"
       PYTHON_VERSION: "3.7.0"
       PYTHON_ARCH: "64"
+      CHECK_WARNINGS: "true"
 
     - PYTHON: "C:\\Python27"
       PYTHON_VERSION: "2.7.8"
@@ -45,7 +46,7 @@ install:
         Where-Object pullRequestId -eq $env:APPVEYOR_PULL_REQUEST_NUMBER)[0].buildNumber) { `
         throw "There are newer queued builds for this pull request, failing early." }
 
-  # Install Python (from the official .msi of http://python.org) and pip when
+  # Install Python (from the official .msi of https://python.org) and pip when
   # not already installed.
   - "powershell ./build_tools/appveyor/install.ps1"
   - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
@@ -72,7 +73,13 @@ test_script:
   # installed library.
   - mkdir "../empty_folder"
   - cd "../empty_folder"
-  - pytest --showlocals --durations=20 --pyargs sklearn
+  - ps: >-
+        if (Test-Path variable:global:CHECK_WARNINGS) {
+            $env:PYTEST_ARGS = "-Werror::DeprecationWarning -Werror::FutureWarning"
+        } else {
+            $env:PYTEST_ARGS = ""
+        }
+  - "pytest --showlocals --durations=20 %PYTEST_ARGS% --pyargs sklearn"
   # Move back to the project folder
   - cd "../scikit-learn"
 

diff --git a/benchmarks/bench_covertype.py b/benchmarks/bench_covertype.py
@@ -34,10 +34,10 @@
    S. Shalev-Shwartz, Y. Singer, N. Srebro - In Proceedings of ICML '07.
 
  * `"Training Linear SVMs in Linear Time"
-   <www.cs.cornell.edu/People/tj/publications/joachims_06a.pdf>`_
+   <https://www.cs.cornell.edu/people/tj/publications/joachims_06a.pdf>`_
    T. Joachims - In SIGKDD '06
 
-[1] http://archive.ics.uci.edu/ml/datasets/Covertype
+[1] https://archive.ics.uci.edu/ml/datasets/Covertype
 
 """
 from __future__ import division, print_function

diff --git a/benchmarks/bench_plot_nmf.py b/benchmarks/bench_plot_nmf.py
@@ -96,7 +96,7 @@ def _nls_subproblem(X, W, H, tol, max_iter, alpha=0., l1_ratio=0.,
     ----------
     C.-J. Lin. Projected gradient methods for non-negative matrix
     factorization. Neural Computation, 19(2007), 2756-2779.
-    http://www.csie.ntu.edu.tw/~cjlin/nmf/
+    https://www.csie.ntu.edu.tw/~cjlin/nmf/
     """
     WtX = safe_sparse_dot(W.T, X)
     WtW = np.dot(W.T, W)

diff --git a/benchmarks/bench_plot_randomized_svd.py b/benchmarks/bench_plot_randomized_svd.py
@@ -52,7 +52,7 @@
 ----------
 (1) Finding structure with randomness: Stochastic algorithms for constructing
     approximate matrix decompositions
-    Halko, et al., 2009 http://arxiv.org/abs/arXiv:0909.4061
+    Halko, et al., 2009 https://arxiv.org/abs/0909.4061
 
 (2) A randomized algorithm for the decomposition of matrices
     Per-Gunnar Martinsson, Vladimir Rokhlin and Mark Tygert
@@ -106,7 +106,7 @@
 MAX_MEMORY = np.int(2e9)
 
 # The following datasets can be dowloaded manually from:
-# CIFAR 10: http://www.cs.toronto.edu/~kriz/cifar-10-python.tar.gz
+# CIFAR 10: https://www.cs.toronto.edu/~kriz/cifar-10-python.tar.gz
 # SVHN: http://ufldl.stanford.edu/housenumbers/train_32x32.mat
 CIFAR_FOLDER = "./cifar-10-batches-py/"
 SVHN_FOLDER = "./SVHN/"

diff --git a/build_tools/Makefile b/build_tools/Makefile
@@ -0,0 +1,4 @@
+# Makefile for maintenance tools
+
+authors:
+	python generate_authors_table.py > ../doc/authors.rst
diff --git a/build_tools/appveyor/install.ps1 b/build_tools/appveyor/install.ps1
@@ -1,8 +1,8 @@
 # Sample script to install Python and pip under Windows
 # Authors: Olivier Grisel, Jonathan Helmus, Kyle Kastner, and Alex Willmer
-# License: CC0 1.0 Universal: http://creativecommons.org/publicdomain/zero/1.0/
+# License: CC0 1.0 Universal: https://creativecommons.org/publicdomain/zero/1.0/
 
-$MINICONDA_URL = "http://repo.continuum.io/miniconda/"
+$MINICONDA_URL = "https://repo.continuum.io/miniconda/"
 $BASE_URL = "https://www.python.org/ftp/python/"
 $GET_PIP_URL = "https://bootstrap.pypa.io/get-pip.py"
 $GET_PIP_PATH = "C:\get-pip.py"