scikit-learn · amueller · Nov 21, 2018 · Sep 25, 2018 · Sep 25, 2018 · Sep 26, 2018
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -64,6 +64,19 @@ jobs:
           path: ~/log.txt
           destination: log.txt
 
+  lint:
+    docker:
+      - image: circleci/python:3.6.1
+    steps:
+      - checkout
+      - run: ./build_tools/circle/checkout_merge_commit.sh
+      - run:
+          name: dependencies
+          command: sudo pip install flake8
+      - run:
+          name: flake8
+          command: ./build_tools/circle/flake8_diff.sh
+
   pypy3:
     docker:
       - image: pypy:3-6.0.0
@@ -103,6 +116,7 @@ workflows:
     jobs:
       - python3
       - python2
+      - lint
       - pypy3:
           filters:
             branches:

diff --git a/.travis.yml b/.travis.yml
@@ -38,6 +38,12 @@ matrix:
            NUMPY_VERSION="1.10.4" SCIPY_VERSION="0.16.1" CYTHON_VERSION="0.25.2"
            PILLOW_VERSION="4.0.0" COVERAGE=true
       if: type != cron
+    # Python 3.5 build
+    - env: DISTRIB="conda" PYTHON_VERSION="3.5" INSTALL_MKL="false"
+           NUMPY_VERSION="1.10.4" SCIPY_VERSION="0.16.1" CYTHON_VERSION="0.25.2"
+           PILLOW_VERSION="4.0.0" COVERAGE=true
+           SKLEARN_SITE_JOBLIB=1 JOBLIB_VERSION="0.11"
+      if: type != cron
     # This environment tests the latest available dependencies.
     # It runs tests requiring pandas and PyAMG.
     # It also runs with the site joblib instead of the vendored copy of joblib.
@@ -48,12 +54,6 @@ matrix:
            CHECK_PYTEST_SOFT_DEPENDENCY="true" TEST_DOCSTRINGS="true"
            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"
-           DISTRIB="conda" PYTHON_VERSION="3.5" INSTALL_MKL="true"
-           NUMPY_VERSION="1.13.1" SCIPY_VERSION="0.19.1"
-           CYTHON_VERSION="0.26.1"
-      if: type != cron
     # This environment tests scikit-learn against numpy and scipy master
     # installed from their CI wheels in a virtualenv with the Python
     # interpreter provided by travis.
@@ -62,7 +62,10 @@ matrix:
        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/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.
 
@@ -57,13 +58,14 @@ scikit-learn requires:
 Scikit-learn 0.21 and later will require Python 3.5 or newer.
 
 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.
+require scikit-image >= 0.11.3, a few examples require pandas >= 0.17.1
+and a few example require joblib >= 0.11.
 
 scikit-learn also uses CBLAS, the C interface to the Basic Linear Algebra
 Subprograms library. scikit-learn comes with a reference implementation, but
 the system CBLAS will be detected by the build system and used if present.
 CBLAS exists in many implementations; see `Linear algebra libraries
-<http://scikit-learn.org/stable/modules/computational_performance.html#linear-algebra-libraries>`_
+<http://scikit-learn.org/stable/modules/computing#linear-algebra-libraries>`_
 for known issues.
 
 User installation
@@ -100,7 +102,7 @@ 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
@@ -143,7 +145,8 @@ 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 +168,7 @@ 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:
@@ -46,7 +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%"

diff --git a/benchmarks/bench_covertype.py b/benchmarks/bench_covertype.py
@@ -50,6 +50,7 @@
 from time import time
 import argparse
 import numpy as np
+from joblib import Memory
 
 from sklearn.datasets import fetch_covtype, get_data_home
 from sklearn.svm import LinearSVC
@@ -59,7 +60,6 @@
 from sklearn.ensemble import RandomForestClassifier, ExtraTreesClassifier
 from sklearn.ensemble import GradientBoostingClassifier
 from sklearn.metrics import zero_one_loss
-from sklearn.utils import Memory
 from sklearn.utils import check_array
 
 # Memoize the data extraction and memory map the resulting

diff --git a/benchmarks/bench_mnist.py b/benchmarks/bench_mnist.py
@@ -35,13 +35,13 @@
 from time import time
 import argparse
 import numpy as np
+from joblib import Memory
 
 from sklearn.datasets import fetch_mldata
 from sklearn.datasets import get_data_home
 from sklearn.ensemble import ExtraTreesClassifier
 from sklearn.ensemble import RandomForestClassifier
 from sklearn.dummy import DummyClassifier
-from sklearn.utils import Memory
 from sklearn.kernel_approximation import Nystroem
 from sklearn.kernel_approximation import RBFSampler
 from sklearn.metrics import zero_one_loss

diff --git a/benchmarks/bench_plot_nmf.py b/benchmarks/bench_plot_nmf.py
@@ -14,6 +14,7 @@
 
 import numpy as np
 import matplotlib.pyplot as plt
+from joblib import Memory
 import pandas
 
 from sklearn.utils.testing import ignore_warnings
@@ -22,7 +23,6 @@
 from sklearn.decomposition.nmf import _initialize_nmf
 from sklearn.decomposition.nmf import _beta_divergence
 from sklearn.decomposition.nmf import INTEGER_TYPES, _check_init
-from sklearn.utils import Memory
 from sklearn.exceptions import ConvergenceWarning
 from sklearn.utils.extmath import safe_sparse_dot, squared_norm
 from sklearn.utils import check_array
@@ -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/benchmarks/bench_rcv1_logreg_convergence.py b/benchmarks/bench_rcv1_logreg_convergence.py
@@ -4,11 +4,11 @@
 # License: BSD 3 clause
 
 import matplotlib.pyplot as plt
+from joblib import Memory
 import numpy as np
 import gc
 import time
 
-from sklearn.utils import Memory
 from sklearn.linear_model import (LogisticRegression, SGDClassifier)
 from sklearn.datasets import fetch_rcv1
 from sklearn.linear_model.sag import get_auto_step_size

diff --git a/benchmarks/bench_saga.py b/benchmarks/bench_saga.py
@@ -7,12 +7,12 @@
 import time
 from os.path import expanduser
 
+from joblib import delayed, Parallel, Memory
 import matplotlib.pyplot as plt
 import numpy as np
 
 from sklearn.datasets import fetch_rcv1, load_iris, load_digits, \
     fetch_20newsgroups_vectorized
-from sklearn.utils import delayed, Parallel, Memory
 from sklearn.linear_model import LogisticRegression
 from sklearn.metrics import log_loss
 from sklearn.model_selection import train_test_split

diff --git a/benchmarks/bench_tsne_mnist.py b/benchmarks/bench_tsne_mnist.py
@@ -14,8 +14,8 @@
 import numpy as np
 import json
 import argparse
+from joblib import Memory
 
-from sklearn.utils import Memory
 from sklearn.datasets import fetch_mldata
 from sklearn.manifold import TSNE
 from sklearn.neighbors import NearestNeighbors

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"

diff --git a/build_tools/appveyor/run_with_env.cmd b/build_tools/appveyor/run_with_env.cmd
@@ -14,10 +14,10 @@
 ::
 :: More details at:
 :: https://github.com/cython/cython/wiki/64BitCythonExtensionsOnWindows
-:: http://stackoverflow.com/a/13751649/163740
+:: https://stackoverflow.com/a/13751649/163740
 ::
 :: Author: Olivier Grisel
-:: License: CC0 1.0 Universal: http://creativecommons.org/publicdomain/zero/1.0/
+:: License: CC0 1.0 Universal: https://creativecommons.org/publicdomain/zero/1.0/
 ::
 :: Notes about batch files for Python people:
 ::

diff --git a/build_tools/circle/build_doc.sh b/build_tools/circle/build_doc.sh
@@ -120,7 +120,8 @@ conda update --yes --quiet conda
 conda create -n $CONDA_ENV_NAME --yes --quiet python="${PYTHON_VERSION:-*}" \
   numpy="${NUMPY_VERSION:-*}" scipy="${SCIPY_VERSION:-*}" cython \
   pytest coverage matplotlib="${MATPLOTLIB_VERSION:-*}" sphinx=1.6.2 pillow \
-  scikit-image="${SCIKIT_IMAGE_VERSION:-*}" pandas="${PANDAS_VERSION:-*}"
+  scikit-image="${SCIKIT_IMAGE_VERSION:-*}" pandas="${PANDAS_VERSION:-*}" \
+  joblib
 
 source activate testenv
 pip install sphinx-gallery

diff --git a/build_tools/circle/build_test_pypy.sh b/build_tools/circle/build_test_pypy.sh
@@ -19,7 +19,7 @@ python --version
 which python
 
 pip install --extra-index https://antocuni.github.io/pypy-wheels/ubuntu numpy Cython pytest
-pip install "scipy>=1.1.0" sphinx numpydoc docutils
+pip install "scipy>=1.1.0" sphinx numpydoc docutils joblib
 
 ccache -M 512M
 export CCACHE_COMPRESS=1

diff --git a/build_tools/travis/flake8_diff.sh → build_tools/circle/flake8_diff.sh b/build_tools/travis/flake8_diff.sh → build_tools/circle/flake8_diff.sh
diff --git a/build_tools/travis/after_success.sh b/build_tools/travis/after_success.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # This script is meant to be called by the "after_success" step defined in
-# .travis.yml. See http://docs.travis-ci.com/ for more details.
+# .travis.yml. See https://docs.travis-ci.com/ for more details.
 
 # License: 3-clause BSD