scikit-learn · Przemo10 · Mar 17, 2017
diff --git a/.codecov.yml b/.codecov.yml
@@ -0,0 +1 @@
+comment: off
diff --git a/.gitignore b/.gitignore
@@ -62,3 +62,6 @@ benchmarks/bench_covertype_data/
 !*/src/*.cpp
 *.sln
 *.pyproj
+
+# Used by py.test
+.cache
diff --git a/.mailmap b/.mailmap
@@ -23,10 +23,10 @@ Brian Holt <bh00038@cvplws63.eps.surrey.ac.uk> <bdholt1@gmail.com>
 Christian Osendorfer <osendorf@gmail.com>
 Clay Woolam <clay@woolam.org>
 Danny Sullivan <dsullivan7@hotmail.com> <dbsullivan23@gmail.com>
-Denis Engemann <d.engemann@fz-juelich.de>
-Denis Engemann <d.engemann@fz-juelich.de> <denis.engemann@gmail.com>
-Denis Engemann <d.engemann@fz-juelich.de> <dengemann@Deniss-MacBook-Pro.local>
-Denis Engemann <d.engemann@fz-juelich.de> <dengemann <denis.engemann@gmail.com>
+Denis Engemann <denis-alexander.engemann@inria.fr>
+Denis Engemann <denis-alexander.engemann@inria.fr> <denis.engemann@gmail.com>
+Denis Engemann <denis-alexander.engemann@inria.fr> <dengemann@Deniss-MacBook-Pro.local>
+Denis Engemann <denis-alexander.engemann@inria.fr> <dengemann <denis.engemann@gmail.com>
 Diego Molla <dmollaaliod@gmail.com> <diego@diego-desktop.(none)>
 DraXus <draxus@gmail.com> draxus <draxus@hammer.ugr>
 Edouard DUCHESNAY <ed203246@is206877.intra.cea.fr> <duchesnay@is143433.(none)>
@@ -61,7 +61,7 @@ Jake VanderPlas <vanderplas@astro.washington.edu> <jakevdp@gmail.com>
 Jake VanderPlas <vanderplas@astro.washington.edu> <vanderplas@astro.washington.edu>
 James Bergstra <james.bergstra@gmail.com>
 Jaques Grobler <jaques.grobler@inria.fr> <jaquesgrobler@gmail.com>
-Jan Schl�ter <scikit-learn@jan-schlueter.de>
+Jan Schlüter <scikit-learn@jan-schlueter.de>
 Jean Kossaifi <jean.kossaifi@gmail.com>
 Jean Kossaifi <jean.kossaifi@gmail.com> <jkossaifi@is208616.intra.cea.fr>
 Jean Kossaifi <jean.kossaifi@gmail.com> <kossaifi@is208616.intra.cea.fr>

diff --git a/.travis.yml b/.travis.yml
@@ -12,11 +12,10 @@ cache:
 addons:
   apt:
     packages:
+      # these only required by the DISTRIB="ubuntu" builds:
+      - python-scipy
       - libatlas3gf-base
       - libatlas-dev
-      # only required by the DISTRIB="ubuntu" build:
-      - python-scipy
-
 env:
   global:
     # Directory where tests are run from
@@ -31,11 +30,17 @@ env:
     # This environment tests the oldest supported anaconda env
     - DISTRIB="conda" PYTHON_VERSION="2.7" INSTALL_MKL="false"
       NUMPY_VERSION="1.6.2" SCIPY_VERSION="0.11.0" CYTHON_VERSION="0.23"
+      COVERAGE=true
     # This environment tests the newest supported anaconda env
     # It also runs tests requiring Pandas.
-    - DISTRIB="conda" PYTHON_VERSION="3.5" INSTALL_MKL="true"
-      NUMPY_VERSION="1.10.4" SCIPY_VERSION="0.17.0" PANDAS_VERSION="0.18.0"
-      CYTHON_VERSION="0.23.4"
+    - DISTRIB="conda" PYTHON_VERSION="3.6" INSTALL_MKL="true"
+      NUMPY_VERSION="1.11.2" SCIPY_VERSION="0.18.1" PANDAS_VERSION="0.19.1"
+      CYTHON_VERSION="0.25.2" COVERAGE=true
+    # This environment use pytest to run the tests. It uses the newest
+    # supported anaconda env. It also runs tests requiring Pandas.
+    - USE_PYTEST="true" DISTRIB="conda" PYTHON_VERSION="3.6" INSTALL_MKL="true"
+      NUMPY_VERSION="1.11.2" SCIPY_VERSION="0.18.1" PANDAS_VERSION="0.19.1"
+      CYTHON_VERSION="0.25.2"
     # flake8 linting on diff wrt common ancestor with upstream/master
     - RUN_FLAKE8="true" SKIP_TESTS="true"
       DISTRIB="conda" PYTHON_VERSION="3.5" INSTALL_MKL="true"
@@ -52,15 +57,8 @@ matrix:
     # 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.
-    # Note: libatlas3gf-base is not allowed yet so we need 'sudo':
-    # https://github.com/travis-ci/apt-package-whitelist/issues/2407
-    # Once libatlas3gf-base is on the whitelist it will be possible to replace
-    # the before_install step with and addons/apt/packages declaration.
     -  python: 3.5
        env: DISTRIB="scipy-dev-wheels"
-       sudo: True
-       before_install: sudo apt-get install -yqq libatlas3gf-base libatlas-dev
-
 
 install: source build_tools/travis/install.sh
 script: bash build_tools/travis/test_script.sh

diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -67,5 +67,5 @@ The following people have been core contributors to scikit-learn's development a
 
 Please do not email the authors directly to ask for assistance or report issues.
 Instead, please see `What's the best way to ask questions about scikit-learn
-<http://scikit-learn.org/stable/faq.html#what-s-the-best-way-to-ask-questions-about-scikit-learn>`_
+<http://scikit-learn.org/stable/faq.html#what-s-the-best-way-to-get-help-on-scikit-learn-usage>`_
 in the FAQ.
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -4,35 +4,36 @@ Contributing to scikit-learn
 
 **Note: This document is a 'getting started' summary for contributing code,
 documentation, testing, and filing issues.** Visit the [**Contributing
-page**](http://scikit-learn.org/stable/developers/index.html)
+page**](http://scikit-learn.org/stable/developers/contributing.html)
 for the full contributor's guide. Please read it carefully to help make
 the code review process go as smoothly as possible and maximize the
-likelihood of your contribution being merged.**
+likelihood of your contribution being merged.
 
 How to contribute
 -----------------
 
-The preferred workflow for contributing to scikit-learn is to fork the 
+The preferred workflow for contributing to scikit-learn is to fork the
 [main repository](https://github.com/scikit-learn/scikit-learn) on
 GitHub, clone, and develop on a branch. Steps:
 
 1. Fork the [project repository](https://github.com/scikit-learn/scikit-learn)
    by clicking on the 'Fork' button near the top right of the page. This creates
-   a copy of the code under your GitHub user account.
+   a copy of the code under your GitHub user account. For more details on
+   how to fork a repository see [this guide](https://help.github.com/articles/fork-a-repo/).
 
 2. Clone your fork of the scikit-learn repo from your GitHub account to your local disk:
 
    ```bash
    $ git clone git@github.com:YourLogin/scikit-learn.git
    $ cd scikit-learn
    ```
-   
+
 3. Create a ``feature`` branch to hold your development changes:
 
    ```bash
    $ git checkout -b my-feature
    ```
-   
+
    Always use a ``feature`` branch. It's good practice to never work on the ``master`` branch!
 
 4. Develop the feature on your feature branch. Add changed files using ``git add`` and then ``git commit`` files:
@@ -48,11 +49,10 @@ GitHub, clone, and develop on a branch. Steps:
    $ git push -u origin my-feature
    ```
 
-5. Go to the GitHub web page of your fork of the scikit-learn repo.
-Click the 'Pull request' button to send your changes to the project's maintainers for
-review. This will send an email to the committers.
+5. Follow [these instructions](https://help.github.com/articles/creating-a-pull-request-from-a-fork)
+to create a pull request from your fork. This will send an email to the committers.
 
-(If any of the above seems like magic to you, please look up the 
+(If any of the above seems like magic to you, please look up the
 [Git documentation](https://git-scm.com/documentation) on the web, or ask a friend or another contributor for help.)
 
 Pull Request Checklist
@@ -79,7 +79,10 @@ following rules before you submit a pull request:
 
 -  Please prefix the title of your pull request with `[MRG]` (Ready for
    Merge), if the contribution is complete and ready for a detailed review.
-   Incomplete contributions should be prefixed `[WIP]` (to indicate a work
+   Two core developers will review your code and change the prefix of the pull
+   request to `[MRG + 1]` and `[MRG + 2]` on approval, making it eligible
+   for merging. An incomplete contribution -- where you expect to do more work before
+   receiving a full review -- should be prefixed `[WIP]` (to indicate a work
    in progress) and changed to `[MRG]` when it matures. WIPs may be useful
    to: indicate you are working on something to avoid duplicated work,
    request broad review of functionality or API, or seek collaborators.
@@ -179,7 +182,7 @@ following rules before submitting:
   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
@@ -228,5 +231,5 @@ Further Information
 -------------------
 
 Visit the [Contributing Code](http://scikit-learn.org/stable/developers/index.html#coding-guidelines)
-section of the website for more information including conforming to the 
+section of the website for more information including conforming to the
 API spec and profiling contributed code.
diff --git a/COPYING b/COPYING
@@ -1,6 +1,6 @@
 New BSD License
 
-Copyright (c) 2007–2016 The scikit-learn developers.
+Copyright (c) 2007–2017 The scikit-learn developers.
 All rights reserved.
 
 

diff --git a/README.rst b/README.rst
@@ -1,15 +1,15 @@
 .. -*- mode: rst -*-
 
-|Travis|_ |AppVeyor|_ |Coveralls|_ |CircleCI|_ |Python27|_ |Python35|_ |PyPi|_ |DOI|_
+|Travis|_ |AppVeyor|_ |Codecov|_ |CircleCI|_ |Python27|_ |Python35|_ |PyPi|_ |DOI|_
 
 .. |Travis| image:: https://api.travis-ci.org/scikit-learn/scikit-learn.svg?branch=master
 .. _Travis: https://travis-ci.org/scikit-learn/scikit-learn
 
 .. |AppVeyor| image:: https://ci.appveyor.com/api/projects/status/github/scikit-learn/scikit-learn?branch=master&svg=true
 .. _AppVeyor: https://ci.appveyor.com/project/sklearn-ci/scikit-learn/history
 
-.. |Coveralls| image:: https://coveralls.io/repos/scikit-learn/scikit-learn/badge.svg?branch=master&service=github
-.. _Coveralls: https://coveralls.io/r/scikit-learn/scikit-learn
+.. |Codecov| image:: https://codecov.io/github/scikit-learn/scikit-learn/badge.svg?branch=master&service=github
+.. _Codecov: https://codecov.io/github/scikit-learn/scikit-learn?branch=master
 
 .. |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
@@ -53,6 +53,8 @@ scikit-learn requires:
 - NumPy (>= 1.6.1)
 - SciPy (>= 0.9)
 
+For running the examples Matplotlib >= 1.1.1 is required.
+
 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.
@@ -158,7 +160,7 @@ Communication
 ~~~~~~~~~~~~~
 
 - Mailing list: https://mail.python.org/mailman/listinfo/scikit-learn
-- IRC channel: ``#scikit-learn`` at ``irc.freenode.net``
+- IRC channel: ``#scikit-learn`` at ``webchat.freenode.net``
 - Stack Overflow: http://stackoverflow.com/questions/tagged/scikit-learn
 - Website: http://scikit-learn.org
 

diff --git a/benchmarks/bench_mnist.py b/benchmarks/bench_mnist.py
@@ -94,11 +94,11 @@ def load_data(dtype=np.float32, order='F'):
     'LinearRegression-SAG': LogisticRegression(solver='sag', tol=1e-1, C=1e4),
     'MultilayerPerceptron': MLPClassifier(
         hidden_layer_sizes=(100, 100), max_iter=400, alpha=1e-4,
-        algorithm='sgd', learning_rate_init=0.2, momentum=0.9, verbose=1,
+        solver='sgd', learning_rate_init=0.2, momentum=0.9, verbose=1,
         tol=1e-4, random_state=1),
     'MLP-adam': MLPClassifier(
         hidden_layer_sizes=(100, 100), max_iter=400, alpha=1e-4,
-        algorithm='adam', learning_rate_init=0.001, verbose=1,
+        solver='adam', learning_rate_init=0.001, verbose=1,
         tol=1e-4, random_state=1)
 }