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‎.gitignore‎

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@@ -23,7 +23,7 @@ scikit_learn.egg-info/
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.coverage
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coverage
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*.py,cover
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.tags
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.tags*
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tags
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covtype.data.gz
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20news-18828/

‎.mailmap‎

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Alexandre Gramfort <alexandre.gramfort@inria.fr> <alexandre.gramfort@gmail.com>
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Alexandre Gramfort <alexandre.gramfort@inria.fr> <alexandre.gramfort@m4x.org>
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Alexandre Gramfort <alexandre.gramfort@inria.fr> <gramfort@localhost.(none)>
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Alexandre Saint <snt.alex@gmail.com>
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Andreas Mueller <amueller@ais.uni-bonn.de>
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Andreas Mueller <amueller@ais.uni-bonn.de> <Andreas Mueller@MSRC-3645211.europe.corp.microsoft.com>
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Andreas Mueller <amueller@ais.uni-bonn.de> <amueller@ais.uni-bonn.de>
@@ -42,12 +43,16 @@ Federico Vaggi <vaggi.federico@gmail.com> <vaggi.federico@GMAIL.COM>
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Gael Varoquaux <gael.varoquaux@inria.fr>
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Gael Varoquaux <gael.varoquaux@inria.fr> <gael.varoquaux@normalesup.org>
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Gael Varoquaux <gael.varoquaux@inria.fr> <varoquau@normalesup.org>
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Giorgio Patrini <giorgio.patrini@nicta.com.au>
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Giorgio Patrini <giorgio.patrini@nicta.com.au> <giorgiop@users.noreply.github.com>
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Gilles Louppe <g.louppe@gmail.com> <g.louppe@ulg.ac.be>
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Hamzeh Alsalhi <93hamsal@gmail.com>
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Harikrishnan S <hihari777@gmail.com>
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Hendrik Heuer <hendrikheuer@gmail.com>
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Henry Lin <hlin117@gmail.com>
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Hrishikesh Huilgolkar <hrishikesh911@gmail.com> <hrishikesh@QE-IND-WKS007.(none)>
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Hugo Bowne-Anderson <hugobowne@gmail.com>
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Imaculate <imaculatemosha@yahoo.com>
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Immanuel Bayer <mane.desk@gmail.com>
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Jacob Schreiber <jmschreiber91@gmail.com>
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Jacob Schreiber <jmschreiber91@gmail.com> <jmschr@cs.washington.edu>
@@ -79,6 +84,7 @@ Sergio Medina <sergio.medina@inria.fr> <smedina@work4labs.com>
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Nelle Varoquaux <nelle.varoquaux@gmail.com>
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Nelle Varoquaux <nelle.varoquaux@gmail.com> <nelle@phgroup.com>
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Nelle Varoquaux <nelle.varoquaux@gmail.com> <nelle@varoquaux@gmail.com>
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Nicolas Goix <goix.nicolas@gmail.com>
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Nicolas Pinto <pinto@alum.mit.edu> <pinto@mit.edu>
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Noel Dawe <Noel.Dawe@cern.ch> <noel.dawe@gmail.com>
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Noel Dawe <Noel.Dawe@cern.ch> <noel.dAwe@cern.ch>
@@ -87,11 +93,14 @@ Olivier Grisel <olivier.grisel@ensta.org> <olivier.grisel@ensta.org>
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Olivier Hervieu <olivier.hervieu@gmail.com> <olivier.hervieu@tinyclues.com>
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Paul Butler <paulgb@gmail.com>
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Peter Prettenhofer <peter.prettenhofer@gmail.com>
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Raghav R V <rvraghav93@gmail.com>
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Robert Layton <robertlayton@gmail.com>
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Roman Sinayev <roman.sinayev@gmail.com>
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Roman Sinayev <roman.sinayev@gmail.com> <roman@y570.(none)>
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Ronald Phlypo <Ronald.Phlypo@inria.fr>
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Satrajit Ghosh <satra@mit.edu> <satrajit.ghosh@gmail.com>
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Sebastian Raschka <se.raschka@me.com>
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Sebastian Raschka <mail@sebastianraschka.com> <se.raschka@me.com>
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Shiqiao Du <lucidfrontier.45@gmail.com>
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Shiqiao Du <lucidfrontier.45@gmail.com> <s.du@freebit.net>
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Thomas Unterthiner <thomas.unterthiner@gmx.net>

‎.travis.yml‎

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@@ -39,9 +39,10 @@ env:
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NUMPY_VERSION="1.6.2" SCIPY_VERSION="0.11.0" CYTHON_VERSION="0.21"
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CACHED_BUILD_DIR="$HOME/sklearn_build_oldest"
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# This environment tests the newest supported anaconda env
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# It also runs tests requiring Pandas.
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- DISTRIB="conda" PYTHON_VERSION="3.5" INSTALL_MKL="true"
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NUMPY_VERSION="1.10.4" SCIPY_VERSION="0.17.0" CYTHON_VERSION="0.23.4"
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CACHED_BUILD_DIR="$HOME/sklearn_build_latest"
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NUMPY_VERSION="1.10.4" SCIPY_VERSION="0.17.0" PANDAS_VERSION="0.18.0"
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CYTHON_VERSION="0.23.4" CACHED_BUILD_DIR="$HOME/sklearn_build_latest"
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# flake8 linting on diff wrt common ancestor with upstream/master
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- RUN_FLAKE8="true" SKIP_TESTS="true"
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DISTRIB="conda" PYTHON_VERSION="3.5" INSTALL_MKL="true"

‎README.rst‎

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.. -*- mode: rst -*-
2-
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|Travis|_ |AppVeyor|_ |Coveralls|_ |CircleCI|_ |Python27|_ |Python35|_ |PyPi|_ |DOI|_
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.. |Travis| image:: https://api.travis-ci.org/scikit-learn/scikit-learn.svg?branch=master
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.. |PyPi| image:: https://badge.fury.io/py/scikit-learn.svg
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.. _PyPi: https://badge.fury.io/py/scikit-learn
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.. |DOI| image:: https://zenodo.org/badge/21369/scikit-learn/scikit-learn.svg
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.. _DOI: https://zenodo.org/badge/latestdoi/21369/scikit-learn/scikit-learn
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scikit-learn
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============
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It is currently maintained by a team of volunteers.
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**Note** `scikit-learn` was previously referred to as `scikits.learn`.
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Important links
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===============
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Website: http://scikit-learn.org
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- Official source code repo: https://github.com/scikit-learn/scikit-learn
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- HTML documentation (stable release): http://scikit-learn.org
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- HTML documentation (development version): http://scikit-learn.org/dev/
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- Download releases: http://sourceforge.net/projects/scikit-learn/files/
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- Issue tracker: https://github.com/scikit-learn/scikit-learn/issues
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- Mailing list: https://lists.sourceforge.net/lists/listinfo/scikit-learn-general
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- IRC channel: ``#scikit-learn`` at ``irc.freenode.net``
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Installation
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------------
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Dependencies
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============
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scikit-learn is tested to work under Python 2.6, Python 2.7, and Python 3.5.
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(using the same codebase thanks to an embedded copy of
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`six <http://pythonhosted.org/six/>`_). It should also work with Python 3.3 and 3.4.
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The required dependencies to build the software are NumPy >= 1.6.1,
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SciPy >= 0.9 and a working C/C++ compiler. For the development version,
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you will also require Cython >=0.23.
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~~~~~~~~~~~~
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For running the examples Matplotlib >= 1.1.1 is required and for running the
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tests you need nose >= 1.1.2.
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Scikit-learn requires::
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This configuration matches the Ubuntu Precise 12.04 LTS release from April
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2012.
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- Python (>= 2.6 or >= 3.3),
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- NumPy (>= 1.6.1),
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- SciPy (>= 0.9).
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scikit-learn also uses CBLAS, the C interface to the Basic Linear Algebra
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Subprograms library. scikit-learn comes with a reference implementation, but
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<http://scikit-learn.org/stable/modules/computational_performance.html#linear-algebra-libraries>`_
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for known issues.
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User installation
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~~~~~~~~~~~~~~~~~
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Install
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=======
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If you already have a working installation of numpy and scipy,
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the easiest way to install scikit-learn is using ``pip`` ::
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This package uses distutils, which is the default way of installing
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python modules. To install in your home directory, use::
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pip install -U scikit-learn
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python setup.py install --user
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or ``conda``::
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To install for all users on Unix/Linux::
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conda install scikit-learn
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python setup.py build
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sudo python setup.py install
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The documentation includes more detailed `installation instructions <http://scikit-learn.org/stable/install.html>`_.
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For more detailed installation instructions,
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see the web page http://scikit-learn.org/stable/install.html
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Development
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===========
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-----------
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Code
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----
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We welcome new contributors of all experience levels. The scikit-learn
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community goals are to be helpful, welcoming, and effective. The
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`Contributor's Guide <http://scikit-learn.org/stable/developers/index.html>`_
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has detailed information about contributing code, documentation, tests, and
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more. We've included some basic information in this README.
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GIT
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~~~
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Important links
86+
~~~~~~~~~~~~~~~
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- Official source code repo: https://github.com/scikit-learn/scikit-learn
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- Download releases: http://sourceforge.net/projects/scikit-learn/files/
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- Issue tracker: https://github.com/scikit-learn/scikit-learn/issues
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Source code
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~~~~~~~~~~~
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You can check the latest sources with the command::
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git clone https://github.com/scikit-learn/scikit-learn.git
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Contributing
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~~~~~~~~~~~~
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Setting up a development environment
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Quick tutorial on how to go about setting up your environment to
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contribute to scikit-learn: https://github.com/scikit-learn/scikit-learn/blob/master/CONTRIBUTING.md
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Before opening a Pull Request, have a look at the
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full Contributing page to make sure your code complies
120-
with our guidelines: http://scikit-learn.org/stable/developers/index.html
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Testing
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-------
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~~~~~~~
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After installation, you can launch the test suite from outside the
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source directory (you will need to have the ``nose`` package installed)::
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Random number generation can be controlled during testing by setting
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the ``SKLEARN_SEED`` environment variable.
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Submitting a Pull Request
126+
~~~~~~~~~~~~~~~~~~~~~~~~~
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Before opening a Pull Request, have a look at the
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full Contributing page to make sure your code complies
130+
with our guidelines: http://scikit-learn.org/stable/developers/index.html
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132+
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Project history
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---------------
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The project was started in 2007 by David Cournapeau as a Google Summer
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of Code project, and since then many volunteers have contributed. See
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the AUTHORS.rst file for a complete list of contributors.
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The project is currently maintained by a team of volunteers.
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**Note** `scikit-learn` was previously referred to as `scikits.learn`.
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Help and Support
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----------------
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Documentation
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~~~~~~~~~~~~~
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- HTML documentation (stable release): http://scikit-learn.org
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- HTML documentation (development version): http://scikit-learn.org/dev/
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- FAQ: http://scikit-learn.org/stable/faq.html
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Communication
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~~~~~~~~~~~~~
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- Mailing list: https://mail.python.org/mailman/listinfo/scikit-learn
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- IRC channel: ``#scikit-learn`` at ``irc.freenode.net``
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- Stack Overflow: http://stackoverflow.com/questions/tagged/scikit-learn
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- Website: http://scikit-learn.org

‎build_tools/circle/push_doc.sh‎

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DOC_REPO="scikit-learn.github.io"
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MSG="Pushing the docs for revision for branch: $CIRCLE_BRANCH, commit $CIRCLE_SHA1"
15+
if [ "$CIRCLE_BRANCH" = "master" ]
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then
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dir=dev
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else
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# Strip off .X
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dir="${CIRCLE_BRANCH::-2}"
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fi
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MSG="Pushing the docs to $dir/ for branch: $CIRCLE_BRANCH, commit $CIRCLE_SHA1"
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cd $HOME
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if [ ! -d $DOC_REPO ];
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then git clone "git@github.com:scikit-learn/"$DOC_REPO".git";
2028
fi
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cd $DOC_REPO
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git checkout master
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git reset --hard origin/master
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git rm -rf dev/ && rm -rf dev/
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cp -R $HOME/scikit-learn/doc/_build/html/stable dev
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git checkout $CIRCLE_BRANCH
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git reset --hard origin/$CIRCLE_BRANCH
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git rm -rf $dir/ && rm -rf $dir/
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cp -R $HOME/scikit-learn/doc/_build/html/stable $dir
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git config --global user.email "olivier.grisel+sklearn-ci@gmail.com"
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git config --global user.name $USERNAME
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git config --global push.default matching
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git add -f dev/
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git commit -m "$MSG" dev
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git add -f $dir/
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git commit -m "$MSG" $dir
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git push
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echo $MSG

‎build_tools/travis/flake8_diff.sh‎

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PROJECT=scikit-learn/scikit-learn
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echo "Remotes:"
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git remote --verbose
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# Find the remote with the project name (upstream in most cases)
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REMOTE=$(git remote -v | grep $PROJECT | cut -f1 | head -1 || echo '')
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git remote add $REMOTE $PROJECT_URL
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fi
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echo "Remotes:"
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echo '--------------------------------------------------------------------------------'
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git remote --verbose
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# Travis does the git clone with a limited depth (50 at the time of
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# writing). This may not be enough to find the common ancestor with
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# $REMOTE/master so we unshallow the git checkout
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if [[ -a .git/shallow ]]; then
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echo -e '\nTrying to unshallow the repo:'
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echo '--------------------------------------------------------------------------------'
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git fetch --unshallow
46+
fi
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if [[ "$TRAVIS" == "true" ]]; then
3949
if [[ "$TRAVIS_PULL_REQUEST" == "false" ]]
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then
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exit 0
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fi
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COMMIT_RANGE=$TRAVIS_COMMIT_RANGE
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else
50-
# Travis does the git clone with a limited depth (50 at the time of
51-
# writing). This may not be enough to find the common ancestor with
52-
# $REMOTE/master so we unshallow the git checkout
53-
git fetch --unshallow || echo "Unshallowing the git checkout failed"
5459
fi
5560
else
5661
# We want to fetch the code as it is in the PR branch and not
5762
# the result of the merge into master. This way line numbers
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# reported by Travis will match with the local code.
59-
BRANCH_NAME=travis_pr_$TRAVIS_PULL_REQUEST
60-
git fetch $REMOTE pull/$TRAVIS_PULL_REQUEST/head:$BRANCH_NAME
61-
git checkout $BRANCH_NAME
64+
LOCAL_BRANCH_REF=travis_pr_$TRAVIS_PULL_REQUEST
65+
# In Travis the PR target is always origin
66+
git fetch origin pull/$TRAVIS_PULL_REQUEST/head:refs/$LOCAL_BRANCH_REF
6267
fi
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fi
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echo -e '\nLast 2 commits:'
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echo '--------------------------------------------------------------------------------'
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git log -2 --pretty=short
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# If not using the commit range from Travis we need to find the common
71-
# ancestor between HEAD and $REMOTE/master
71+
# ancestor between $LOCAL_BRANCH_REF and $REMOTE/master
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if [[ -z "$COMMIT_RANGE" ]]; then
73+
if [[ -z "$LOCAL_BRANCH_REF" ]]; then
74+
LOCAL_BRANCH_REF=$(git rev-parse --abbrev-ref HEAD)
75+
fi
76+
echo -e "\nLast 2 commits in $LOCAL_BRANCH_REF:"
77+
echo '--------------------------------------------------------------------------------'
78+
git log -2 $LOCAL_BRANCH_REF
79+
7380
REMOTE_MASTER_REF="$REMOTE/master"
7481
# Make sure that $REMOTE_MASTER_REF is a valid reference
75-
git fetch $REMOTE master:refs/$REMOTE_MASTER_REF
82+
echo -e "\nFetching $REMOTE_MASTER_REF"
83+
echo '--------------------------------------------------------------------------------'
84+
git fetch $REMOTE master:refs/remotes/$REMOTE_MASTER_REF
85+
LOCAL_BRANCH_SHORT_HASH=$(git rev-parse --short $LOCAL_BRANCH_REF)
86+
REMOTE_MASTER_SHORT_HASH=$(git rev-parse --short $REMOTE_MASTER_REF)
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77-
COMMIT=$(git merge-base @ $REMOTE_MASTER_REF) || \
78-
echo "No common ancestor found for $(git show @ -q) and $(git show $REMOTE_MASTER_REF -q)"
79-
80-
if [[ -n "$TMP_REMOTE" ]]; then
81-
git remote remove $TMP_REMOTE
82-
fi
88+
COMMIT=$(git merge-base $LOCAL_BRANCH_REF $REMOTE_MASTER_REF) || \
89+
echo "No common ancestor found for $(git show $LOCAL_BRANCH_REF -q) and $(git show $REMOTE_MASTER_REF -q)"
8390

8491
if [ -z "$COMMIT" ]; then
8592
exit 1
8693
fi
8794

88-
echo -e "\nCommon ancestor between HEAD and $REMOTE_MASTER_REF is:"
95+
COMMIT_SHORT_HASH=$(git rev-parse --short $COMMIT)
96+
97+
echo -e "\nCommon ancestor between $LOCAL_BRANCH_REF ($LOCAL_BRANCH_SHORT_HASH)"\
98+
"and $REMOTE_MASTER_REF ($REMOTE_MASTER_SHORT_HASH) is $COMMIT_SHORT_HASH:"
8999
echo '--------------------------------------------------------------------------------'
90-
git show --no-patch $COMMIT
100+
git show --no-patch $COMMIT_SHORT_HASH
101+
102+
COMMIT_RANGE="$COMMIT_SHORT_HASH..$LOCAL_BRANCH_SHORT_HASH"
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92-
COMMIT_RANGE="$(git rev-parse --short $COMMIT)..$(git rev-parse --short @)"
104+
if [[ -n "$TMP_REMOTE" ]]; then
105+
git remote remove $TMP_REMOTE
106+
fi
93107

94108
else
95109
echo "Got the commit range from Travis: $COMMIT_RANGE"

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