Merge commit '0.14a1-239-g0872592' into dfsg

* commit '0.14a1-239-g0872592': (2048 commits)
  DOC copyedit SGDClassifier docstring
  DOC: also point installation menu to stable
  DOC home always points to stable
  DOC now building to html/stable
  comments added to the changes
  DOC: few small doc fixes to layout bugs on new website
  FIX: remove dupplicate entry in What's new
  DOC: DBSCAN misc doc formatting
  MISC: fix reference to example
  MISC: update whats_new
  DOC credit to @ephes and myself for log loss in metrics
  DBSCAN BallTree implementation
  DOC added link from banner to example.
  DOC Update what's new
  DOC fix comment on svm probability param
  Also clean the dist folder when calling make
  Ignore the generated MANIFEST file
  partial_fit for naive Bayes was done for 0.14-rc, not 0.11...
  Re-align the what's new file with the new ordering of items from master
  Fixed a typo in a contributor's name
  ...

Conflicts: joblib has its own destiny
	sklearn/externals/joblib/__init__.py
	sklearn/externals/joblib/format_stack.py
	sklearn/externals/joblib/func_inspect.py
	sklearn/externals/joblib/hashing.py
	sklearn/externals/joblib/logger.py
	sklearn/externals/joblib/memory.py
	sklearn/externals/joblib/numpy_pickle.py
	sklearn/externals/joblib/parallel.py
	sklearn/externals/joblib/test/test_memory.py
	sklearn/externals/joblib/test/test_parallel.py

Author: yarikoptic

.gitattributes

@@ -1,5 +1,6 @@
 /sklearn/__check_build/_check_build.c -diff
 /sklearn/_hmmc.c -diff
+/sklearn/_isotonic.c -diff
 /sklearn/cluster/_hierarchical.c -diff
 /sklearn/cluster/_k_means.c -diff
 /sklearn/datasets/_svmlight_format.c -diff
@@ -17,6 +18,7 @@
 /sklearn/utils/arrayfuncs.c -diff
 /sklearn/utils/graph_shortest_path.c -diff
 /sklearn/utils/lgamma.c -diff
+/sklearn/utils/_logistic_sigmoid.c -diff
 /sklearn/utils/murmurhash.c -diff
 /sklearn/utils/seq_dataset.c -diff
 /sklearn/utils/sparsefuncs.c -diff

.gitignore

@@ -1,7 +1,9 @@
 *.pyc
 *.so
+*.pyd
 *~
 .#*
+*.lprof
 *.swp
 *.swo
 .DS_Store
@@ -10,10 +12,12 @@ sklearn/datasets/__config__.py
 sklearn/**/*.html
 
 dist/
+MANIFEST
 doc/_build/
 doc/auto_examples/
 doc/modules/generated/
 doc/datasets/generated/
+*.pdf
 pip-log.txt
 scikit_learn.egg-info/
 .coverage
@@ -30,6 +34,7 @@ coverages
 samples
 doc/coverages
 doc/samples
+*.prof
 
 lfw_preprocessed/
 nips2010_pdf/
@@ -39,4 +44,9 @@ nips2010_pdf/
 *.tgz
 
 examples/cluster/joblib
+reuters/
 benchmarks/bench_covertype_data/
+
+*.prefs
+.pydevproject
+.idea

.mailmap

@@ -1,82 +1,80 @@
-Gael Varoquaux <[email protected]> gvaroquaux <[email protected]>
-Gael Varoquaux <[email protected]> Gael varoquaux <[email protected]>
-Gael Varoquaux <[email protected]> GaelVaroquaux <[email protected]>
-Gael Varoquaux <[email protected]> Varoquaux <[email protected]>
-Olivier Grisel <[email protected]> ogrisel <[email protected]>
-Olivier Grisel <[email protected]> Olivier Grisel <ogrisel@turingcarpet.(none)>
-Alexandre Gramfort <[email protected]> Alexandre Gramfort <[email protected]>
-Alexandre Gramfort <[email protected]> Alexandre Gramfort <[email protected]>
-Alexandre Gramfort <[email protected]> Alexandre Gramfort <gramfort@localhost.(none)>
-Matthieu Perrot <[email protected]> Matthieu Perrot <revilyo@earth.(none)>
-Matthieu Perrot <[email protected]> revilyo <revilyo@earth.(none)>
-Vincent Michel <[email protected]> vincent <[email protected]>
-Vincent Michel <[email protected]> vincent <vincent@axon.(none)>
-Vincent Michel <[email protected]> vincent M <[email protected]>
-Vincent Michel <[email protected]> Vincent M <[email protected]>
-Vincent Michel <[email protected]> Vincent Michel <[email protected]>
-Vincent Michel <[email protected]> Vincent M <[email protected]>
-Vincent Michel <[email protected]> Vincent michel <[email protected]>
-Vincent Michel <[email protected]> Vincent Michel <[email protected]>
+Alexandre Gramfort <[email protected]> <[email protected]>
+Alexandre Gramfort <[email protected]> <[email protected]>
+Alexandre Gramfort <[email protected]> <gramfort@localhost.(none)>
+Andreas Mueller <[email protected]>
+Andreas Mueller <[email protected]> <Andreas [email protected]>
+Andreas Mueller <[email protected]> <[email protected]>
+Andreas Mueller <[email protected]> <[email protected]>
+Andreas Mueller <[email protected]> <andy@marvin>
+Arnaud Joly <[email protected]>
+Arnaud Joly <[email protected]> <[email protected]>
+Arnaud Joly <[email protected]> <[email protected]>
+Anne-Laure Fouque <afouque@is208050.(none)> <[email protected]>
 Ariel Rokem <[email protected]> arokem <[email protected]>
-Bertrand Thirion <[email protected]> bthirion <[email protected]>
-Peter Prettenhofer <[email protected]> pprett <[email protected]>
-Anne-Laure Fouque <afouque@is208050.(none)> Anne-Laure FOUQUE <[email protected]>
-Vincent Dubourg <[email protected]> dubourg <[email protected]>
-Vincent Dubourg <[email protected]> dubourg <dubourg@PTlami14.(none)>
-Christian Osendorfer <[email protected]> osdf <[email protected]> 
-James Bergstra <[email protected]> james.bergstra <[email protected]>
-Xinfan Meng <[email protected]> mxf <[email protected]>
-Jan Schlüter <[email protected]> f0k <[email protected]>
-Vlad Niculae <[email protected]> vene <[email protected]>
-Virgile Fritsch <[email protected]> VirgileFritsch <[email protected]>
-Virgile Fritsch <[email protected]> Virgile <[email protected]>
-Virgile Fritsch <[email protected]> Virgile <virgile@virgile-Precision-M4400.(none)>
-Jean Kossaifi <[email protected]> Jean  KOSSAIFI <[email protected]>
-Jean Kossaifi <[email protected]> JeanKossaifi <[email protected]>
-Jean Kossaifi <[email protected]> Jean Kossaifi <[email protected]>
-Jake VanderPlas <[email protected]> Jacob Vanderplas <[email protected]>
-Jake VanderPlas <[email protected]> Jake Vanderplas <[email protected]>
-Jake VanderPlas <[email protected]> Jake Vanderplas <[email protected]>
-Andreas Mueller <[email protected]> Andy <[email protected]>
-Andreas Mueller <[email protected]> unknown <Andreas [email protected]>
-Andreas Mueller <[email protected]> andy <andy@marvin>
-Andreas Mueller <[email protected]> Andreas Mueller <[email protected]>
-Andreas Mueller <[email protected]> Andreas Müller <[email protected]>
-Brian Holt <[email protected]> bdholt1 <[email protected]>
-Brian Holt <[email protected]> Brian Holt <[email protected]>
-Robert Layton <[email protected]> robertlayton <[email protected]>
-Robert Layton <[email protected]> = <[email protected]>
-Fabian Pedregosa <[email protected]> Fabian Pedregosa <[email protected]>
-Lars Buitinck <[email protected]> Lars Buitinck <[email protected]>
-Lars Buitinck <[email protected]> unknown <Lars@.(none)>
-Lars Buitinck <[email protected]> Lars Buitinck <[email protected]>
-DraXus <[email protected]> draxus <[email protected]>
-Edouard DUCHESNAY <[email protected]>  Edouard Duchesnay <duchesnay@is143433.(none)>
-Edouard DUCHESNAY <[email protected]> Edouard Duchesnay <[email protected]>
-Edouard DUCHESNAY <[email protected]> duchesnay <[email protected]>
-Edouard DUCHESNAY <[email protected]> duchesnay <edouard@is2206219.(none)> 
-Emmanuelle Gouillart <[email protected]> Emmanuelle Gouillart <emma@aleph.(none)>
-Emmanuelle Gouillart <[email protected]> emmanuelle <[email protected]> 
-Gilles Louppe <[email protected]> Gilles Louppe <[email protected]>
-Nelle Varoquaux <[email protected]> Nelle Varoquaux <[email protected]>
-Nicolas Pinto <[email protected]> Nicolas Pinto <[email protected]>
-Olivier Hervieu <[email protected]> Olivier Hervieu <[email protected]>
-Satrajit Ghosh <[email protected]> Satrajit Ghosh <[email protected]>
-Shiqiao Du <[email protected]> Shiqiao Du <[email protected]>
-Shiqiao Du <[email protected]> Shiqiao <[email protected]>
-Tim Sheerman-Chase <[email protected]> Tim Sheerman-Chase <ts00051@ts00051-desktop.(none)>
-Vincent Schut <[email protected]> Vincent Schut <vincent@TIMO.(none)>
-iBayer <[email protected]> ibayer <[email protected]>
-Wei Li <[email protected]> kuantkid <[email protected]>
-Wei Li <[email protected]> Wei LI <[email protected]>
-Hrishikesh Huilgolkar <[email protected]> <hrishikesh@QE-IND-WKS007.(none)>
+Bertrand Thirion <[email protected]>
 Brian Cheung <[email protected]> <[email protected]>
-Brian Cheung <[email protected]> cow <briancheung>
-Brian Cheung <[email protected]> cow <cow@rusty.(none)>
+Brian Cheung <[email protected]> <briancheung>
+Brian Cheung <[email protected]> <cow@rusty.(none)>
+Brian Holt <[email protected]> <[email protected]>
+Christian Osendorfer <[email protected]>
+Clay Woolam <[email protected]>
 Diego Molla <[email protected]> <diego@diego-desktop.(none)>
-Michael EICKENBERG <[email protected]> Michael EICKENBERG <[email protected]>
-Michael EICKENBERG <[email protected]> Michael <[email protected]>
-Nelle Varoquaux <[email protected]> <nelle@[email protected]><nelle@[email protected]>
+DraXus <[email protected]> draxus <[email protected]>
+Edouard DUCHESNAY <[email protected]> <duchesnay@is143433.(none)>
+Edouard DUCHESNAY <[email protected]> <[email protected]>
+Edouard DUCHESNAY <[email protected]> <edouard@is2206219.(none)>
+Emmanuelle Gouillart <[email protected]>
+Emmanuelle Gouillart <[email protected]> <emma@aleph.(none)>
+Fabian Pedregosa <[email protected]> <[email protected]>
+Federico Vaggi <[email protected]>
+Gael Varoquaux <[email protected]>
+Gael Varoquaux <[email protected]> <[email protected]>
+Gilles Louppe <[email protected]> <[email protected]>
+Harikrishnan S <[email protected]>
+Hrishikesh Huilgolkar <[email protected]> <hrishikesh@QE-IND-WKS007.(none)>
+Immanuel Bayer <[email protected]>
+Jake VanderPlas <[email protected]> <[email protected]>
+Jake VanderPlas <[email protected]> <[email protected]>
+Jake VanderPlas <[email protected]> <[email protected]>
+James Bergstra <[email protected]>
+Jan Schl�ter <[email protected]>
+Jean Kossaifi <[email protected]>
+Jean Kossaifi <[email protected]> <[email protected]>
+Jean Kossaifi <[email protected]> <[email protected]>
+Joel Nothman <[email protected]> <[email protected]>
+Lars Buitinck <[email protected]> <Lars@.(none)>
+Lars Buitinck <[email protected]> <[email protected]>
+Lars Buitinck <[email protected]> <[email protected]>
+Matthieu Perrot <[email protected]> <revilyo@earth.(none)>
+Michael Eickenberg <[email protected]>
+Michael Eickenberg <[email protected]> <[email protected]>
+Nelle Varoquaux <[email protected]>
+Nelle Varoquaux <[email protected]> <[email protected]> <nelle@[email protected]>
+Nicolas Pinto <[email protected]> <[email protected]>
 Noel Dawe <[email protected]> <[email protected]>
-Noel Dawe <[email protected]> <[email protected]>
-X006 <x006@x006-icsl.(none)> x006 <x006@x006laptop.(none)>
+Olivier Grisel <[email protected]> <ogrisel@turingcarpet.(none)>
+Olivier Grisel <[email protected]> <[email protected]>
+Olivier Hervieu <[email protected]> <[email protected]>
+Peter Prettenhofer <[email protected]>
+Robert Layton <[email protected]>
+Roman Sinayev <[email protected]>
+Roman Sinayev <[email protected]> <roman@y570.(none)>
+Satrajit Ghosh <[email protected]> <[email protected]>
+Shiqiao Du <[email protected]>
+Shiqiao Du <[email protected]> <[email protected]>
+Tim Sheerman-Chase <[email protected]> <ts00051@ts00051-desktop.(none)>
+Vincent Dubourg <[email protected]>
+Vincent Dubourg <[email protected]> <dubourg@PTlami14.(none)>
+Vincent Michel <[email protected]> <[email protected]>
+Vincent Michel <[email protected]> <vincent@axon.(none)>
+Vincent Michel <[email protected]> <[email protected]>
+Vincent Michel <[email protected]> <[email protected]>
+Vincent Michel <[email protected]> <[email protected]>
+Vincent Schut <[email protected]> <vincent@TIMO.(none)>
+Virgile Fritsch <[email protected]>
+Virgile Fritsch <[email protected]> <virgile@virgile-Precision-M4400.(none)>
+Vlad Niculae <[email protected]>
+Wei Li <[email protected]>
+Wei Li <[email protected]> <[email protected]>
+X006 <x006@x006-icsl.(none)> <x006@x006laptop.(none)>
+Xinfan Meng <[email protected]> <[email protected]>

.travis.yml

@@ -1,10 +1,10 @@
 language: python
 python:
     - "2.7"
-virtualenv: 
+virtualenv:
     system_site_packages: true
 before_install:
     - sudo apt-get update -qq
-    - sudo apt-get install -qq python-scipy
+    - sudo apt-get install -qq python-scipy python-nose
 install: python setup.py build_ext --inplace
 script: make test

AUTHORS.rst

@@ -87,3 +87,5 @@ People
   * `Wei Li <http://kuantkid.github.com>`_
 
   * `Arnaud Joly <http://www.ajoly.org>`_
+
+  * `Kemal Eren <http://www.kemaleren.com>`_

MANIFEST.in

@@ -1,5 +1,5 @@
 include *.rst
 recursive-include doc *
 recursive-include examples *
-recursive-include sklearn *.c *.h *.pyx
+recursive-include sklearn *.c *.h *.pyx *.pxd
 recursive-include sklearn/datasets *.csv *.csv.gz *.rst *.jpg *.txt

Makefile

@@ -15,9 +15,11 @@ clean-pyc:
 clean-so:
 	find sklearn -name "*.so" | xargs rm -f
 	find sklearn -name "*.pyd" | xargs rm -f
+	find sklearn -name "__pycache__" | xargs rm -rf
 
 clean-build:
 	rm -rf build
+	rm -rf dist
 
 clean-ctags:
 	rm -f tags

README-py3k.rst

@@ -34,8 +34,12 @@ Important links
 Dependencies
 ============
 
-The required dependencies to build the software are Python >= 2.6,
-setuptools, Numpy >= 1.3, SciPy >= 0.7 and a working C/C++ compiler.
+scikit-learn is tested to work under Python 2.6+ and Python 3.3+
+(using the same codebase thanks to an embedded copy of [six](
+http://pythonhosted.org/six/)).
+
+The required dependencies to build the software Numpy >= 1.3, SciPy >= 0.7
+and a working C/C++ compiler.
 
 For running the examples Matplotlib >= 0.99.1 is required and for running the
 tests you need nose >= 0.10.
@@ -49,7 +53,7 @@ Install
 This package uses distutils, which is the default way of installing
 python modules. To install in your home directory, use::
 
-  python setup.py install --home
+  python setup.py install --user
 
 To install for all users on Unix/Linux::