Merge branch 'release/3.0.0'

Conflicts:
	src/shogun/lib/tapkee/tapkee_defines.hpp

Author: vigsterkr

.clang_complete

@@ -0,0 +1 @@
+-Isrc

.gitignore

@@ -26,6 +26,7 @@ configure.log
 *.mex*
 *.oct
 .localvimrc
+*.DS_Store
 
 *~
 \#*\#
@@ -34,6 +35,8 @@ configure.log
 
 
 # /doc/
+/doc/Doxyfile_en
+/doc/Doxyfile_cn
 /doc/html
 /doc/html_cn
 /doc/pages/Configure.generated
@@ -48,7 +51,7 @@ configure.log
 /src/examples
 /src/shogun/.clang_complete
 /src/configure-*-*.c*
-
+/src/build-local
 
 # static interfaces
 /src/interfaces/cmdline_static/shogun
@@ -81,19 +84,23 @@ configure.log
 /src/interfaces/*_modular/Loss.i
 /src/interfaces/*_modular/Statistics.i
 /src/interfaces/*_modular/Latent.i
-
+/src/interfaces/*_modular/GaussianProcess.i
 
 # particular modular ones
 /src/interfaces/csharp_modular/*.cs
+/src/interfaces/csharp_modular/abstract_types_extension.i
+/src/interfaces/csharp_modular/modshogun.dll
 /src/interfaces/java_modular/*.java
 /src/interfaces/java_modular/*.jar
 /src/interfaces/java_modular/*.class
 /src/interfaces/java_modular/org/*
 /src/interfaces/java_modular/shogun/*
 /src/interfaces/python_modular/*.py
+/src/interfaces/python_modular/abstract_types_extension.i
 /src/interfaces/r_modular/*.R
 /src/interfaces/r_modular/*.RData
 /src/interfaces/perl_modular/*.pm
+/src/interfaces/octave_modular/abstract_types_extension.i
 /.duped_py_pl.pb
 
 # /examples/
@@ -103,10 +110,23 @@ configure.log
 /examples/missing.log
 /examples/undocumented/libshogun/*
 !/examples/undocumented/libshogun/*.cpp
+!/examples/undocumented/libshogun/CMakeLists.txt
 examples/undocumented/python_modular/*
 !/examples/undocumented/libshogun/tools/
 !examples/undocumented/python_modular/graphical/
 !examples/undocumented/python_modular/*.py
+!examples/undocumented/python_modular/CMakeLists.txt
 
 # /tests
 /tests/unit/shogun-unit-test
+/tests/unit/*.txt
+/tests/unit/*.xml
+/tests/unit/*.hdf5
+/tests/unit/*.json
+/tests/unit/combined_kernel.weights
+
+# cmake
+/CMakeFiles/
+CMakeCache.txt
+/build
+/third_party

.travis.yml

@@ -2,9 +2,6 @@ language: cpp
 compiler:
   - gcc
   - clang
-branches:
-  only:
-    - master
 notifications:
   email: false
   irc:
@@ -14,8 +11,61 @@ notifications:
     on_failure: always
     template:
       - "it's %{author}'s turn to pay the next round of drinks for the massacre he caused in %{repository}: %{build_url}"
+matrix:
+  include:
+    - compiler: clang
+      python: 2.7
+      language: python
+      env: CMAKE_OPTIONS="-DPythonModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON" EXTRA_PACKAGES="python-scipy swig2.0" CC=clang CXX=clang++
+    - compiler: clang
+      python: 3.3
+      language: python
+      env: CMAKE_OPTIONS="-DPythonModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON" EXTRA_PACKAGES="swig2.0" CC=clang CXX=clang++ PIP_ARGS=" -I --use-wheel --find-links=http://cache27diy-cpycloud.rhcloud.com/3.3/"
+    - compiler: clang
+      rvm: 1.8.7
+      language: ruby
+      env: CMAKE_OPTIONS="-DRubyModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON" CUSTOM_PKG="gem install narray" EXTRA_PACKAGES="swig2.0" CC=clang CXX=clang++
+    - compiler: clang
+      jdk: oraclejdk7
+      language: java
+      env: CMAKE_OPTIONS="-DJavaModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON" EXTRA_PACKAGES="jblas swig2.0" CC=clang CXX=clang++
+    - compiler: clang
+      env: CMAKE_OPTIONS="-DCSharpModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON" EXTRA_PACKAGES="mono-devel mono-gmcs cli-common-dev swig2.0" CC=clang CXX=clang++
+    - compiler: clang
+      env: CMAKE_OPTIONS="-DLuaModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON" EXTRA_PACKAGES="lua5.1 liblua5.1-0-dev swig2.0" CC=clang CXX=clang++
+    - compiler: gcc
+      env: CMAKE_OPTIONS="-DOctaveModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON" EXTRA_PACKAGES="octave liboctave-dev swig2.0"
+    - compiler: clang
+      env: CMAKE_OPTIONS="-DRModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON" EXTRA_PACKAGES="r-base-core swig2.0" CC=clang CXX=clang++
+    - language: objective-c
+      env: OSX=1
+  allow_failures:
+    - compiler: clang
+      env: CMAKE_OPTIONS="-DRModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON" EXTRA_PACKAGES="r-base-core swig2.0" CC=clang CXX=clang++
+    - compiler: clang
+      python: 3.3
+      language: python
+      env: CMAKE_OPTIONS="-DPythonModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON" EXTRA_PACKAGES="swig2.0" CC=clang CXX=clang++ PIP_ARGS=" -I --use-wheel --find-links=http://cache27diy-cpycloud.rhcloud.com/3.3/"
+    - language: objective-c
+      env: OSX=1
+virtualenv:
+  system_site_packages: true
 before_install:
- - sudo apt-get update -qq
- - sudo apt-get install -qq cdbs libeigen3-dev libarpack2-dev libatlas-base-dev libblas-dev libglpk-dev libhdf5-serial-dev libjson0-dev swig zlib1g-dev libxml2-dev libreadline6-dev libreadline-dev libsnappy-dev liblzo2-dev liblzma-dev liblapack-dev
-before_script: cd ./src
-script: ./configure --disable-optimization --interfaces=cmdline_static && make -j 4 && sudo make install && make tests
+ - if [ -z $OSX ] ; then sudo apt-add-repository -y ppa:dr-graef/octave-3.6.precise ; sudo apt-get update -qq ; else brew update ; fi
+ - if [ -z $OSX ] ; then sudo apt-get install -qq libbz2-dev cdbs libarpack2-dev libatlas-base-dev libblas-dev libglpk-dev libhdf5-serial-dev zlib1g-dev libxml2-dev libreadline6-dev libreadline-dev libsnappy-dev liblzo2-dev liblzma-dev liblapack-dev gdb cmake python-jinja2 $EXTRA_PACKAGES ; else brew install cmake ; fi
+ - if [ $OSX ] ; then curl -O https://raw.github.com/rudix-mac/package-manager/master/rudix.py && sudo python rudix.py install rudix && sudo rudix install jinja2 ; fi
+ - $CUSTOM_PKG
+ - if [[ $TRAVIS_PYTHON_VERSION == '3.3' ]] ; then pip install -I git+https://github.com/pypa/pip@42102e9deaea99db08b681d06906c2945f6f95e2#egg=pip ; fi
+ - if [[ $TRAVIS_PYTHON_VERSION == '3.3' ]] ; then pip install -I -U setuptools ; fi
+ - if [[ $TRAVIS_PYTHON_VERSION == '3.3' ]] ; then pip install wheel ; fi
+ - if [[ $TRAVIS_PYTHON_VERSION == '3.3' ]] ; then pip install $PIP_ARGS numpy ; fi
+ - if [[ $TRAVIS_PYTHON_VERSION == '3.3' ]] ; then pip install $PIP_ARGS scipy ; fi
+ - if [[ $TRAVIS_PYTHON_VERSION == '3.3' ]] ; then pip install --use-mirrors jinja2 ; fi
+before_script:
+  - mkdir build
+  - cd build
+script:
+  - cmake -DENABLE_TESTING=ON -DBUNDLE_EIGEN=ON -DBUNDLE_JSON=ON -DBUNDLE_NLOPT=ON $CMAKE_OPTIONS ..
+  - if [ -z $CMAKE_OPTIONS ] ; then make -j 2 ; else make -j 4 ; fi
+  - sudo make install
+  - ctest --output-on-failure -j 2

AUTHORS.md

@@ -0,0 +1,9 @@
+* Soeren Sonnenburg <sonne@debian.org>
+* Heiko Strathmann <heiko.strathmann@gmail.com>
+* Sergey Lisitsyn <lisitsyn.s.o@gmail.com>
+* Viktor Gal <vigsterkr@gmail.com>
+* Fernando Iglesias <fernando.iglesiasg@gmail.com>
+* Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>
+* Shashwat Lal Das <fraggerx@gmail.com>
+* Sebastian Henschel <shogun@kodeaffe.de>
+* Christian Widmer <cwidmer@tuebingen.mpg.de>