Merge branch 'release/3.2.0'

Author: Soeren Sonnenburg

.gitignore

@@ -111,7 +111,6 @@ configure.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

.travis.yml

@@ -13,14 +13,16 @@ notifications:
       - "it's %{author}'s turn to pay the next round of drinks for the massacre he caused in %{repository}: %{build_url}"
 matrix:
   include:
+    - compiler: gcc
+      env: CMAKE_OPTIONS="-DCMAKE_BUILD_TYPE=Debug -DENABLE_COVERAGE=ON" CUSTOM_PKG="sudo pip install -q cpp-coveralls" COVERALLS=1
     - 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/"
+      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 --no-index --find-links=http://cache27diy-cpycloud.rhcloud.com/3.3/"
     - compiler: clang
       rvm: 1.8.7
       language: ruby
@@ -42,21 +44,15 @@ matrix:
   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:
  - if [ -z $OSX ] ; then sudo apt-add-repository -y ppa:kubuntu-ppa/backports ; sudo apt-get update -qq ; fi
  - 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 [ -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 list cmake || 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 git+https://github.com/pypa/pip@1.5#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
@@ -67,6 +63,9 @@ before_script:
   - cd build
 script:
   - cmake -DENABLE_TESTING=ON -DBUNDLE_EIGEN=ON -DBUNDLE_JSON=ON -DBUNDLE_NLOPT=ON $CMAKE_OPTIONS ..
-  - if [ -z $CMAKE_OPTIONS ] ; then make -j 2 ; else make -j 4 ; fi
+  - if [ -z "$CMAKE_OPTIONS" -o -n "$COVERALLS" ] ; then make -j 2 ; else make -j 4 ; fi
   - sudo make install
   - ctest --output-on-failure -j 2
+after_success:
+  - cd ..
+  - coveralls -e tests -e examples -e cmake -e benchmarks -e src/interfaces -e /usr/include -e build/GoogleMock -e build/NLopt -e build/Eigen3 -e build/JSON -e build/CMakeFiles -E '.*\.h' > /dev/null

CMakeLists.txt

@@ -44,6 +44,11 @@ SET(THIRD_PARTY_DIR ${CMAKE_SOURCE_DIR}/third_party)
 SET(LIBSHOGUN_SRC_DIR ${CMAKE_SOURCE_DIR}/src/shogun)
 SET(COMMON_MODULAR_SRC_DIR ${CMAKE_SOURCE_DIR}/src/interfaces/modular/)
 
+INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/src
+	${CMAKE_SOURCE_DIR}/src/shogun
+	${CMAKE_BINARY_DIR}/src
+	${CMAKE_BINARY_DIR}/src/shogun)
+
 # check whether any of the modular interfaces are turned ON
 IF (
 	PythonModular OR LuaModular OR RModular OR
@@ -184,15 +189,9 @@ ENDIF()
 # clang with -std=c++11 and -stdlib=libc++ does not work
 # well with swig generated cxx hence disable c++11 for this case.
 
-# TODO: until swig 2.0.11 does not support compilation with libc++
-# There are PRs against SWIG HEAD to fix this hence it needs to be checked
-# which later version can support compilation with libc++
-IF (COMPILE_MODULAR_INTERFACE AND ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang") AND NOT SWIG_VERSION VERSION_GREATER "2.0.11")
-	SET(CMAKE_CXX_FLAGS "-stdlib=libstdc++ ${CMAKE_CXX_FLAGS}")
-	SET(SWIG_CXX_COMPILER_FLAGS "-stdlib=libstdc++ ${SWIG_CXX_COMPILER_FLAGS}")
-ENDIF()
-
-IF (NOT ((CYGWIN AND ENABLE_TESTING) OR (DARWIN AND COMPILE_MODULAR_INTERFACE)))
+# this has been only fixed in swig 2.0.12 or later.
+IF (NOT ((CYGWIN AND ENABLE_TESTING) OR (DARWIN AND COMPILE_MODULAR_INTERFACE
+	AND SWIG_VERSION VERSION_LESS "2.0.12")))
 	INCLUDE(CheckCXX11Features)
 
 	IF(_HAS_CXX11_FLAG)
@@ -212,6 +211,12 @@ IF (NOT ((CYGWIN AND ENABLE_TESTING) OR (DARWIN AND COMPILE_MODULAR_INTERFACE)))
 	IF (HAVE_CXX11_ATOMIC)
 		LIST(APPEND DEFINES HAVE_CXX11_ATOMIC)
 	ENDIF()
+ELSEIF(DARWIN AND ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang") AND NOT (CMAKE_CXX_COMPILER_VERSION VERSION_LESS "5.0.0"))
+	# osx clang 5.0.0 or later uses libc++ by default
+	# this is causing problems with source generated by swig version earlier than 3.0.0
+	# force to use libstdc++ for compilation of sources
+	SET(CMAKE_CXX_FLAGS "-stdlib=libstdc++ ${CMAKE_CXX_FLAGS}")
+	SET(SWIG_CXX_COMPILER_FLAGS "-stdlib=libstdc++ ${SWIG_CXX_COMPILER_FLAGS}")
 ENDIF()
 
 include(CheckIncludeFileCXX)
@@ -825,11 +830,15 @@ IF (PythonModular OR PythonStatic)
 			SET(TARGET_SWIGFLAGS "-builtin\;-modern\;-modernargs")
 		ENDIF()
 
-		add_subdirectory(src/interfaces/python_modular)
+		IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/python_modular)
+			add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/python_modular)
+		ENDIF()
 	ENDIF()
 
 	IF(PythonStatic)
-		add_subdirectory(src/interfaces/python_static)
+		IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/python_static)
+			add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/python_static)
+		ENDIF()
 	ENDIF()
 ENDIF()
 
@@ -843,7 +852,9 @@ IF (LuaModular)
     ENDIF ()
 	SET(LUA_EXECUTABLE lua)
 	UNSET(TARGET_SWIGFLAGS)
-	add_subdirectory(src/interfaces/lua_modular)
+	IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/lua_modular)
+		add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/lua_modular)
+	ENDIF()
 ENDIF()
 
 # java modular
@@ -865,7 +876,9 @@ IF (JavaModular)
 	ENDIF()
 
 	SET(TARGET_SWIGFLAGS "-package\;org.shogun")
-	add_subdirectory(src/interfaces/java_modular)
+	IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/java_modular)
+		add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/java_modular)
+	ENDIF()
 ENDIF()
 
 # ruby modular
@@ -874,7 +887,7 @@ IF (RubyModular)
 	FIND_PACKAGE(RubyNArray REQUIRED)
 	SET(NARRAY_LIB ${RUBY_NARRAY_LIBRARY})
 	UNSET(TARGET_SWIGFLAGS)
-	add_subdirectory(src/interfaces/ruby_modular)
+	add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/ruby_modular)
 ENDIF()
 
 # octave modular
@@ -886,19 +899,25 @@ IF (OctaveModular OR OctaveStatic)
 
 	IF(OctaveModular)
 		UNSET(TARGET_SWIGFLAGS)
-		add_subdirectory(src/interfaces/octave_modular)
+		IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/octave_modular)
+			add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/octave_modular)
+		ENDIF()
 	ENDIF()
 
 	IF(OctaveStatic)
-		add_subdirectory(src/interfaces/octave_static)
+		IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/octave_static)
+			add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/octave_static)
+		ENDIF()
 	ENDIF()
 ENDIF()
 
 # csharp modular
 IF (CSharpModular)
 	FIND_PACKAGE(CSharp REQUIRED)
 	UNSET(TARGET_SWIGFLAGS)
-	add_subdirectory(src/interfaces/csharp_modular)
+	IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/csharp_modular)
+		add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/csharp_modular)
+	ENDIF()
 ENDIF()
 
 # r modular
@@ -907,32 +926,42 @@ IF (RModular OR RStatic)
 
 	IF (RModular)
 		UNSET(TARGET_SWIGFLAGS)
-		add_subdirectory(src/interfaces/r_modular)
+		IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/r_modular)
+			add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/r_modular)
+		ENDIF()
 	ENDIF()
 
 	IF (RStatic)
-		add_subdirectory(src/interfaces/r_static)
+		IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/r_static)
+			add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/r_static)
+		ENDIF()
 	ENDIF()
 ENDIF()
 
 # perl modular
 IF (PerlModular)
 	FIND_PACKAGE(FindPerlLibs REQUIRED)
 	UNSET(TARGET_SWIGFLAGS)
-	#add_subdirectory(src/interfaces/perl_modular)
+	IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/perl_modular)
+		#add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/perl_modular)
+	ENDIF()
 ENDIF()
 
 IF (MatlabStatic)
 	FIND_PACKAGE(Matlab REQUIRED)
 	IF(MATLAB_FOUND)
-		add_subdirectory(src/interfaces/matlab_static)
+		IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/matlab_modular)
+			add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/matlab_static)
+		ENDIF()
 	ELSE()
 		MESSAGE(FATAL_ERROR "Could not find Matlab, which is required for compiling matlab_static interface. Try setting MATLAB_ROOT enviroment variable to the right path")
 	ENDIF()
 ENDIF()
 
 IF (CmdLineStatic)
-	add_subdirectory(src/interfaces/cmdline_static)
+	IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/cmdline_static)
+		add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/cmdline_static)
+	ENDIF()
 ENDIF()
 
 IF (SVMLight)
@@ -945,6 +974,7 @@ OPTION(BUILD_DASHBOARD_REPORTS "Set to ON to activate reporting of Shogun builds
 IF(BUILD_DASHBOARD_REPORTS)
 	file(TO_CMAKE_PATH "${CMAKE_SOURCE_DIR}/configs/valgrind.supp" VALGRIND_SUPPRESSION_FILE)
 	SET(MEMORYCHECK_SUPPRESSIONS_FILE ${VALGRIND_SUPPRESSION_FILE} CACHE FILEPATH "File that contains suppressions for the memory checker")
+	SET(MEMORYCHECK_COMMAND_OPTIONS "-q --tool=memcheck --leak-check=full --track-origins=yes --num-callers=50 --error-exitcode=1")
 	include(CTest)
 ENDIF()
 
@@ -957,13 +987,15 @@ IF(ENABLE_TESTING)
 		enable_testing()
 	ENDIF()
 
-	# add integration tests
-	add_subdirectory(tests/integration)
+	IF(EXISTS ${CMAKE_SOURCE_DIR}/tests)
+		# add integration tests
+		add_subdirectory(${CMAKE_SOURCE_DIR}/tests/integration)
 
 
-	# add unit tests
-	IF (NOT TRAVIS_DISABLE_UNIT_TESTS)
-		add_subdirectory(tests/unit)
+		# add unit tests
+		IF (NOT TRAVIS_DISABLE_UNIT_TESTS)
+			add_subdirectory(${CMAKE_SOURCE_DIR}/tests/unit)
+		ENDIF()
 	ENDIF()
 ENDIF()
 
@@ -973,10 +1005,14 @@ SET(CONFIGURE_OPTIONS "TODO")
 SET(COMPFLAGS_CPP "${MERGED_CXX_FLAGS}")
 SET(LINKFLAGS "${POSTLINKFLAGS}")
 
-add_subdirectory(src/shogun)
+IF(EXISTS ${CMAKE_SOURCE_DIR}/src/shogun)
+	add_subdirectory(${CMAKE_SOURCE_DIR}/src/shogun)
+ENDIF()
 
-IF(BUILD_EXAMPLES OR ENABLE_TESTING)
-	add_subdirectory(examples)
+IF(EXISTS ${CMAKE_SOURCE_DIR}/examples)
+	IF(BUILD_EXAMPLES OR ENABLE_TESTING)
+		add_subdirectory(${CMAKE_SOURCE_DIR}/examples)
+	ENDIF()
 ENDIF()
 
 # general cpack settings

NEWS

@@ -1,3 +1,23 @@
+2014-02-17 Soeren Sonnenburg <sonne@debian.org>
+
+	* SHOGUN Release version 3.2.0 (libshogun 16.0, data 0.8, parameter 1)
+	* This release also contains several cleanups and bugfixes:
+	* Features:
+		- Fully support python3 now
+		- Add mini-batch k-means [Parijat Mazumdar]
+		- Add k-means++ [Parijat Mazumdar]
+		- Add sub-sequence string kernel [lambday]
+	* Bugfixes:
+		- Compile fixes for upcoming swig3.0
+		- Speedup for gaussian process' apply()
+		- Improve unit / integration test checks
+		- libbmrm uninitialized memory reads
+		- libocas uninitialized memory reads
+		- Octave 3.8 compile fixes [Orion Poplawski]
+		- Fix java modular compile error [Bjoern Esser]
+	* Cleanup and API Changes:
+		- None
+
 2014-01-06 Soeren Sonnenburg <sonne@debian.org>
 
 	* SHOGUN Release version 3.1.1 (libshogun 15.1, data 0.7, parameter 1)

README.md

@@ -4,11 +4,13 @@
 Develop branch build status:
 
 [![Build Status](https://travis-ci.org/shogun-toolbox/shogun.png?branch=develop)](https://travis-ci.org/shogun-toolbox/shogun)
+[![Coverage Status](https://coveralls.io/repos/shogun-toolbox/shogun/badge.png?branch=develop)](https://coveralls.io/r/shogun-toolbox/shogun?branch=develop)
 
 Buildbot: http://buildbot.shogun-toolbox.org/waterfall.
 
 Quick links to this file:
 
+* [Quickstart](doc/md/QUICKSTART.md)
 * [Introduction](#introduction)
 * [Interfaces](#interfaces)
 * [Platforms](#platforms)

cmake/CommonModularInterface.cmake

@@ -2,7 +2,7 @@ MACRO(GENERATE_MODULAR_TARGET MODULAR_NAME MODULAR_DIR MODULAR_LIBARIES)
 if(SYSTEM_INCLUDES)
 	INCLUDE_DIRECTORIES(SYSTEM ${SYSTEM_INCLUDES})
 endif()
-INCLUDE_DIRECTORIES(${INCLUDES} ${CMAKE_SOURCE_DIR}/src)
+INCLUDE_DIRECTORIES(${INCLUDES})
 
 # transform defines to -D<definition> string
 foreach(D IN LISTS DEFINES)
@@ -78,4 +78,4 @@ ELSE()
 	#TODO add scrubing
 ENDIF()
 
-ENDMACRO()
+ENDMACRO()

cmake/FindOctave.cmake

@@ -119,14 +119,16 @@ find_library( OCTAVE_OCTAVE_LIBRARY
               NAMES octave liboctave
               HINTS ${OCTAVE_LIBRARIES_PATHS}
             )
-find_library( OCTAVE_CRUFT_LIBRARY
-              NAMES cruft libcruft
-              HINTS ${OCTAVE_LIBRARIES_PATHS}
-            )
-
 set ( OCTAVE_LIBRARIES ${OCTAVE_OCTINTERP_LIBRARY} )
 list ( APPEND OCTAVE_LIBRARIES ${OCTAVE_OCTAVE_LIBRARY} )
-list ( APPEND OCTAVE_LIBRARIES ${OCTAVE_CRUFT_LIBRARY} )
+
+if ( ${OCTAVE_VERSION_STRING} LESS 3.8.0 )
+  find_library( OCTAVE_CRUFT_LIBRARY
+                NAMES cruft libcruft
+                HINTS ${OCTAVE_LIBRARIES_PATHS}
+              )
+  list ( APPEND OCTAVE_LIBRARIES ${OCTAVE_CRUFT_LIBRARY} )
+endif ()
 
 find_path ( OCTAVE_INCLUDE_DIR
             NAMES mex.h

cmake/checkgdb.cmake

@@ -6,4 +6,5 @@ if (RESULT)
 	#		--args ${EXECUTABLE} ${FILE} ${ARGS}
 	#			RESULT_VARIABLE GDB_RESULT)
 	#endif()
-endif()
+	MESSAGE( FATAL_ERROR "FAIL:  ${ARGS}, EXITCODE:  ${RESULT}" )
+endif (RESULT)

cmake/version.cmake

@@ -65,7 +65,7 @@ ELSEIF(EXISTS "${ROOT_DIR}/NEWS")
 		SET(VERSION_SUB "0${VERSION_SUB}")
 	ENDIF()
 	SET(REVISION ${VERSION_MAJOR}${VERSION_MINOR}${VERSION_SUB})
-	EXECUTE_PROCESS(COMMAND ${PYTHON_EXECUTABLE} -c "import os.path,time;print time.strftime('%Y-%m-%d %H:%M', time.gmtime(os.path.getmtime('${ROOT_DIR}/NEWS')))"
+	EXECUTE_PROCESS(COMMAND ${PYTHON_EXECUTABLE} -c "import os.path,time;print (time.strftime('%Y-%m-%d %H:%M', time.gmtime(os.path.getmtime('${ROOT_DIR}/NEWS'))))"
 		OUTPUT_VARIABLE DATEINFO
 		OUTPUT_STRIP_TRAILING_WHITESPACE
 	)