Merge branch 'master' of https://github.com/shogun-toolbox/shogun

Author: Soeren Sonnenburg

.gitignore

@@ -130,3 +130,6 @@ examples/undocumented/python_modular/*
 CMakeCache.txt
 /build
 /third_party
+
+# protobuf
+src/shogun/io/protobuf/*.pb.*

.gitmodules

@@ -1,6 +1,7 @@
 [submodule "data"]
 	path = data
 	url = git://github.com/shogun-toolbox/shogun-data.git
+	branch = master
 [submodule "doc/tutorial"]
 	path = doc/tutorial
 	url = git://github.com/shogun-toolbox/shogun-tutorial.git

.travis.yml

@@ -51,6 +51,7 @@ matrix:
 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 [ $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

CMakeLists.txt

@@ -5,7 +5,7 @@
 # $ make
 
 project(shogun)
-cmake_minimum_required(VERSION 2.8.4)
+cmake_minimum_required(VERSION 2.8.8)
 SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake")
 include(ShogunUtils)
 
@@ -69,11 +69,7 @@ ELSEIF(${CMAKE_SYSTEM_NAME} MATCHES "FreeBSD")
 ENDIF()
 
 # Get processor type, sets MACHINE macro
-IF(NOT WIN32)
-	execute_process(COMMAND uname -m
-	    OUTPUT_VARIABLE MACHINE_OUTPUT OUTPUT_STRIP_TRAILING_WHITESPACE)
-	SET(MACHINE ${MACHINE_OUTPUT})
-ENDIF()
+SET(MACHINE ${CMAKE_SYSTEM_PROCESSOR})
 
 SET(EXT_LIB_SWIG_RUBY_MODULAR ".so")
 if(DARWIN)
@@ -186,8 +182,16 @@ ENDIF()
 # check for supported c++11 features
 #
 # clang with -std=c++11 and -stdlib=libc++ does not work
-# well with swig generated cxx
-# hence disable c++11 for this case.
+# 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)))
 	INCLUDE(CheckCXX11Features)
 
@@ -210,6 +214,12 @@ IF (NOT ((CYGWIN AND ENABLE_TESTING) OR (DARWIN AND COMPILE_MODULAR_INTERFACE)))
 	ENDIF()
 ENDIF()
 
+include(CheckIncludeFileCXX)
+CHECK_INCLUDE_FILE_CXX("unordered_map" HAVE_STD_UNORDERED_MAP)
+IF (HAVE_STD_UNORDERED_MAP)
+	LIST(APPEND DEFINES HAVE_STD_UNORDERED_MAP)
+ENDIF()
+
 IF(CMAKE_BUILD_TYPE MATCHES "Release")
 	# there's a bug on FreeBSD -march=native.
 	# for some CPU types it does not detect the right flags
@@ -396,6 +406,20 @@ ENDIF()
 
 ######################### LIBRARIES #########################
 
+#check for symbols
+include (CheckCXXSymbolExists)
+CHECK_CXX_SYMBOL_EXISTS(isfinite "cmath" HAVE_DECL_ISFINITE)
+AppendToDefines(HAVE_DECL_ISFINITE)
+
+CHECK_CXX_SYMBOL_EXISTS(isinf "cmath" HAVE_DECL_ISINF)
+AppendToDefines(HAVE_DECL_ISINF)
+
+CHECK_CXX_SYMBOL_EXISTS(isnan "cmath" HAVE_DECL_ISNAN)
+AppendToDefines(HAVE_DECL_ISNAN)
+
+CHECK_CXX_SYMBOL_EXISTS(signgam "cmath" HAVE_DECL_SIGNGAM)
+AppendToDefines(HAVE_DECL_SIGNGAM)
+
 # check for math functions
 include(CheckFunctionExists)
 IF(UNIX)
@@ -421,6 +445,37 @@ IF(HAVE_SQRTL)
 	LIST(APPEND DEFINES HAVE_SQRTL)
 ENDIF()
 
+CHECK_FUNCTION_EXISTS(finite HAVE_FPCLASS)
+AppendToDefines(HAVE_FPCLASS)
+
+CHECK_FUNCTION_EXISTS(fpclass HAVE_FPCLASS)
+AppendToDefines(HAVE_FPCLASS)
+
+CHECK_FUNCTION_EXISTS(isfinite HAVE_ISFINITE)
+AppendToDefines(HAVE_ISFINITE)
+
+CHECK_FUNCTION_EXISTS(isinf HAVE_ISINF)
+AppendToDefines(HAVE_ISINF)
+
+CHECK_FUNCTION_EXISTS(isnan HAVE_ISNAN)
+AppendToDefines(HAVE_ISNAN)
+
+include(CheckCXXSourceCompiles)
+CHECK_CXX_SOURCE_COMPILES(
+  "#include <cmath>\nint main() { return std::isinf( 0 ); }\n"
+  HAVE_STD_ISINF )
+AppendToDefines(HAVE_STD_ISINF)
+
+CHECK_CXX_SOURCE_COMPILES(
+  "#include <cmath>\nint main() { return std::isfinite( 0 ); }\n"
+  HAVE_STD_ISFINITE )
+AppendToDefines(HAVE_STD_ISFINITE)
+
+CHECK_CXX_SOURCE_COMPILES(
+  "#include <cmath>\nint main() { return std::isnan( 0 ); }\n"
+  HAVE_STD_ISNAN )
+AppendToDefines(HAVE_STD_ISNAN)
+
 # check SSE and SSE2 intrinsics header
 IF(NOT CYGWIN)
 include(CheckIncludeFile)
@@ -431,6 +486,17 @@ IF(HAVE_SSE2)
 ENDIF(HAVE_SSE2)
 ENDIF(NOT CYGWIN)
 
+###### checks for random
+CHECK_FUNCTION_EXISTS(arc4random HAVE_ARC4RANDOM)
+IF(NOT HAVE_ARC4RANDOM)
+    # assume that /dev/random is non-blocking if /dev/urandom does not exist
+    if(EXISTS /dev/urandom)
+      set(DEV_RANDOM "/dev/urandom" CACHE INTERNAL "" FORCE)
+    elseif( EXISTS /dev/random )
+      set(DEV_RANDOM "/dev/random" CACHE INTERNAL "" FORCE)
+    endif()
+ENDIF()
+
 FIND_PACKAGE(GDB)
 IF (GDB_FOUND)
 	SET(GDB_DEFAULT_SCRIPT ${CMAKE_CURRENT_SOURCE_DIR}/src/.gdb)
@@ -667,7 +733,6 @@ IF (HDF5_FOUND)
 	SET(HAVE_HDF5 1)
 	LIST(APPEND DEFINES HAVE_HDF5)
 	LIST(APPEND INCLUDES ${HDF5_INCLUDE_DIRS})
-	SET(HDF5_LIBRARIES "${HDF5_LIBRARIES_RELEASE}")
 	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${HDF5_LIBRARIES})
 ENDIF()
 
@@ -725,18 +790,21 @@ IF (SPINLOCK_FOUND)
 	LIST(APPEND DEFINES USE_SPINLOCKS)
 ENDIF()
 
-#FIND_PACKAGE(Protobuf)
-#IF (PROTOBUF_FOUND)
-#	SET(HAVE_PROTOBUF 1)
-#	LIST(APPEND DEFINES HAVE_PROTOBUF)
-#	LIST(APPEND INCUDES ${PROTOBUF_INCLUDE_DIRS})
-#	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${PROTOBUF_LIBRARIES})
-#ENDIF()
+FIND_PACKAGE(Protobuf)
+IF (PROTOBUF_FOUND)
+	SET(HAVE_PROTOBUF 1)
+	LIST(APPEND DEFINES HAVE_PROTOBUF)
+	LIST(APPEND INCUDES ${PROTOBUF_INCLUDE_DIRS})
+	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${PROTOBUF_LIBRARIES})
+ENDIF()
 
 #SWIG Interfaces
 SET(CMAKE_SWIG_FLAGS "${CMAKE_SWIG_FLAGS};-w473;-w454;-w312;-w325;-fvirtual")
 
-OPTION(USE_SWIG_DIRECTORS "" OFF)
+OPTION(USE_SWIG_DIRECTORS "Enable SWIG director classes" OFF)
+IF(USE_SWIG_DIRECTORS)
+	LIST(APPEND DEFINES USE_SWIG_DIRECTORS)
+ENDIF()
 
 # python modular
 IF (PythonModular OR PythonStatic)

NEWS

@@ -1,3 +1,36 @@
+2014-01-06 Soeren Sonnenburg <sonne@debian.org>
+
+	* SHOGUN Release version 3.1.1 (libshogun 15.1, data 0.7, parameter 1)
+	* This is a bugfix release:
+	* Bugfixes:
+		- Fix compile error occurring with CXX0X
+		- Bump data version to required version
+
+2014-01-05 Soeren Sonnenburg <sonne@debian.org>
+
+	* SHOGUN Release version 3.1.0 (libshogun 15.0, data 0.6, parameter 1)
+	* This release also contains several cleanups and bugfixes:
+	* Features:
+		- Add option to set k-means cluster centers [Parijat Mazumdar]
+		- Add leave one out crossvalidation scheme [Saurabh Mahindre]
+		- Add multiclass ipython notebook tutorials [Chiyuan Zhang]
+		- Add learning of StreamingSparseFeatures in OnlineLibLinear [Thoralf Klein]
+	* Bugfixes:
+		- Decrease memory footprint of SGObject
+		- Fix protobuf detection
+		- Fix doxygen files and various doxygen errors
+		- Fix compile error with directors
+		- Fix memory leak in modular interfaces and apply*()
+		- Fix leak in KNN::store_model_features
+		- Notebook fixes
+		- Allow custom kernel matrices of size 2^31-1 x 2^31-1 [Koen van de Sande]
+		- Fix Protobuf cmake detection
+		- Fix LabelsFactory methods' object ownership in SWIG interfaces with the %newobject directive.
+	* Cleanup and API Changes:
+		- Introduce slim SGRefObject for refcounted objects as base class of
+		SGObject [Thoralf Klein]
+
+
 2013-10-28 Soeren Sonnenburg <sonne@debian.org>
 
 	* SHOGUN Release version 3.0.0 (libshogun 14.0, data 0.6, parameter 1)

README.md

@@ -12,18 +12,18 @@ Quick links to this file:
 * [Introduction](#introduction)
 * [Interfaces](#interfaces)
 * [Platforms](#platforms)
-* [Directory Contents](#contents)
+* [Contents](#contents)
 * [Applications](#applications)
 * [License](#license)
 * [Download](#download)
 * [References](#references)
 
 Other links that may be useful:
 
-* See [INSTALL](INSTALL.md) for first steps on installation and running SHOGUN.
-* See [README.developer](README_developer.md) for the developer documentation.
-* See [README.data](README_data.md) for how to download example data sets accompanying SHOGUN.
-* See [README.cmake](README_cmake.md) for setting particular build options with SHOGUN and cmake.
+* See [INSTALL](doc/md/INSTALL.md) for first steps on installation and running SHOGUN.
+* See [README.developer](doc/md/README_developer.md) for the developer documentation.
+* See [README.data](doc/md/README_data.md) for how to download example data sets accompanying SHOGUN.
+* See [README.cmake](doc/md/README_cmake.md) for setting particular build options with SHOGUN and cmake.
 
 ## Introduction
 ---------------
@@ -53,9 +53,9 @@ each feature object allowing for on-the-fly pre-processing.
 
 Shogun got initiated by Soeren Sonnenburg and Gunnar Raetsch (thats where the
 name ShoGun originates from). It is now developed by a much larger Team
-cf. [AUTHORS](AUTHORS.md) and would not have been possible without the patches
+cf. [AUTHORS](doc/md/AUTHORS.md) and would not have been possible without the patches
 and bug reports by various people and by the various authors of other machine
-learning packages that we utilize. See [CONTRIBUTIONS](CONTRIBUTIONS.md) for
+learning packages that we utilize. See [CONTRIBUTIONS](doc/md/CONTRIBUTIONS.md) for
 a detailled list.
 
 ## Interfaces
@@ -91,9 +91,9 @@ Visit http://www.shogun-toolbox.org/doc/en/current for further information.
 ------------
 
 Debian GNU/Linux, Mac OSX and WIN32/CYGWIN are supported platforms (see
-the [INSTALL](INSTALL.md) file for generic and platform specific installation instructions).
+the [INSTALL](doc/md/INSTALL.md) file for generic and platform specific installation instructions).
 
-## Directory Contents
+## Contents
 -----------
 
 The following directories are found in the source distribution.
@@ -125,11 +125,11 @@ Except for the files classifier/svm/Optimizer.{cpp,h},
 classifier/svm/SVM_light.{cpp,h}, regression/svr/SVR_light.{cpp,h}
 and the kernel caching functions in kernel/Kernel.{cpp,h}
 which are (C) Torsten Joachims and follow a different
-licensing scheme (cf. [LICENSE\_SVMlight](LICENSE_SVMlight.md)) SHOGUN is
+licensing scheme (cf. [LICENSE\_SVMlight](doc/md/LICENSE_SVMlight.md)) SHOGUN is
 generally licensed under the GPL version 3 or any later version (cf.
-[LICENSE](LICENSE.md)) with code borrowed from various GPL compatible
-libraries from various places (cf. [CONTRIBUTIONS](CONTRIBUTIONS.md)). See also
-[LICENSE\_msufsort](LICENSE_msufsort.md) and  [LICENSE\_tapkee](LICENSE_tapkee.md).
+[LICENSE](doc/md/LICENSE.md)) with code borrowed from various GPL compatible
+libraries from various places (cf. [CONTRIBUTIONS](doc/md/CONTRIBUTIONS.md)). See also
+[LICENSE\_msufsort](doc/md/LICENSE_msufsort.md) and  [LICENSE\_tapkee](doc/md/LICENSE_tapkee.md).
 
 ## Download
 -----------
@@ -207,3 +207,5 @@ https://github.com/shogun-toolbox/shogun.
 [17] S. Sonnenburg, G. Raetsch, C.Schaefer, and B.Schoelkopf, Large Scale
 	Multiple Kernel Learning, Journal of Machine Learning Research, 2006,
 	K.Bennett and E.P. Hernandez Editors.
+
+[![githalytics.com alpha](https://cruel-carlota.pagodabox.com/3e5ff04ff56513867eedb5b2f4261702 "githalytics.com")](http://githalytics.com/shogun-toolbox/shogun)

README_cmake.md

@@ -34,6 +34,12 @@ MACRO(PrintInterfaceStatus INTERFACE_NAME INTERFACE_FLAG)
 	ENDIF()
 ENDMACRO()
 
+MACRO(AppendToDefines MACRO)
+	IF (${MACRO})
+		LIST(APPEND DEFINES ${MACRO})
+	ENDIF()
+ENDMACRO()
+
 # based on compiz_discover_tests
 function (shogun_discover_tests EXECUTABLE)