2010-05-31 Soeren Sonnenburg <sonne@debian.org>

	* SHOGUN Release version 0.9.3 (libshogun 8.0, libshogunui 5.0)
	* This release contains several enhancements, cleanups and bugfixes:
	* Features:
		- Experimental lp-norm MCMKL
		- New Kernels: SpectrumRBFKernelRBF, SpectrumMismatchRBFKernel, WeightedDegreeRBFKernel
		- WDK kernel supports amino acids
		- String Features now support append operations (and creation of
		- python-dbg support
		- Allow floats as input for custom kernel (and matrices > 4GB in size)
	* Bugfixes:
		- Static linking fix.
		- Fix sparse linear kernel's add_to_normal
	* Cleanup and API Changes:
		- Remove init() function in Performance Measures
		- Adjust .so suffix for python and use python distutils to figure out
		install paths

2010-03-31 Soeren Sonnenburg <sonne@debian.org>

	* SHOGUN Release version 0.9.2 (libshogun 7.0, libshogunui 4.0)
	* This release contains several enhancements, cleanups and bugfixes:
	* Features:
		- Direct reading and writing of ASCII/Binary files/HDF5 based files.
		- Implemented multi task kernel normalizer.
		- Implement SNP kernel.
		- Implement time limit for libsvm/libsvr.
		- Integrate Elastic Net MKL (thanks Ryoata Tomioka for the patch).
		- Implement Hashed WD Features.
		- Implement Hashed Sparse Poly Features.
		- Integrate liblinear 1.51
		- LibSVM can now be trained with bias disabled.
		- Add functions to set/get global and local io/parallel/... objects.
	* Bugfixes:
		- Fix set_w() for linear classifiers.
		- Static Octave, Python, Cmdline and Modular Python interfaces Compile
		cleanly under Windows/Cygwin again.
		- In static interfaces testing could fail when not directly done after
		training.
	* Cleanup and API Changes:
		- None

2009-11-16 Soeren Sonnenburg <sonne@debian.org>

	* SHOGUN Release version 0.9.1 (libshogun 6.0, libshogunui 3.1)
	* This release contains several enhancements, cleanups and bugfixes:
	* Features:
		- Integrate LaRank.
		- Memory Mapped Features (for data sets that don't fit into memory).
        - Compressor module with compression and decompression support for
        lzo, gzip, bzip2 and lzma.
		- Compressed String Features with on-the-fly decompression
		(CDecompressString preproc).
		- Parallel computation of get_kernel_matrix().
		- One may now prefix all shogun print/outputs with file name and
		line number (obj.io.enable_file_and_line())
		- Chinese Documentation thanks Elpmis Lee.
	* Bugfixes:
		- Fix One class MKL testing in static interfaces.
		- Configure fixes: Let octave not write history on configure; fail
		when cplex is forcefully enabled but not found; add cplex 12 support.
		- Fix a problem with regression and CombinedKernels employing only
		Custom kernels.
	* Cleanup and API Changes:
		- String Features now (like SimpleFeatures) upon get_feature_vector
		require an additional do_free argument and need to be freed using
		free_feature_vector.

2009-10-23 Soeren Sonnenburg <sonne@debian.org>

	* SHOGUN Release version 0.9.0 (libshogun 5.0, libshogunui 3.0)
	* This release contains several cleanups and enhancements:
	* Features:
	    - Implement set_linear_classifier for static interfaces.
		- Implement Polynomial DotFeatures.
		- Implement domain adaptation SVM.
		- Speed up ScatterSVM.
		- Initial implementation for saving and Loading of shogun objects.
		- Examples have been polished/split up into separate files.
		- Documentation and webpage improvements.
	* Bugfixes:
		- Fix one class MKL for static interfaces.
		- Fix performance measures integer overflow.
		- Configure fixes to run under OSX's snow leopard.
		- Compiles and runs under solaris both using suncc and gcc.
	* Cleanup and API Changes:
		- It is no longer necessary to call init_kernel TRAIN/TEST.
		- Removed kernel {load,save}_init.
		- Removed preproc {load,save}_init.
		- Move the mkl code from classifier/svm to classifier/mkl.
		- Removed obsolete mindy support.
		- Rename MCSVM to ScatterSVM
		- Move distributions to distributions/ directory.
		- CClassifier::classify() no longer has a label as argument.
		- Introduce CClassifier::train(CFeatures* ) and classify(CFeatures*)
          for more effective training/testing.
		- Remove unnecessary global symbols.

2009-08-16 Soeren Sonnenburg <sonne@debian.org>

	* SHOGUN Release version 0.8.0 (libshogun 4.0, libshogunui 2.0)
	* This release contains several cleanups, features and bugfixes:
	* Features:
		- Implements new multiclass svm formulation.
		- 1,2 and general q-norm MKL for classification, regression and
		one-class for wrapper and chunking algorithm for arbitrary (dual) SVM
		solvers.
		- Dynamic Programming code is now accessible from python.
		- Implements Regulatory Modules kernel.
		- Documentation updates (Tutorial, improved installation instructions,
				overview about the implemented algorithms).
	* Bugfixes:
		- Correct q-norm MKL for Newton.
		- Upon make install of elwms don't install files into R/octave/python
		if these interfaces were not configured
		- Svm-nu parameter was not set correctly.
		- Fix custom kernel initialization.
		- Correct get_subkernel_weights.
		- Proper Intel core2 compile flags detection
		- Fix number of outputs for KNN.
		- Run tests with proper LD_LIBRARY_PATH set.
		- Fix several memory leaks.
	* Cleanup and API Changes:
		- Rename svm_one_class_nu to svm_nu.
		- Clean up dynamic programming code.
		- Remove commands from_position_list and slide_window and move
		functionallity into set/add_features,
		- Remove now obsolete legacy examples.

2009-05-02 Soeren Sonnenburg <sonne@debian.org>

	* SHOGUN Release version 0.7.3 (libshogun 3.0, libshogunui 1.1)
	* This release contains several bugfixes:
	* Features:
		- Improve libshogun/developer tutorial.
		- Implement convenience function for parallel quicksort.
		- Fasta/fastq file loading for StringFeatures.
	* Bugfixes:
		- get_name function was undefined in Evaluation causing the
		PerformanceMeasures class to be defunct.
		- Workaround bugs in the std template library for math functions.
		- Compiles cleanly under OSX now, thanks to James Kyle.
	* Cleanup and API Changes:
		- Make sure that all destructors are declared virtual.

2009-03-23 Soeren Sonnenburg <sonne@debian.org>

	* SHOGUN Release version 0.7.2 (libshogun 2.0, libshogunui 1.1)
	* This release contains several cleanups and enhancements:
	* Features:
		- Support all data types from python_modular: dense, scipy-sparse
		csc_sparse matrices and strings of type bool, char, (u)int{8,16,32,64},
		float{32,64,96}. In addition, individual vectors/strings can now be
		obtained and even changed.  See examples/python_modular/features_*.py
		for examples.
		- AUC maximization now works with arbitrary kernel SVMs.
		- Documentation updates, many examples have been polished.
		- Slightly speedup Oligo kernel.
	* Bugfixes:
		- Fix reading strings from directory (f.load_from_directory()).
		- Update copyright to 2009.
	* Cleanup and API Changes:
		- Remove {Char,Short,Word,Int,Real}Features and only ever use the
		templated SimpleFeatures.
		- Split up examples in examples/python_modular to separate files.
		- Now use s.set_features(strs) instead of s.set_string_features(strs)
          to set string features.
		- The meaning of the width parameter for the Oligo Kernel changed, the
		OligoKernel has been renamed to OligoStringKernel.

2009-03-08 Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.7.1 (libshogun 1.0, libshogunui 1.0)
	* This release contains several cleanups and bugfixes:
	* Features:
		- configure now detects libshogun/ui installed in /usr/(local/)lib if
		libshogun/ui dirs are removed.
		- Improved documentation (and path and doxygen fixes).
		- Tutorial on how to develop with libshogun and to extend shogun.
		- Added the elwms (eilergendewollmilchsau) interface that is a
		chimera that in one file interfaces to python,octave,r,matlab and
		provides the run_{octave,python,r} command to run code in
		{octave,python,r} from within octave,r,matlab,python transparently
		making variables available to the target interface avoiding file i/o.
		- Implement AttributeFeatures for (attr,value) pairs, trees etc.
	* Bugfixes:
		- fix a crasher occurring with combined kernel and multiple threads.
		- configure now allows building of modular interfaces only.
		- n-dimensional arrays work now in octave.
	* Cleanup and API Changes:
		- Custom Kernel no longer requires features nor initialization, even
		not when used in CombinedKernel (the combined kernel will skip over
		custom kernels on init).

2009-02-20 Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.7.0 (libshogun 0.0, libshogunui 0.0)
	* This release contains major feature enhancements and bugfixes:
		- Implement DotFeatures and CombinedDotFeatures. DotFeatures need
		  to provide dot-product and similar operations (hence the name).
		  This enables training of linear methods with mixed datatypes
		  (sparse and dense and other even the newly implemented string
		  based SpecFeatures and WDFeatures).
		- MKL now does not require CPLEX any longer.
		- Add q-norm MKL support based on internal Newton implementation.
		- Add 1-norm MKL support based on GLPK.
		- Add multiclass MKL support based on the GLPK and the GMNP svm solver.
		- Implement Tensor Product Pair Kernel (TPPK).
		- Support compilation on the iPhone :)
		- Add an option to set wds kernel position weights.
		- Build static libshogun.a for libshogun target.
		- Testsuite can also test the modular R interface, added test for
		  OligoKernel.
		- Ocas and WDOcas can be used with a bias feature now.
		- Update to LibSVM 2.88.
		- Enable parallelized HMM code by default.
	* Cleanup and API Changes:
		- Shogun has been split up into libshogun and the static and modular
		interfaces linking to it.
		- Static interfaces now do proper reference counting.
		- Remove SparseLinearClassifier: LinearClassifier is a drop-in
		  replacement.
		- WDOcas and SVMOcas now have the bias term enabled by default.
	* Bugfixes:
		- Fix regression for COMM* kernels (normalization argument was ignored).
		- Use C99 variadic macros, instead of gcc's own variant.
		- Disable lp_solve, it is not required as we are using GLPK now.
		- Fix HMM training.

2008-11-25 Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.6.7
	* Cleanup:
		- Replace ambigous self-defined data types for char/int/float etc.
		by 'standardized' types.
		- Method classify() in WDSVMOcas now has a default value for its
		  argument.
		- Removed a few stderr debug outputs.
	* Features:
		- Testsuite now covers subSVMs in MultiClassSVMs, static interfaces
		  now support commands GET_NUM_SVMS and GET_SVM for MultiClassSVMs.
	* Bugfixes:
		- Fix for contigous arrays/vectors in interface for Python modular.
		- Fixed improper assignment of labels in constructor of WDSVMOcas
		  leading to segfaults on destruction in (python) modular interface.
		- Fixed a segfault opportunity in MultiClassSVM.

2008-10-11  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.6.6
	* Bugfixes:
		- Include missing file regression/Regression.h.
		- Fix formula in CosineDistance.

2008-10-10  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.6.5
	* This release contains several cleanups and bugfixes:
		- Implement KernelNormalizer class with a couple of normalization
		functions that can now be attached to almost any kernel via
		set_normalizer() in the modular and set_kernel_normalization in the
		static interfaces. This fixes a long standing bug in the
		WeightedDegreePositionStringKernel normalization WARNING will break
		compatibility to all previously trained WD-shift kernel models, use
		FIRSTELEMENT / CFirstElementKernelNormalizer for an *approximation* to
		the previous buggy behaviour. Also breaks WordMatchKernel as for this
		kernel normalization is now enabled by default.
		- The custom kernel no longer requires lhs/rhs features (it will create
				its own dummy features)
		- Linear kernels don't use kernel cache (only slows down things)
		- Integrate the Oligo string-kernel (from Meinecke et.al 2004)
		- Remove use_precompute hack from SVMLight.
		- Add precompute_kernels function to turn kernels appended to a
		combined kernel into CustomKernels (i.e. precomputed ones).
		- Add distances BrayCurtis, ChiSquare, Cosine and Tanimoto.
	* Bugfixes:
		- Support Intel MKL on 32bit archs.
		- Fix compilation when atlas/lapack is not available.

2008-08-15  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.6.4
	* This release contains major feature enhancements and bugfixes:
		- Implement 2-norm Multiple Kernel Learning.
		- Much extended documentation.
		- Add Gaussian kernel for 32bit floating point features.
		- Testsuite is now available for static interfaces python, octave,
		  matlab and R and modular interface octave.
	* Bugfixes:
		- Tests are now run in the examples/interface directory, with paths set
		to the installation directory.
		- Filter out duplicate signals in signal handler and make sure the
		handler is removed.
		- Fix random number generator initialization.

2008-06-13  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.6.3
	* This release contains several cleanups and bugfixes:
		- Fail nicely in out of memory situations.
		- Drop R package, now configure; make; make install will work for all
		interfaces.
		- Disable progress output by default. Ocas now uses a progress bar and
		  hence is less verbose.
		- Revised directory structure with /doc, /examples, /src, /testsuite.
		- Add common toy data repository and make all examples from all interfaces
		use it.
		- Add examples for cmdline interface.
		- Dynamically generate a reference documentation for the static interfaces.
		- Syntax highlight commands again.
		- Support for cplex 11.
		- Port MKL examples to R.
		- Merge structure learning branch.
	* Bugfixes:
		- Don't render string if it is not printed in current loglevel anyway
		and throw exceptions for messages with priority ERROR or higher.
		- Compile fix when lapack is not available.
		- Fix when only lapack and blas (but not atlas) are available.
		- Fix bug in batch/linadd occurring for WD kernel of order 1.
		- Check that strings have same length on initing WD kernels.
		- Remove signal handler on Ctrl+C to fix Ctrl+C pressed twice bug.
		- All derived classes now call their parent class on construction.
		- Fix a crasher occuring with SVRLight on multiple threads.

2008-05-15  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.6.2
		- Experimental support for r-modular thanks to the swig team!
		- All python-modular examples describing the use of kernels,
		classifier, distributions, features, distances, regression and
		preprocessors have been ported to r-modular (requires swig from svn).
		- The 'send_command' legacy is no longer necessary, numbers can be used
		as such and don't have to be given as strings. All examples for
		r,python,octave,matlab have been converted to the new syntax.
		- Resurrected the command line interface. Basic functionionality,
		like training a classifier on strings/real valued (sparse) features
		was restored. Readline completion was added.
		- Documentation updates.
	* Bugfixes:
		- The weighted spectrum kernel is now working again.
		- Fix the testsuite to reliably check methods that use random().
		- Off-by-one bug fix in FixedDegreeStringKernel.
		- Fix reading strings from file, when strings don't have the same length.
		- Fix massive slowdown in modular interfaces for WD based kernels (it
		is 5-30 times faster now).

2008-04-19  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.6.1
		- Now fully support octave-modular thanks to the swig team!
		- All python-modular examples describing the use of kernels,
		classifier, distributions, features, distances, regression and
		preprocessors have been ported to octave-modular.
		- Minor documentation updates.
		- Unconditionally disable swig director. This reduces wrapper code size
		and compile time and also speeds up calls to virtual functions *a lot*.
		Expect big speed improvements if you were using the python-modular
		interface.
	* Bugfixes:
		- Include missing files in documentation.
		- The 'send_command' legacy is no longer necessary.
		- Improved cmdline help, categorized in topic sg('help', 'topic')

2008-04-12  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.6.0
	* This release contains several major enhancements:
		- The static R,octave,matlab,python interfaces have been rewritten from
		scratch simplifying future extensions. They now use the same syntax and
		support the same set of shogun commands.
		- Toy examples describing the use of kernels, classifier,
		distributions, features, distances, regression and preprocessors
		for the static python, R, octave and matlab interface have been added.
		- Improved user documentation
		- Support for ACML and Intel MKL
	* New methods:
		- POIMs for python-modular interface
	* Bugfixes:
		- Fixed memory leaks in Classifiers, Kernels, Distributions
		- Fixed severale delete[]/free mismatches
		- Fixed reading and writing of svm light format
		- Enable ctrl-c support in octave

2008-02-19  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.5.1
	* This release contains minor bugfixes
		- Allow building w/o doxygen
		- Code cleanups
		- Support newer lapack/atlas/blas
	* New methods:
		- Added several performance measures
		- SVMSGD
		- Efficient reading/writing of svmlight format

2008-01-31  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.5.0
	* This release contains several major enhancements:
		- Full fledged test suite for python-modular interface
		- Toy examples describing the use of kernels, classifier,
		distributions, features, distances, regression and preprocessors
		for the python-modular interface
		- Doxygen generated documentation for python-modular interface
		- Many cleanups to make python-modular interface more consistent
	* New methods:
		- WDSVMOcas
		- Update liblinear to version 1.22
	* Bugfixes:
		- StringFeatures may now directly read DNA strings from a single file
		- Option to quieten progress output
		- Several memory leaks and valgrind errors
		- Fixed rarely ocurring convergence problem in OCAS
		- Division by zero in Chi2Kernel
		- WD kernel now dynamically allocates Tries
		- Matlab clear sg ; sg crasher
		- Salzberg/HistogramWordkernel crasher
		- Fix build dependency generation using gcc -MM
	* Switched license to GPL v3

2007-11-23  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.4.4
	* This release contains several bugfixes:
		- Memory leak fix in libsvm wrapper
		- Enable error checking in matlab interface
		- Free memory after batch computation
		- Parallel (num_threads>1) bug occurring with batch computation
		- Several python-modular interface cleanups
		- Fix for Chi2 kernel
		- Use gcc now to generate build dependencies
		- Test for existance of log2 (enables building on interix)
		- Python build fix
		- Double free fix for combined kernel (python modular interface)
	* New methods: SVMOcas, GaussianShiftKernel

2007-10-10  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.4.3
	* This release contains minor bugfixes for the
	weighted spectrum kernel and poims

2007-09-19  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.4.2
	* This release contains minor bugfixes and improvements
		- fix POIMs
		- compile fix when atlas/lapack is not available
		- minor code cleanup (Tries now use templates)
		- added KMeans and Hierarchical Clustering

2007-09-01  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.4.1
	* This release contains minor bugfixes and improvements
	* Fixes for:
		- SVMLin
		- python examples
		- R examples
		- cplex 10 compatibility fixes
		- compilation fix when configured with --disable-svm-light
		- sliding window/position list fixes
	* New methods
		- Liblinear
		- Local Alignment Kernel
		- support for transfering StringFeatures of type word to matlab
		- python modular support for custom kernel

2007-07-30  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.4.0
	* new methods: 
		- SubgradientSVM
		- GMNPSVM (multiclass b-SVM)
		- SubgradientLPM
		- CplexLPM
		- LPBoost (for LPM)
		- SVMLin
		- weighted spectrum kernel
	* linadd support for GPDTSVM
	* new commands new_classifier / train_classifier / get_classifier
	* support for sparse features (from matlab)
	* cleaned and added many more examples 
	* removed suffixarray code due to license conflicts
	* Matlab R2007a support
	* all string kernels now work on strings (not charfeatures)

2007-03-06  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.3.2
	* workaround for python-numpy, when long==int==int32, add bool support
	* fix autodetection of atlas/lapack
	* fix uninitialized variables in (GUI)HMM, valgrind errors

2007-02-20  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.3.1
	* update README
	* fix autodetection of powl() and _SC_NPROCESSORS_ONLN

2007-02-14  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.3.0

2007-02-13  Soeren Sonnenburg <debian@nn7.de>

	* added vojtechs SVM
	* finished (regularized) LDA
	* conservational weights in WD kernel
	* added mikios kernel ridge regression (KRR)
	* many fixes in python swig interface
	* build fixes for archs that don't have powl()
	* much improved build system
	* updated coding conventions (though still in a flux)
	* enable warnings for shadowed variables
	* lots of build fixes 

2006-12-05  Soeren Sonnenburg <debian@nn7.de>

	* SHOGUN Release version 0.2.1

2006-10-13  Soeren Sonnenburg <Soeren.Sonnenburg@first.fraunhofer.de>

	* swig python interface (works w/ multiple svms etc etc)

2006-10-09  Soeren Sonnenburg <Soeren.Sonnenburg@first.fraunhofer.de>

	* some autodetection magic in ./configure
	* fixed a serious bug occuring with shrinking & SVM light (target epsilon
			was not achieved as we erreanously terminated optimization)
	* fixed a serious bug when using charfeatures (or strings) w/ mxGetString
	in matlab interface (the mxGetString function has the undocumented
			`feature' of returning locale dependent results!)
	* new command use_shrinking 0/1
	* new svm classifier SVM LIBSVM_ONECLASS
	* new function get_WD_scoring
	* make much more use of templates, i.e. remove all the
	{Real,Char,Word,Byte,*}Kernel.* files

2006-09-11  Soeren Sonnenburg <Soeren.Sonnenburg@first.fraunhofer.de>

	* incorporated MINDY support
	* new alphabet class, all string features now have a defined
	alphabet plus mapping function
	* RAW (i.e. 8bit) alphabet added
	* fixes for CommStringUlongKernel (was buggy when strings have different
			lengths)
	* new get_WD_scoring function
	* compile fixes for octave and matlab on osx
	* configure now scans a number of variants to detect include and library paths
	* configure obeys INCLUDES LIBS environment variables and optional
	  paths specified by --libraries --includes 
	* updated copyright infos
	* updated license infos

2006-06-30  Soeren Sonnenburg <Soeren.Sonnenburg@first.fraunhofer.de>

	* SHOGUN Release 0.1.2
	* compile fixes for R on MaxOSX
	* some compile fixes for cygwin/WIN32
	* Weighted Degree/Weighted Degree Shift kernel speedups & fixes
	* python build fixes
	* initial *workin* swig support 
	* entropy example

2006-06-15  Soeren Sonnenburg <Soeren.Sonnenburg@first.fraunhofer.de>

	* SHOGUN Release version 0.1-pre1
