April-ANN v0.3.0-beta: deploying April-ANN as a Lua 5.2 module

The more important changes are:

• April-ANN could be loaded as a Lua 5.2 module.
• The ANNs learning algorithm has been splitted in two parts:
  • The gradient computation, done in ANN components.
  • The optimization procedure implemented in specific Lua objects.
• Some bugs and memory leaks has been solved.

API Changes

• Added loss parameter to trainable.supervised_trainer methods.
• Added optimizer parameter to trainable.supervised_trainer methods.
• Added ann.optimizer package, which has the implementation of weight update
  based on weight gradient. So, the ANN components only compute gradients.
  This allows to implement different optimization methods (as "Conjugate
  Gradient", or "Linear Search Brack-Propagation") with the same gradient
  computation.
• Loss functions ann.loss API has been changed, now the loss computation is
  done in two separated steps:
  - matrix = loss:compute_loss(output,target): which returns a matrix with
  the loss of every pair of patterns, allowing to perform several loss
  computations without taken them into account.
  - matrix = loss:accum_loss(matrix): which accumulates the loss in the
  internal state of the class.
• Added a new version of loss function, which computes mean and
  sample variance of the loss. Besides, the loss computation is done
  with doubles, being more accurated than before.
• replacement parameter in SDAE doesn't force on_the_fly parameter, they are
  independent.
• SDAE training has been changed in order to allow the use of LUA datasets,
• Replaced cpp_class_binding_extension by class_extension function,
  adding Lua classes support besides to CPP binded classes.
• Modified class and class_instance functions to be more homogeneous
  with C++ binding.
• Added support for GZipped matrices load and save from C++, so functions
  matrix.savefile and matrix.loadfile (and its correspondence for complex
  numbers, double, int32, and char) were removed. Methods matrix.fromFilename
  and matrix.toFilename accept '.gz' extension.

Packages rename

• Changed package sdae to ann.autoencoders.
• Changed package loss_functions to ann.loss.
• Splitted mathcore package into mathcore and complex packages.
• Renamed math package to mathcore to avoid the collision with Lua standard
  math library.

New features

• April-ANN is deployed as a standalone executable and as a shared library for
  Lua 5.2.
• Modified lua.h to incorporate the GIT commit number in the disclaimer.
• Added Lua autocompletion when readline is available.
• Implemented SignalHandler class in C++.
• Added signal.register and signal.receive functions to Lua.
• Added to matrix the methods map, contiguous, join, abs, tan,
  atan, atanh, sinh, asin, asinh, cosh, acos, acosh, fromMMap,
  toMMap, div, max, min.
• Added iterator class, which is a wrapper around Lua iterators, but
  provides a more natural interface with functional programming procedures
  as map, filter, apply, or reduce.
• Added methods iterate, field, select to iterator Lua class.
• table.insert returns the table, which is useful for reduction operations.
• Added table method to iterator class.
• Added naive L1_norm regularization.
• Added dataset.clamp.
• Added mathcore.set_mmap_allocation function, which allows to forces the
  use of mmap for matrix memory allocation.
• Added ann.components.slice.
• Added GS-PCA algorithm for efficient computation of PCA (iterative algorithm),
  stats.iterative_pca Lua function.
• Added basic MapReduce implementation in Lua.
• Added stats.correlation.pearson Lua class.
• Added stats.bootstrap_resampling function.
• Added math.add, math.sub, math.mul, math.div functions.
• trainable and ann.mlp.all_all are using matrix:to_lua_string()
  method.
• Added method to_lua_string() in all matrix types, so the method produce
  a Lua chunk which is loadable and produce a matrix.
• Added serialization to parallel_foreach, allowing to produce outputs which
  could be loaded by the caller process.
• Declaration of luatype function as global, it wasn't.
• Added iterable_map and multiple_ipairs functions to the Lua utilities.
• Added SubAndDivNormalizationDataSet, applies a substraction and a division of
  the feature vectors.
• Added stepDataset.

Bugs removed

• Solved bug at luabind_template.cc, which introduced spurious segmentation
  faults due to Lua execution of garbage collection in the middle of a
  lua_pushClassName.
• Solved bug at glob function.
• Solved bug at matrix iterators operator=.
• Solved bug at method matrix::best_span_iterator::setAtWindow. Becaose of It
  the method didn't works when the matrix was a sub-matrix (slice) of other
  matrix.
• Solved bugs at Matrix template constructor which affects to rewrap lua
  method, and to select method, which affects to select lua method.
• Added binarizer::init() to a binded static_constructor, it is needed to
  execute init() before decode/encode double numbers, because of endianism.
• Solved bug at constString when extracting double numbers in binary format.
• MacOS compilation problems solved.
• Solved problems with CUDA, it is working again.
• Dynamic loading of C modules is working now.

C/C++ code changes

• Added BIND_STRING_CONSTANT to luabind, so it is possible to export C string
  constants to Lua.
• Removed warning of clang about unused variables, adding a new macro
  UNUSED_VARIABLE(x) defined in the header utils/c_src/unused_variable.h.
• Matrix fromString and toString Lua methods have been improved to write/read
  directly from Lua string buffer, so the memory print has been reduced.
• The C++ routines to write and read files is generalized to work with streams,
  under the BufferedStream template, and it is instantiated to FILE and gzFile
  formats.
• Added sanity check to cross-entropy and multi-class cross-entropy loss
  functions, to detect the use of non logarithmic outputs.