Theano 0.5rc1

TODO for final 0.5 release:
- test python 2.4
- test theano-cache with "pip install Theano": issue 101
- Re-write this NEWS.txt file!

if time check issue: 98.

Modifications in the trunk since the 0.4.1 release (12 August 2011) up to 2 Dec 2011


Every body is recommented to update Theano to 0.5 when released after
they checked there code don't return deprecation warning. Otherwise,
in one case the result can change. In other case, the warning are
transformed to error. See bellow.


Important change:
 * Moved to github: https://github.com/Theano/Theano/
 * Old trac ticket moved to assembla ticket: https://www.assembla.com/spaces/theano/tickets
 * Theano vision: https://deeplearning.net/software/theano/introduction.html#theano-vision (Many people)
 * 


Interface Behavior Change (was deprecated and generated a warning since Theano 0.3 released the 23 Nov 2010):
* The current default value of the parameter axis of
  theano.{max,min,argmax,argmin,max_and_argmax} is now the same as
  numpy: None. i.e. operate on all dimensions of the tensor.


Interface Feature Removed (was deprecated):
 * The string mode FAST_RUN_NOGC and STABILIZE are not accepted. It was accepted only by theano.function(). Use Mode(linker='c|py_nogc') or Mode(optimizer='stabilize') instead.
 * tensor.grad(cost, wrt) now return an object of the "same type" as wrt 
   (list/tuple/TensorVariable).
 * a few tag.shape and Join.vec_length left.

 * scan interface change: RP
   * The use of `return_steps` for specifying how many entries of the output
     scan has been deprecated

     * The same thing can be done by applying a subtensor on the output
       return by scan to select a certain slice
   * The inner function (that scan receives) should return its outputs and
     updates following this order:

        [outputs], [updates], [condition]. One can skip any of the three if not
        used, but the order has to stay unchanged.
 * shared.value is moved, use shared.set_value() or shared.get_value() instead.


New Deprecation (will be removed in Theano 0.6, warning generated if you use them):
 * tensor.shared() renamed to tensor._shared (Olivier D.)
   * You probably want to call theano.shared()!


Interface Bug Fix:
 * Rop in some case should have returned a list of 1 theano varible, but returned directly that variable.
 * Theano flags "home" is not used anymore as it was a duplicate. If you use it, theano should raise an error.

New features:
 * adding 1d advanced indexing support to inc_subtensor and set_subtensor (James
 * tensor.{zeros,ones}_like now support the dtype param as numpy (Fred)
 * config flags "exception_verbosity" to control the verbosity of exception (Ian 
 * theano-cache list: list the content of the theano cache(Fred)
 * tensor.ceil_int_div FB
 * MaxAndArgMax.grad now work with any axis(The op support only 1 axis) FB
   * used by tensor.{max,min,max_and_argmax}
 * tensor.{all,any} RP
 * tensor.roll as numpy: (Matthew Rocklin, DWF)
 * on Windows work. Still experimental. (Sebastian Urban)
 * IfElse now allow to have a list/tuple as the result of the if/else branches.
   * They must have the same length and correspondig type) RP
 * argmax dtype as int64. OD



New Optimizations:
 * AdvancedSubtensor1 reuse preallocated memory if available(scan, c|py_nogc linker)(Fred)
 * tensor_variable.size (as numpy) product of the shape elements OD
 * sparse_variable.size (as scipy) the number of stored value.OD
 * dot22, dot22scalar work with complex(Fred)
 * Doc how to wrap in Theano an existing python function(in numpy, scipy, ...) Fred
 * added arccos IG
 * sparse dot with full output. (Yann Dauphin)
   * Optimized to Usmm and UsmmCscDense in some case (YD)
   * Note: theano.dot, sparse.dot return a structured_dot grad(
 * Generate Gemv/Gemm more often JB
 * scan move computation outside the inner loop when the remove everything from the inner loop RP
 * scan optimization done earlier. This allow other optimization to be applied FB, RP, GD
 * exp(x) * sigmoid(-x) is now correctly optimized to a more stable form.


GPU:
 * GpuAdvancedSubtensor1 support broadcasted dimensions


Bugs fixed:
 * On cpu, if the convolution had received explicit shape information, they where not checked at run time. This caused wrong result if the input shape was not the one expected. (Fred, reported by Sander Dieleman)
 * Scan grad when the input of scan has sequence of different length. (RP reported by Michael Forbes)
 * Scan.infer_shape now work correctly when working with a condition for the number of loop. In the past, it returned n_stepts as the shape, witch is not always true. RP
 * Theoritic bug: in some case we could have GPUSum return bad value. Was not able to produce the error.. 
   * pattern affected({0,1}*nb dim, 0 no reduction on this dim, 1 reduction on this dim )
     01, 011, 0111, 010, 10, 001, 0011, 0101: FB
 * div by zeros in verify_grad. This hidded a bug in the grad of Images2Neibs. (JB)
 * theano.sandbox.neighbors.Images2Neibs grad was returning wrong value. The grad is now disabled and return an error. FB



Crash fixed:
 * T.mean crash at graph building timeby Ian G.
 * "Interactive debugger" crash fix (Ian, Fred)
 * "Interactive Debugger" renamed to "Using Test Values"
 * Do not call gemm with strides 0, some blas refuse it. (PL)
 * optimization crash with gemm and complex.(Fred
 * Gpu crash with elemwise Fred
 * compilation crash with amdlibm and the gpu. Fred
 * IfElse crash Fred
 * Execution crash fix in AdvancedSubtensor1 on 32 bits computer(PL)
 * gpu compilation crash on MacOS X OD
 * gpu compilation crash on MacOS X Fred
 * Support for OSX Enthought Python Distribution 7.x (Graham Taylor, OD)
 * When the subtensor inputs had 0 dimensions and the outputs 0 dimensions
 * Crash when the step to subtensor was not 1 in conjonction with some optimization


Optimization:
 * Added Subtensor(Rebroadcast(x)) => Rebroadcast(Subtensor(x)) optimization (GD)
 * Scan optimization are executed earlier. This make other optimization being applied(like blas optimization, gpu optimization...)(GD, Fred, RP)
 * Make the optimization process faster JB
 * Allow fusion of elemwise when the scalar op need support code. JB


Know bug:
 * CAReduce with nan in inputs don't return the good output (`Ticket <http://trac-hg.assembla.com/theano/ticket/763>`_).

   * This is used in tensor.{max,mean,prod,sum} and in the grad of PermuteRowElements.
 * If you do grad of grad of scan you can have wrong number in some case.


Sandbox:
 * cvm, interface more consistent with current linker (James)
 * vm linker have a callback parameter (JB)
 * review/finish/doc: diag/extract_diag AB,FB,GD
 * review/finish/doc: AllocDiag/diag AB,FB,GD
 * review/finish/doc: MatrixInverse, matrix_inverse RP
 * review/finish/doc: matrix_dot RP
 * review/finish/doc: det PH determinent op
 * review/finish/doc: Cholesky David determinent op
 * review/finish/doc: ensure_sorted_indices Li Yao
 * review/finish/doc: spectral_radius_boud Xavier Glorot
 * review/finish/doc: sparse sum Valentin Bisson


Sandbox New features(not enabled by default):
 * CURAND_RandomStreams for uniform and normal(not pickable, gpu only)(James)


Documentation:
 * Many update by many people: Olivier Delalleau, Fred, RP, David, 
 * Updates to install doc on MacOS (OD)
 * Updates to install doc on Windows(DWF, OD)
 * Doc how to use scan to loop with a condition as the number of iteration RP


Others:
 * Better error message at many places: David Warde-Farley, Ian, Fred, Olivier D.
 * pep8: James, 
 * min_informative_str to print graph: Ian G.
 * Fix catching of exception. (Sometimes we catched interupt): Fred, David, Ian, OD,
 * Better support for uft string(David WF)
 * Fix pydotprint with a function compiled with a ProfileMode (Fred)
   * Was broken with change to the profiler.
 * warning when people have old cache entry (OD)
 * More test for join on the gpu and cpu.
 * Don't request to load the gpu module by default in scan module. RP
 * Better opt that lift transpose around dot JB
 * Fix some import problem
 * Filtering update JB


Reviewers:
 James, David, Ian, Fred, Razvan, delallea
