Merge pull request #2069 from abergeron/doc

doc/index.txt

@@ -67,16 +67,17 @@ installation and configuration, see :ref:`installing Theano <install>`.
   Status
   ======
 
-  .. image:: https://secure.travis-ci.org/Theano/Theano.png?branch=master
-      :target: http://travis-ci.org/Theano/Theano/builds
+  .. raw:: html
 
-  .. image:: https://pypip.in/v/Theano/badge.png
-      :target: https://crate.io/packages/Theano/
-      :alt: Latest PyPI version
+     <a href="http://travis-ci.org/Theano/Theano/builds"><img src="https://secure.travis-ci.org/Theano/Theano.png?branch=master" /></a>&nbsp;
 
-  .. image:: https://pypip.in/d/Theano/badge.png
-      :target: https://crate.io/packages/Theano/
-      :alt: Number of PyPI downloads
+  .. raw:: html
+
+     <a href="https://crate.io/packages/Theano/"><img src="https://pypip.in/v/Theano/badge.png" alt="Latest PyPI version" /></a>&nbsp;
+
+  .. raw:: html
+
+     <a href="https://crate.io/packages/Theano/"><img src="https://pypip.in/d/Theano/badge.png" alt="Number of PyPI downloads" /></a>&nbsp;
 
   .. _available on PyPI: http://pypi.python.org/pypi/Theano
   .. _Related Projects: https://github.com/Theano/Theano/wiki/Related-projects

doc/library/sandbox/linalg.txt

 ..  ../../../../theano/sandbox/linalg/ops.py
 ..  ../../../../theano/sandbox/linalg
 
-.. _libdoc_linalg:
+.. _libdoc_sandbox_linalg:
 
 ===================================================================
 :mod:`sandbox.linalg` --  Linear Algebra Ops

doc/library/tensor/nnet/conv.txt

@@ -32,18 +32,20 @@ TODO: Give examples on how to use these things! They are pretty complicated.
       Most of the more efficient GPU implementations listed below can be used
       as an automatic replacement for nnet.conv2d by enabling specific graph
       optimizations.
-    - :func:`conv2d_fft <theano.sandbox.cuda.fftconv.conv2d_fft>`
-      This is a GPU-only version of nnet.conv2d that uses an FFT transform
-      to perform the work. conv2d_fft should not be called directly as it
-      does not provide a gradient. Instead, use nnet.conv2d and allow
-      Theano's graph optimizer to replace it by the FFT version by setting
-      ``THEANO_FLAGS=optimizer_including=conv_fft_valid:conv_fft_full``
+    - :func:`conv2d_fft <theano.sandbox.cuda.fftconv.conv2d_fft>` This
+      is a GPU-only version of nnet.conv2d that uses an FFT transform
+      to perform the work. conv2d_fft should not be used directly as
+      it does not provide a gradient. Instead, use nnet.conv2d and
+      allow Theano's graph optimizer to replace it by the FFT version
+      by setting
+      'THEANO_FLAGS=optimizer_including=conv_fft_valid:conv_fft_full'
       in your environement.  This is not enabled by default because it
-      has some restrictions on input and uses a lot more memory.  Also note
-      that it requires CUDA >= 5.0, scikits.cuda >= 0.5.0 and PyCUDA to run.
-      To deactivate the FFT optimization on a specific nnet.conv2d
-      while the optimization flags are active, you can set its ``version``
-      parameter to ``'no_fft'``. To enable it for just one Theano function:
+      has some restrictions on input and uses a lot more memory.  Also
+      note that it requires CUDA >= 5.0, scikits.cuda >= 0.5.0 and
+      PyCUDA to run.  To deactivate the FFT optimization on a specific
+      nnet.conv2d while the optimization flags are active, you can set
+      its ``version`` parameter to ``'no_fft'``. To enable it for just
+      one Theano function:
 
       .. code-block:: python
 

doc/library/tensor/slinalg.txt

 ..  ../../../../theano/sandbox/slinalg.py
 
-.. _libdoc_linalg:
+.. _libdoc_slinalg:
 
 ===================================================================
 :mod:`tensor.slinalg` --  Linear Algebra Ops Using Scipy

theano/sandbox/cuda/blas.py

@@ -7,8 +7,8 @@ from theano import tensor
 from theano.compat.six import StringIO
 from theano.sandbox.cuda.type import CudaNdarrayType
 from theano.sandbox.cuda import GpuOp
-from theano.sandbox.cuda import as_cuda_ndarray_variable
-from theano.sandbox.cuda.basic_ops import gpu_contiguous
+from theano.sandbox.cuda.basic_ops import (as_cuda_ndarray_variable,
+                                           gpu_contiguous)
 
 
 class GpuDot22(GpuOp):

theano/sandbox/cuda/nnet.py

 from theano import Op, Apply
 from theano.compat.six import StringIO
 
-from theano.sandbox.cuda import GpuOp, as_cuda_ndarray_variable
+from theano.sandbox.cuda import GpuOp
+from theano.sandbox.cuda.basic_ops import as_cuda_ndarray_variable
 
 from theano.sandbox.cuda.kernel_codegen import (nvcc_kernel,
                                                 inline_softmax,

theano/sparse/basic.py

@@ -1143,11 +1143,12 @@ class GetItem2Lists(gof.op.Op):
 get_item_2lists = GetItem2Lists()
 """Select elements of sparse matrix, returning them in a vector.
 
-:param x: Sparse matrix.
-:param index: List of two lists, first list indicating the row 
-of each element and second list indicating its column.
+  :param x: Sparse matrix.
 
-:return: The corresponding elements in `x`.
+  :param index: List of two lists, first list indicating the row of
+                each element and second list indicating its column.
+
+  :return: The corresponding elements in `x`.
 """
 
 
@@ -1737,13 +1738,14 @@ class Diag(gof.op.Op):
 diag = Diag()
 """Extract the diagonal of a square sparse matrix as a dense vector.
 
-:param x: A square sparse matrix in csc format.
+  :param x: A square sparse matrix in csc format.
 
-:return: A dense vector representing the diagonal elements.
+  :return: A dense vector representing the diagonal elements.
 
-:note: The grad implemented is regular, i.e. not structured, since
-the output is a dense vector.
+.. note::
 
+  The grad implemented is regular, i.e. not structured, since the
+  output is a dense vector.
 """
 
 

theano/tensor/extra_ops.py

@@ -863,18 +863,21 @@ class FillDiagonalOffset(gof.Op):
 
         return [wr_a, wr_val,wr_offset]
 
-fill_diagonal_offset = FillDiagonalOffset()
-""" Returns a copy of an array with all
+fill_diagonal_offset_ = FillDiagonalOffset()
+
+def fill_diagonal_offset(a, val, offset):
+    """
+    Returns a copy of an array with all
     elements of the main diagonal set to a specified scalar value.
 
       :param a: Rectangular array of two dimensions.
       :param val: Scalar value to fill the diagonal whose type must be
           compatible with that of array 'a' (i.e. 'val' cannot be viewed
           as an upcast of 'a').
-    :params offset : Scalar value Offset of the diagonal from the main 
+      :param offset: Scalar value Offset of the diagonal from the main
           diagonal. Can be positive or negative integer.
       :return: An array identical to 'a' except that its offset diagonal
           is filled with scalar 'val'. The output is unwrapped.
-
-"""
+    """
+    return fill_diagonal_offset_(a, val, offset)
 

theano/tensor/nlinalg.py

@@ -496,20 +496,35 @@ def qr(a, mode="full"):
     Factor the matrix a as qr, where q
     is orthonormal and r is upper-triangular.
 
-    Parameters :
-    ------------
-
-    a : array_like, shape (M, N)
+    :type a:
+        array_like, shape (M, N)
+    :param a:
         Matrix to be factored.
 
-    mode : {'reduced', 'complete', 'r', 'raw', 'full', 'economic'}, optional
+    :type mode:
+        one of 'reduced', 'complete', 'r', 'raw', 'full' and
+        'economic', optional
+    :keyword mode:
         If K = min(M, N), then
-        'reduced' : returns q, r with dimensions (M, K), (K, N) (default)
-        'complete' : returns q, r with dimensions (M, M), (M, N)
-        'r' : returns r only with dimensions (K, N)
-        'raw' : returns h, tau with dimensions (N, M), (K,)
-        'full' : alias of 'reduced', deprecated
-        'economic' : returns h from 'raw', deprecated. The options 'reduced',
+
+        'reduced'
+          returns q, r with dimensions (M, K), (K, N)
+
+        'complete'
+           returns q, r with dimensions (M, M), (M, N)
+
+        'r'
+          returns r only with dimensions (K, N)
+
+        'raw'
+          returns h, tau with dimensions (N, M), (K,)
+
+        'full'
+          alias of 'reduced', deprecated (default)
+
+        'economic'
+          returns h from 'raw', deprecated. The options 'reduced',
+
         'complete', and 'raw' are new in numpy 1.8, see the notes for more
         information. The default is 'reduced' and to maintain backward
         compatibility with earlier versions of numpy both it and the old
@@ -518,21 +533,25 @@ def qr(a, mode="full"):
         deprecated. The modes 'full' and 'economic' may be passed using only
         the first letter for backwards compatibility, but all others
         must be spelled out.
+
         Default mode is 'full' which is also default for numpy 1.6.1.
 
-        Note:   Default mode was left to full as full and reduced are both doing
-                the same thing in the new numpy version but only full works on the old
-                previous numpy version.
-    Returns :
-    ---------
-    q : matrix of float or complex, optional
-    A matrix with orthonormal columns. When mode = 'complete'
-    the result is an orthogonal/unitary matrix depending on whether
-    or not a is real/complex. The determinant may be either +/- 1 in that case.
-
-    r : matrix of float or complex, optional
+        :note: Default mode was left to full as full and reduced are
+           both doing the same thing in the new numpy version but only
+           full works on the old previous numpy version.
+
+    :rtype q:
+      matrix of float or complex, optional
+    :return q:
+      A matrix with orthonormal columns. When mode = 'complete' the
+      result is an orthogonal/unitary matrix depending on whether or
+      not a is real/complex. The determinant may be either +/- 1 in
+      that case.
+
+    :rtype r:
+      matrix of float or complex, optional
+    :return r:
       The upper-triangular matrix.
-
     """
     x = [[2, 1], [3, 4]]
     if isinstance(numpy.linalg.qr(x,mode), tuple):
@@ -549,8 +568,6 @@ class SVD(Op):
 
     def __init__(self, full_matrices=True, compute_uv=True):
         """
-        inputs :
-        --------
         full_matrices : bool, optional
             If True (default), u and v have the shapes (M, M) and (N, N),
             respectively.
@@ -582,21 +599,18 @@ def svd(a, full_matrices=1, compute_uv=1):
     """
     This function performs the SVD on CPU.
 
-    Parameters :
-    ------------
-
-    full_matrices : bool, optional
+    :type full_matrices: bool, optional
+    :param full_matrices:
         If True (default), u and v have the shapes (M, M) and (N, N),
         respectively.
         Otherwise, the shapes are (M, K) and (K, N), respectively,
         where K = min(M, N).
-    compute_uv : bool, optional
+    :type compute_uv: bool, optional
+    :param compute_uv:
         Whether or not to compute u and v in addition to s.
         True by default.
 
-    Returns :
-    -------
-    U, V and D matrices.
+    :returns: U, V and D matrices.
     """
     return SVD(full_matrices, compute_uv)(a)
 

theano/tensor/nnet/Conv3D.py

@@ -533,31 +533,33 @@ class Conv3D(theano.Op):
 
         return strutil.render_string(codeSource,locals())
 
+_conv3D = Conv3D()
 
-conv3D = Conv3D()
-"""
-3D "convolution" of multiple filters on a minibatch
-(does not flip the kernel, moves kernel with a user specified stride)
+def conv3D(V, W, b, d):
+    """
+    3D "convolution" of multiple filters on a minibatch
+    (does not flip the kernel, moves kernel with a user specified stride)
 
-:param V: Visible unit, input.
+    :param V: Visible unit, input.
         dimensions: (batch, row, column, time, in channel)
-:param W: Weights, filter.
+    :param W: Weights, filter.
         dimensions: (out channel, row, column, time ,in channel)
-:param b: bias, shape == (W.shape[0],)
-:param d: strides when moving the filter over the input(dx, dy, dt)
+    :param b: bias, shape == (W.shape[0],)
+    :param d: strides when moving the filter over the input(dx, dy, dt)
 
-:note: The order of dimensions does not correspond to the one in `conv2d`.
+    :note: The order of dimensions does not correspond to the one in `conv2d`.
            This is for optimization.
 
-:note: The GPU implementation is very slow. You should use
-    :func:`conv3d2d <theano.tensor.nnet.conv3d2d.conv3d>` for a GPU
-    graph instead.
-
-:see: Someone made a script that shows how to swap the axes between
-      both 3d convolution implementations in Theano. See the last
-      `attachment <https://groups.google.com/d/msg/theano-users/1S9_bZgHxVw/0cQR9a4riFUJ>`_.
+    :note: The GPU implementation is very slow. You should use
+           :func:`conv3d2d <theano.tensor.nnet.conv3d2d.conv3d>` for a
+           GPU graph instead.
 
+    :see: Someone made a script that shows how to swap the axes
+          between both 3d convolution implementations in Theano. See
+          the last `attachment
+          <https://groups.google.com/d/msg/theano-users/1S9_bZgHxVw/0cQR9a4riFUJ>`_.
 """
+    return _conv3D(V, W, b, d)
 
 def computeH(V,W,b,d):
     assert len(W.shape) == 5