license changes, reexport modules

20 files changed, 304 insertions, 67 deletions

diff --git a/packages/base/hmatrix-base.cabal b/packages/base/hmatrix-base.cabal
index 3f12dad..638390a 100644
--- a/packages/base/hmatrix-base.cabal
+++ b/packages/base/hmatrix-base.cabal
@@ -39,10 +39,12 @@ library
                         Numeric.LinearAlgebra.LAPACK
                         Numeric.LinearAlgebra.Algorithms
                         Numeric.Container
-                        Numeric.LinearAlgebra
                         Numeric.LinearAlgebra.Util
                         Numeric.LinearAlgebra.Util.Convolution
                         Data.Packed.IO
+                        Numeric.LinearAlgebra.Base
+                        Numeric.LinearAlgebra.Devel
+                        Numeric.LinearAlgebra.Data
                         
     other-modules:      Data.Packed.Internal,
                         Data.Packed.Internal.Common,
diff --git a/packages/base/src/Data/Packed.hs b/packages/base/src/Data/Packed.hs
index c66718a..129bd22 100644
--- a/packages/base/src/Data/Packed.hs
+++ b/packages/base/src/Data/Packed.hs
@@ -10,6 +10,7 @@ Types for dense 'Vector' and 'Matrix' of 'Storable' elements.
 
 -}
 -----------------------------------------------------------------------------
+{-# OPTIONS_HADDOCK hide #-}
 
 module Data.Packed (
     -- * Vector
diff --git a/packages/base/src/Data/Packed/Development.hs b/packages/base/src/Data/Packed/Development.hs
index 6dfd551..1efedc9 100644
--- a/packages/base/src/Data/Packed/Development.hs
+++ b/packages/base/src/Data/Packed/Development.hs
@@ -13,6 +13,7 @@
 -- in the @examples\/devel@ folder included in the package.
 --
 -----------------------------------------------------------------------------
+{-# OPTIONS_HADDOCK hide #-}
 
 module Data.Packed.Development (
     createVector, createMatrix,
diff --git a/packages/base/src/Data/Packed/Foreign.hs b/packages/base/src/Data/Packed/Foreign.hs
index efa51ca..1ec3694 100644
--- a/packages/base/src/Data/Packed/Foreign.hs
+++ b/packages/base/src/Data/Packed/Foreign.hs
@@ -6,6 +6,7 @@
 -- @ glUniformMatrix4fv 0 1 (fromIntegral gl_TRUE) \`appMatrix\` perspective 0.01 100 (pi\/2) (4\/3) 
 -- @
 --
+{-# OPTIONS_HADDOCK hide #-}
 module Data.Packed.Foreign 
     ( app
     , appVector, appVectorLen
diff --git a/packages/base/src/Data/Packed/Internal.hs b/packages/base/src/Data/Packed/Internal.hs
index 537e51e..59a72fc 100644
--- a/packages/base/src/Data/Packed/Internal.hs
+++ b/packages/base/src/Data/Packed/Internal.hs
@@ -2,11 +2,9 @@
 -- |
 -- Module      :  Data.Packed.Internal
 -- Copyright   :  (c) Alberto Ruiz 2007
--- License     :  GPL-style
---
--- Maintainer  :  Alberto Ruiz <aruiz@um.es>
+-- License     :  BSD3
+-- Maintainer  :  Alberto Ruiz
 -- Stability   :  provisional
--- Portability :  portable
 --
 -- Reexports all internal modules
 --
diff --git a/packages/base/src/Data/Packed/Matrix.hs b/packages/base/src/Data/Packed/Matrix.hs
index d94d167..b3be823 100644
--- a/packages/base/src/Data/Packed/Matrix.hs
+++ b/packages/base/src/Data/Packed/Matrix.hs
@@ -8,9 +8,8 @@
 -- |
 -- Module      :  Data.Packed.Matrix
 -- Copyright   :  (c) Alberto Ruiz 2007-10
--- License     :  GPL
---
--- Maintainer  :  Alberto Ruiz <aruiz@um.es>
+-- License     :  BSD3
+-- Maintainer  :  Alberto Ruiz
 -- Stability   :  provisional
 --
 -- A Matrix representation suitable for numerical computations using LAPACK and GSL.
diff --git a/packages/base/src/Data/Packed/Numeric.hs b/packages/base/src/Data/Packed/Numeric.hs
index 4892089..c13e91d 100644
--- a/packages/base/src/Data/Packed/Numeric.hs
+++ b/packages/base/src/Data/Packed/Numeric.hs
@@ -10,7 +10,6 @@
 -- Module      :  Data.Packed.Numeric
 -- Copyright   :  (c) Alberto Ruiz 2010-14
 -- License     :  BSD3
---
 -- Maintainer  :  Alberto Ruiz
 -- Stability   :  provisional
 --
diff --git a/packages/base/src/Data/Packed/ST.hs b/packages/base/src/Data/Packed/ST.hs
index dae457c..5c45c7b 100644
--- a/packages/base/src/Data/Packed/ST.hs
+++ b/packages/base/src/Data/Packed/ST.hs
@@ -9,12 +9,12 @@
 -- License     :  BSD3
 -- Maintainer  :  Alberto Ruiz
 -- Stability   :  provisional
--- Portability :  portable
 --
 -- In-place manipulation inside the ST monad.
 -- See examples/inplace.hs in the distribution.
 --
 -----------------------------------------------------------------------------
+{-# OPTIONS_HADDOCK hide #-}
 
 module Data.Packed.ST (
     -- * Mutable Vectors
diff --git a/packages/base/src/Data/Packed/Vector.hs b/packages/base/src/Data/Packed/Vector.hs
index a8f6bb1..53fe563 100644
--- a/packages/base/src/Data/Packed/Vector.hs
+++ b/packages/base/src/Data/Packed/Vector.hs
@@ -4,9 +4,8 @@
 -- |
 -- Module      :  Data.Packed.Vector
 -- Copyright   :  (c) Alberto Ruiz 2007-10
--- License     :  GPL
---
--- Maintainer  :  Alberto Ruiz <aruiz@um.es>
+-- License     :  BSD3
+-- Maintainer  :  Alberto Ruiz
 -- Stability   :  provisional
 --
 -- 1D arrays suitable for numeric computations using external libraries.
diff --git a/packages/base/src/Numeric/Container.hs b/packages/base/src/Numeric/Container.hs
index b7d3b80..240e5f5 100644
--- a/packages/base/src/Numeric/Container.hs
+++ b/packages/base/src/Numeric/Container.hs
@@ -9,11 +9,9 @@
 -- |
 -- Module      :  Numeric.Container
 -- Copyright   :  (c) Alberto Ruiz 2010-14
--- License     :  GPL
---
--- Maintainer  :  Alberto Ruiz <aruiz@um.es>
+-- License     :  BSD3
+-- Maintainer  :  Alberto Ruiz
 -- Stability   :  provisional
--- Portability :  portable
 --
 -- Basic numeric operations on 'Vector' and 'Matrix', including conversion routines.
 --
diff --git a/packages/base/src/Numeric/LinearAlgebra.hs b/packages/base/src/Numeric/LinearAlgebra.hs
deleted file mode 100644
index 1db860c..0000000
--- a/packages/base/src/Numeric/LinearAlgebra.hs
+++ /dev/null
@@ -1,30 +0,0 @@
------------------------------------------------------------------------------
-{- |
-Module      :  Numeric.LinearAlgebra
-Copyright   :  (c) Alberto Ruiz 2006-10
-License     :  GPL-style
-
-Maintainer  :  Alberto Ruiz (aruiz at um dot es)
-Stability   :  provisional
-Portability :  uses ffi
-
-This module reexports all normally required functions for Linear Algebra applications.
-
-It also provides instances of standard classes 'Show', 'Read', 'Eq',
-'Num', 'Fractional', and 'Floating' for 'Vector' and 'Matrix'.
-In arithmetic operations one-component vectors and matrices automatically
-expand to match the dimensions of the other operand.
-
--}
------------------------------------------------------------------------------
-{-# OPTIONS_HADDOCK hide #-}
-
-module Numeric.LinearAlgebra (
-    module Numeric.Container,
-    module Numeric.LinearAlgebra.Algorithms
-) where
-
-import Numeric.Container
-import Numeric.LinearAlgebra.Algorithms
-import Numeric.Matrix()
-import Numeric.Vector()
diff --git a/packages/base/src/Numeric/LinearAlgebra/Algorithms.hs b/packages/base/src/Numeric/LinearAlgebra/Algorithms.hs
index 6f40683..92761be 100644
--- a/packages/base/src/Numeric/LinearAlgebra/Algorithms.hs
+++ b/packages/base/src/Numeric/LinearAlgebra/Algorithms.hs
@@ -7,12 +7,10 @@
 -----------------------------------------------------------------------------
 {- |
 Module      :  Numeric.LinearAlgebra.Algorithms
-Copyright   :  (c) Alberto Ruiz 2006-9
-License     :  GPL-style
-
-Maintainer  :  Alberto Ruiz (aruiz at um dot es)
+Copyright   :  (c) Alberto Ruiz 2006-14
+License     :  BSD3
+Maintainer  :  Alberto Ruiz
 Stability   :  provisional
-Portability :  uses ffi
 
 High level generic interface to common matrix computations.
 
@@ -20,6 +18,7 @@ Specific functions for particular base types can also be explicitly
 imported from "Numeric.LinearAlgebra.LAPACK".
 
 -}
+{-# OPTIONS_HADDOCK hide #-}
 -----------------------------------------------------------------------------
 
 module Numeric.LinearAlgebra.Algorithms (
diff --git a/packages/base/src/Numeric/LinearAlgebra/Base.hs b/packages/base/src/Numeric/LinearAlgebra/Base.hs
new file mode 100644
index 0000000..8aa7846
--- /dev/null
+++ b/packages/base/src/Numeric/LinearAlgebra/Base.hs
@@ -0,0 +1,139 @@
+-----------------------------------------------------------------------------
+{- |
+Module      :  Numeric.LinearAlgebra
+Copyright   :  (c) Alberto Ruiz 2006-14
+License     :  BSD3
+Maintainer  :  Alberto Ruiz
+Stability   :  provisional
+
+This module reexports the most common Linear Algebra functions.
+
+-}
+-----------------------------------------------------------------------------
+module Numeric.LinearAlgebra.Base (
+
+    -- * Basic types and data processing    
+    module Numeric.LinearAlgebra.Data,
+    
+    -- | The standard numeric classes are defined elementwise:
+    --
+    -- >>> fromList [1,2,3] * fromList [3,0,-2 :: Double]
+    -- fromList [3.0,0.0,-6.0]
+    -- 
+    -- >>> (3><3) [1..9] * ident 3 :: Matrix Double
+    -- (3><3)
+    --  [ 1.0, 0.0, 0.0
+    --  , 0.0, 5.0, 0.0
+    --  , 0.0, 0.0, 9.0 ]
+    --
+    -- In arithmetic operations single-element vectors and matrices
+    -- (created from numeric literals or using 'scalar') automatically
+    -- expand to match the dimensions of the other operand:
+    -- 
+    -- >>> 5 + 2*ident 3 :: Matrix Double
+    -- (3><3)
+    --  [ 7.0, 5.0, 5.0
+    --  , 5.0, 7.0, 5.0
+    --  , 5.0, 5.0, 7.0 ]
+    --
+
+    -- * Products
+    (<.>),
+    
+    -- | The matrix product is also implemented in the "Data.Monoid" instance for Matrix, where
+    -- single-element matrices (created from numeric literals or using 'scalar')
+    -- are used for scaling.
+    --
+    -- >>> let m = (2><3)[1..] :: Matrix Double
+    -- >>> m <> 2 <> diagl[0.5,1,0]
+    -- (2><3)
+    -- [ 1.0,  4.0, 0.0
+    -- , 4.0, 10.0, 0.0 ]
+    --
+    -- mconcat uses 'optimiseMult' to get the optimal association order.
+ 
+    (◇),
+    outer, kronecker, cross,
+    scale,
+    sumElements, prodElements, absSum,
+    
+    -- * Linear Systems
+    (<\>),
+    linearSolve,
+    linearSolveLS,
+    linearSolveSVD,
+    luSolve,
+    cholSolve,
+    
+    -- * Inverse and pseudoinverse
+    inv, pinv, pinvTol,
+
+    -- * Determinant and rank
+    rcond, rank, ranksv, 
+    det, invlndet,
+    
+    -- * Singular value decomposition
+    svd,
+    fullSVD,
+    thinSVD,
+    compactSVD,
+    singularValues,
+    leftSV, rightSV,
+    
+    -- * Eigensystems
+    eig, eigSH, eigSH',
+    eigenvalues, eigenvaluesSH, eigenvaluesSH',
+    geigSH',
+
+    -- * QR
+    qr, rq, qrRaw, qrgr,
+
+    -- * Cholesky
+    chol, cholSH, mbCholSH,
+
+    -- * Hessenberg
+    hess,
+
+    -- * Schur
+    schur,
+
+    -- * LU
+    lu, luPacked,
+    
+    -- * Matrix functions
+    expm,
+    sqrtm,
+    matFunc,
+
+    -- * Nullspace
+    nullspacePrec,
+    nullVector,
+    nullspaceSVD,
+    null1, null1sym,
+    
+    orth,
+
+    -- * Norms
+    norm1, norm2, normInf, pnorm, NormType(..),
+
+    -- * Correlation and Convolution
+    corr, conv, corrMin, corr2, conv2,
+
+    -- * Random arrays
+
+    -- |    rand, randn, RandDist(..), randomVector, gaussianSample, uniformSample
+    
+    -- * Misc
+    meanCov, peps, relativeError, haussholder, optimiseMult, udot
+) where
+
+import Numeric.LinearAlgebra.Data
+
+import Numeric.Matrix()
+import Numeric.Vector()
+import Numeric.Container
+import Numeric.LinearAlgebra.Algorithms
+import Numeric.LinearAlgebra.Util
+
+
+
diff --git a/packages/base/src/Numeric/LinearAlgebra/Data.hs b/packages/base/src/Numeric/LinearAlgebra/Data.hs
new file mode 100644
index 0000000..3bc88f9
--- /dev/null
+++ b/packages/base/src/Numeric/LinearAlgebra/Data.hs
@@ -0,0 +1,68 @@
+--------------------------------------------------------------------------------
+{- |
+Module      :  Numeric.LinearAlgebra.Data
+Copyright   :  (c) Alberto Ruiz 2014
+License     :  BSD3
+Maintainer  :  Alberto Ruiz
+Stability   :  provisional
+
+Basic data processing.
+
+-}
+--------------------------------------------------------------------------------
+
+module Numeric.LinearAlgebra.Data(
+
+    -- * Vector
+    -- | 1D arrays are storable vectors from the vector package.
+    
+    Vector, (|>), dim, (@>),
+    
+    -- * Matrix
+    Matrix, (><), size, (@@>), trans, ctrans,
+    
+    -- * Construction
+    scalar, konst, build, assoc, accum, linspace, -- ones, zeros,
+
+    -- * Diagonal
+    ident, diag, diagl, diagRect, takeDiag,
+
+    -- * Data manipulation
+    fromList, toList, subVector, takesV, vjoin,
+    flatten, reshape, asRow, asColumn, row, col,
+    fromRows, toRows, fromColumns, toColumns, fromLists, toLists, fromArray2D,
+    takeRows, dropRows, takeColumns, dropColumns, subMatrix, (?), (¿), fliprl, flipud,
+  
+    -- * Block matrix
+    fromBlocks, (¦), (——), diagBlock, repmat, toBlocks, toBlocksEvery,
+
+    -- * Mapping functions
+    conj, cmap, step, cond,
+    
+    -- * Find elements
+    find, maxIndex, minIndex, maxElement, minElement, atIndex,
+
+    -- * IO
+    disp, dispf, disps, dispcf, latexFormat, format, readMatrix,
+
+    -- | loadMatrix, saveMatrix, fromFile, fileDimensions, fscanfVector, fprintfVector, freadVector, fwriteVector
+
+-- * Conversion
+    Convert(..),
+    
+    -- * Misc
+    arctan2,
+    rows, cols,
+    separable,
+
+    module Data.Complex
+
+) where
+
+import Data.Packed.Vector
+import Data.Packed.Matrix
+import Numeric.Container
+import Data.Packed.IO
+import Numeric.LinearAlgebra.Util
+import Data.Complex
+
diff --git a/packages/base/src/Numeric/LinearAlgebra/Devel.hs b/packages/base/src/Numeric/LinearAlgebra/Devel.hs
new file mode 100644
index 0000000..c41db2d
--- /dev/null
+++ b/packages/base/src/Numeric/LinearAlgebra/Devel.hs
@@ -0,0 +1,68 @@
+--------------------------------------------------------------------------------
+{- |
+Module      :  Numeric.HMatrix.Devel
+Copyright   :  (c) Alberto Ruiz 2014
+License     :  BSD3
+Maintainer  :  Alberto Ruiz
+Stability   :  provisional
+
+The library can be easily extended using the tools in this module.
+
+-}
+--------------------------------------------------------------------------------
+
+module Numeric.LinearAlgebra.Devel(
+    -- * FFI helpers
+    -- | Sample usage, to upload a perspective matrix to a shader.
+    --
+    -- @ glUniformMatrix4fv 0 1 (fromIntegral gl_TRUE) \`appMatrix\` perspective 0.01 100 (pi\/2) (4\/3)
+    -- @
+    module Data.Packed.Foreign,
+
+    -- * FFI tools
+    -- | Illustrative usage examples can be found
+    --   in the @examples\/devel@ folder included in the package.
+    module Data.Packed.Development,
+
+    -- * ST
+    -- | In-place manipulation inside the ST monad.
+    -- See examples\/inplace.hs in the distribution.
+    
+    -- ** Mutable Vectors
+    STVector, newVector, thawVector, freezeVector, runSTVector,
+    readVector, writeVector, modifyVector, liftSTVector,
+    -- ** Mutable Matrices
+    STMatrix, newMatrix, thawMatrix, freezeMatrix, runSTMatrix,
+    readMatrix, writeMatrix, modifyMatrix, liftSTMatrix,
+    -- ** Unsafe functions
+    newUndefinedVector,
+    unsafeReadVector, unsafeWriteVector,
+    unsafeThawVector, unsafeFreezeVector,
+    newUndefinedMatrix,
+    unsafeReadMatrix, unsafeWriteMatrix,
+    unsafeThawMatrix, unsafeFreezeMatrix,
+
+    -- * Special maps and zips
+    mapVectorWithIndex, zipVector, zipVectorWith, unzipVector, unzipVectorWith,
+    mapVectorM, mapVectorM_, mapVectorWithIndexM, mapVectorWithIndexM_,
+    foldLoop, foldVector, foldVectorG, foldVectorWithIndex,
+    mapMatrixWithIndex, mapMatrixWithIndexM, mapMatrixWithIndexM_,
+    liftMatrix, liftMatrix2, liftMatrix2Auto,
+
+    -- * Auxiliary classes
+    Element, Container, Product, Contraction, LSDiv,
+    Complexable(), RealElement(),
+    RealOf, ComplexOf, SingleOf, DoubleOf,
+    IndexOf,
+    Field, Normed
+) where
+
+import Data.Packed.Foreign
+import Data.Packed.Development
+import Data.Packed.ST
+import Numeric.Container(Container,Contraction,LSDiv,Product,
+                         Complexable(),RealElement(),
+                         RealOf, ComplexOf, SingleOf, DoubleOf, IndexOf)
+import Data.Packed
+import Numeric.LinearAlgebra.Algorithms(Field,Normed)
+
diff --git a/packages/base/src/Numeric/LinearAlgebra/LAPACK.hs b/packages/base/src/Numeric/LinearAlgebra/LAPACK.hs
index 9cb67d4..40fef45 100644
--- a/packages/base/src/Numeric/LinearAlgebra/LAPACK.hs
+++ b/packages/base/src/Numeric/LinearAlgebra/LAPACK.hs
@@ -3,7 +3,6 @@
 -- Module      :  Numeric.LinearAlgebra.LAPACK
 -- Copyright   :  (c) Alberto Ruiz 2006-14
 -- License     :  BSD3
--- 
 -- Maintainer  :  Alberto Ruiz
 -- Stability   :  provisional
 --
diff --git a/packages/base/src/Numeric/LinearAlgebra/Util.hs b/packages/base/src/Numeric/LinearAlgebra/Util.hs
index 533c54b..f0470ab 100644
--- a/packages/base/src/Numeric/LinearAlgebra/Util.hs
+++ b/packages/base/src/Numeric/LinearAlgebra/Util.hs
@@ -3,9 +3,8 @@
 {- |
 Module      :  Numeric.LinearAlgebra.Util
 Copyright   :  (c) Alberto Ruiz 2013
-License     :  GPL
-
-Maintainer  :  Alberto Ruiz (aruiz at um dot es)
+License     :  BSD3
+Maintainer  :  Alberto Ruiz
 Stability   :  provisional
 
 -}
diff --git a/packages/base/src/Numeric/LinearAlgebra/Util/Convolution.hs b/packages/base/src/Numeric/LinearAlgebra/Util/Convolution.hs
index d04c46b..1775f14 100644
--- a/packages/base/src/Numeric/LinearAlgebra/Util/Convolution.hs
+++ b/packages/base/src/Numeric/LinearAlgebra/Util/Convolution.hs
@@ -3,9 +3,8 @@
 {- |
 Module      :  Numeric.LinearAlgebra.Util.Convolution
 Copyright   :  (c) Alberto Ruiz 2012
-License     :  GPL
-
-Maintainer  :  Alberto Ruiz (aruiz at um dot es)
+License     :  BSD3
+Maintainer  :  Alberto Ruiz
 Stability   :  provisional
 
 -}
@@ -17,7 +16,7 @@ module Numeric.LinearAlgebra.Util.Convolution(
    corr2, conv2, separable
 ) where
 
-import Numeric.LinearAlgebra
+import Numeric.Container
 
 
 vectSS :: Element t => Int -> Vector t -> Matrix t
diff --git a/packages/base/src/Numeric/Matrix.hs b/packages/base/src/Numeric/Matrix.hs
index 3478aae..962ee84 100644
--- a/packages/base/src/Numeric/Matrix.hs
+++ b/packages/base/src/Numeric/Matrix.hs
@@ -7,12 +7,11 @@
 -----------------------------------------------------------------------------
 -- |
 -- Module      :  Numeric.Matrix
--- Copyright   :  (c) Alberto Ruiz 2010
--- License     :  GPL-style
+-- Copyright   :  (c) Alberto Ruiz 2014
+-- License     :  BSD3
 --
--- Maintainer  :  Alberto Ruiz <aruiz@um.es>
+-- Maintainer  :  Alberto Ruiz
 -- Stability   :  provisional
--- Portability :  portable
 --
 -- Provides instances of standard classes 'Show', 'Read', 'Eq',
 -- 'Num', 'Fractional', and 'Floating' for 'Matrix'.
diff --git a/packages/base/src/Numeric/Vector.hs b/packages/base/src/Numeric/Vector.hs
index 2769cd9..3a425f5 100644
--- a/packages/base/src/Numeric/Vector.hs
+++ b/packages/base/src/Numeric/Vector.hs
@@ -7,11 +7,10 @@
 -- |
 -- Module      :  Numeric.Vector
 -- Copyright   :  (c) Alberto Ruiz 2011
--- License     :  GPL-style
+-- License     :  BSD3
 --
--- Maintainer  :  Alberto Ruiz <aruiz@um.es>
+-- Maintainer  :  Alberto Ruiz
 -- Stability   :  provisional
--- Portability :  portable
 --
 -- Provides instances of standard classes 'Show', 'Read', 'Eq',
 -- 'Num', 'Fractional',  and 'Floating' for 'Vector'.