23 files changed, 92 insertions, 134 deletions

diff --git a/packages/base/hmatrix.cabal b/packages/base/hmatrix.cabal
index a487928..0ab4821 100644
--- a/packages/base/hmatrix.cabal
+++ b/packages/base/hmatrix.cabal
@@ -47,8 +47,7 @@ library
                         Numeric.LinearAlgebra.HMatrix
                         Numeric.LinearAlgebra.Static
 
-    other-modules:      Internal.Tools
-                        Internal.Vector
+    other-modules:      Internal.Vector
                         Internal.Devel
                         Internal.Vectorized
                         Internal.Matrix
diff --git a/packages/base/src/Internal/Algorithms.hs b/packages/base/src/Internal/Algorithms.hs
index 328af22..aaf6fbb 100644
--- a/packages/base/src/Internal/Algorithms.hs
+++ b/packages/base/src/Internal/Algorithms.hs
@@ -27,12 +27,9 @@ import Internal.Matrix
 import Internal.Element
 import Internal.Conversion
 import Internal.LAPACK as LAPACK
+import Internal.Numeric
 import Data.List(foldl1')
 import Data.Array
-import Internal.Numeric
-import Data.Vector.Storable(fromList)
-
--- :i mul
 
 {- | Generic linear algebra functions for double precision real and complex matrices.
 
diff --git a/packages/base/src/Internal/CG.hs b/packages/base/src/Internal/CG.hs
index 1193b18..fd14212 100644
--- a/packages/base/src/Internal/CG.hs
+++ b/packages/base/src/Internal/CG.hs
@@ -16,7 +16,6 @@ import Internal.Sparse
 import Numeric.Vector()
 import Internal.Algorithms(linearSolveLS, relativeError, pnorm, NormType(..))
 import Control.Arrow((***))
-import Data.Vector.Storable(fromList)
 
 {-
 import Util.Misc(debug, debugMat)
@@ -30,7 +29,6 @@ infix 0 ///
 v /// b = debugMat b 2 asRow v
 -}
 
-type R = Double
 type V = Vector R
 
 data CGState = CGState
diff --git a/packages/base/src/Internal/Container.hs b/packages/base/src/Internal/Container.hs
index 216e31e..f6355b2 100644
--- a/packages/base/src/Internal/Container.hs
+++ b/packages/base/src/Internal/Container.hs
@@ -24,14 +24,12 @@
 
 module Internal.Container where
 
-import Internal.Tools
 import Internal.Vector
 import Internal.Matrix
 import Internal.Element
 import Internal.Numeric
 import Data.Complex
 import Internal.Algorithms(Field,linearSolveSVD)
-import Data.Vector.Storable(fromList)
 
 ------------------------------------------------------------------
 
diff --git a/packages/base/src/Internal/Devel.hs b/packages/base/src/Internal/Devel.hs
index 61d2c85..b8e04ef 100644
--- a/packages/base/src/Internal/Devel.hs
+++ b/packages/base/src/Internal/Devel.hs
@@ -11,7 +11,6 @@
 module Internal.Devel where
 
 
-import Internal.Tools ( (//) )
 import Control.Monad ( when )
 import Foreign.C.Types ( CInt )
 --import Foreign.Storable.Complex ()
@@ -19,6 +18,11 @@ import Foreign.Ptr(Ptr)
 import Control.Exception as E ( SomeException, catch )
 
 
+-- | postfix function application (@flip ($)@)
+(//) :: x -> (x -> y) -> y
+infixl 0 //
+(//) = flip ($)
+
 -- hmm..
 ww2 w1 o1 w2 o2 f = w1 o1 $ w2 o2 . f
 ww3 w1 o1 w2 o2 w3 o3 f = w1 o1 $ ww2 w2 o2 w3 o3 . f
diff --git a/packages/base/src/Internal/Element.hs b/packages/base/src/Internal/Element.hs
index 61a75d8..55bff67 100644
--- a/packages/base/src/Internal/Element.hs
+++ b/packages/base/src/Internal/Element.hs
@@ -21,15 +21,14 @@
 
 module Internal.Element where
 
-import Internal.Tools
 import Internal.Vector
 import Internal.Matrix
 import Internal.Vectorized
 import qualified Internal.ST as ST
 import Data.Array
 import Text.Printf
-import Data.Vector.Storable(fromList)
 import Data.List(transpose,intersperse)
+import Data.List.Split(chunksOf)
 import Foreign.Storable(Storable)
 import Control.Monad(liftM)
 
@@ -165,6 +164,15 @@ m ?? (er,ec) = extractR m moder rs modec cs
 
 --------------------------------------------------------------------------------
 
+-- | obtains the common value of a property of a list
+common :: (Eq a) => (b->a) -> [b] -> Maybe a
+common f = commonval . map f
+  where
+    commonval :: (Eq a) => [a] -> Maybe a
+    commonval [] = Nothing
+    commonval [a] = Just a
+    commonval (a:b:xs) = if a==b then commonval (b:xs) else Nothing
+
 
 -- | creates a matrix from a vertical list of matrices
 joinVert :: Element t => [Matrix t] -> Matrix t
@@ -210,7 +218,7 @@ adaptBlocks ms = ms' where
     rs = map (compatdim . map rows) ms
     cs = map (compatdim . map cols) (transpose ms)
     szs = sequence [rs,cs]
-    ms' = splitEvery bc $ zipWith g szs (concat ms)
+    ms' = chunksOf bc $ zipWith g szs (concat ms)
 
     g [Just nr,Just nc] m
                 | nr == r && nc == c = m
diff --git a/packages/base/src/Internal/IO.hs b/packages/base/src/Internal/IO.hs
index e594a1c..a899cfd 100644
--- a/packages/base/src/Internal/IO.hs
+++ b/packages/base/src/Internal/IO.hs
@@ -16,16 +16,26 @@ module Internal.IO (
     loadMatrix, loadMatrix', saveMatrix
 ) where
 
-import Internal.Tools
 import Internal.Devel
 import Internal.Vector
 import Internal.Matrix
 import Internal.Vectorized
 import Text.Printf(printf)
-import Data.List(intersperse)
+import Data.List(intersperse,transpose)
 import Data.Complex
 
 
+-- | Formatting tool
+table :: String -> [[String]] -> String
+table sep as = unlines . map unwords' $ transpose mtp
+  where
+    mt = transpose as
+    longs = map (maximum . map length) mt
+    mtp = zipWith (\a b -> map (pad a) b) longs mt
+    pad n str = replicate (n - length str) ' ' ++ str
+    unwords' = concat . intersperse sep
+
+
 
 {- | Creates a string from a matrix given a separator and a function to show each entry. Using
 this function the user can easily define any desired display function:
diff --git a/packages/base/src/Internal/LAPACK.hs b/packages/base/src/Internal/LAPACK.hs
index 9cab3f8..d6a2e6e 100644
--- a/packages/base/src/Internal/LAPACK.hs
+++ b/packages/base/src/Internal/LAPACK.hs
@@ -20,19 +20,15 @@ import Internal.Vector
 import Internal.Matrix
 import Internal.Conversion
 import Internal.Element
-
 import Foreign.Ptr(nullPtr)
 import Foreign.C.Types
 import Control.Monad(when)
 import System.IO.Unsafe(unsafePerformIO)
-import Data.Vector.Storable(fromList)
 
 -----------------------------------------------------------------------------------
 
 type TMMM t = t ..> t ..> t ..> Ok
 
-type R = Double
-type C = Complex Double
 type F = Float
 type Q = Complex Float
 
diff --git a/packages/base/src/Internal/Matrix.hs b/packages/base/src/Internal/Matrix.hs
index 44365d0..d715cbf 100644
--- a/packages/base/src/Internal/Matrix.hs
+++ b/packages/base/src/Internal/Matrix.hs
@@ -16,12 +16,9 @@
 
 module Internal.Matrix where
 
-
-import Internal.Tools ( splitEvery, fi, compatdim, (//) )
 import Internal.Vector
 import Internal.Devel
 import Internal.Vectorized
-import Data.Vector.Storable ( unsafeWith, fromList )
 import Foreign.Marshal.Alloc ( free )
 import Foreign.Ptr ( Ptr )
 import Foreign.Storable ( Storable )
@@ -30,7 +27,7 @@ import Foreign.C.Types ( CInt(..) )
 import Foreign.C.String ( CString, newCString )
 import System.IO.Unsafe ( unsafePerformIO )
 import Control.DeepSeq ( NFData(..) )
-
+import Data.List.Split(chunksOf)
 
 -----------------------------------------------------------------
 
@@ -150,7 +147,22 @@ type t ::> s = Mt t s
 
 -- | the inverse of 'Data.Packed.Matrix.fromLists'
 toLists :: (Element t) => Matrix t -> [[t]]
-toLists m = splitEvery (cols m) . toList . flatten $ m
+toLists m = chunksOf (cols m) . toList . flatten $ m
+
+
+
+-- | common value with \"adaptable\" 1
+compatdim :: [Int] -> Maybe Int
+compatdim [] = Nothing
+compatdim [a] = Just a
+compatdim (a:b:xs)
+    | a==b = compatdim (b:xs)
+    | a==1 = compatdim (b:xs)
+    | b==1 = compatdim (a:xs)
+    | otherwise = Nothing
+
+
+
 
 -- | Create a matrix from a list of vectors.
 -- All vectors must have the same dimension,
diff --git a/packages/base/src/Internal/Modular.hs b/packages/base/src/Internal/Modular.hs
index 1116b96..cf50a05 100644
--- a/packages/base/src/Internal/Modular.hs
+++ b/packages/base/src/Internal/Modular.hs
@@ -29,13 +29,11 @@ import Internal.Vector
 import Internal.Matrix hiding (mat,size)
 import Internal.Numeric
 import Internal.Element
-import Internal.Tools
 import Internal.Container
 import Internal.Util(Indexable(..),gaussElim)
 import GHC.TypeLits
 import Data.Proxy(Proxy)
 import Foreign.ForeignPtr(castForeignPtr)
-import Data.Vector.Storable(fromList,unsafeToForeignPtr, unsafeFromForeignPtr)
 import Foreign.Storable
 import Data.Ratio
 
diff --git a/packages/base/src/Internal/Numeric.hs b/packages/base/src/Internal/Numeric.hs
index af665a4..879daf8 100644
--- a/packages/base/src/Internal/Numeric.hs
+++ b/packages/base/src/Internal/Numeric.hs
@@ -18,7 +18,6 @@
 
 module Internal.Numeric where
 
-import Internal.Tools
 import Internal.Vector
 import Internal.Matrix
 import Internal.Element
@@ -26,7 +25,7 @@ import Internal.ST as ST
 import Internal.Conversion
 import Internal.Vectorized
 import Internal.LAPACK(multiplyR,multiplyC,multiplyF,multiplyQ,multiplyI)
-import Data.Vector.Storable(fromList)
+import Data.List.Split(chunksOf)
 
 --------------------------------------------------------------------------------
 
@@ -617,7 +616,7 @@ m2=(4><3)
 -}
 kronecker :: (Product t) => Matrix t -> Matrix t -> Matrix t
 kronecker a b = fromBlocks
-              . splitEvery (cols a)
+              . chunksOf (cols a)
               . map (reshape (cols b))
               . toRows
               $ flatten a `outer` flatten b
diff --git a/packages/base/src/Internal/Random.hs b/packages/base/src/Internal/Random.hs
index c44c272..8c792eb 100644
--- a/packages/base/src/Internal/Random.hs
+++ b/packages/base/src/Internal/Random.hs
@@ -25,8 +25,6 @@ import Internal.Matrix
 import Internal.Numeric
 import Internal.Algorithms
 import System.Random(randomIO)
-import Data.Vector.Storable(fromList)
-
 
 -- | Obtains a matrix whose rows are pseudorandom samples from a multivariate
 -- Gaussian distribution.
diff --git a/packages/base/src/Internal/ST.hs b/packages/base/src/Internal/ST.hs
index 25e7969..ae75a1b 100644
--- a/packages/base/src/Internal/ST.hs
+++ b/packages/base/src/Internal/ST.hs
@@ -32,9 +32,6 @@ module Internal.ST (
 import Internal.Vector
 import Internal.Matrix
 import Internal.Vectorized
-import Data.Vector.Storable(unsafeWith)
-
-
 import Control.Monad.ST(ST, runST)
 import Foreign.Storable(Storable, peekElemOff, pokeElemOff)
 
diff --git a/packages/base/src/Internal/Sparse.hs b/packages/base/src/Internal/Sparse.hs
index 930bc99..b365c15 100644
--- a/packages/base/src/Internal/Sparse.hs
+++ b/packages/base/src/Internal/Sparse.hs
@@ -14,9 +14,7 @@ import Internal.Vector
 import Internal.Matrix
 import Internal.Numeric
 import Internal.Container
-import Internal.Tools
 import qualified Data.Vector.Storable as V
-import Data.Vector.Storable(fromList)
 import Data.Function(on)
 import Control.Arrow((***))
 import Control.Monad(when)
diff --git a/packages/base/src/Internal/Static.hs b/packages/base/src/Internal/Static.hs
index 48327e5..01c2205 100644
--- a/packages/base/src/Internal/Static.hs
+++ b/packages/base/src/Internal/Static.hs
@@ -25,8 +25,8 @@ module Internal.Static where
 
 import GHC.TypeLits
 import qualified Numeric.LinearAlgebra as LA
-import Numeric.LinearAlgebra hiding (konst,size)
-import Internal.Vector as D
+import Numeric.LinearAlgebra hiding (konst,size,R,C)
+import Internal.Vector as D hiding (R,C)
 import Internal.ST
 import Data.Proxy(Proxy)
 import Foreign.Storable(Storable)
diff --git a/packages/base/src/Internal/Tools.hs b/packages/base/src/Internal/Tools.hs
deleted file mode 100644
index 47115bc..0000000
--- a/packages/base/src/Internal/Tools.hs
+++ /dev/null
@@ -1,61 +0,0 @@
--- |
--- Module      :  Internal.Tools
--- Copyright   :  (c) Alberto Ruiz 2007-15
--- License     :  BSD3
--- Maintainer  :  Alberto Ruiz
--- Stability   :  provisional
---
-
-module Internal.Tools where
-
-import Data.List(transpose,intersperse)
-import Foreign.C.Types(CInt)
-import Data.List.Split
-
-type I = CInt
-
-splitEvery :: Int -> [e] -> [[e]]
-splitEvery = chunksOf
-
--- | postfix function application (@flip ($)@)
-(//) :: x -> (x -> y) -> y
-infixl 0 //
-(//) = flip ($)
-
--- | specialized fromIntegral
-fi :: Int -> CInt
-fi = fromIntegral
-
--- | specialized fromIntegral
-ti :: CInt -> Int
-ti = fromIntegral
-
--- | obtains the common value of a property of a list
-common :: (Eq a) => (b->a) -> [b] -> Maybe a
-common f = commonval . map f
-  where
-    commonval :: (Eq a) => [a] -> Maybe a
-    commonval [] = Nothing
-    commonval [a] = Just a
-    commonval (a:b:xs) = if a==b then commonval (b:xs) else Nothing
-
--- | common value with \"adaptable\" 1
-compatdim :: [Int] -> Maybe Int
-compatdim [] = Nothing
-compatdim [a] = Just a
-compatdim (a:b:xs)
-    | a==b = compatdim (b:xs)
-    | a==1 = compatdim (b:xs)
-    | b==1 = compatdim (a:xs)
-    | otherwise = Nothing
-
--- | Formatting tool
-table :: String -> [[String]] -> String
-table sep as = unlines . map unwords' $ transpose mtp
-  where 
-    mt = transpose as
-    longs = map (maximum . map length) mt
-    mtp = zipWith (\a b -> map (pad a) b) longs mt
-    pad n str = replicate (n - length str) ' ' ++ str
-    unwords' = concat . intersperse sep
-
diff --git a/packages/base/src/Internal/Util.hs b/packages/base/src/Internal/Util.hs
index 9900770..e9cf155 100644
--- a/packages/base/src/Internal/Util.hs
+++ b/packages/base/src/Internal/Util.hs
@@ -56,7 +56,6 @@ module Internal.Util(
     gaussElim
 ) where
 
-import Internal.Tools
 import Internal.Vector
 import Internal.Matrix hiding (size)
 import Internal.Numeric
@@ -76,7 +75,6 @@ import Data.List(intercalate,sortBy)
 import Data.Function(on)
 import Control.Arrow((&&&))
 import Data.Complex
-import Data.Vector.Storable(fromList)
 
 type ℝ = Double
 type ℕ = Int
diff --git a/packages/base/src/Internal/Vector.hs b/packages/base/src/Internal/Vector.hs
index 27ee13c..0e9161d 100644
--- a/packages/base/src/Internal/Vector.hs
+++ b/packages/base/src/Internal/Vector.hs
@@ -10,38 +10,56 @@
 -- Stability   :  provisional
 --
 
-module Internal.Vector where
-
-import Internal.Tools
-import Foreign.Marshal.Array ( peekArray, copyArray, advancePtr )
-import Foreign.ForeignPtr ( ForeignPtr, castForeignPtr )
-import Foreign.Ptr ( Ptr )
+module Internal.Vector(
+    I,Z,R,C,
+    fi,ti,
+    Vector, fromList, unsafeToForeignPtr, unsafeFromForeignPtr, unsafeWith,
+    createVector, vec,
+    toList, dim, (@>), at', (|>),
+    vjoin, subVector, takesV, idxs,
+    buildVector,
+    asReal, asComplex,
+    toByteString,fromByteString,
+    zipVector, unzipVector, zipVectorWith, unzipVectorWith,
+    foldVector, foldVectorG, foldVectorWithIndex, foldLoop,
+    mapVector, mapVectorM, mapVectorM_,
+    mapVectorWithIndex, mapVectorWithIndexM, mapVectorWithIndexM_
+) where
+
+import Foreign.Marshal.Array
+import Foreign.ForeignPtr
+import Foreign.Ptr
 import Foreign.Storable
-    ( Storable, peekElemOff, pokeElemOff, sizeOf )
-import Foreign.C.Types ( CInt )
-import Data.Complex ( Complex )
-import System.IO.Unsafe ( unsafePerformIO )
-import GHC.ForeignPtr ( mallocPlainForeignPtrBytes )
-import GHC.Base ( realWorld#, IO(IO), when )
+import Foreign.C.Types(CInt)
+import Data.Int(Int64)
+import Data.Complex
+import System.IO.Unsafe(unsafePerformIO)
+import GHC.ForeignPtr(mallocPlainForeignPtrBytes)
+import GHC.Base(realWorld#, IO(IO), when)
 import qualified Data.Vector.Storable as Vector
-    ( Vector, slice, length )
-import Data.Vector.Storable
-    ( fromList, unsafeToForeignPtr, unsafeFromForeignPtr, unsafeWith )
-
+import Data.Vector.Storable(Vector, fromList, unsafeToForeignPtr, unsafeFromForeignPtr, unsafeWith)
 
 #ifdef BINARY
-
 import Data.Binary
 import Control.Monad(replicateM)
 import qualified Data.ByteString.Internal as BS
 import Data.Vector.Storable.Internal(updPtr)
-import Foreign.Ptr(plusPtr)
-
 #endif
 
+type I = CInt
+type Z = Int64
+type R = Double
+type C = Complex Double
+
+
+-- | specialized fromIntegral
+fi :: Int -> CInt
+fi = fromIntegral
 
+-- | specialized fromIntegral
+ti :: CInt -> Int
+ti = fromIntegral
 
-type Vector = Vector.Vector
 
 -- | Number of elements
 dim :: (Storable t) => Vector t -> Int
diff --git a/packages/base/src/Internal/Vectorized.hs b/packages/base/src/Internal/Vectorized.hs
index ddb14c9..b9b8239 100644
--- a/packages/base/src/Internal/Vectorized.hs
+++ b/packages/base/src/Internal/Vectorized.hs
@@ -14,10 +14,8 @@
 
 module Internal.Vectorized where
 
-import Internal.Tools
 import Internal.Vector
 import Internal.Devel
-
 import Data.Complex
 import Foreign.Marshal.Alloc(free,malloc)
 import Foreign.Marshal.Array(newArray,copyArray)
@@ -26,9 +24,8 @@ import Foreign.Storable(peek,Storable)
 import Foreign.C.Types
 import Foreign.C.String
 import System.IO.Unsafe(unsafePerformIO)
-
 import Control.Monad(when)
-import Data.Vector.Storable ( unsafeWith )
+
 
 
 fromei x = fromIntegral (fromEnum x) :: CInt
diff --git a/packages/base/src/Numeric/LinearAlgebra/Data.hs b/packages/base/src/Numeric/LinearAlgebra/Data.hs
index 196ada9..06485e6 100644
--- a/packages/base/src/Numeric/LinearAlgebra/Data.hs
+++ b/packages/base/src/Numeric/LinearAlgebra/Data.hs
@@ -88,12 +88,11 @@ module Numeric.LinearAlgebra.Data(
     separable,
     fromArray2D,
     module Data.Complex,
-    I,F,
+    R,C,I,Z,F,
     Vector, Matrix, GMatrix, nRows, nCols
 
 ) where
 
-import Internal.Tools
 import Internal.Vector
 import Internal.Vectorized
 import Internal.Matrix hiding (size)
@@ -105,6 +104,5 @@ import Internal.Util hiding ((&),(#))
 import Data.Complex
 import Internal.Sparse
 import Internal.Modular
-import Data.Vector.Storable(fromList)
 
 
diff --git a/packages/base/src/Numeric/LinearAlgebra/Devel.hs b/packages/base/src/Numeric/LinearAlgebra/Devel.hs
index 4d5b5cb..1a70663 100644
--- a/packages/base/src/Numeric/LinearAlgebra/Devel.hs
+++ b/packages/base/src/Numeric/LinearAlgebra/Devel.hs
@@ -68,7 +68,6 @@ module Numeric.LinearAlgebra.Devel(
 
 ) where
 
-import Internal.Tools
 import Internal.Foreign
 import Internal.Devel
 import Internal.ST
@@ -76,5 +75,4 @@ import Internal.Vector
 import Internal.Matrix
 import Internal.Element
 import Internal.Sparse
-import Data.Vector.Storable (unsafeToForeignPtr, unsafeFromForeignPtr )
 
diff --git a/packages/base/src/Numeric/LinearAlgebra/Static.hs b/packages/base/src/Numeric/LinearAlgebra/Static.hs
index 04c4151..dee5b2c 100644
--- a/packages/base/src/Numeric/LinearAlgebra/Static.hs
+++ b/packages/base/src/Numeric/LinearAlgebra/Static.hs
@@ -65,7 +65,7 @@ import Numeric.LinearAlgebra hiding (
     row,col,vector,matrix,linspace,toRows,toColumns,
     (<\>),fromList,takeDiag,svd,eig,eigSH,eigSH',
     eigenvalues,eigenvaluesSH,eigenvaluesSH',build,
-    qr,size,app,mul,dot,chol,range)
+    qr,size,app,mul,dot,chol,range,R,C)
 import qualified Numeric.LinearAlgebra as LA
 import Data.Proxy(Proxy)
 import Internal.Static
diff --git a/packages/base/src/Numeric/Vector.hs b/packages/base/src/Numeric/Vector.hs
index 7525890..076f485 100644
--- a/packages/base/src/Numeric/Vector.hs
+++ b/packages/base/src/Numeric/Vector.hs
@@ -19,11 +19,9 @@
 
 module Numeric.Vector () where
 
-import Internal.Tools
 import Internal.Vectorized
 import Internal.Vector
 import Internal.Numeric
-import Data.Vector.Storable(fromList)
 import Internal.Conversion
 
 -------------------------------------------------------------------