update other pkgs to ghc-7.10

13 files changed, 63 insertions, 54 deletions

diff --git a/packages/gsl/hmatrix-gsl.cabal b/packages/gsl/hmatrix-gsl.cabal
index 95fa3ed..70e4246 100644
--- a/packages/gsl/hmatrix-gsl.cabal
+++ b/packages/gsl/hmatrix-gsl.cabal
@@ -1,5 +1,5 @@
 Name:               hmatrix-gsl
-Version:            0.16.0.3
+Version:            0.17.0.0
 License:            GPL
 License-file:       LICENSE
 Author:             Alberto Ruiz
@@ -25,7 +25,7 @@ flag onlygsl
 
 library
 
-    Build-Depends:      base<5, hmatrix>=0.16, array, vector,
+    Build-Depends:      base<5, hmatrix>=0.17, array, vector,
                         process, random
 
 
diff --git a/packages/gsl/src/Graphics/Plot.hs b/packages/gsl/src/Graphics/Plot.hs
index 0ea41ac..d2ea192 100644
--- a/packages/gsl/src/Graphics/Plot.hs
+++ b/packages/gsl/src/Graphics/Plot.hs
@@ -27,13 +27,13 @@ module Graphics.Plot(
 
 ) where
 
-import Numeric.Container
+import Numeric.LinearAlgebra.HMatrix
 import Data.List(intersperse)
 import System.Process (system)
 
 -- | From vectors x and y, it generates a pair of matrices to be used as x and y arguments for matrix functions.
 meshdom :: Vector Double -> Vector Double -> (Matrix Double , Matrix Double)
-meshdom r1 r2 = (outer r1 (constant 1 (dim r2)), outer (constant 1 (dim r1)) r2)
+meshdom r1 r2 = (outer r1 (konst 1 (size r2)), outer (konst 1 (size r1)) r2)
 
 
 {- | Draws a 3D surface representation of a real matrix.
diff --git a/packages/gsl/src/Numeric/GSL/Fitting.hs b/packages/gsl/src/Numeric/GSL/Fitting.hs
index 0a92373..db9d82f 100644
--- a/packages/gsl/src/Numeric/GSL/Fitting.hs
+++ b/packages/gsl/src/Numeric/GSL/Fitting.hs
@@ -1,3 +1,5 @@
+{-# LANGUAGE FlexibleContexts #-}
+
 {- |
 Module      :  Numeric.GSL.Fitting
 Copyright   :  (c) Alberto Ruiz 2010
@@ -50,7 +52,7 @@ module Numeric.GSL.Fitting (
     fitModelScaled, fitModel
 ) where
 
-import Numeric.LinearAlgebra
+import Numeric.LinearAlgebra.HMatrix
 import Numeric.GSL.Internal
 
 import Foreign.Ptr(FunPtr, freeHaskellFunPtr)
@@ -80,13 +82,13 @@ nlFitting :: FittingMethod
 nlFitting method epsabs epsrel maxit fun jac xinit = nlFitGen (fi (fromEnum method)) fun jac xinit epsabs epsrel maxit
 
 nlFitGen m f jac xiv epsabs epsrel maxit = unsafePerformIO $ do
-    let p   = dim xiv
-        n   = dim (f xiv)
+    let p   = size xiv
+        n   = size (f xiv)
     fp <- mkVecVecfun (aux_vTov (checkdim1 n p . f))
     jp <- mkVecMatfun (aux_vTom (checkdim2 n p . jac))
     rawpath <- createMatrix RowMajor maxit (2+p)
     app2 (c_nlfit m fp jp epsabs epsrel (fi maxit) (fi n)) vec xiv mat rawpath "c_nlfit"
-    let it = round (rawpath @@> (maxit-1,0))
+    let it = round (rawpath `atIndex` (maxit-1,0))
         path = takeRows it rawpath
         [sol] = toRows $ dropRows (it-1) path
     freeHaskellFunPtr fp
@@ -99,7 +101,7 @@ foreign import ccall safe "nlfit"
 -------------------------------------------------------
 
 checkdim1 n _p v
-    | dim v == n = v
+    | size v == n = v
     | otherwise = error $ "Error: "++ show n
                         ++ " components expected in the result of the function supplied to nlFitting"
 
@@ -114,9 +116,9 @@ err (model,deriv) dat vsol = zip sol errs where
     sol = toList vsol
     c = max 1 (chi/sqrt (fromIntegral dof))
     dof = length dat - (rows cov)
-    chi = norm2 (fromList $ cost (resMs model) dat sol)
+    chi = norm_2 (fromList $ cost (resMs model) dat sol)
     js = fromLists $ jacobian (resDs deriv) dat sol
-    cov = inv $ trans js <> js
+    cov = inv $ tr js <> js
     errs = toList $ scalar c * sqrt (takeDiag cov)
 
 
diff --git a/packages/gsl/src/Numeric/GSL/Fourier.hs b/packages/gsl/src/Numeric/GSL/Fourier.hs
index 734325b..d824b4f 100644
--- a/packages/gsl/src/Numeric/GSL/Fourier.hs
+++ b/packages/gsl/src/Numeric/GSL/Fourier.hs
@@ -16,14 +16,13 @@ module Numeric.GSL.Fourier (
     ifft
 ) where
 
-import Data.Packed
+import Numeric.LinearAlgebra.HMatrix
 import Numeric.GSL.Internal
-import Data.Complex
 import Foreign.C.Types
 import System.IO.Unsafe (unsafePerformIO)
 
 genfft code v = unsafePerformIO $ do
-    r <- createVector (dim v)
+    r <- createVector (size v)
     app2 (c_fft code) vec v vec r "fft"
     return r
 
diff --git a/packages/gsl/src/Numeric/GSL/IO.hs b/packages/gsl/src/Numeric/GSL/IO.hs
index 0d6031a..936f6bf 100644
--- a/packages/gsl/src/Numeric/GSL/IO.hs
+++ b/packages/gsl/src/Numeric/GSL/IO.hs
@@ -14,7 +14,7 @@ module Numeric.GSL.IO (
     fileDimensions, loadMatrix, fromFile
 ) where
 
-import Data.Packed
+import Numeric.LinearAlgebra.HMatrix hiding(saveMatrix, loadMatrix)
 import Numeric.GSL.Vector
 import System.Process(readProcess)
 
diff --git a/packages/gsl/src/Numeric/GSL/Internal.hs b/packages/gsl/src/Numeric/GSL/Internal.hs
index a1c4e0c..a269224 100644
--- a/packages/gsl/src/Numeric/GSL/Internal.hs
+++ b/packages/gsl/src/Numeric/GSL/Internal.hs
@@ -22,14 +22,13 @@ module Numeric.GSL.Internal(
     aux_vTom,
     createV,
     createMIO,
-    module Data.Packed.Development,
+    module Numeric.LinearAlgebra.Devel,
     check,
     Res,TV,TM,TCV,TCM
 ) where
 
-import Data.Packed
-import Data.Packed.Development hiding (check)
-import Data.Complex
+import Numeric.LinearAlgebra.HMatrix
+import Numeric.LinearAlgebra.Devel hiding (check)
 
 import Foreign.Marshal.Array(copyArray)
 import Foreign.Ptr(Ptr, FunPtr)
diff --git a/packages/gsl/src/Numeric/GSL/LinearAlgebra.hs b/packages/gsl/src/Numeric/GSL/LinearAlgebra.hs
index 17e2258..cb78bf4 100644
--- a/packages/gsl/src/Numeric/GSL/LinearAlgebra.hs
+++ b/packages/gsl/src/Numeric/GSL/LinearAlgebra.hs
@@ -15,7 +15,7 @@ module Numeric.GSL.LinearAlgebra (
     fileDimensions, loadMatrix, fromFile
 ) where
 
-import Data.Packed
+import Numeric.LinearAlgebra.HMatrix hiding (RandDist,randomVector,saveMatrix,loadMatrix)
 import Numeric.GSL.Internal hiding (TV,TM,TCV,TCM)
 
 import Foreign.Marshal.Alloc(free)
diff --git a/packages/gsl/src/Numeric/GSL/Minimization.hs b/packages/gsl/src/Numeric/GSL/Minimization.hs
index 056d463..00e0619 100644
--- a/packages/gsl/src/Numeric/GSL/Minimization.hs
+++ b/packages/gsl/src/Numeric/GSL/Minimization.hs
@@ -1,3 +1,6 @@
+{-# LANGUAGE FlexibleContexts #-}
+
+
 {- |
 Module      :  Numeric.GSL.Minimization
 Copyright   :  (c) Alberto Ruiz 2006-9
@@ -56,7 +59,7 @@ module Numeric.GSL.Minimization (
 ) where
 
 
-import Data.Packed
+import Numeric.LinearAlgebra.HMatrix hiding(step)
 import Numeric.GSL.Internal
 
 import Foreign.Ptr(Ptr, FunPtr, freeHaskellFunPtr)
@@ -99,7 +102,7 @@ uniMinimizeGen m f xmin xl xu epsrel maxit = unsafePerformIO $ do
     rawpath <- createMIO maxit 4
                          (c_uniMinize m fp epsrel (fi maxit) xmin xl xu)
                          "uniMinimize"
-    let it = round (rawpath @@> (maxit-1,0))
+    let it = round (rawpath `atIndex` (maxit-1,0))
         path = takeRows it rawpath
         [sol] = toLists $ dropRows (it-1) path
     freeHaskellFunPtr fp
@@ -137,13 +140,13 @@ minimize method eps maxit sz f xi = v2l $ minimizeV method eps maxit (fromList s
 ww2 w1 o1 w2 o2 f = w1 o1 $ \a1 -> w2 o2 $ \a2 -> f a1 a2
 
 minimizeV method eps maxit szv f xiv = unsafePerformIO $ do
-    let n   = dim xiv
+    let n   = size xiv
     fp <- mkVecfun (iv f)
     rawpath <- ww2 vec xiv vec szv $ \xiv' szv' ->
                    createMIO maxit (n+3)
                          (c_minimize (fi (fromEnum method)) fp eps (fi maxit) // xiv' // szv')
                          "minimize"
-    let it = round (rawpath @@> (maxit-1,0))
+    let it = round (rawpath `atIndex` (maxit-1,0))
         path = takeRows it rawpath
         sol = flatten $ dropColumns 3 $ dropRows (it-1) path
     freeHaskellFunPtr fp
@@ -191,7 +194,7 @@ minimizeD method eps maxit istep tol f df xi = v2l $ minimizeVD
 
 
 minimizeVD method eps maxit istep tol f df xiv = unsafePerformIO $ do
-    let n = dim xiv
+    let n = size xiv
         f' = f
         df' = (checkdim1 n . df)
     fp <- mkVecfun (iv f')
@@ -200,7 +203,7 @@ minimizeVD method eps maxit istep tol f df xiv = unsafePerformIO $ do
                     createMIO maxit (n+2)
                          (c_minimizeD (fi (fromEnum method)) fp dfp istep tol eps (fi maxit) // xiv')
                          "minimizeD"
-    let it = round (rawpath @@> (maxit-1,0))
+    let it = round (rawpath `atIndex` (maxit-1,0))
         path = takeRows it rawpath
         sol = flatten $ dropColumns 2 $ dropRows (it-1) path
     freeHaskellFunPtr fp
@@ -217,6 +220,6 @@ foreign import ccall safe "gsl-aux.h minimizeD"
 ---------------------------------------------------------------------
 
 checkdim1 n v
-    | dim v == n = v
+    | size v == n = v
     | otherwise = error $ "Error: "++ show n
                         ++ " components expected in the result of the gradient supplied to minimizeD"
diff --git a/packages/gsl/src/Numeric/GSL/ODE.hs b/packages/gsl/src/Numeric/GSL/ODE.hs
index 7549a65..3258b83 100644
--- a/packages/gsl/src/Numeric/GSL/ODE.hs
+++ b/packages/gsl/src/Numeric/GSL/ODE.hs
@@ -1,3 +1,6 @@
+{-# LANGUAGE FlexibleContexts #-}
+
+
 {- |
 Module      :  Numeric.GSL.ODE
 Copyright   :  (c) Alberto Ruiz 2010
@@ -32,7 +35,7 @@ module Numeric.GSL.ODE (
     odeSolve, odeSolveV, ODEMethod(..), Jacobian
 ) where
 
-import Data.Packed
+import Numeric.LinearAlgebra.HMatrix
 import Numeric.GSL.Internal
 
 import Foreign.Ptr(FunPtr, nullFunPtr, freeHaskellFunPtr)
@@ -68,7 +71,7 @@ odeSolve
     -> Vector Double   -- ^ desired solution times
     -> Matrix Double   -- ^ solution
 odeSolve xdot xi ts = odeSolveV RKf45 hi epsAbs epsRel (l2v xdot) (fromList xi) ts
-    where hi = (ts@>1 - ts@>0)/100
+    where hi = (ts!1 - ts!0)/100
           epsAbs = 1.49012e-08
           epsRel = 1.49012e-08
           l2v f = \t -> fromList  . f t . toList
@@ -107,14 +110,14 @@ odeSolveV'
     -> Vector Double     -- ^ desired solution times
     -> Matrix Double     -- ^ solution
 odeSolveV' method mbjac h epsAbs epsRel f  xiv ts = unsafePerformIO $ do
-    let n   = dim xiv
+    let n   = size xiv
     fp <- mkDoubleVecVecfun (\t -> aux_vTov (checkdim1 n . f t))
     jp <- case mbjac of
         Just jac -> mkDoubleVecMatfun (\t -> aux_vTom (checkdim2 n . jac t))
         Nothing  -> return nullFunPtr
     sol <- vec xiv $ \xiv' ->
             vec (checkTimes ts) $ \ts' ->
-             createMIO (dim ts) n
+             createMIO (size ts) n
               (ode_c (method) h epsAbs epsRel fp jp // xiv' // ts' )
               "ode"
     freeHaskellFunPtr fp
@@ -126,7 +129,7 @@ foreign import ccall safe "ode"
 -------------------------------------------------------
 
 checkdim1 n v
-    | dim v == n = v
+    | size v == n = v
     | otherwise = error $ "Error: "++ show n
                         ++ " components expected in the result of the function supplied to odeSolve"
 
@@ -135,6 +138,7 @@ checkdim2 n m
     | otherwise = error $ "Error: "++ show n ++ "x" ++ show n
                         ++ " Jacobian expected in odeSolve"
 
-checkTimes ts | dim ts > 1 && all (>0) (zipWith subtract ts' (tail ts')) = ts
+checkTimes ts | size ts > 1 && all (>0) (zipWith subtract ts' (tail ts')) = ts
               | otherwise = error "odeSolve requires increasing times"
     where ts' = toList ts
+
diff --git a/packages/gsl/src/Numeric/GSL/Polynomials.hs b/packages/gsl/src/Numeric/GSL/Polynomials.hs
index b1be85d..246e301 100644
--- a/packages/gsl/src/Numeric/GSL/Polynomials.hs
+++ b/packages/gsl/src/Numeric/GSL/Polynomials.hs
@@ -16,9 +16,8 @@ module Numeric.GSL.Polynomials (
     polySolve
 ) where
 
-import Data.Packed
+import Numeric.LinearAlgebra.HMatrix
 import Numeric.GSL.Internal
-import Data.Complex
 import System.IO.Unsafe (unsafePerformIO)
 
 #if __GLASGOW_HASKELL__ >= 704
@@ -47,8 +46,8 @@ polySolve :: [Double] -> [Complex Double]
 polySolve = toList . polySolve' . fromList
 
 polySolve' :: Vector Double -> Vector (Complex Double)
-polySolve' v | dim v > 1 = unsafePerformIO $ do
-    r <- createVector (dim v-1)
+polySolve' v | size v > 1 = unsafePerformIO $ do
+    r <- createVector (size v-1)
     app2 c_polySolve vec v vec r "polySolve"
     return r
              | otherwise = error "polySolve on a polynomial of degree zero"
diff --git a/packages/gsl/src/Numeric/GSL/Random.hs b/packages/gsl/src/Numeric/GSL/Random.hs
index f1f49e5..139c921 100644
--- a/packages/gsl/src/Numeric/GSL/Random.hs
+++ b/packages/gsl/src/Numeric/GSL/Random.hs
@@ -21,11 +21,13 @@ module Numeric.GSL.Random (
 ) where
 
 import Numeric.GSL.Vector
-import Numeric.LinearAlgebra(cholSH)
-import Numeric.Container hiding (
+import Numeric.LinearAlgebra.HMatrix hiding (
     randomVector,
     gaussianSample,
-    uniformSample
+    uniformSample,
+    Seed,
+    rand,
+    randn
     )
 import System.Random(randomIO)
 
@@ -40,10 +42,10 @@ gaussianSample :: Seed
                -> Matrix Double -- ^ covariance matrix
                -> Matrix Double -- ^ result
 gaussianSample seed n med cov = m where
-    c = dim med
+    c = size med
     meds = konst 1 n `outer` med
     rs = reshape c $ randomVector seed Gaussian (c * n)
-    m = rs `mXm` cholSH cov `add` meds
+    m = rs <> cholSH cov + meds
 
 -- | Obtains a matrix whose rows are pseudorandom samples from a multivariate
 -- uniform distribution.
@@ -55,10 +57,10 @@ uniformSample seed n rgs = m where
     (as,bs) = unzip rgs
     a = fromList as
     cs = zipWith subtract as bs
-    d = dim a
+    d = size a
     dat = toRows $ reshape n $ randomVector seed Uniform (n*d)
     am = konst 1 n `outer` a
-    m = fromColumns (zipWith scale cs dat) `add` am
+    m = fromColumns (zipWith scale cs dat) + am
 
 -- | pseudorandom matrix with uniform elements between 0 and 1
 randm :: RandDist
diff --git a/packages/gsl/src/Numeric/GSL/Root.hs b/packages/gsl/src/Numeric/GSL/Root.hs
index b9f3b94..724f32f 100644
--- a/packages/gsl/src/Numeric/GSL/Root.hs
+++ b/packages/gsl/src/Numeric/GSL/Root.hs
@@ -1,3 +1,5 @@
+{-# LANGUAGE  FlexibleContexts #-}
+
 {- |
 Module      :  Numeric.GSL.Root
 Copyright   :  (c) Alberto Ruiz 2009
@@ -39,7 +41,7 @@ module Numeric.GSL.Root (
     rootJ, RootMethodJ(..),
 ) where
 
-import Data.Packed
+import Numeric.LinearAlgebra.HMatrix
 import Numeric.GSL.Internal
 import Foreign.Ptr(FunPtr, freeHaskellFunPtr)
 import Foreign.C.Types
@@ -69,7 +71,7 @@ uniRootGen m f xl xu epsrel maxit = unsafePerformIO $ do
     rawpath <- createMIO maxit 4
                          (c_root m fp epsrel (fi maxit) xl xu)
                          "root"
-    let it = round (rawpath @@> (maxit-1,0))
+    let it = round (rawpath `atIndex` (maxit-1,0))
         path = takeRows it rawpath
         [sol] = toLists $ dropRows (it-1) path
     freeHaskellFunPtr fp
@@ -100,7 +102,7 @@ uniRootJGen m f df x epsrel maxit = unsafePerformIO $ do
     rawpath <- createMIO maxit 2
                          (c_rootj m fp dfp epsrel (fi maxit) x)
                          "rootj"
-    let it = round (rawpath @@> (maxit-1,0))
+    let it = round (rawpath `atIndex` (maxit-1,0))
         path = takeRows it rawpath
         [sol] = toLists $ dropRows (it-1) path
     freeHaskellFunPtr fp
@@ -132,13 +134,13 @@ root method epsabs maxit fun xinit = rootGen (fi (fromEnum method)) fun xinit ep
 
 rootGen m f xi epsabs maxit = unsafePerformIO $ do
     let xiv = fromList xi
-        n   = dim xiv
+        n   = size xiv
     fp <- mkVecVecfun (aux_vTov (checkdim1 n . fromList . f . toList))
     rawpath <- vec xiv $ \xiv' ->
                    createMIO maxit (2*n+1)
                          (c_multiroot m fp epsabs (fi maxit) // xiv')
                          "multiroot"
-    let it = round (rawpath @@> (maxit-1,0))
+    let it = round (rawpath `atIndex` (maxit-1,0))
         path = takeRows it rawpath
         [sol] = toLists $ dropRows (it-1) path
     freeHaskellFunPtr fp
@@ -169,14 +171,14 @@ rootJ method epsabs maxit fun jac xinit = rootJGen (fi (fromEnum method)) fun ja
 
 rootJGen m f jac xi epsabs maxit = unsafePerformIO $ do
     let xiv = fromList xi
-        n   = dim xiv
+        n   = size xiv
     fp <- mkVecVecfun (aux_vTov (checkdim1 n . fromList . f . toList))
     jp <- mkVecMatfun (aux_vTom (checkdim2 n . fromLists . jac . toList))
     rawpath <- vec xiv $ \xiv' ->
                    createMIO maxit (2*n+1)
                          (c_multirootj m fp jp epsabs (fi maxit) // xiv')
                          "multiroot"
-    let it = round (rawpath @@> (maxit-1,0))
+    let it = round (rawpath `atIndex` (maxit-1,0))
         path = takeRows it rawpath
         [sol] = toLists $ dropRows (it-1) path
     freeHaskellFunPtr fp
@@ -189,7 +191,7 @@ foreign import ccall safe "multirootj"
 -------------------------------------------------------
 
 checkdim1 n v
-    | dim v == n = v
+    | size v == n = v
     | otherwise = error $ "Error: "++ show n
                         ++ " components expected in the result of the function supplied to root"
 
diff --git a/packages/gsl/src/Numeric/GSL/Vector.hs b/packages/gsl/src/Numeric/GSL/Vector.hs
index af79f32..0cd99eb 100644
--- a/packages/gsl/src/Numeric/GSL/Vector.hs
+++ b/packages/gsl/src/Numeric/GSL/Vector.hs
@@ -14,8 +14,7 @@ module Numeric.GSL.Vector (
     fwriteVector, freadVector, fprintfVector, fscanfVector
 ) where
 
-import Data.Packed
-import Numeric.LinearAlgebra(RandDist(..))
+import Numeric.LinearAlgebra.HMatrix hiding(randomVector, saveMatrix)
 import Numeric.GSL.Internal hiding (TV,TM,TCV,TCM)
 
 import Foreign.Marshal.Alloc(free)