instances moved to base

8 files changed, 18 insertions, 175 deletions

diff --git a/packages/base/hmatrix-base.cabal b/packages/base/hmatrix-base.cabal
index 8571e7a..8eeb97e 100644
--- a/packages/base/hmatrix-base.cabal
+++ b/packages/base/hmatrix-base.cabal
@@ -39,12 +39,15 @@ library
                         Numeric.LinearAlgebra.LAPACK
                         Data.Packed.Numeric
                         Numeric.Vectorized
+                        Numeric.Vector
+                        Numeric.Matrix
                         
     other-modules:      Data.Packed.Internal,
                         Data.Packed.Internal.Common,
                         Data.Packed.Internal.Signatures,
                         Data.Packed.Internal.Vector,
                         Data.Packed.Internal.Matrix
+                        Numeric.Chain
 
     C-sources:          src/C/lapack-aux.c
                         src/C/vector-aux.c
diff --git a/packages/hmatrix/src/Numeric/Chain.hs b/packages/base/src/Numeric/Chain.hs
index de6a86f..fbdb01b 100644
--- a/packages/hmatrix/src/Numeric/Chain.hs
+++ b/packages/base/src/Numeric/Chain.hs
@@ -130,7 +130,7 @@ chain_paren (r,c) ixes ma = let ((lr,lc),(rr,rc)) = fromJust $ (ixes A.! r) A.!
 
 --------------------------------------------------------------------------
 
-{- TESTS -}
+{- TESTS
 
 -- optimal association is ((m1*(m2*m3))*m4)
 m1, m2, m3, m4 :: Matrix Double
@@ -138,3 +138,6 @@ m1 = (10><15) [1..]
 m2 = (15><20) [1..]
 m3 = (20><5) [1..]
 m4 = (5><10) [1..]
+
+-}
+
diff --git a/packages/hmatrix/src/Numeric/Matrix.hs b/packages/base/src/Numeric/Matrix.hs
index e285ff2..3478aae 100644
--- a/packages/hmatrix/src/Numeric/Matrix.hs
+++ b/packages/base/src/Numeric/Matrix.hs
@@ -27,9 +27,11 @@ module Numeric.Matrix (
 
 -------------------------------------------------------------------
 
-import Numeric.Container
+import Data.Packed
+import Data.Packed.Numeric
 import qualified Data.Monoid as M
 import Data.List(partition)
+import Numeric.Chain
 
 -------------------------------------------------------------------
 
diff --git a/packages/hmatrix/src/Numeric/Vector.hs b/packages/base/src/Numeric/Vector.hs
index 4c59d32..2769cd9 100644
--- a/packages/hmatrix/src/Numeric/Vector.hs
+++ b/packages/base/src/Numeric/Vector.hs
@@ -21,7 +21,8 @@
 module Numeric.Vector () where
 
 import Numeric.Vectorized
-import Numeric.Container
+import Data.Packed.Vector
+import Data.Packed.Numeric
 
 -------------------------------------------------------------------
 
diff --git a/packages/hmatrix/Config.hs b/packages/hmatrix/Config.hs
deleted file mode 100644
index 5145d1a..0000000
--- a/packages/hmatrix/Config.hs
+++ /dev/null
@@ -1,154 +0,0 @@
-{-
-    GSL and LAPACK may require auxiliary libraries which depend on OS,
-    distribution, and implementation. This script tries to to find out
-    the correct link command for your system.
-    Suggestions and contributions are welcome.
-
-    By default we try to link -lgsl -llapack. This works in ubuntu/debian,
-    both with and without ATLAS.
-    If this fails we try different sets of additional libraries which are
-    known to work in some systems.
-
-    The desired libraries can also be explicitly given by the user using cabal
-    flags (e.g., -fmkl, -faccelerate) or --configure-option=link:lib1,lib2,lib3,...
-
--}
-
-module Config(config) where
-
-import System.Process
-import System.Exit
-import System.Environment
-import System.Directory(createDirectoryIfMissing)
-import System.FilePath((</>))
-import Data.List(isPrefixOf, intercalate)
-import Distribution.Simple.LocalBuildInfo
-import Distribution.Simple.Configure
-import Distribution.PackageDescription
-
--- possible additional dependencies for the desired libs (by default gsl lapack)
-
-opts = [ ""                              -- Ubuntu/Debian
-       , "blas"
-       , "blas cblas"
-       , "cblas"
-       , "gslcblas"
-       , "blas gslcblas"
-       , "f77blas"
-       , "f77blas cblas atlas gcc_s"     -- Arch Linux (older version of atlas-lapack)
-       , "blas gslcblas gfortran"        -- Arch Linux with normal blas and lapack
-       ]
-
--- location of test program
-testProgLoc bInfo = buildDir bInfo </> "dummy.c"
-testOutLoc bInfo = buildDir bInfo </> "dummy"
-
--- write test program
-writeTestProg bInfo contents = writeFile (testProgLoc bInfo) contents
-
--- compile, discarding error messages
-compile cmd = do
-    let processRecord = (shell $ unwords cmd) { std_out = CreatePipe
-                                           , std_err = CreatePipe }
-    ( _, _, _, h) <- createProcess processRecord
-    waitForProcess h
-
--- command to compile the test program
-compileCmd bInfo buildInfo = [ "gcc "
-                             , (unwords $ ccOptions buildInfo)  
-                             , (unwords $ cppOptions buildInfo) 
-                             , (unwords $ map ("-I"++) $ includeDirs buildInfo) 
-                             , testProgLoc bInfo
-                             , "-o"
-                             , testOutLoc bInfo 
-                             , (unwords $ map ("-L"++) $ extraLibDirs buildInfo) 
-                             ]
- 
--- compile a simple program with symbols from GSL and LAPACK with the given libs
-testprog bInfo buildInfo libs fmks = do
-    writeTestProg bInfo "#include <gsl/gsl_sf_gamma.h>\nint main(){dgemm_(); zgesvd_(); gsl_sf_gamma(5);}"
-    compile $ compileCmd bInfo 
-                         buildInfo 
-                            ++ [ (prepend "-l" $ libs)
-                               , (prepend "-framework " fmks) ] 
-
-prepend x = unwords . map (x++) . words
-
-check bInfo buildInfo libs fmks = (ExitSuccess ==) `fmap` testprog bInfo buildInfo libs fmks
-
--- simple test for GSL
-gsl bInfo buildInfo = do
-    writeTestProg bInfo "#include <gsl/gsl_sf_gamma.h>\nint main(){gsl_sf_gamma(5);}"
-    compile $ compileCmd bInfo buildInfo ++ ["-lgsl", "-lgslcblas"]
-
--- test for gsl >= 1.12
-gsl112 bInfo buildInfo = do
-    writeTestProg bInfo "#include <gsl/gsl_sf_exp.h>\nint main(){gsl_sf_exprel_n_CF_e(1,1,0);}"
-    compile $ compileCmd bInfo buildInfo ++ ["-lgsl", "-lgslcblas"]
-
--- test for odeiv2
-gslodeiv2 bInfo buildInfo = do
-    writeTestProg bInfo "#include <gsl/gsl_odeiv2.h>\nint main(){return 0;}"
-    compile $ compileCmd bInfo buildInfo ++ ["-lgsl", "-lgslcblas"]
-
-checkCommand c = (ExitSuccess ==) `fmap` c
-
--- test different configurations until the first one works
-try _ _ _ _ [] = return Nothing
-try l i b f (opt:rest) = do
-    ok <- check l i (b ++ " " ++ opt) f
-    if ok then return (Just opt)
-          else try l i b f rest
-
--- read --configure-option=link:lib1,lib2,lib3,etc
-linkop = "--configure-option=link:"
-getUserLink = concatMap (g . drop (length linkop)) . filter (isPrefixOf linkop)
-    where g = map cs
-          cs ',' = ' '
-          cs x   = x
-
-config :: LocalBuildInfo -> IO HookedBuildInfo
-          
-config bInfo = do
-    putStr "Checking foreign libraries..."
-    args <- getArgs
-
-    let Just lib = library . localPkgDescr $ bInfo
-        buildInfo = libBuildInfo lib
-        base = unwords . extraLibs $ buildInfo
-        fwks = unwords . frameworks $ buildInfo
-        auxpref = getUserLink args
-
-    -- We extract the desired libs from hmatrix.cabal (using a cabal flags)
-    -- and from a posible --configure-option=link:lib1,lib2,lib3
-    -- by default the desired libs are gsl lapack.
-
-    let pref = if null (words (base ++ " " ++ auxpref)) then "gsl lapack" else auxpref
-        fullOpts = map ((pref++" ")++) opts
-
-    -- create the build directory (used for tmp files) if necessary
-    createDirectoryIfMissing True $ buildDir bInfo
-    
-    r <- try bInfo buildInfo base fwks fullOpts
-
-    case r of
-        Nothing -> do
-            putStrLn " FAIL"
-            g  <- checkCommand $ gsl bInfo buildInfo
-            if g
-                then putStrLn " *** Sorry, I can't link LAPACK."
-                else putStrLn " *** Sorry, I can't link GSL."
-            putStrLn " *** Please make sure that the appropriate -dev packages are installed."
-            putStrLn " *** You can also specify the required libraries using"
-            putStrLn " *** cabal install hmatrix --configure-option=link:lib1,lib2,lib3,etc."            
-            return (Just emptyBuildInfo { buildable = False }, [])
-        Just ops -> do
-            putStrLn $ " OK " ++ ops
-            g1 <- checkCommand $ gsl112 bInfo buildInfo
-            let op1 = if g1 then "" else "-DGSL110"
-            g2 <- checkCommand $ gslodeiv2 bInfo buildInfo
-            let op2 = if g2 then "" else "-DGSLODE1"
-                opts = filter (not.null) [op1,op2]
-            let hbi = emptyBuildInfo { extraLibs = words ops, ccOptions = opts }
-            return (Just hbi, [])
-
diff --git a/packages/hmatrix/Setup.lhs b/packages/hmatrix/Setup.lhs
index e3f9847..4b19c19 100644
--- a/packages/hmatrix/Setup.lhs
+++ b/packages/hmatrix/Setup.lhs
@@ -1,18 +1,5 @@
 #! /usr/bin/env runhaskell
 
 > import Distribution.Simple
-> import Distribution.Simple.Setup
-> import Distribution.PackageDescription
-> import Distribution.Simple.LocalBuildInfo
-
-> import System.Process(system)
-> import Config(config)
-
-> main = defaultMainWithHooks simpleUserHooks { confHook = c }
-
-> c x y = do
->     binfo <- confHook simpleUserHooks x y
->     pbi <- config binfo
->     let pkg_descr = localPkgDescr binfo
->     return $ binfo { localPkgDescr = updatePackageDescription pbi pkg_descr }
+> main = defaultMain
 
diff --git a/packages/hmatrix/hmatrix.cabal b/packages/hmatrix/hmatrix.cabal
index 73edac4..369c412 100644
--- a/packages/hmatrix/hmatrix.cabal
+++ b/packages/hmatrix/hmatrix.cabal
@@ -102,9 +102,6 @@ library
                         Numeric.GSL.Internal,
                         Numeric.GSL.Vector,
                         Numeric.IO,
-                        Numeric.Chain,
-                        Numeric.Vector,
-                        Numeric.Matrix,
                         Numeric.LinearAlgebra.Util.Convolution
                         
 
diff --git a/packages/hmatrix/src/Numeric/Container.hs b/packages/hmatrix/src/Numeric/Container.hs
index 645a83f..e7f23d4 100644
--- a/packages/hmatrix/src/Numeric/Container.hs
+++ b/packages/hmatrix/src/Numeric/Container.hs
@@ -66,11 +66,11 @@ module Numeric.Container (
 
 import Data.Packed hiding (stepD, stepF, condD, condF, conjugateC, conjugateQ)
 import Data.Packed.Numeric
-import Numeric.Chain
 import Numeric.IO
 import Data.Complex
 import Numeric.LinearAlgebra.Algorithms(Field,linearSolveSVD)
 import Numeric.Random
+import Data.Monoid(Monoid(mconcat))
 
 ------------------------------------------------------------------
 
@@ -268,4 +268,8 @@ infixl 7 ◇
 dot :: (Container Vector t, Product t) => Vector t -> Vector t -> t
 dot u v = udot (conj u) v
 
+--------------------------------------------------------------------------------
+
+optimiseMult :: Monoid (Matrix t) => [Matrix t] -> Matrix t
+optimiseMult = mconcat