hmatrix 0.15.2.0 → 0.15.2.1

raw patch · 10 files changed

+103/−61 lines, 10 filesdep ~arraydep ~basedep ~binary

Dependency ranges changed: array, base, binary, process

Files

• Config.hs +5/−6
• INSTALL.md +9/−2
• THANKS.md +12/−0
• hmatrix.cabal +7/−2
• lib/Data/Packed/Internal/Matrix.hs +1/−1
• lib/Data/Packed/Internal/Vector.hs +3/−7
• lib/Numeric/ContainerBoot.hs +25/−5
• lib/Numeric/GSL/Integration.hs +27/−24
• lib/Numeric/GSL/gsl-aux.c +12/−12
• lib/Numeric/LinearAlgebra/Util.hs +2/−2

@@ -48,20 +48,20 @@  -- compile, discarding error messages compile cmd = do-    let processRecord = (shell $ join cmd) { std_out = CreatePipe+    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 "-                             , (join $ ccOptions buildInfo)  -                             , (join $ cppOptions buildInfo) -                             , (join $ map ("-I"++) $ includeDirs buildInfo) +                             , (unwords $ ccOptions buildInfo)  +                             , (unwords $ cppOptions buildInfo) +                             , (unwords $ map ("-I"++) $ includeDirs buildInfo)                               , testProgLoc bInfo                              , "-o"                              , testOutLoc bInfo -                             , (join $ map ("-L"++) $ extraLibDirs buildInfo) +                             , (unwords $ map ("-L"++) $ extraLibDirs buildInfo)                               ]   -- compile a simple program with symbols from GSL and LAPACK with the given libs@@ -72,7 +72,6 @@                             ++ [ (prepend "-l" $ libs)                                , (prepend "-framework " fmks) ]  -join = intercalate " " prepend x = unwords . map (x++) . words  check bInfo buildInfo libs fmks = (ExitSuccess ==) `fmap` testprog bInfo buildInfo libs fmks

@@ -21,12 +21,19 @@ ## Mac OS/X ###############################################  -GSL must be installed via MacPorts:+GSL must be installed via Homebrew or MacPorts. +Via Homebrew:++    $ brew install gsl+    $ cabal install hmatrix++Via MacPorts:+     $ sudo port install gsl +universal     $ cabal install hmatrix -(Contributed by Heinrich Apfelmus and Torsten Kemps-Benedix).+(Contributed by Heinrich Apfelmus, Torsten Kemps-Benedix and Ted Fujimoto).  ## Windows ############################################### 

@@ -141,3 +141,15 @@  - Henning Thielemann reported the pinv inefficient implementation. +- bdoering reported the problem of zero absolute tolerance in the integration functions.++- Alexei Uimanov replaced fromList by Vector.fromList.++- Adam Vogt updated the code for ghc-7.7++- Mike Meyer (mwm) added freeBSD library configuration information.++- tfgit updated the OSX installation instructions via Homebrew+++

@@ -1,5 +1,5 @@ Name:               hmatrix-Version:            0.15.2.0+Version:            0.15.2.1 License:            GPL License-file:       LICENSE Author:             Alberto Ruiz@@ -21,7 +21,7 @@                     .                     - "Numeric.LinearAlgebra": everything + instances of standard Haskell numeric classes Category:           Math-tested-with:        GHC ==7.6+tested-with:        GHC ==7.8  cabal-version:      >=1.8 @@ -185,6 +185,11 @@         if arch(i386)             cc-options: -arch i386         frameworks: Accelerate++    if os(freebsd)+       extra-lib-dirs: /usr/local/lib+       include-dirs: /usr/local/include+       extra-libraries: gsl blas lapack      if os(windows)         extra-libraries: gsl-0 blas lapack

@@ -154,7 +154,7 @@ fromRows :: Element t => [Vector t] -> Matrix t fromRows vs = case compatdim (map dim vs) of     Nothing -> error "fromRows applied to [] or to vectors with different sizes"-    Just c  -> reshape c . join . map (adapt c) $ vs+    Just c  -> reshape c . Data.Packed.Internal.Vector.join . map (adapt c) $ vs   where     adapt c v | dim v == c = v               | otherwise = constantD (v@>0) c

@@ -16,7 +16,7 @@ module Data.Packed.Internal.Vector (     Vector, dim,     fromList, toList, (|>),-    join, (@>), safe, at, at', subVector, takesV,+    Data.Packed.Internal.Vector.join, (@>), safe, at, at', subVector, takesV,     mapVector, mapVectorWithIndex, zipVectorWith, unzipVectorWith,     mapVectorM, mapVectorM_, mapVectorWithIndexM, mapVectorWithIndexM_,     foldVector, foldVectorG, foldLoop, foldVectorWithIndex,@@ -34,7 +34,7 @@ import Data.Packed.Internal.Common import Data.Packed.Internal.Signatures import Foreign.Marshal.Alloc(free)-import Foreign.Marshal.Array(peekArray, pokeArray, copyArray, advancePtr)+import Foreign.Marshal.Array(peekArray, copyArray, advancePtr) import Foreign.ForeignPtr(ForeignPtr, castForeignPtr) import Foreign.Ptr(Ptr) import Foreign.Storable(Storable, peekElemOff, pokeElemOff, sizeOf)@@ -57,6 +57,7 @@  import qualified Data.Vector.Storable as Vector import Data.Vector.Storable(Vector,+                            fromList,                             unsafeToForeignPtr,                             unsafeFromForeignPtr,                             unsafeWith)@@ -102,11 +103,6 @@ 4 |> [2.0,3.0,5.0,7.0]@  -}-fromList :: Storable a => [a] -> Vector a-fromList l = unsafePerformIO $ do-    v <- createVector (length l)-    unsafeWith v $ \ p -> pokeArray p l-    return v  safeRead v = inlinePerformIO . unsafeWith v {-# INLINE safeRead #-}

@@ -510,20 +510,40 @@ class Build f where     build' :: BoundsOf f -> f -> ContainerOf f -type family BoundsOf x +#if MIN_VERSION_base(4,7,0)+-- ghc >= 7.7 considers:+--+-- > a -> a+-- > b -> b -> b+--+-- to overlap+type family BoundsOf x where+    BoundsOf (a -> a) = Int+    BoundsOf (a->a->a) = (Int,Int)+type family ContainerOf x where+    ContainerOf (a->a) = Vector a+    ContainerOf (a->a->a) = Matrix a+#else+type family BoundsOf x+type family ContainerOf x type instance BoundsOf (a->a) = Int type instance BoundsOf (a->a->a) = (Int,Int)--type family ContainerOf x- type instance ContainerOf (a->a) = Vector a type instance ContainerOf (a->a->a) = Matrix a+#endif + instance (Element a, Num a) => Build (a->a) where     build' = buildV -instance (Element a, Num a) => Build (a->a->a) where+instance (Element a,+#if MIN_VERSION_base(4,7,0)+        BoundsOf (a -> a -> a) ~ (Int,Int),+        ContainerOf (a -> a -> a) ~ Matrix a,+#endif+        Num a)+        => Build (a->a->a) where     build' = buildM  buildM (rc,cc) f = fromLists [ [f r c | c <- cs] | r <- rs ]

@@ -31,6 +31,8 @@ import Data.Packed.Internal(check,(//)) import System.IO.Unsafe(unsafePerformIO) +eps = 1e-12+ {- | conversion of Haskell functions into function pointers that can be used in the C side -} foreign import ccall safe "wrapper" mkfun:: (Double -> Ptr() -> Double) -> IO( FunPtr (Double -> Ptr() -> Double)) @@ -55,7 +57,7 @@     r <- malloc     e <- malloc     fp <- mkfun (\x _ -> f x) -    c_integrate_qags fp a b prec (fromIntegral n) r e // check "integrate_qags"+    c_integrate_qags fp a b eps prec (fromIntegral n) r e // check "integrate_qags"     vr <- peek r     ve <- peek e     let result = (vr,ve)@@ -64,9 +66,9 @@     freeHaskellFunPtr fp     return result -foreign import ccall safe "gsl-aux.h integrate_qags" - c_integrate_qags :: FunPtr (Double-> Ptr() -> Double) -> Double -> Double -> Double -> CInt-                     -> Ptr Double -> Ptr Double -> IO CInt+foreign import ccall safe "integrate_qags" c_integrate_qags+    :: FunPtr (Double-> Ptr() -> Double) -> Double -> Double+    -> Double -> Double -> CInt -> Ptr Double -> Ptr Double -> IO CInt  ----------------------------------------------------------------- {- | Numerical integration using /gsl_integration_qng/ (useful for fast integration of smooth functions). For example:@@ -86,7 +88,7 @@     r <- malloc     e <- malloc     fp <- mkfun (\x _ -> f x) -    c_integrate_qng fp a b prec r e  // check "integrate_qng"+    c_integrate_qng fp a b eps prec r e  // check "integrate_qng"     vr <- peek r     ve <- peek e     let result = (vr,ve)@@ -95,9 +97,9 @@     freeHaskellFunPtr fp     return result -foreign import ccall safe "gsl-aux.h integrate_qng" - c_integrate_qng :: FunPtr (Double-> Ptr() -> Double) -> Double -> Double -> Double -                    -> Ptr Double -> Ptr Double -> IO CInt+foreign import ccall safe "integrate_qng" c_integrate_qng+    :: FunPtr (Double-> Ptr() -> Double) -> Double -> Double+    -> Double -> Double -> Ptr Double -> Ptr Double -> IO CInt  -------------------------------------------------------------------- {- | Numerical integration using /gsl_integration_qagi/ (integration over the infinite integral -Inf..Inf using QAGS). @@ -118,7 +120,7 @@     r <- malloc     e <- malloc     fp <- mkfun (\x _ -> f x) -    c_integrate_qagi fp prec (fromIntegral n) r e // check "integrate_qagi"+    c_integrate_qagi fp eps prec (fromIntegral n) r e // check "integrate_qagi"     vr <- peek r     ve <- peek e     let result = (vr,ve)@@ -127,9 +129,9 @@     freeHaskellFunPtr fp     return result -foreign import ccall safe "gsl-aux.h integrate_qagi" - c_integrate_qagi :: FunPtr (Double-> Ptr() -> Double) -> Double -> CInt-                     -> Ptr Double -> Ptr Double -> IO CInt+foreign import ccall safe "integrate_qagi" c_integrate_qagi+    :: FunPtr (Double-> Ptr() -> Double) -> Double -> Double+    -> CInt -> Ptr Double -> Ptr Double -> IO CInt  -------------------------------------------------------------------- {- | Numerical integration using /gsl_integration_qagiu/ (integration over the semi-infinite integral a..Inf). @@ -151,7 +153,7 @@     r <- malloc     e <- malloc     fp <- mkfun (\x _ -> f x) -    c_integrate_qagiu fp a prec (fromIntegral n) r e // check "integrate_qagiu"+    c_integrate_qagiu fp a eps prec (fromIntegral n) r e // check "integrate_qagiu"     vr <- peek r     ve <- peek e     let result = (vr,ve)@@ -160,9 +162,9 @@     freeHaskellFunPtr fp     return result -foreign import ccall safe "gsl-aux.h integrate_qagiu" - c_integrate_qagiu :: FunPtr (Double-> Ptr() -> Double) -> Double -> Double -> CInt-                     -> Ptr Double -> Ptr Double -> IO CInt+foreign import ccall safe "integrate_qagiu" c_integrate_qagiu+    :: FunPtr (Double-> Ptr() -> Double) -> Double -> Double+    -> Double -> CInt -> Ptr Double -> Ptr Double -> IO CInt  -------------------------------------------------------------------- {- | Numerical integration using /gsl_integration_qagil/ (integration over the semi-infinite integral -Inf..b). @@ -184,7 +186,7 @@     r <- malloc     e <- malloc     fp <- mkfun (\x _ -> f x) -    c_integrate_qagil fp b prec (fromIntegral n) r e // check "integrate_qagil"+    c_integrate_qagil fp b eps prec (fromIntegral n) r e // check "integrate_qagil"     vr <- peek r     ve <- peek e     let result = (vr,ve)@@ -193,9 +195,9 @@     freeHaskellFunPtr fp     return result -foreign import ccall safe "gsl-aux.h integrate_qagil" - c_integrate_qagil :: FunPtr (Double-> Ptr() -> Double) -> Double -> Double -> CInt-                     -> Ptr Double -> Ptr Double -> IO CInt+foreign import ccall safe "gsl-aux.h integrate_qagil" c_integrate_qagil+    :: FunPtr (Double-> Ptr() -> Double) -> Double -> Double+    -> Double -> CInt -> Ptr Double -> Ptr Double -> IO CInt   --------------------------------------------------------------------@@ -231,7 +233,7 @@     e <- malloc     neval <- malloc     fp <- mkfun (\x _ -> f x)-    c_integrate_cquad fp a b prec (fromIntegral n) r e neval // check "integrate_cquad"+    c_integrate_cquad fp a b eps prec (fromIntegral n) r e neval // check "integrate_cquad"     vr <- peek r     ve <- peek e     vneval <- peek neval@@ -242,6 +244,7 @@     freeHaskellFunPtr fp     return result -foreign import ccall safe "gsl-aux.h integrate_cquad" - c_integrate_cquad :: FunPtr (Double-> Ptr() -> Double) -> Double -> Double -> Double -> CInt-                     -> Ptr Double -> Ptr Double -> Ptr Int -> IO CInt+foreign import ccall safe "integrate_cquad" c_integrate_cquad+    :: FunPtr (Double-> Ptr() -> Double) -> Double -> Double+    -> Double -> Double -> CInt -> Ptr Double -> Ptr Double -> Ptr Int -> IO CInt+

@@ -737,80 +737,80 @@ }  -int integrate_qng(double f(double, void*), double a, double b, double prec,+int integrate_qng(double f(double, void*), double a, double b, double aprec, double prec,                    double *result, double*error) {     DEBUGMSG("integrate_qng");     gsl_function F;     F.function = f;     F.params = NULL;     size_t neval;-    int res = gsl_integration_qng (&F, a,b, 0, prec, result, error, &neval); +    int res = gsl_integration_qng (&F, a,b, aprec, prec, result, error, &neval);     CHECK(res,res);     OK } -int integrate_qags(double f(double,void*), double a, double b, double prec, int w, +int integrate_qags(double f(double,void*), double a, double b, double aprec, double prec, int w,                double *result, double* error) {     DEBUGMSG("integrate_qags");     gsl_integration_workspace * wk = gsl_integration_workspace_alloc (w);     gsl_function F;     F.function = f;     F.params = NULL;-    int res = gsl_integration_qags (&F, a,b, 0, prec, w,wk, result, error); +    int res = gsl_integration_qags (&F, a,b, aprec, prec, w,wk, result, error);     CHECK(res,res);     gsl_integration_workspace_free (wk);      OK } -int integrate_qagi(double f(double,void*), double prec, int w, +int integrate_qagi(double f(double,void*), double aprec, double prec, int w,                double *result, double* error) {     DEBUGMSG("integrate_qagi");     gsl_integration_workspace * wk = gsl_integration_workspace_alloc (w);     gsl_function F;     F.function = f;     F.params = NULL;-    int res = gsl_integration_qagi (&F, 0, prec, w,wk, result, error); +    int res = gsl_integration_qagi (&F, aprec, prec, w,wk, result, error);     CHECK(res,res);     gsl_integration_workspace_free (wk);      OK }  -int integrate_qagiu(double f(double,void*), double a, double prec, int w, +int integrate_qagiu(double f(double,void*), double a, double aprec, double prec, int w,                double *result, double* error) {     DEBUGMSG("integrate_qagiu");     gsl_integration_workspace * wk = gsl_integration_workspace_alloc (w);     gsl_function F;     F.function = f;     F.params = NULL;-    int res = gsl_integration_qagiu (&F, a, 0, prec, w,wk, result, error); +    int res = gsl_integration_qagiu (&F, a, aprec, prec, w,wk, result, error);     CHECK(res,res);     gsl_integration_workspace_free (wk);      OK }  -int integrate_qagil(double f(double,void*), double b, double prec, int w, +int integrate_qagil(double f(double,void*), double b, double aprec, double prec, int w,                double *result, double* error) {     DEBUGMSG("integrate_qagil");     gsl_integration_workspace * wk = gsl_integration_workspace_alloc (w);     gsl_function F;     F.function = f;     F.params = NULL;-    int res = gsl_integration_qagil (&F, b, 0, prec, w,wk, result, error); +    int res = gsl_integration_qagil (&F, b, aprec, prec, w,wk, result, error);     CHECK(res,res);     gsl_integration_workspace_free (wk);      OK } -int integrate_cquad(double f(double,void*), double a, double b, double prec,+int integrate_cquad(double f(double,void*), double a, double b, double aprec, double prec,                     int w, double *result, double* error, int *neval) {     DEBUGMSG("integrate_cquad");     gsl_integration_cquad_workspace * wk = gsl_integration_cquad_workspace_alloc (w);     gsl_function F;     F.function = f;     F.params = NULL;-    int res = gsl_integration_cquad (&F, a, b, 0, prec, wk, result, error, neval); +    int res = gsl_integration_cquad (&F, a, b, aprec, prec, wk, result, error, neval);     CHECK(res,res);     gsl_integration_cquad_workspace_free (wk);      OK

@@ -97,7 +97,7 @@ -- | concatenation of real vectors infixl 3 & (&) :: Vector Double -> Vector Double -> Vector Double-a & b = join [a,b]+a & b = Numeric.Container.join [a,b]  -- | horizontal concatenation of real matrices infixl 3 !@@ -206,7 +206,7 @@  vech :: Element t => Matrix t -> Vector t -- ^ half-vectorization (of the lower triangular part)-vech m = join . zipWith f [0..] . toColumns $ m+vech m = Numeric.Container.join . zipWith f [0..] . toColumns $ m   where     f k v = subVector k (dim v - k) v