hmatrix 0.11.0.1 → 0.11.0.3

raw patch · 8 files changed

+210/−155 lines, 8 filessetup-changedPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• Config.hs +145/−0
• Setup.lhs +36/−1
• THANKS +9/−0
• configure +0/−3
• configure.hs +0/−145
• hmatrix.cabal +9/−5
• lib/Data/Packed/Internal/Vector.hs +10/−0
• lib/Numeric/LinearAlgebra/Tests.hs +1/−1

@@ -0,0 +1,145 @@+{-+    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 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+       ]++-- compile a simple program with symbols from GSL and LAPACK with the given libs+testprog bInfo buildInfo libs fmks =+    "echo \"#include <gsl/gsl_sf_gamma.h>\nint main(){zgesvd_(); gsl_sf_gamma(5);}\""+                     ++" > " ++ (buildDir bInfo) ++ "/dummy.c; gcc "+                     ++ (join $ ccOptions buildInfo) ++ " "+                     ++ (join $ cppOptions buildInfo) ++ " "+                     ++ (join $ map ("-I"++) $ includeDirs buildInfo) ++ " " +                     ++ (buildDir bInfo) ++ "/dummy.c -o "+                     ++ (buildDir bInfo) ++ "/dummy "+                     ++ (join $ map ("-L"++) $ extraLibDirs buildInfo) ++ " "+                     ++ (prepend "-l" $ libs) ++ " "+                     ++ (prepend "-framework " fmks) ++ " > /dev/null 2> /dev/null"++join = intercalate " "+prepend x = unwords . map (x++) . words++check bInfo buildInfo libs fmks = (ExitSuccess ==) `fmap` system (testprog bInfo buildInfo libs fmks)++-- simple test for GSL+gsl bInfo buildInfo = "echo \"#include <gsl/gsl_sf_gamma.h>\nint main(){gsl_sf_gamma(5);}\""+           ++" > " ++ (buildDir bInfo) ++ "/dummy.c; gcc "+           ++ (join $ ccOptions buildInfo) ++ " "+           ++ (join $ cppOptions buildInfo) ++ " "+           ++ (join $ map ("-I"++) $ includeDirs buildInfo) ++ " " +           ++ (buildDir bInfo) ++ "/dummy.c -o "+           ++ (buildDir bInfo) ++ "/dummy "+           ++ (join $ map ("-L"++) $ extraLibDirs buildInfo) ++ " -lgsl -lgslcblas"+           ++ " > /dev/null 2> /dev/null"++-- test for gsl >= 1.12+gsl112 bInfo buildInfo =+    "echo \"#include <gsl/gsl_sf_exp.h>\nint main(){gsl_sf_exprel_n_CF_e(1,1,0);}\""+           ++" > " ++ (buildDir bInfo) ++ "/dummy.c; gcc " +           ++ (buildDir bInfo) ++ "/dummy.c "+           ++ (join $ ccOptions buildInfo) ++ " "+           ++ (join $ cppOptions buildInfo) ++ " "+           ++ (join $ map ("-I"++) $ includeDirs buildInfo)+           ++" -o " ++ (buildDir bInfo) ++ "/dummy "+           ++ (join $ map ("-L"++) $ extraLibDirs buildInfo) ++ " -lgsl -lgslcblas"+           ++ " > /dev/null 2> /dev/null"+++checkCommand c = (ExitSuccess ==) `fmap` system 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 = "link:"+getUserLink = concatMap (g . drop (length linkop)) . filter (isPrefixOf linkop)+    where g = map cs+          cs ',' = ' '+          cs x   = x++config = do+    info <- maybeGetPersistBuildConfig "dist"+    case info of+        Nothing -> putStrLn "Please run \"cabal clean\" first." >> exitFailure+        Just bInfo -> mainOk bInfo+        +mainOk 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."+            writeFile "hmatrix.buildinfo" ("buildable: False\n")+        Just ops -> do+            putStrLn " OK"+            g <- checkCommand $ gsl112 bInfo buildInfo+            writeFile "hmatrix.buildinfo" $ "extra-libraries: " +++                ops ++ "\n" +++                if g+                    then ""+                    else "cc-options: -DGSL110\n"+

@@ -2,7 +2,42 @@  > import Distribution.Simple > import System.Process(system)+>+> import Config(config)+>+> import Distribution.Simple.Setup+> import Distribution.PackageDescription+> import Distribution.Simple.LocalBuildInfo+> import Distribution.Simple.Command+> import Distribution.PackageDescription.Parse+> import Distribution.Simple.Utils(info)+> import Distribution.Verbosity -> main = defaultMainWithHooks autoconfUserHooks {runTests = t}+> main = do+>    defaultMainWithHooks autoconfUserHooks {+>        runTests = t, +>        postConf = modifiedPostConf }+>   where modifiedPostConf :: Args -> ConfigFlags -> PackageDescription -> LocalBuildInfo -> IO ()+>         modifiedPostConf args flags pkg_descr lbi+>              = do let verbosity = fromFlag (configVerbosity flags)+>                   noExtraFlags args+>+>                   config+>+>                   pbi <- getHookedBuildInfo verbosity+>                   let pkg_descr' = updatePackageDescription pbi pkg_descr+>                   postConf simpleUserHooks args flags pkg_descr' lbi ++> getHookedBuildInfo :: Verbosity -> IO HookedBuildInfo+> getHookedBuildInfo verbosity = do+>   maybe_infoFile <- defaultHookedPackageDesc+>   case maybe_infoFile of+>     Nothing       -> return emptyHookedBuildInfo+>     Just infoFile -> do+>       info verbosity $ "Reading parameters from " ++ infoFile+>       readHookedBuildInfo verbosity infoFile++ > t _ _ _ _ = system ( "runhaskell examples/tests.hs") >> return()+

@@ -85,3 +85,12 @@  - Stefan Kersten fixed hmatrix.cabal for 64-bit ghc-7 in OS/X +- Sacha Sokoloski reported an installation problem on Arch Linux and+  helped with the configuration.++- Carter Schonwald helped with the configuration for Homebrew OS X and+  found a tolerance problem in test "1E5 rots".++- Duncan Coutts reported a problem with configure.hs and contributed+  a solution.+

@@ -1,3 +0,0 @@-#! /bin/sh--runhaskell configure.hs $*

@@ -1,145 +0,0 @@-#! /usr/bin/env runhaskell-{- configure.hs for hmatrix-   --------------------------    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,...---}--import System.Process-import System.Exit-import System.Environment-import System.Directory(createDirectoryIfMissing)-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-       ]---- compile a simple program with symbols from GSL and LAPACK with the given libs-testprog bInfo buildInfo libs fmks =-    "echo \"#include <gsl/gsl_sf_gamma.h>\nint main(){zgesvd_(); gsl_sf_gamma(5);}\""-                     ++" > " ++ (buildDir bInfo) ++ "/dummy.c; gcc "-                     ++ (join $ ccOptions buildInfo) ++ " "-                     ++ (join $ cppOptions buildInfo) ++ " "-                     ++ (join $ map ("-I"++) $ includeDirs buildInfo) ++ " " -                     ++ (buildDir bInfo) ++ "/dummy.c -o "-                     ++ (buildDir bInfo) ++ "/dummy "-                     ++ (join $ map ("-L"++) $ extraLibDirs buildInfo) ++ " "-                     ++ (prepend "-l" $ libs) ++ " "-                     ++ (prepend "-framework " fmks) ++ " > /dev/null 2> /dev/null"--join = intercalate " "-prepend x = unwords . map (x++) . words--check bInfo buildInfo libs fmks = (ExitSuccess ==) `fmap` system (testprog bInfo buildInfo libs fmks)---- simple test for GSL-gsl bInfo buildInfo = "echo \"#include <gsl/gsl_sf_gamma.h>\nint main(){gsl_sf_gamma(5);}\""-           ++" > " ++ (buildDir bInfo) ++ "/dummy.c; gcc "-           ++ (join $ ccOptions buildInfo) ++ " "-           ++ (join $ cppOptions buildInfo) ++ " "-           ++ (join $ map ("-I"++) $ includeDirs buildInfo) ++ " " -           ++ (buildDir bInfo) ++ "/dummy.c -o "-           ++ (buildDir bInfo) ++ "/dummy "-           ++ (join $ map ("-L"++) $ extraLibDirs buildInfo) ++ " -lgsl -lgslcblas"-           ++ " > /dev/null 2> /dev/null"---- test for gsl >= 1.12-gsl112 bInfo buildInfo =-    "echo \"#include <gsl/gsl_sf_exp.h>\nint main(){gsl_sf_exprel_n_CF_e(1,1,0);}\""-           ++" > " ++ (buildDir bInfo) ++ "/dummy.c; gcc " -           ++ (buildDir bInfo) ++ "/dummy.c "-           ++ (join $ ccOptions buildInfo) ++ " "-           ++ (join $ cppOptions buildInfo) ++ " "-           ++ (join $ map ("-I"++) $ includeDirs buildInfo)-           ++" -o " ++ (buildDir bInfo) ++ "/dummy "-           ++ (join $ map ("-L"++) $ extraLibDirs buildInfo) ++ " -lgsl -lgslcblas"-           ++ " > /dev/null 2> /dev/null"---checkCommand c = (ExitSuccess ==) `fmap` system 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 = "link:"-getUserLink = concatMap (g . drop (length linkop)) . filter (isPrefixOf linkop)-    where g = map cs-          cs ',' = ' '-          cs x   = x--main = do-    info <- maybeGetPersistBuildConfig "dist"-    case info of-        Nothing -> putStrLn "Please run \"cabal clean\" first." >> exitFailure-        Just bInfo -> mainOk bInfo-        -mainOk 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."-            writeFile "hmatrix.buildinfo" ("buildable: False\n")-        Just ops -> do-            putStrLn " OK"-            g <- checkCommand $ gsl112 bInfo buildInfo-            writeFile "hmatrix.buildinfo" $ "extra-libraries: " ++-                ops ++ "\n" ++-                if g-                    then ""-                    else "cc-options: -DGSL110\n"

@@ -1,5 +1,5 @@ Name:               hmatrix-Version:            0.11.0.1+Version:            0.11.0.3 License:            GPL License-file:       LICENSE Author:             Alberto Ruiz@@ -21,14 +21,14 @@                     .                     - "Numeric.LinearAlgebra": everything + instances of standard Haskell numeric classes Category:           Math-tested-with:        GHC ==6.10.4, GHC ==6.12.1, GHC ==6.12.3+tested-with:        GHC ==6.10.4, GHC ==6.12.1, GHC ==6.12.3, GHC ==7.0.1, GHC==7.0.2  cabal-version:      >=1.6  build-type:         Custom  extra-source-files: lib/Numeric/LinearAlgebra/Tests/quickCheckCompat.h-                    configure configure.hs THANKS INSTALL CHANGES+                    Config.hs THANKS INSTALL CHANGES extra-tmp-files:    hmatrix.buildinfo  extra-source-files: examples/tests.hs@@ -164,12 +164,14 @@     if impl(ghc < 6.10.2)         cpp-options: -DFINIT +    if impl(ghc >= 7.0.1)+        cpp-options: -DFINIT+     if flag(finit)         cpp-options: -DFINIT      if impl(ghc == 7.0.1)         cpp-options: -DNONORMVTEST-        cpp-options: -DFINIT      if flag(mkl)       if arch(x86_64)@@ -179,7 +181,9 @@      if os(OSX)         extra-lib-dirs: /opt/local/lib/-        include-dirs: /opt/local/include+        include-dirs: /opt/local/include/+        extra-lib-dirs: /usr/local/lib/+        include-dirs: /usr/local/include/         extra-libraries: gsl         if arch(i386)             cc-options: -arch i386

@@ -201,12 +201,21 @@  subVector = Vector.slice +{-+subVector k l v+    | k<0 || k >= n || k+l > n || l < 0 = error "subVector out of range"+    | otherwise = unsafeFromForeignPtr fp (i+k) l+  where+    (fp, i, n) = unsafeToForeignPtr v+-}+ #else  subVector k l v@V{idim = n, ioff = i}     | k<0 || k >= n || k+l > n || l < 0 = error "subVector out of range"     | otherwise = v {idim = l, ioff = i+k} +{- subVectorCopy k l (v@V {idim=n})     | k<0 || k >= n || k+l > n || l < 0 = error "subVector out of range"     | otherwise = unsafePerformIO $ do@@ -214,6 +223,7 @@         let f _ s _ d = copyArray d (advancePtr s k) l >> return 0         app2 f vec v vec r "subVector"         return r+-}  #endif 

@@ -213,7 +213,7 @@     where c = cos a           s = sin a -rotTest = fun (10^5) :~12~: rot 5E4+rotTest = fun (10^5) :~11~: rot 5E4     where fun n = foldl1' (<>) (map rot angles)               where angles = toList $ linspace n (0,1)