PrimitiveArray 0.6.0.0 → 0.6.1.0

raw patch · 8 files changed

+122/−25 lines, 8 filesdep ~OrderedBitsdep ~aesonPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependency ranges changed: OrderedBits, aeson

API changes (from Hackage documentation)

Files

• Data/PrimitiveArray/Dense.hs +12/−8
• Data/PrimitiveArray/Index.hs +2/−0
• Data/PrimitiveArray/Index/PhantomInt.hs +76/−0
• Data/PrimitiveArray/Index/Subword.hs +1/−1
• PrimitiveArray.cabal +13/−9
• README.md +7/−4
• changelog.md +7/−1
• tests/properties.hs +4/−2

@@ -45,13 +45,15 @@ instance (ToJSON    sh, ToJSON    e, Unbox e) => ToJSON    (Unboxed sh e) instance (FromJSON  sh, FromJSON  e, Unbox e) => FromJSON  (Unboxed sh e) -instance NFData (Unboxed sh e) where-  rnf !_ = ()+instance (NFData sh) => NFData (Unboxed sh e) where+  rnf (Unboxed l h xs) = rnf l `seq` rnf h `seq` rnf xs+  {-# Inline rnf #-}  data instance MutArr m (Unboxed sh e) = MUnboxed !sh !sh !(VU.MVector (PrimState m) e) -instance NFData (MutArr m (Unboxed sh e)) where-  rnf !_ = ()+instance (NFData sh) => NFData (MutArr m (Unboxed sh e)) where+  rnf (MUnboxed l h xs) = rnf l `seq` rnf h `seq` rnf xs+  {-# Inline rnf #-}  instance (Index sh, Unbox elm) => MPrimArrayOps Unboxed sh elm where   boundsM (MUnboxed l h _) = (l,h)@@ -103,13 +105,15 @@ instance (ToJSON    sh, ToJSON    e)  => ToJSON    (Boxed sh e) instance (FromJSON  sh, FromJSON  e)  => FromJSON  (Boxed sh e) -instance NFData (Boxed sh e) where-  rnf !_ = ()+instance (NFData sh, NFData e) => NFData (Boxed sh e) where+  rnf (Boxed l h xs) = rnf l `seq` rnf h `seq` rnf xs+  {-# Inline rnf #-}  data instance MutArr m (Boxed sh e) = MBoxed !sh !sh !(V.MVector (PrimState m) e) -instance NFData (MutArr m (Boxed sh e)) where-  rnf !_ = ()+instance (NFData sh) => NFData (MutArr m (Boxed sh e)) where+  rnf (MBoxed l h _) = rnf l `seq` rnf h -- no rnf for the data !+  {-# Inline rnf #-}  instance (Index sh) => MPrimArrayOps Boxed sh elm where   boundsM (MBoxed l h _) = (l,h)

@@ -4,6 +4,7 @@   , module Data.PrimitiveArray.Index.Complement   , module Data.PrimitiveArray.Index.Int   , module Data.PrimitiveArray.Index.Outside+  , module Data.PrimitiveArray.Index.PhantomInt   , module Data.PrimitiveArray.Index.Point   , module Data.PrimitiveArray.Index.Set   , module Data.PrimitiveArray.Index.Subword@@ -13,6 +14,7 @@ import Data.PrimitiveArray.Index.Complement import Data.PrimitiveArray.Index.Int import Data.PrimitiveArray.Index.Outside+import Data.PrimitiveArray.Index.PhantomInt import Data.PrimitiveArray.Index.Point import Data.PrimitiveArray.Index.Set import Data.PrimitiveArray.Index.Subword

@@ -0,0 +1,76 @@++-- | A linear 0-based int-index with a phantom type.++module Data.PrimitiveArray.Index.PhantomInt where++import Control.DeepSeq (NFData(..))+import Data.Aeson (FromJSON,ToJSON)+import Data.Binary (Binary)+import Data.Data+import Data.Ix(Ix)+import Data.Serialize (Serialize)+import Data.Typeable+import Data.Vector.Fusion.Stream.Monadic (flatten,map,Step(..))+import Data.Vector.Fusion.Stream.Size+import Data.Vector.Unboxed.Deriving+import GHC.Generics (Generic)+import Prelude hiding (map)++import Data.PrimitiveArray.Index.Class++++-- | A 'PInt' behaves exactly like an @Int@, but has an attached phantom+-- type @p@. In particular, the @Index@ and @IndexStream@ instances are the+-- same as for raw @Int@s.++newtype PInt p = PInt { getPInt :: Int }+  deriving (Read,Show,Eq,Ord,Enum,Num,Integral,Real,Generic,Data,Typeable,Ix)+++derivingUnbox "PInt"+  [t| forall p . PInt p -> Int |]  [| getPInt |]  [| PInt |]++instance Binary    (PInt p)+instance Serialize (PInt p)+instance FromJSON  (PInt p)+instance ToJSON    (PInt p)++instance NFData (PInt p)++instance Index (PInt p) where+  linearIndex _ _ (PInt k) = k+  {-# Inline linearIndex #-}+  smallestLinearIndex _ = error "still needed?"+  {-# Inline smallestLinearIndex #-}+  largestLinearIndex (PInt h) = h+  {-# Inline largestLinearIndex #-}+  size _ (PInt h) = h+1+  {-# Inline size #-}+  inBounds l h k = l <= k && k <= h+  {-# Inline inBounds #-}++instance IndexStream z => IndexStream (z:.(PInt p)) where+  streamUp (ls:.l) (hs:.h) = flatten mk step Unknown $ streamUp ls hs+    where mk z = return (z,l)+          step (z,k)+            | k > h     = return $ Done+            | otherwise = return $ Yield (z:.k) (z,k+1)+          {-# Inline [0] mk   #-}+          {-# Inline [0] step #-}+  {-# Inline streamUp #-}+  streamDown (ls:.l) (hs:.h) = flatten mk step Unknown $ streamDown ls hs+    where mk z = return (z,h)+          step (z,k)+            | k < l     = return $ Done+            | otherwise = return $ Yield (z:.k) (z,k-1)+          {-# Inline [0] mk   #-}+          {-# Inline [0] step #-}+  {-# Inline streamDown #-}++instance IndexStream (PInt p) where+  streamUp l h = map (\(Z:.k) -> k) $ streamUp (Z:.l) (Z:.h)+  {-# Inline streamUp #-}+  streamDown l h = map (\(Z:.k) -> k) $ streamDown (Z:.l) (Z:.h)+  {-# Inline streamDown #-}+

@@ -86,7 +86,7 @@   {-# Inline linearIndex #-}   smallestLinearIndex _ = error "still needed?"   {-# Inline smallestLinearIndex #-}-  largestLinearIndex = upperTri+  largestLinearIndex h = upperTri h -1   {-# Inline largestLinearIndex #-}   size _ h = upperTri h   {-# Inline size #-}

@@ -1,11 +1,13 @@ Name:           PrimitiveArray-Version:        0.6.0.0+Version:        0.6.1.0 License:        BSD3 License-file:   LICENSE Maintainer:     choener@bioinf.uni-leipzig.de author:         Christian Hoener zu Siederdissen, 2011-2015 copyright:      Christian Hoener zu Siederdissen, 2011-2015 homepage:       http://www.bioinf.uni-leipzig.de/Software/gADP/+homepage:       https://github.com/choener/PrimitiveArray+bug-reports:    https://github.com/choener/PrimitiveArray/issues Stability:      Experimental Category:       Data Build-type:     Simple@@ -46,24 +48,26 @@     Data.PrimitiveArray.Index.Complement     Data.PrimitiveArray.Index.Int     Data.PrimitiveArray.Index.Outside+    Data.PrimitiveArray.Index.PhantomInt     Data.PrimitiveArray.Index.Point     Data.PrimitiveArray.Index.Set     Data.PrimitiveArray.Index.Subword     Data.PrimitiveArray.QuickCheck.Index.Set   build-depends: base                     >= 4.7      && < 4.9-               , aeson                    == 0.8.*-               , binary                   == 0.7.*-               , bits                     == 0.4.*-               , cereal                   == 0.4.*+               , aeson                    >= 0.8      && < 0.10+               , binary                   >= 0.7      && < 0.8+               , bits                     >= 0.4      && < 0.5+               , cereal                   >= 0.4      && < 0.5                , deepseq                  >= 1.3      && < 1.5-               , OrderedBits              == 0.0.0.*+               , OrderedBits              >= 0.0.0.1  && < 0.0.1.0                , primitive                >= 0.5.4    && < 0.7                , QuickCheck               >= 2.7      && < 2.9-               , vector                   == 0.10.*-               , vector-binary-instances  == 0.2.*-               , vector-th-unbox          == 0.2.*+               , vector                   >= 0.10     && < 0.11+               , vector-binary-instances  >= 0.2      && < 0.3+               , vector-th-unbox          >= 0.2      && < 0.3   default-extensions: BangPatterns                     , DefaultSignatures+                    , DeriveDataTypeable                     , DeriveGeneric                     , FlexibleContexts                     , FlexibleInstances

@@ -1,6 +1,8 @@+[![Build Status](https://travis-ci.org/choener/PrimitiveArray.svg?branch=master)](https://travis-ci.org/choener/PrimitiveArray)+ # PrimitiveArray -[![Build Status](https://travis-ci.org/choener/PrimitiveArray.svg?branch=master)](https://travis-ci.org/choener/PrimitiveArray)+[*generalized ADPfusion Homepage*](http://www.bioinf.uni-leipzig.de/Software/gADP/)  PrimitiveArray provides operations on multi-dimensional arrays. Internally, the representation is based on the vector library, while the multi-dimensional@@ -12,7 +14,8 @@  #### Contact -Christian Hoener zu Siederdissen-choener@bioinf.uni-leipzig.de-http://www.bioinf.uni-leipzig.de/~choener/+Christian Hoener zu Siederdissen  +Leipzig University, Leipzig, Germany  +choener@bioinf.uni-leipzig.de  +http://www.bioinf.uni-leipzig.de/~choener/   

@@ -1,8 +1,14 @@+0.6.1.0+-------++- OrderedBits < 0.0.1+- travis.yml update+ 0.6.0.0 -------  - moved primitive array classes to Data.PrimitiveArray.Class-- added _from / _to lenses+- added from / to lenses - Field1 .. Field6 lenses for indices (Z:.a:.b...) (with Z being Field0)   - lens stuff currently commented out; aiming to have an extra package [lens     is fairly heavy]

@@ -4,11 +4,13 @@ import           Test.Framework.Providers.QuickCheck2 import           Test.Framework.TH --- import qualified Data.Bits.Ordered.QuickCheck as QC+import qualified  Data.PrimitiveArray.QuickCheck.Index.Set as QCS   --- prop_PopCountSet = QC.prop_PopCountSet+-- prop_Fixed_BitSet_setSucc = QCS.prop_Fixed_BitSet_setSucc++  main :: IO () main = $(defaultMainGenerator)