diff --git a/Biobase/Types/Accession.hs b/Biobase/Types/Accession.hs --- a/Biobase/Types/Accession.hs +++ b/Biobase/Types/Accession.hs @@ -7,15 +7,16 @@ import Control.DeepSeq import Data.Aeson import Data.Binary +import Data.Char (isLetter) import Data.Hashable (Hashable) import Data.Ix (Ix) import Data.Serialize import Data.Serialize.Text import Data.String -import Data.Stringable +import Data.String.Conversions (ConvertibleStrings(..), cs) +import Data.String.Conversions.Monomorphic (toST, fromST) import Data.Text.Binary -import Data.Text (Text, span) -import Data.Char (isLetter) +import Data.Text (Text, span, length) import GHC.Generics (Generic) import Prelude hiding (length,span) @@ -45,14 +46,14 @@ -- | Generate an accession with an explicit phantom type: @accession' -- Nucleotide "Bla"@ has type @:: Accession Nucleotide@. -accession' :: Stringable s => t -> s -> Accession t -accession' t = Accession . toText +accession' :: ConvertibleStrings s Text => t -> s -> Accession t +accession' t = Accession . toST -- | Generate an accession when the type @Accession t@ is clear from the -- context. -accession :: Stringable s => s -> Accession t -accession = Accession . toText +accession :: ConvertibleStrings s Text => s -> Accession t +accession = Accession . toST {-# Inline accession #-} -- | Retag an accession diff --git a/Biobase/Types/Names.hs b/Biobase/Types/Names.hs --- a/Biobase/Types/Names.hs +++ b/Biobase/Types/Names.hs @@ -14,16 +14,17 @@ import Data.Aeson as A import Data.Binary as DB import Data.Hashable +import Data.Interned +import Data.Interned.Text import Data.Serialize as DS import Data.Serialize.Text -import Data.Stringable as SA import Data.String as IS +import Data.String.Conversions (ConvertibleStrings(..), cs) +import Data.String.Conversions.Monomorphic (toST, fromST) import Data.Text.Binary -import Data.Text (Text,pack) +import Data.Text (Text, pack, unpack) import Data.Vector.Unboxed.Deriving import GHC.Generics -import Data.Interned.Text -import Data.Interned import Biobase.Types.Names.Internal @@ -56,7 +57,7 @@ {-# Inline fromString #-} instance Show SpeciesName where - showsPrec p i r = showsPrec p (toString i) r + showsPrec p i r = showsPrec p (unpack $ toST i) r {-# Inline showsPrec #-} instance Read SpeciesName where @@ -65,38 +66,32 @@ instance Hashable SpeciesName -instance Stringable SpeciesName where - toString = toString . speciesNameBimapLookupInt . getSpeciesNameRep - fromString = speciesName . SA.fromString - length = SA.length . speciesNameBimapLookupInt . getSpeciesNameRep - toText = toText . speciesNameBimapLookupInt . getSpeciesNameRep - fromText = speciesName . fromText - {-# Inline toString #-} - {-# Inline fromString #-} - {-# Inline length #-} - {-# Inline toText #-} - {-# Inline fromText #-} +instance ConvertibleStrings Text SpeciesName where + convertString = speciesName +instance ConvertibleStrings SpeciesName Text where + convertString = speciesNameBimapLookupInt . getSpeciesNameRep + instance NFData SpeciesName instance Binary SpeciesName where - put = DB.put . toText - get = fromText <$> DB.get + put = DB.put . toST + get = fromST <$> DB.get {-# Inline put #-} {-# Inline get #-} instance Serialize SpeciesName where - put = DS.put . toText - get = fromText <$> DS.get + put = DS.put . toST + get = fromST <$> DS.get {-# Inline put #-} {-# Inline get #-} instance FromJSON SpeciesName where - parseJSON s = fromText <$> parseJSON s + parseJSON s = fromST <$> parseJSON s {-# Inline parseJSON #-} instance ToJSON SpeciesName where - toJSON = toJSON . toText + toJSON = toJSON . toST {-# Inline toJSON #-} @@ -112,18 +107,12 @@ rnf (TaxonomicRank it) = rnf (internedTextId it) {-# Inline rnf #-} -instance Stringable TaxonomicRank where - toString = toString . unintern . getTaxonomicRank - fromString = fromText . pack - length = SA.length . toText - toText = unintern . getTaxonomicRank - fromText = TaxonomicRank . intern - {-# Inline toString #-} - {-# Inline fromString #-} - {-# Inline length #-} - {-# Inline toText #-} - {-# Inline fromText #-} +instance ConvertibleStrings Text TaxonomicRank where + convertString = TaxonomicRank . intern +instance ConvertibleStrings TaxonomicRank Text where + convertString = unintern . getTaxonomicRank + instance Hashable TaxonomicRank where hashWithSalt s (TaxonomicRank it) = hashWithSalt s (internedTextId it) {-# Inline hashWithSalt #-} @@ -133,22 +122,22 @@ {-# Inline readsPrec #-} instance Binary TaxonomicRank where - put = DB.put . toText - get = fromText <$> DB.get + put = DB.put . toST + get = fromST <$> DB.get {-# Inline put #-} {-# Inline get #-} instance Serialize TaxonomicRank where - put = DS.put . toText - get = fromText <$> DS.get + put = DS.put . toST + get = fromST <$> DS.get {-# Inline put #-} {-# Inline get #-} instance FromJSON TaxonomicRank where - parseJSON s = fromText <$> parseJSON s + parseJSON s = fromST <$> parseJSON s {-# Inline parseJSON #-} instance ToJSON TaxonomicRank where - toJSON = toJSON . toText + toJSON = toJSON . toST {-# Inline toJSON #-} diff --git a/BiobaseTypes.cabal b/BiobaseTypes.cabal --- a/BiobaseTypes.cabal +++ b/BiobaseTypes.cabal @@ -1,5 +1,5 @@ name: BiobaseTypes -version: 0.1.2.0 +version: 0.1.2.1 author: Christian Hoener zu Siederdissen, 2015 - 2016 copyright: Christian Hoener zu Siederdissen, 2015 - 2016 homepage: https://github.com/choener/BiobaseTypes @@ -11,7 +11,7 @@ build-type: Simple stability: experimental cabal-version: >= 1.10.0 -tested-with: GHC == 7.8.4, GHC == 7.10.3, GHC == 8.0.1 +tested-with: GHC == 7.10.3, GHC == 8.0.1 synopsis: Collection of types for bioinformatics description: Types used in a number of bioinformatics libraries. @@ -32,27 +32,26 @@ library build-depends: base >= 4.7 && < 5.0 - , aeson >= 0.8 && < 1.1 - , binary >= 0.7 && < 0.8 - , cereal >= 0.4 && < 0.6 - , cereal-text >= 0.1 && < 0.2 - , cereal-vector >= 0.2 && < 0.3 - , data-default >= 0.5 && < 0.6 - , deepseq >= 1.3 && < 1.5 - , hashable >= 1.2 && < 1.3 - , intern >= 0.9 && < 0.10 - , log-domain >= 0.10 && < 0.11 - , primitive >= 0.5 && < 0.7 - , QuickCheck >= 2.7 && < 2.9 - , stringable >= 0.1.3 && < 0.2 - , text >= 1.0 && < 1.3 - , text-binary >= 0.2 && < 0.3 - , vector >= 0.10 && < 0.12 - , vector-binary-instances >= 0.2 && < 0.3 - , vector-th-unbox >= 0.2 && < 0.3 + , aeson >= 0.8 + , binary >= 0.7 + , cereal >= 0.4 + , cereal-text >= 0.1 + , cereal-vector >= 0.2 + , data-default >= 0.5 + , deepseq >= 1.3 + , hashable >= 1.2 + , intern >= 0.9 + , primitive >= 0.5 + , QuickCheck >= 2.7 + , string-conversions >= 0.4 + , text >= 1.0 + , text-binary >= 0.2 + , vector >= 0.10 + , vector-binary-instances >= 0.2 + , vector-th-unbox >= 0.2 -- , bimaps == 0.1.0.* - , PrimitiveArray == 0.7.1.* + , PrimitiveArray == 0.8.0.* exposed-modules: Biobase.Types.Accession Biobase.Types.Bitscore @@ -71,6 +70,7 @@ default-extensions: BangPatterns , DataKinds , DeriveGeneric + , FlexibleContexts , FlexibleInstances , GeneralizedNewtypeDeriving , KindSignatures @@ -101,11 +101,12 @@ default-extensions: ScopedTypeVariables , TemplateHaskell build-depends: base - , BiobaseTypes , QuickCheck , tasty >= 0.11 , tasty-quickcheck >= 0.8 , tasty-th >= 0.1 + -- + , BiobaseTypes diff --git a/changelog.md b/changelog.md --- a/changelog.md +++ b/changelog.md @@ -1,3 +1,10 @@ +0.1.2.1 +------- + +- increased minimal required PrimitiveArray version +- removed almost all upper bounds +- removed ghc 7.8.4 as viable compiler + 0.1.2.0 -------