BiobaseTypes 0.1.2.0 → 0.1.2.1

raw patch · 4 files changed

+66/−68 lines, 4 filesdep +string-conversionsdep −log-domaindep −stringabledep ~PrimitiveArraydep ~QuickCheckdep ~aesonPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependencies added: string-conversions

Dependencies removed: log-domain, stringable

Dependency ranges changed: PrimitiveArray, QuickCheck, aeson, binary, cereal, cereal-text, cereal-vector, data-default, deepseq, hashable, intern, primitive, text, text-binary, vector, vector-binary-instances, vector-th-unbox

API changes (from Hackage documentation)

Files

• Biobase/Types/Accession.hs +8/−7
• Biobase/Types/Names.hs +28/−39
• BiobaseTypes.cabal +23/−22
• changelog.md +7/−0

@@ -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

@@ -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 #-} 

@@ -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   

@@ -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 -------