cobot-io 0.1.5.2 → 0.1.5.3
raw patch · 4 files changed
+39/−20 lines, 4 filesdep ~bytestringdep ~deepseqdep ~hspecPVP ok
version bump matches the API change (PVP)
Dependency ranges changed: bytestring, deepseq, hspec, megaparsec, text
API changes (from Hackage documentation)
Files
- ChangeLog.md +3/−0
- cobot-io.cabal +12/−9
- src/Bio/Uniprot/Parser.hs +7/−1
- test/FASTASpec.hs +17/−10
ChangeLog.md view
@@ -2,6 +2,9 @@ ## [Unreleased] +## [0.1.5.3] - 2023-12-08+- Update tests and dependencies.+ ## [0.1.5.2] - 2023-11-09 - Add Ord for Fasta and related types.
cobot-io.cabal view
@@ -5,7 +5,7 @@ -- see: https://github.com/sol/hpack name: cobot-io-version: 0.1.5.2+version: 0.1.5.3 synopsis: Biological data file formats and IO description: Please see the README on GitHub at <https://github.com/biocad/cobot-io#readme> category: Bio@@ -21,6 +21,9 @@ GHC ==8.10.7 || ==9.0.2 || ==9.2.8+ || ==9.4.8+ || ==9.6.3+ || ==9.8.1 extra-source-files: README.md@@ -187,11 +190,11 @@ , attoparsec >=0.10 && <0.15 , base >=4.14 && <5 , binary >=0.8.3.0 && <1.0- , bytestring >=0.10.8.1 && <0.12+ , bytestring >=0.10.8.1 && <0.13 , cobot >=0.1.1.7 , containers >=0.5.7.1 && <0.7 , data-msgpack >=0.0.9 && <0.1- , deepseq ==1.4.*+ , deepseq >=1.4 && <1.6 , filepath , http-conduit ==2.3.* , hyraxAbif >=0.2.3.27 && <0.2.5.0@@ -201,7 +204,7 @@ , mtl >=2.2.1 && <2.4 , parser-combinators >=1.2.1 , split- , text >=1.2.2.1 && <2.1+ , text >=1.2.2.1 && <2.2 , vector default-language: Haskell2010 if impl(ghc >= 9.0)@@ -240,24 +243,24 @@ , attoparsec >=0.10 && <0.15 , base >=4.14 && <5 , binary >=0.8.3.0 && <1.0- , bytestring >=0.10.8.1 && <0.12+ , bytestring >=0.10.8.1 && <0.13 , cobot >=0.1.1.7 , cobot-io , containers >=0.5.7.1 && <0.7 , data-msgpack >=0.0.9 && <0.1- , deepseq ==1.4.*+ , deepseq >=1.4 && <1.6 , directory , filepath- , hspec >=2.4.1 && <2.11+ , hspec >=2.4.1 && <2.12 , http-conduit ==2.3.* , hyraxAbif >=0.2.3.27 && <0.2.5.0 , lens >=4.16 && <5.3 , linear- , megaparsec <9.3+ , megaparsec , mtl >=2.2.1 && <2.4 , neat-interpolation >=0.3 , parser-combinators >=1.2.1 , split- , text >=1.2.2.1 && <2.1+ , text >=1.2.2.1 && <2.2 , vector default-language: Haskell2010
src/Bio/Uniprot/Parser.hs view
@@ -1,3 +1,4 @@+{-# LANGUAGE CPP #-} {-# LANGUAGE TupleSections #-} {-# OPTIONS_GHC -fno-warn-unused-do-bind #-} {-# OPTIONS_GHC -fno-warn-name-shadowing #-}@@ -9,8 +10,13 @@ import Prelude hiding (null) import qualified Prelude as P (concat, init, last, null, tail) -import Bio.Uniprot.Type+#if MIN_VERSION_base(4, 18, 0)+import Control.Applicative ((<|>))+#else import Control.Applicative (liftA2, (<|>))+#endif++import Bio.Uniprot.Type import Control.Monad (unless) import Data.Attoparsec.Text import Data.Bifunctor (second)
test/FASTASpec.hs view
@@ -2,16 +2,19 @@ module FASTASpec where -import Bio.FASTA (fastaP, fromFile, toFile)-import Bio.FASTA.Parser (parseOnly)-import Bio.FASTA.Type (Fasta, FastaItem (..))-import Bio.Sequence (bareSequence)-import Control.Monad.IO.Class (liftIO)-import Data.Text.IO (readFile)-import Prelude hiding (readFile, writeFile)-import System.Directory (removeFile)-import Test.Hspec+import Control.Monad.IO.Class (liftIO)+import Data.Bifunctor (first)+import qualified Data.Text as T+import Data.Text.IO (readFile)+import Prelude hiding (readFile, writeFile)+import System.Directory (removeFile)+import Test.Hspec +import Bio.FASTA (fastaP, fromFile, toFile)+import Bio.FASTA.Parser (parseOnly)+import Bio.FASTA.Type (Fasta, FastaItem (..))+import Bio.Sequence (bareSequence)+ correctFasta1 :: Fasta Char correctFasta1 = [ FastaItem "3HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL") , FastaItem "7HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL")@@ -70,7 +73,7 @@ it ("correctly parses bad fasta from file " <> path) $ do res <- liftIO (readFile path) let badRes = parseOnly fastaP res- badRes `shouldBe` cf+ noSpaces badRes `shouldBe` noSpaces cf writeFile :: FilePath -> Fasta Char -> Spec writeFile path cf =@@ -79,3 +82,7 @@ fasta <- fromFile path removeFile path fasta `shouldBe` cf++-- | megaparsec >= 9.3 added more spaces to error messages, so that our old ones do not match.+noSpaces :: Either String a -> Either String a+noSpaces = first $ T.unpack . T.replace " " "" . T.pack