currycarbon 0.4.0.1 → 0.5.0.0

raw patch · 7 files changed

+59/−27 lines, 7 filesdep ~optparse-applicativePVP ok

version bump matches the API change (PVP)

Dependency ranges changed: optparse-applicative

API changes (from Hackage documentation)

Files

• CHANGELOG.md +4/−0
• README.md +2/−2
• currycarbon.cabal +3/−3
• src-executables/Main-currycarbon.hs +1/−2
• src/Currycarbon/CalCurves.hs +24/−11
• src/Currycarbon/ParserHelpers.hs +16/−0
• src/Currycarbon/Parsers.hs +9/−9

@@ -1,3 +1,7 @@+- V 0.5.0.0: Cleaned up parser error behaviour:+    - Parsing errors are now more helpful with better positional information, using a modified `showParsecErr` and a new `showParsecErrOneLine`.+    - Breaking change: The type of `readCalCurve` changed. It is now safe, returning `Either String CalCurveBP`. The old version is preserved in `readCalCurveUnsafe`.+- V 0.4.0.2: Support for `optparse-applicative-0.19.0.0`. - V 0.4.0.1: Support for `random-1.3`. Now possible, because MonadRandom supports it as well (https://github.com/byorgey/MonadRandom/blob/master/CHANGES.markdown#062-5-march-2025). - V 0.4.0.0: Another major update:     - Added more calibration curves next to `intcal20`: `shcal20` and `marine20`. Renamed the `Currycarbon.CalCurves.IntCal20` module to just `Currycarbon.CalCurves`. In the CLI, `--calCurveFile` is now just `--calCurve`, and it allows to either select the different packaged curves or read arbitrary .14c files.

@@ -32,7 +32,7 @@ ```  ```-currycarbon v0.4.0.0 (UTF-8)+currycarbon v0.4.0.2 (UTF-8) Method: Bchron {distribution = StudentTDist {ndf = 100.0}} Curve: IntCal20 Calibrating...@@ -74,7 +74,7 @@                    [[--seed INT] (-n|--nrSamples INT) --samplesFile FILE]                    [--calCurveSegFile FILE] [--calCurveMatFile FILE] -  Intercept calibration of radiocarbon dates+  currycarbon calibrates radiocarbon dates  Available options:   -h,--help                Show this help text

@@ -1,7 +1,7 @@ name:                currycarbon-version:             0.4.0.1+version:             0.5.0.0 synopsis:            A package for simple, fast radiocarbon calibration-description:         Radiocarbon calibration with the intercept method optimised for fast calibration of many dates.+description:         Radiocarbon calibration library and command line tool. homepage:            https://github.com/nevrome/currycarbon category:            Archaeoinformatics author:              Clemens Schmid@@ -54,7 +54,7 @@     build-depends:               currycarbon       , base >= 4.14 && < 5-      , optparse-applicative >= 0.16 && < 0.19+      , optparse-applicative >= 0.16 && < 0.21       , filepath >= 1.4 && < 1.6     other-modules:       Paths_currycarbon

@@ -47,8 +47,7 @@  optParserInfo :: OP.ParserInfo Options optParserInfo = OP.info (OP.helper <*> versionOption <*> optParser) (-    OP.briefDesc <>-    OP.progDesc "Intercept calibration of radiocarbon dates"+    OP.progDesc "currycarbon calibrates radiocarbon dates"     )  versionOption :: OP.Parser (a -> a)

@@ -4,7 +4,9 @@  import           Currycarbon.ParserHelpers import           Currycarbon.Types+import           Currycarbon.Utils +import           Control.Exception         (throwIO) import qualified Data.FileEmbed            as FE import qualified Data.Vector.Unboxed       as VU import qualified Text.Parsec               as P@@ -22,8 +24,8 @@  readCalCurveSelection :: String -> Either String CalCurveSelection readCalCurveSelection s =-    case P.runParser parseCalCurveSelection () "" s of-        Left err -> Left $ showParsecErr err+    case P.runParser parseCalCurveSelection () s s of+        Left err -> Left $ showParsecErrOneLine err         Right x  -> Right x  parseCalCurveSelection :: P.Parser CalCurveSelection@@ -44,18 +46,29 @@ -- | Read a calibration curve file. The file must adhere to the .14c file format. readCalCurveFromFile :: FilePath -> IO CalCurveBP readCalCurveFromFile calCurveFile = do-    calCurve <- readFile calCurveFile-    return $ readCalCurve calCurve+    calCurveString <- readFile calCurveFile+    case readCalCurve calCurveString of+        Left err -> throwIO $ CurrycarbonCLIParsingException err+        Right x  -> return x -readCalCurve :: String -> CalCurveBP+readCalCurve :: String -> Either String CalCurveBP readCalCurve calCurveString = do-    case P.runParser parseCalCurve () "" calCurveString of-        Left p  -> error $ "This should never happen." ++ show p-        Right x -> CalCurveBP+    case P.runParser parseCalCurve () "calCurve" calCurveString of+        Left err -> Left $ showParsecErr err+        Right x  -> Right $ CalCurveBP             (VU.fromList $ map (\(a,_,_) -> a) x)             (VU.fromList $ map (\(_,b,_) -> b) x)             (VU.fromList $ map (\(_,_,c) -> c) x) +readCalCurveUnsafe :: String -> CalCurveBP+readCalCurveUnsafe calCurveString = do+    case P.runParser parseCalCurve () "calCurve" calCurveString of+        Left err -> error $ "Error when reading calCurve " ++ show err+        Right x  -> CalCurveBP+            (VU.fromList $ map (\(a,_,_) -> a) x)+            (VU.fromList $ map (\(_,b,_) -> b) x)+            (VU.fromList $ map (\(_,_,c) -> c) x)+ parseCalCurve :: P.Parser [(YearBP, YearBP, YearRange)] parseCalCurve = do     P.skipMany comments@@ -79,20 +92,20 @@ -- | The intcal20 calibration curve -- (Reimer et al. 2020, doi: [10.1017/RDC.2020.41](https://doi.org/10.1017/RDC.2020.41)) intcal20 :: CalCurveBP-intcal20 = readCalCurve intcal20String+intcal20 = readCalCurveUnsafe intcal20String intcal20String :: String intcal20String = $(FE.makeRelativeToProject "data/intcal20.14c" >>= FE.embedStringFile)  -- | The shcal20 calibration curve -- (Hogg et al. 2020, doi: [10.1017/RDC.2020.59](https://doi.org/10.1017/RDC.2020.59)) shcal20 :: CalCurveBP-shcal20 = readCalCurve shcal20String+shcal20 = readCalCurveUnsafe shcal20String shcal20String :: String shcal20String = $(FE.makeRelativeToProject "data/shcal20.14c" >>= FE.embedStringFile)  -- | The shcal20 calibration curve -- (Heaton et al. 2020, doi: [10.1017/RDC.2020.68](https://doi.org/10.1017/RDC.2020.68)) marine20 :: CalCurveBP-marine20 = readCalCurve marine20String+marine20 = readCalCurveUnsafe marine20String marine20String :: String marine20String = $(FE.makeRelativeToProject "data/marine20.14c" >>= FE.embedStringFile)

@@ -158,6 +158,22 @@  showParsecErr :: P.ParseError -> String showParsecErr err =+    let pos = P.errorPos err+        posStr = P.sourceName pos +++                     " (issue in line " ++ show (P.sourceLine pos) +++                     ", column " ++ show (P.sourceColumn pos) +++                     ")"+    in posStr ++ ": " ++ cleanParsecErr err++showParsecErrOneLine :: P.ParseError -> String+showParsecErrOneLine err =+    let pos = P.errorPos err+        posStr = P.sourceName pos +++                     " (issue in column " ++ show (P.sourceColumn pos) ++ ")"+    in posStr ++ ": " ++ cleanParsecErr err++cleanParsecErr :: P.ParseError -> String+cleanParsecErr err =     P.showErrorMessages         "or" "unknown parse error"         "expecting" "unexpected" "end of input"

@@ -26,8 +26,8 @@  readCalibrationMethod :: String -> Either String CalibrationMethod readCalibrationMethod s =-    case P.runParser parseCalibrationMethod () "" s of-        Left err -> Left $ showParsecErr err+    case P.runParser parseCalibrationMethod () s s of+        Left err -> Left $ showParsecErrOneLine err         Right x  -> Right x  parseCalibrationMethod :: P.Parser CalibrationMethod@@ -201,8 +201,8 @@  readNamedCalExprs :: String -> Either String [NamedCalExpr] readNamedCalExprs s =-    case P.runParser parseCalExprSepBySemicolon () "" s of-        Left err -> Left $ showParsecErr err+    case P.runParser parseCalExprSepBySemicolon () s s of+        Left err -> Left $ showParsecErrOneLine err         Right x  -> Right x         where         parseCalExprSepBySemicolon :: P.Parser [NamedCalExpr]@@ -210,8 +210,8 @@  readOneNamedCalExpr :: String -> Either String NamedCalExpr readOneNamedCalExpr s =-    case P.runParser namedExpr () "" s of-        Left err -> Left $ showParsecErr err+    case P.runParser namedExpr () s s of+        Left err -> Left $ showParsecErrOneLine err         Right x  -> Right x  readNamedCalExprsFromFile :: FilePath -> IO [NamedCalExpr]@@ -244,7 +244,7 @@ readUncalC14FromFile :: FilePath -> IO [UncalC14] readUncalC14FromFile uncalFile = do     s <- readFile uncalFile-    case P.runParser uncalC14SepByNewline () "" s of+    case P.runParser uncalC14SepByNewline () uncalFile s of         Left err -> throwIO $ CurrycarbonCLIParsingException $ showParsecErr err         Right x  -> return x     where@@ -253,8 +253,8 @@  readUncalC14 :: String -> Either String [UncalC14] readUncalC14 s =-    case P.runParser uncalC14SepBySemicolon () "" s of-        Left err -> Left $ showParsecErr err+    case P.runParser uncalC14SepBySemicolon () s s of+        Left err -> Left $ showParsecErrOneLine err         Right x  -> Right x     where         uncalC14SepBySemicolon :: P.Parser [UncalC14]