Merge 'thunk' tool into 'ouch' tool

Expand with CLI options with usage:

  ouch -e C4Cl6               # enumeration
  ouch -f some_compounds.smi  # list compounds in SMILES file

In general `ouch -?`:

  Common flags:
    -f --file=FILE          List compounds from SMILES file
    -e --enumerate=FORMULA  Enumerate molecular formula
    -? --help               Display help message
    -V --version            Print version information

ouch.cabal

@@ -58,6 +58,6 @@ executable ouch
   main-is: tools/ouch.hs
   ghc-options: -Wall -O2
   build-depends: base >=3 && <5, binary -any, bytestring -any,
-                containers -any, deepseq -any, parallel -any, parsec >=3.1.0,
-                time -any, vector -any
+                 containers -any, deepseq -any, parallel -any, parsec >=3.1.0,
+                 time -any, vector -any, cmdargs
 

tools/ouch.hs

@@ -1,24 +1,50 @@
+{-# LANGUAGE RecordWildCards, DeriveDataTypeable #-}
 --
--- So far simple SMILES file CLI printer without options.
+-- CLI OUCH tool.
 --
--- Usage: ouch <SMILES_file>
+-- Common flags:
+--   -f --file=FILE          List compounds from SMILES file
+--   -e --enumerate=FORMULA  Enumerate molecular formula
+--   -? --help               Display help message
+--   -V --version            Print version information
 --
 
-import Control.Monad(when)
+import Control.Monad(unless)
 import Data.Functor((<$>))
+import Ouch.Enumerate.Formula(expand, Formula)
 import Ouch.Input.Smiles(readSmi)
 import Ouch.Property.Composition(molecularFormula, molecularWeight)
 import Ouch.Structure.Molecule
-import System.Environment
-import System.Exit(exitFailure)
+import System.Console.CmdArgs.Implicit
+import System.Environment(getArgs, withArgs)
 import Text.Printf(printf)
 import qualified Ouch.Property.Builder as OPB
 
-showMolecule :: String -- ^ SMILES string
-             -> String -- ^ description
-showMolecule smile = smile ++ "\n  --> " ++ showProperty molecularFormula mol ++ ", " ++ showMolWeight mol
-  where
-    mol = readSmi smile
+ouchVersion, ouchProgram, ouchSummary :: String
+ouchVersion   = "0.0.1"
+ouchProgram   = "ouch"
+ouchSummary   = ouchProgram ++ " v" ++ ouchVersion
+
+data CmdOptions = CmdOptions {
+  file      :: String,
+  enumerate :: String
+} deriving (Show, Data, Typeable)
+
+defOpts :: CmdOptions
+defOpts = CmdOptions
+  { file      = "" &= typ "FILE" &= help "List compounds from SMILES file"
+  , enumerate = "" &= typ "FORMULA" &= help "Enumerate molecular formula"
+  } &= summary ouchSummary
+    &= program ouchProgram
+    &= help "OUCH CLI tool"
+
+
+showMolecule :: Molecule -> String
+showMolecule mol = showProperty molecularFormula mol ++ ", " ++ showMolWeight mol
+
+showSmile :: String -- ^ SMILES string
+          -> String -- ^ description
+showSmile smile = smile ++ "\n  --> " ++ showMolecule (readSmi smile)
 
 showProperty :: OPB.Property -> Molecule -> String
 showProperty p m = show $ getPropertyValue p m
@@ -32,12 +58,20 @@ getPropertyValue prop m = case OPB.value prop of
                             Left  v -> v
                             Right f -> f m
 
+-- | If no arguments are passed to a program, displays help message and exits,
+-- returns parsed arguments otherwise.
+cmdArgsOrHelp :: Data a => a -> IO a
+cmdArgsOrHelp opts = do
+  mainArgs <- getArgs
+  (if null mainArgs then withArgs ["-?"] else id) (cmdArgs opts)
+
 main :: IO ()
 main = do
-  args <- getArgs
-  when (null args) $ do
-    putStrLn "ouch: SMILES file operand required"
-    exitFailure
-  smiles <- lines <$> readFile (head args)
-  mapM_ (putStrLn . showMolecule) smiles
+  CmdOptions{..} <- cmdArgsOrHelp defOpts
+  unless (null file) $ do
+    smiles <- lines <$> readFile file
+    mapM_ (putStrLn . showSmile) smiles
+  unless (null enumerate) $
+    mapM_ print (expand (read enumerate::Formula))
+