flat-mcmc 1.2.2 → 1.3.0

raw patch · 3 files changed

+47/−13 lines, 3 filesdep ~basedep ~pipesdep ~primitivenew-component:exe:bnn-examplePVP ok

version bump matches the API change (PVP)

Dependency ranges changed: base, pipes, primitive, text, transformers, vector

API changes (from Hackage documentation)

Files

• flat-mcmc.cabal +16/−5
• lib/Numeric/MCMC/Flat.hs +8/−8
• src/Main.hs +23/−0

@@ -1,5 +1,5 @@ name:                flat-mcmc-version:             1.2.2+version:             1.3.0 synopsis:            Painless general-purpose sampling. homepage:            https://github.com/jtobin/flat-mcmc license:             MIT@@ -59,10 +59,10 @@     , monad-par        >= 0.3.4.7 && < 1     , monad-par-extras >= 0.3.3 && < 1     , mwc-probability  >= 1.0.1 && < 2-    , pipes            >  4     && < 5-    , primitive-    , text-    , transformers+    , pipes            >= 4     && < 5+    , primitive        >= 0.6   && < 1+    , text             >= 1.2   && < 2+    , transformers     >= 0.2   && < 0.6     , vector           >= 0.10  && < 1  Test-suite rosenbrock@@ -84,6 +84,17 @@   default-language:    Haskell2010   ghc-options:     -rtsopts -threaded+  build-depends:+      base+    , flat-mcmc+    , vector++executable bnn-example+  hs-source-dirs:      src+  main-is:             Main.hs+  default-language:    Haskell2010+  ghc-options:+    -O2 -Wall -rtsopts -threaded   build-depends:       base     , flat-mcmc

@@ -1,4 +1,5 @@ {-# OPTIONS_GHC -fno-warn-type-defaults #-}+{-# LANGUAGE BangPatterns #-} {-# LANGUAGE OverloadedStrings #-} {-# LANGUAGE RecordWildCards #-} @@ -39,8 +40,8 @@  import Control.Monad (replicateM) import Control.Monad.Par (NFData)-import Control.Monad.Par.Scheds.Direct hiding (put, get) import Control.Monad.Par.Combinator (parMap)+import Control.Monad.Par.Scheds.Sparks hiding (get) import Control.Monad.Primitive (PrimMonad, PrimState, RealWorld) import Control.Monad.Trans.State.Strict (get, put, execStateT) import Data.Monoid@@ -104,8 +105,8 @@ {-# INLINE acceptProb #-}  move :: Target Particle -> Particle -> Particle -> Double -> Double -> Particle-move target p0 p1 z zc =-  let proposal = stretch p0 p1 z+move target !p0 p1 z zc =+  let !proposal = stretch p0 p1 z       pAccept  = acceptProb target p0 proposal z   in  if   zc <= min 1 (exp pAccept)       then proposal@@ -122,17 +123,16 @@ execute target e0 e1 n = do   zs  <- replicateM n symmetric   zcs <- replicateM n uniform-  vjs <- replicateM n (uniformR (1, n))+  js  <- U.replicateM n (uniformR (1, n))    let granularity = truncate (fromIntegral n / 2) -      js      = U.fromList vjs       w0 k    = e0 `V.unsafeIndex` pred k       w1 k ks = e1 `V.unsafeIndex` pred (ks `U.unsafeIndex` pred k)         worker (k, z, zc) = move target (w0 k) (w1 k js) z zc-      result = runPar $+      !result = runPar $         parMapChunk granularity worker (zip3 [1..n] zs zcs)    return $! V.fromList result@@ -151,8 +151,8 @@       e1   = V.unsafeSlice n n chainPosition   result0 <- lift (execute chainTarget e0 e1 n)   result1 <- lift (execute chainTarget e1 result0 n)-  let ensemble = V.concat [result0, result1]-  put (Chain chainTarget ensemble)+  let !ensemble = V.concat [result0, result1]+  put $! (Chain chainTarget ensemble) {-# INLINE flat #-}  chain :: PrimMonad m => Chain -> Gen (PrimState m) -> Producer Chain m ()

@@ -0,0 +1,23 @@+{-# OPTIONS_GHC -fno-warn-type-defaults #-}++module Main where++import Numeric.MCMC.Flat+import qualified Data.Vector.Unboxed as U (toList, fromList)+import qualified Data.Vector as V (fromList)++bnn :: Particle -> Double+bnn xs = -0.5 * (x0 ^ 2 * x1 ^ 2 + x0 ^ 2 + x1 ^ 2 - 8 * x0 - 8 * x1) where+  [x0, x1] = U.toList xs++ensemble :: Ensemble+ensemble = V.fromList [+    U.fromList [negate 1.0, negate 1.0]+  , U.fromList [negate 1.0, 1.0]+  , U.fromList [1.0, negate 1.0]+  , U.fromList [1.0, 1.0]+  ]++main :: IO ()+main = withSystemRandom . asGenIO $ mcmc 10000 ensemble bnn+