Hello community, here is the log from the commit of package ghc-speedy-slice for openSUSE:Factory checked in at 2017-03-03 17:51:50 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/ghc-speedy-slice (Old) and /work/SRC/openSUSE:Factory/.ghc-speedy-slice.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "ghc-speedy-slice" Fri Mar 3 17:51:50 2017 rev:4 rq:461683 version:0.3.0 Changes: -------- --- /work/SRC/openSUSE:Factory/ghc-speedy-slice/ghc-speedy-slice.changes 2017-01-12 15:52:35.351016135 +0100 +++ /work/SRC/openSUSE:Factory/.ghc-speedy-slice.new/ghc-speedy-slice.changes 2017-03-03 17:51:51.219097710 +0100 @@ -1,0 +2,5 @@ +Sun Feb 12 14:20:39 UTC 2017 - [email protected] + +- Update to version 0.3.0 with cabal2obs. + +------------------------------------------------------------------- Old: ---- speedy-slice-0.1.5.tar.gz New: ---- speedy-slice-0.3.0.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ ghc-speedy-slice.spec ++++++ --- /var/tmp/diff_new_pack.qQqujS/_old 2017-03-03 17:51:51.711028230 +0100 +++ /var/tmp/diff_new_pack.qQqujS/_new 2017-03-03 17:51:51.715027666 +0100 @@ -1,7 +1,7 @@ # # spec file for package ghc-speedy-slice # -# Copyright (c) 2016 SUSE LINUX GmbH, Nuernberg, Germany. +# Copyright (c) 2017 SUSE LINUX GmbH, Nuernberg, Germany. # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -19,7 +19,7 @@ %global pkg_name speedy-slice %bcond_with tests Name: ghc-%{pkg_name} -Version: 0.1.5 +Version: 0.3.0 Release: 0 Summary: Speedy slice sampling License: MIT @@ -27,6 +27,7 @@ Url: https://hackage.haskell.org/package/%{pkg_name} Source0: https://hackage.haskell.org/package/%{pkg_name}-%{version}/%{pkg_name}-%{version}.tar.gz BuildRequires: ghc-Cabal-devel +BuildRequires: ghc-kan-extensions-devel BuildRequires: ghc-lens-devel BuildRequires: ghc-mcmc-types-devel BuildRequires: ghc-mwc-probability-devel @@ -50,8 +51,9 @@ Additionally you can sample over anything that's an instance of both 'Num' and 'Variate', which is useful in the case of discrete parameters. -Exports a 'mcmc' function that prints a trace to stdout, as well as a 'slice' -transition operator that can be used more generally. +Exports a 'mcmc' function that prints a trace to stdout, a 'chain' function for +collecting results in memory, and a 'slice' transition operator that can be +used more generally. > import Numeric.MCMC.Slice > import Data.Sequence (Seq, index, fromList) > > bnn :: Seq Double -> Double > bnn xs = -0.5 * (x0 ^ 2 * x1 ^ 2 + x0 ^ 2 + x1 ^ ++++++ speedy-slice-0.1.5.tar.gz -> speedy-slice-0.3.0.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/speedy-slice-0.1.5/Numeric/MCMC/Slice.hs new/speedy-slice-0.3.0/Numeric/MCMC/Slice.hs --- old/speedy-slice-0.1.5/Numeric/MCMC/Slice.hs 2016-10-31 20:45:32.000000000 +0100 +++ new/speedy-slice-0.3.0/Numeric/MCMC/Slice.hs 2016-12-21 21:59:06.000000000 +0100 @@ -1,4 +1,4 @@ --- {-# OPTIONS_GHC -Wall #-} +{-# OPTIONS_GHC -Wall #-} {-# LANGUAGE BangPatterns #-} {-# LANGUAGE RecordWildCards #-} {-# LANGUAGE FlexibleContexts #-} @@ -28,6 +28,7 @@ module Numeric.MCMC.Slice ( mcmc + , chain , slice -- * Re-exported @@ -37,8 +38,11 @@ , MWC.asGenIO ) where +import Control.Monad (replicateM) +import Control.Monad.Codensity (lowerCodensity) import Control.Monad.Trans.State.Strict (put, get, execStateT) -import Control.Monad.Primitive (PrimMonad, PrimState, RealWorld) +import Control.Monad.Primitive (PrimMonad, PrimState) +import Control.Monad.IO.Class (MonadIO, liftIO) import Control.Lens hiding (index) import Data.Maybe (fromMaybe) import Data.Sampling.Types @@ -55,32 +59,62 @@ -- -9.310661272172682e-2,0.2562387977415508 -- -0.48500122500661846,0.46245400501919076 mcmc - :: (Show (t a), FoldableWithIndex (Index (t a)) t, Ixed (t a), + :: (MonadIO m, PrimMonad m, + Show (t a), FoldableWithIndex (Index (t a)) t, Ixed (t a), Num (IxValue (t a)), Variate (IxValue (t a))) => Int -> IxValue (t a) -> t a -> (t a -> Double) - -> Gen RealWorld - -> IO () + -> Gen (PrimState m) + -> m () mcmc n radial chainPosition target gen = runEffect $ - chain radial Chain {..} gen + drive radial Chain {..} gen >-> Pipes.take n - >-> Pipes.mapM_ print + >-> Pipes.mapM_ (liftIO . print) where chainScore = lTarget chainTarget chainPosition chainTunables = Nothing chainTarget = Target target Nothing --- A Markov chain driven by the slice transition operator. +-- | Trace 'n' iterations of a Markov chain and collect them in a list. +-- +-- >>> results <- withSystemRandom . asGenIO $ mcmc 3 1 [0, 0] rosenbrock chain + :: (PrimMonad m, FoldableWithIndex (Index (f a)) f, Ixed (f a) + , Variate (IxValue (f a)), Num (IxValue (f a))) + => Int + -> IxValue (f a) + -> f a + -> (f a -> Double) + -> Gen (PrimState m) + -> m [Chain (f a) b] +chain n radial position target gen = runEffect $ + drive radial origin gen + >-> collect n + where + ctarget = Target target Nothing + + origin = Chain { + chainScore = lTarget ctarget position + , chainTunables = Nothing + , chainTarget = ctarget + , chainPosition = position + } + + collect :: Monad m => Int -> Consumer a m [a] + collect size = lowerCodensity $ + replicateM size (lift Pipes.await) + +-- A Markov chain driven by the slice transition operator. +drive :: (PrimMonad m, FoldableWithIndex (Index (t a)) t, Ixed (t a), Num (IxValue (t a)), Variate (IxValue (t a))) => IxValue (t a) -> Chain (t a) b -> Gen (PrimState m) - -> Producer (Chain (t a) b) m () -chain radial = loop where + -> Producer (Chain (t a) b) m c +drive radial = loop where loop state prng = do next <- lift (MWC.sample (execStateT (slice radial) state) prng) yield next diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/speedy-slice-0.1.5/speedy-slice.cabal new/speedy-slice-0.3.0/speedy-slice.cabal --- old/speedy-slice-0.1.5/speedy-slice.cabal 2016-12-04 09:57:44.000000000 +0100 +++ new/speedy-slice-0.3.0/speedy-slice.cabal 2016-12-21 21:51:51.000000000 +0100 @@ -1,5 +1,5 @@ name: speedy-slice -version: 0.1.5 +version: 0.3.0 synopsis: Speedy slice sampling. homepage: http://github.com/jtobin/speedy-slice license: MIT @@ -20,8 +20,9 @@ Additionally you can sample over anything that's an instance of both 'Num' and 'Variate', which is useful in the case of discrete parameters. . - Exports a 'mcmc' function that prints a trace to stdout, as well as a - 'slice' transition operator that can be used more generally. + Exports a 'mcmc' function that prints a trace to stdout, a 'chain' function + for collecting results in memory, and a 'slice' transition operator that can + be used more generally. . > import Numeric.MCMC.Slice > import Data.Sequence (Seq, index, fromList) @@ -44,6 +45,7 @@ Numeric.MCMC.Slice build-depends: base >= 4 && < 6 + , kan-extensions >= 5 && < 6 , lens >= 4 && < 5 , primitive >= 0.6 && < 1.0 , mcmc-types >= 1.0.1 diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/speedy-slice-0.1.5/test/BNN.hs new/speedy-slice-0.3.0/test/BNN.hs --- old/speedy-slice-0.1.5/test/BNN.hs 2016-10-31 21:37:30.000000000 +0100 +++ new/speedy-slice-0.3.0/test/BNN.hs 2016-12-21 22:00:28.000000000 +0100 @@ -11,5 +11,7 @@ x1 = index xs 1 main :: IO () -main = withSystemRandom . asGenIO $ mcmc 100 1 (fromList [0, 0]) bnn +main = withSystemRandom . asGenIO $ \gen -> do + _ <- chain 50 1 (fromList [0, 0]) bnn gen + mcmc 50 1 (fromList [0, 0]) bnn gen diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/speedy-slice-0.1.5/test/Rosenbrock.hs new/speedy-slice-0.3.0/test/Rosenbrock.hs --- old/speedy-slice-0.1.5/test/Rosenbrock.hs 2016-10-31 21:37:35.000000000 +0100 +++ new/speedy-slice-0.3.0/test/Rosenbrock.hs 2016-12-21 22:00:32.000000000 +0100 @@ -8,6 +8,7 @@ rosenbrock [x0, x1] = negate (5 *(x1 - x0 ^ 2) ^ 2 + 0.05 * (1 - x0) ^ 2) main :: IO () -main = withSystemRandom . asGenIO $ mcmc 100 1 [0, 0] rosenbrock - +main = withSystemRandom . asGenIO $ \gen -> do + _ <- chain 50 1 [0, 0] rosenbrock gen + mcmc 50 1 [0, 0] rosenbrock gen
