3 Mar
2017
3 Mar
'17
16:51
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 - psimons@suse.com
+
+- 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