diff --git a/CHANGELOG.md b/CHANGELOG.md --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,10 @@ +# 1.3.0 + +- Support for GHC 9.6 +- Replaced transformers' `ListT` by + (https://github.com/tweag/monad-bayes/pull/295) +- Naming fixes for `Sampler` and `SamplerT` + # 1.2.0 - Renamed monad transformers idiomatically diff --git a/benchmark/Single.hs b/benchmark/Single.hs --- a/benchmark/Single.hs +++ b/benchmark/Single.hs @@ -1,12 +1,12 @@ {-# LANGUAGE DerivingStrategies #-} {-# LANGUAGE ImportQualifiedPost #-} +import Control.Applicative (Applicative (..)) import Control.Monad.Bayes.Sampler.Strict import Data.Time (diffUTCTime, getCurrentTime) import Helper import Options.Applicative - ( Applicative (liftA2), - ParserInfo, + ( ParserInfo, auto, execParser, fullDesc, @@ -17,6 +17,10 @@ option, short, ) +-- Prelude exports liftA2 from GHC 9.6 on, see https://github.com/haskell/core-libraries-committee/blob/main/guides/export-lifta2-prelude.md +-- import Control.Applicative further up can be removed once we don't support GHC <= 9.4 anymore + +import Prelude hiding (Applicative (..)) infer :: Model -> Alg -> IO () infer model alg = do diff --git a/models/ConjugatePriors.hs b/models/ConjugatePriors.hs --- a/models/ConjugatePriors.hs +++ b/models/ConjugatePriors.hs @@ -4,12 +4,15 @@ module ConjugatePriors where -import Control.Applicative (Applicative (liftA2)) +import Control.Applicative (Applicative (..)) import Control.Foldl (fold) import Control.Foldl qualified as F import Control.Monad.Bayes.Class (Bayesian (..), MonadDistribution (bernoulli, beta, gamma, normal), MonadMeasure, normalPdf) import Numeric.Log (Log (Exp)) -import Prelude +-- Prelude exports liftA2 from GHC 9.6 on, see https://github.com/haskell/core-libraries-committee/blob/main/guides/export-lifta2-prelude.md +-- import Control.Applicative further up can be removed once we don't support GHC <= 9.4 anymore + +import Prelude hiding (Applicative (..)) type GammaParams = (Double, Double) diff --git a/models/Dice.hs b/models/Dice.hs --- a/models/Dice.hs +++ b/models/Dice.hs @@ -3,13 +3,17 @@ -- A toy model for dice rolling from http://dl.acm.org/citation.cfm?id=2804317 -- Exact results can be obtained using Dist monad -import Control.Applicative (liftA2) +import Control.Applicative (Applicative (..)) import Control.Monad.Bayes.Class ( MonadDistribution (uniformD), MonadFactor (score), MonadMeasure, condition, ) +-- Prelude exports liftA2 from GHC 9.6 on, see https://github.com/haskell/core-libraries-committee/blob/main/guides/export-lifta2-prelude.md +-- import Control.Applicative further up can be removed once we don't support GHC <= 9.4 anymore + +import Prelude hiding (Applicative (..)) -- | A toss of a six-sided die. die :: (MonadDistribution m) => m Int diff --git a/monad-bayes.cabal b/monad-bayes.cabal --- a/monad-bayes.cabal +++ b/monad-bayes.cabal @@ -1,16 +1,16 @@ -cabal-version: 2.2 -name: monad-bayes -version: 1.2.0 -license: MIT -license-file: LICENSE.md -copyright: 2015-2020 Adam Scibior -maintainer: dominic.steinitz@tweag.io -author: Adam Scibior -stability: experimental -tested-with: GHC ==9.0.2 || ==9.2.7 || ==9.4.5 -homepage: http://github.com/tweag/monad-bayes#readme -bug-reports: https://github.com/tweag/monad-bayes/issues -synopsis: A library for probabilistic programming. +cabal-version: 2.2 +name: monad-bayes +version: 1.3.0 +license: MIT +license-file: LICENSE.md +copyright: 2015-2020 Adam Scibior +maintainer: dominic.steinitz@tweag.io +author: Adam Scibior +stability: experimental +tested-with: GHC ==9.0.2 || ==9.2.7 || ==9.4.5 || ==9.6.4 +homepage: http://github.com/tweag/monad-bayes#readme +bug-reports: https://github.com/tweag/monad-bayes/issues +synopsis: A library for probabilistic programming. description: A library for probabilistic programming using probability monads. The emphasis is on composition of inference algorithms implemented in @@ -19,12 +19,14 @@ for a quick-start user guide and a reference overview of how it all works" and the included [README](#readme). -category: Statistics -build-type: Simple -extra-source-files: +category: Statistics +build-type: Simple +extra-doc-files: CHANGELOG.md README.md +data-files: test/fixtures/*.txt + source-repository head type: git location: https://github.com/tweag/monad-bayes.git @@ -36,7 +38,7 @@ common deps build-depends: - , base >=4.15 && <4.18 + , base >=4.15 && <4.19 , brick >=1.0 && <2.0 , containers >=0.5.10 && <0.7 , foldl ^>=1.4 @@ -51,7 +53,7 @@ , matrix ^>=0.3 , monad-coroutine ^>=0.9.0 , monad-extras ^>=0.6 - , mtl ^>=2.2.2 + , mtl >=2.2.2 && <2.4 , mwc-random >=0.13.6 && <0.16 , pipes ^>=4.3 , pretty-simple ^>=4.1 @@ -61,22 +63,25 @@ , scientific ^>=0.3 , statistics >=0.14.0 && <0.17 , text >=1.2 && <2.1 + , transformers >=0.5.6 && <0.7 , vector >=0.12.0 && <0.14 , vty ^>=5.38 common test-deps build-depends: , abstract-par ^>=0.3 - , criterion >=1.5 && <1.7 + , criterion >=1.5 && <1.7 , directory ^>=1.3 - , hspec ^>=2.11 + , hspec >=2.10 && <2.12 , monad-bayes - , optparse-applicative >=0.17 && <0.19 + , optparse-applicative >=0.17 && <0.19 , process ^>=1.6 , QuickCheck ^>=2.14 - , time >=1.9 && <1.13 - , transformers ^>=0.5.6 + , time >=1.9 && <1.13 , typed-process ^>=0.2 + + autogen-modules: Paths_monad_bayes + other-modules: Paths_monad_bayes library import: deps diff --git a/src/Control/Monad/Bayes/Class.hs b/src/Control/Monad/Bayes/Class.hs --- a/src/Control/Monad/Bayes/Class.hs +++ b/src/Control/Monad/Bayes/Class.hs @@ -77,11 +77,11 @@ import Control.Arrow (Arrow (second)) import Control.Monad (replicateM, when) import Control.Monad.Cont (ContT) -import Control.Monad.Except (ExceptT, lift) +import Control.Monad.Except (ExceptT) import Control.Monad.Identity (IdentityT) -import Control.Monad.List (ListT) import Control.Monad.Reader (ReaderT) import Control.Monad.State (StateT) +import Control.Monad.Trans.Class (lift) import Control.Monad.Writer (WriterT) import Data.Histogram qualified as H import Data.Histogram.Fill qualified as H @@ -389,16 +389,6 @@ score = lift . score instance (MonadMeasure m) => MonadMeasure (StateT s m) - -instance (MonadDistribution m) => MonadDistribution (ListT m) where - random = lift random - bernoulli = lift . bernoulli - categorical = lift . categorical - -instance (MonadFactor m) => MonadFactor (ListT m) where - score = lift . score - -instance (MonadMeasure m) => MonadMeasure (ListT m) instance (MonadDistribution m) => MonadDistribution (ContT r m) where random = lift random diff --git a/src/Control/Monad/Bayes/Enumerator.hs b/src/Control/Monad/Bayes/Enumerator.hs --- a/src/Control/Monad/Bayes/Enumerator.hs +++ b/src/Control/Monad/Bayes/Enumerator.hs @@ -32,16 +32,18 @@ import Control.Applicative (Alternative) import Control.Arrow (second) +import Control.Monad (MonadPlus) import Control.Monad.Bayes.Class ( MonadDistribution (bernoulli, categorical, logCategorical, random), MonadFactor (..), MonadMeasure, ) -import Control.Monad.Writer +import Control.Monad.Writer (WriterT (..)) import Data.AEq (AEq, (===), (~==)) import Data.List (sortOn) import Data.Map qualified as Map import Data.Maybe (fromMaybe) +import Data.Monoid (Product (..)) import Data.Ord (Down (Down)) import Data.Vector qualified as VV import Data.Vector.Generic qualified as V diff --git a/src/Control/Monad/Bayes/Inference/Lazy/MH.hs b/src/Control/Monad/Bayes/Inference/Lazy/MH.hs --- a/src/Control/Monad/Bayes/Inference/Lazy/MH.hs +++ b/src/Control/Monad/Bayes/Inference/Lazy/MH.hs @@ -7,10 +7,11 @@ import Control.Monad.Bayes.Class (Log (ln)) import Control.Monad.Bayes.Sampler.Lazy - ( SamplerT (runSamplerT), + ( Sampler, Tree (..), Trees (..), randomTree, + runSampler, ) import Control.Monad.Bayes.Weighted (WeightedT, runWeightedT) import Control.Monad.Extra (iterateM) @@ -18,7 +19,7 @@ import System.Random (RandomGen (split), getStdGen, newStdGen) import System.Random qualified as R -mh :: forall a. Double -> WeightedT SamplerT a -> IO [(a, Log Double)] +mh :: forall a. Double -> WeightedT Sampler a -> IO [(a, Log Double)] mh p m = do -- Top level: produce a stream of samples. -- Split the random number generator in two @@ -27,7 +28,7 @@ g <- newStdGen >> getStdGen let (g1, g2) = split g let t = randomTree g1 - let (x, w) = runSamplerT (runWeightedT m) t + let (x, w) = runSampler (runWeightedT m) t -- Now run step over and over to get a stream of (tree,result,weight)s. let (samples, _) = runState (iterateM step (t, x, w)) g2 -- The stream of seeds is used to produce a stream of result/weight pairs. @@ -50,7 +51,7 @@ let t' = mutateTree p g1 t -- Rerun the model with the new tree, to get a new -- weight w'. - let (x', w') = runSamplerT (runWeightedT m) t' + let (x', w') = runSampler (runWeightedT m) t' -- MH acceptance ratio. This is the probability of either -- returning the new seed or the old one. let ratio = w' / w diff --git a/src/Control/Monad/Bayes/Inference/Lazy/WIS.hs b/src/Control/Monad/Bayes/Inference/Lazy/WIS.hs --- a/src/Control/Monad/Bayes/Inference/Lazy/WIS.hs +++ b/src/Control/Monad/Bayes/Inference/Lazy/WIS.hs @@ -1,17 +1,17 @@ module Control.Monad.Bayes.Inference.Lazy.WIS where -import Control.Monad.Bayes.Sampler.Lazy (SamplerT, weightedsamples) +import Control.Monad.Bayes.Sampler.Lazy (SamplerT, weightedSamples) import Control.Monad.Bayes.Weighted (WeightedT) import Numeric.Log (Log (Exp)) import System.Random (Random (randoms), getStdGen, newStdGen) --- | WeightedT Importance Sampling +-- | Weighted Importance Sampling -- | Likelihood weighted importance sampling first draws n weighted samples, -- and then samples a stream of results from that regarded as an empirical distribution -lwis :: Int -> WeightedT SamplerT a -> IO [a] +lwis :: Int -> WeightedT (SamplerT IO) a -> IO [a] lwis n m = do - xws <- weightedsamples m + xws <- weightedSamples m let xws' = take n $ accumulate xws 0 let max' = snd $ last xws' _ <- newStdGen diff --git a/src/Control/Monad/Bayes/Integrator.hs b/src/Control/Monad/Bayes/Integrator.hs --- a/src/Control/Monad/Bayes/Integrator.hs +++ b/src/Control/Monad/Bayes/Integrator.hs @@ -48,6 +48,10 @@ import Numeric.Log (Log (ln)) import Statistics.Distribution qualified as Statistics import Statistics.Distribution.Uniform qualified as Statistics +-- Prelude exports liftA2 from GHC 9.6 on, see https://github.com/haskell/core-libraries-committee/blob/main/guides/export-lifta2-prelude.md +-- import Control.Applicative further up can be removed once we don't support GHC <= 9.4 anymore + +import Prelude hiding (Applicative (..)) newtype Integrator a = Integrator {getIntegrator :: Cont Double a} deriving newtype (Functor, Applicative, Monad) diff --git a/src/Control/Monad/Bayes/Population.hs b/src/Control/Monad/Bayes/Population.hs --- a/src/Control/Monad/Bayes/Population.hs +++ b/src/Control/Monad/Bayes/Population.hs @@ -1,6 +1,7 @@ {-# LANGUAGE DerivingStrategies #-} {-# LANGUAGE GeneralizedNewtypeDeriving #-} {-# LANGUAGE ImportQualifiedPost #-} +{-# LANGUAGE NamedFieldPuns #-} {-# LANGUAGE RankNTypes #-} {-# OPTIONS_GHC -Wno-deprecations #-} @@ -37,11 +38,12 @@ ) where +import Control.Applicative (Alternative) import Control.Arrow (second) -import Control.Monad (replicateM) +import Control.Monad (forM, replicateM) import Control.Monad.Bayes.Class - ( MonadDistribution (categorical, logCategorical, random, uniform), - MonadFactor, + ( MonadDistribution (..), + MonadFactor (..), MonadMeasure, factor, ) @@ -52,7 +54,9 @@ runWeightedT, weightedT, ) -import Control.Monad.List (ListT (..), MonadIO, MonadTrans (..)) +import Control.Monad.IO.Class +import Control.Monad.Trans.Class +import Data.Functor.Compose import Data.List (unfoldr) import Data.List qualified import Data.Maybe (catMaybes) @@ -62,6 +66,40 @@ import Numeric.Log qualified as Log import Prelude hiding (all, sum) +-- | The old-fashioned, broken list transformer, adding a list/nondeterminism/choice effect. +-- It is not a valid monad transformer, but it is a valid 'Applicative'. +newtype ListT m a = ListT {getListT :: Compose m [] a} + deriving newtype (Functor, Applicative, Alternative) + +listT :: m [a] -> ListT m a +listT = ListT . Compose + +runListT :: ListT m a -> m [a] +runListT = getCompose . getListT + +-- | This monad instance is _unlawful_, +-- it is only by accident and careful construction that it can be used here. +instance (Monad m) => Monad (ListT m) where + ma >>= f = ListT $ Compose $ do + as <- runListT ma + fmap concat $ forM as $ runListT . f + +instance MonadTrans ListT where + lift = ListT . Compose . fmap pure + +instance (MonadIO m) => MonadIO (ListT m) where + liftIO = lift . liftIO + +instance (MonadDistribution m) => MonadDistribution (ListT m) where + random = lift random + bernoulli = lift . bernoulli + categorical = lift . categorical + +instance (MonadFactor m) => MonadFactor (ListT m) where + score = lift . score + +instance (MonadMeasure m) => MonadMeasure (ListT m) + -- | A collection of weighted samples, or particles. newtype PopulationT m a = PopulationT {getPopulationT :: WeightedT (ListT m) a} deriving newtype (Functor, Applicative, Monad, MonadIO, MonadDistribution, MonadFactor, MonadMeasure) @@ -80,7 +118,7 @@ -- | Initialize 'PopulationT' with a concrete weighted sample. fromWeightedList :: (Monad m) => m [(a, Log Double)] -> PopulationT m a -fromWeightedList = PopulationT . weightedT . ListT +fromWeightedList = PopulationT . weightedT . listT -- | Increase the sample size by a given factor. -- The weights are adjusted such that their sum is preserved. diff --git a/src/Control/Monad/Bayes/Sampler/Lazy.hs b/src/Control/Monad/Bayes/Sampler/Lazy.hs --- a/src/Control/Monad/Bayes/Sampler/Lazy.hs +++ b/src/Control/Monad/Bayes/Sampler/Lazy.hs @@ -1,4 +1,5 @@ {-# LANGUAGE BangPatterns #-} +{-# LANGUAGE DeriveFunctor #-} {-# LANGUAGE GeneralizedNewtypeDeriving #-} {-# LANGUAGE RankNTypes #-} {-# LANGUAGE ScopedTypeVariables #-} @@ -9,6 +10,9 @@ import Control.Monad (ap) import Control.Monad.Bayes.Class (MonadDistribution (random)) import Control.Monad.Bayes.Weighted (WeightedT, runWeightedT) +import Control.Monad.IO.Class +import Control.Monad.Identity (Identity (runIdentity)) +import Control.Monad.Trans import Numeric.Log (Log (..)) import System.Random ( RandomGen (split), @@ -17,10 +21,11 @@ ) import System.Random qualified as R --- | A 'Tree' is a lazy, infinitely wide and infinitely deep tree, labelled by Doubles --- | Our source of randomness will be a Tree, populated by uniform [0,1] choices for each label. --- | Often people just use a list or stream instead of a tree. --- | But a tree allows us to be lazy about how far we are going all the time. +-- | A 'Tree' is a lazy, infinitely wide and infinitely deep tree, labelled by Doubles. +-- +-- Our source of randomness will be a Tree, populated by uniform [0,1] choices for each label. +-- Often people just use a list or stream instead of a tree. +-- But a tree allows us to be lazy about how far we are going all the time. data Tree = Tree { currentUniform :: Double, lazyUniforms :: Trees @@ -32,48 +37,61 @@ tailTrees :: Trees } --- | A probability distribution over a is --- | a function 'Tree -> a' --- | The idea is that it uses up bits of the tree as it runs -newtype SamplerT a = SamplerT {runSamplerT :: Tree -> a} +-- | A probability distribution over @a@ is a function 'Tree -> a'. +-- The idea is that it uses up bits of the tree as it runs. +type Sampler = SamplerT Identity + +runSampler :: Sampler a -> Tree -> a +runSampler = (runIdentity .) . runSamplerT + +newtype SamplerT m a = SamplerT {runSamplerT :: Tree -> m a} deriving (Functor) --- | Two key things to do with trees: --- | Split tree splits a tree in two (bijectively) --- | Get the label at the head of the tree and discard the rest +-- | Split a tree in two (bijectively). splitTree :: Tree -> (Tree, Tree) splitTree (Tree r (Trees t ts)) = (t, Tree r ts) --- | Preliminaries for the simulation methods. Generate a tree with uniform random labels. This uses 'split' to split a random seed +-- | Generate a tree with uniform random labels. +-- +-- Preliminary for the simulation methods. This uses 'split' to split a random seed. randomTree :: (RandomGen g) => g -> Tree randomTree g = let (a, g') = R.random g in Tree a (randomTrees g') randomTrees :: (RandomGen g) => g -> Trees randomTrees g = let (g1, g2) = split g in Trees (randomTree g1) (randomTrees g2) -instance Applicative SamplerT where - pure = SamplerT . const +instance (Monad m) => Applicative (SamplerT m) where + pure = lift . pure (<*>) = ap --- | probabilities for a monad. -- | Sequencing is done by splitting the tree --- | and using different bits for different computations. -instance Monad SamplerT where +-- and using different bits for different computations. +instance (Monad m) => Monad (SamplerT m) where return = pure - (SamplerT m) >>= f = SamplerT \g -> + (SamplerT m) >>= f = SamplerT \g -> do let (g1, g2) = splitTree g - (SamplerT m') = f (m g1) - in m' g2 + a <- m g1 + let SamplerT m' = f a + m' g2 -instance MonadDistribution SamplerT where - random = SamplerT \(Tree r _) -> r +instance MonadTrans SamplerT where + lift = SamplerT . const -sampler :: SamplerT a -> IO a -sampler m = newStdGen *> (runSamplerT m . randomTree <$> getStdGen) +instance (MonadIO m) => MonadIO (SamplerT m) where + liftIO = lift . liftIO +-- | Sampling gets the label at the head of the tree and discards the rest. +instance (Monad m) => MonadDistribution (SamplerT m) where + random = SamplerT \(Tree r _) -> pure r + +-- | Runs a 'SamplerT' by creating a new 'StdGen'. +runSamplerTIO :: (MonadIO m) => SamplerT m a -> m a +runSamplerTIO m = liftIO newStdGen *> (runSamplerT m =<< randomTree <$> liftIO getStdGen) + +-- | Draw a stream of independent samples. independent :: (Monad m) => m a -> m [a] independent = sequence . repeat --- | 'weightedsamples' runs a probability measure and gets out a stream of (result,weight) pairs -weightedsamples :: WeightedT SamplerT a -> IO [(a, Log Double)] -weightedsamples = sampler . independent . runWeightedT +-- | Runs a probability measure and gets out a stream of @(result,weight)@ pairs +weightedSamples :: (MonadIO m) => WeightedT (SamplerT m) a -> m [(a, Log Double)] +weightedSamples = runSamplerTIO . sequence . repeat . runWeightedT diff --git a/src/Control/Monad/Bayes/Sampler/Strict.hs b/src/Control/Monad/Bayes/Sampler/Strict.hs --- a/src/Control/Monad/Bayes/Sampler/Strict.hs +++ b/src/Control/Monad/Bayes/Sampler/Strict.hs @@ -42,13 +42,14 @@ ) import Control.Monad.Reader (MonadIO, ReaderT (..)) import Control.Monad.ST (ST) +import Control.Monad.Trans (MonadTrans) import Numeric.Log (Log (ln)) import System.Random.MWC.Distributions qualified as MWC import System.Random.Stateful (IOGenM (..), STGenM, StatefulGen, StdGen, initStdGen, mkStdGen, newIOGenM, newSTGenM, uniformDouble01M, uniformRM) -- | The sampling interpretation of a probabilistic program -- Here m is typically IO or ST -newtype SamplerT g m a = SamplerT {runSamplerT :: ReaderT g m a} deriving (Functor, Applicative, Monad, MonadIO) +newtype SamplerT g m a = SamplerT {runSamplerT :: ReaderT g m a} deriving (Functor, Applicative, Monad, MonadIO, MonadTrans) -- | convenient type synonym to show specializations of SamplerT -- to particular pairs of monad and RNG diff --git a/src/Control/Monad/Bayes/Traced/Basic.hs b/src/Control/Monad/Bayes/Traced/Basic.hs --- a/src/Control/Monad/Bayes/Traced/Basic.hs +++ b/src/Control/Monad/Bayes/Traced/Basic.hs @@ -17,7 +17,7 @@ ) where -import Control.Applicative (liftA2) +import Control.Applicative (Applicative (..)) import Control.Monad.Bayes.Class ( MonadDistribution (random), MonadFactor (..), @@ -34,6 +34,10 @@ import Control.Monad.Bayes.Weighted (WeightedT) import Data.Functor.Identity (Identity) import Data.List.NonEmpty as NE (NonEmpty ((:|)), toList) +-- Prelude exports liftA2 from GHC 9.6 on, see https://github.com/haskell/core-libraries-committee/blob/main/guides/export-lifta2-prelude.md +-- import Control.Applicative further up can be removed once we don't support GHC <= 9.4 anymore + +import Prelude hiding (Applicative (..)) -- | Tracing monad that records random choices made in the program. data TracedT m a = TracedT diff --git a/src/Control/Monad/Bayes/Traced/Static.hs b/src/Control/Monad/Bayes/Traced/Static.hs --- a/src/Control/Monad/Bayes/Traced/Static.hs +++ b/src/Control/Monad/Bayes/Traced/Static.hs @@ -18,7 +18,7 @@ ) where -import Control.Applicative (liftA2) +import Control.Applicative (Applicative (..)) import Control.Monad.Bayes.Class ( MonadDistribution (random), MonadFactor (..), @@ -35,6 +35,10 @@ import Control.Monad.Bayes.Weighted (WeightedT) import Control.Monad.Trans (MonadTrans (..)) import Data.List.NonEmpty as NE (NonEmpty ((:|)), toList) +-- Prelude exports liftA2 from GHC 9.6 on, see https://github.com/haskell/core-libraries-committee/blob/main/guides/export-lifta2-prelude.md +-- import Control.Applicative further up can be removed once we don't support GHC <= 9.4 anymore + +import Prelude hiding (Applicative (..)) -- | A tracing monad where only a subset of random choices are traced. -- diff --git a/test/TestBenchmarks.hs b/test/TestBenchmarks.hs --- a/test/TestBenchmarks.hs +++ b/test/TestBenchmarks.hs @@ -3,12 +3,13 @@ import Control.Monad (forM_) import Data.Maybe (fromJust) import Helper +import Paths_monad_bayes (getDataDir) import System.IO (readFile') import System.IO.Error (catchIOError, isDoesNotExistError) import Test.Hspec fixtureToFilename :: Model -> Alg -> String -fixtureToFilename model alg = fromJust (serializeModel model) ++ "-" ++ show alg ++ ".txt" +fixtureToFilename model alg = "/test/fixtures/" ++ fromJust (serializeModel model) ++ "-" ++ show alg ++ ".txt" models :: [Model] models = [LR 10, HMM 10, LDA (5, 10)] @@ -21,7 +22,8 @@ testFixture :: Model -> Alg -> SpecWith () testFixture model alg = do - let filename = "test/fixtures/" ++ fixtureToFilename model alg + dataDir <- runIO getDataDir + let filename = dataDir <> fixtureToFilename model alg it ("should agree with the fixture " ++ filename) $ do fixture <- catchIOError (readFile' filename) $ \e -> if isDoesNotExistError e diff --git a/test/TestSSMFixtures.hs b/test/TestSSMFixtures.hs --- a/test/TestSSMFixtures.hs +++ b/test/TestSSMFixtures.hs @@ -3,16 +3,18 @@ import Control.Monad.Bayes.Sampler.Strict (sampleIOfixed) import NonlinearSSM import NonlinearSSM.Algorithms +import Paths_monad_bayes (getDataDir) import System.IO (readFile') import System.IO.Error (catchIOError, isDoesNotExistError) import Test.Hspec fixtureToFilename :: Alg -> FilePath -fixtureToFilename alg = "test/fixtures/SSM-" ++ show alg ++ ".txt" +fixtureToFilename alg = "/test/fixtures/SSM-" ++ show alg ++ ".txt" testFixture :: Alg -> SpecWith () testFixture alg = do - let filename = fixtureToFilename alg + dataDir <- runIO getDataDir + let filename = dataDir <> fixtureToFilename alg it ("should agree with the fixture " ++ filename) $ do ys <- sampleIOfixed $ generateData t fixture <- catchIOError (readFile' filename) $ \e -> diff --git a/test/TestWeighted.hs b/test/TestWeighted.hs --- a/test/TestWeighted.hs +++ b/test/TestWeighted.hs @@ -2,6 +2,7 @@ module TestWeighted (check, passed, result, model) where +import Control.Monad (unless, when) import Control.Monad.Bayes.Class ( MonadDistribution (normal, uniformD), MonadMeasure, @@ -9,7 +10,6 @@ ) import Control.Monad.Bayes.Sampler.Strict (sampleIOfixed) import Control.Monad.Bayes.Weighted (runWeightedT) -import Control.Monad.State (unless, when) import Data.AEq (AEq ((~==))) import Data.Bifunctor (second) import Numeric.Log (Log (Exp, ln)) diff --git a/test/fixtures/HMM10-MH.txt b/test/fixtures/HMM10-MH.txt new file mode 100644 --- /dev/null +++ b/test/fixtures/HMM10-MH.txt @@ -0,0 +1,1 @@ +["[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,2,1,1,1,2,1,1,2,0]","[1,2,1,1,1,2,1,1,2,0]","[1,2,1,1,1,2,1,1,2,0]","[1,2,1,1,1,2,1,1,2,0]","[1,2,1,1,1,2,1,1,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[2,2,1,1,1,1,1,2,2,0]","[2,2,1,1,1,2,1,1,2,0]","[2,2,1,1,1,2,1,1,2,0]","[2,2,1,1,1,2,1,1,2,0]","[2,2,1,1,1,2,1,1,2,0]","[2,2,1,1,1,2,1,1,2,0]","[2,1,2,1,1,2,1,1,2,0]","[2,1,2,1,1,2,1,1,2,0]","[2,1,2,1,1,2,1,1,2,0]","[2,1,2,1,1,2,1,1,2,0]","[1,1,2,1,1,2,1,1,2,0]","[1,2,1,1,1,2,1,1,2,0]","[1,2,1,1,1,2,1,1,2,0]","[1,1,1,1,1,2,1,1,2,0]","[1,1,1,1,1,2,1,1,2,0]","[1,1,1,1,1,2,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[0,1,1,1,1,0,1,1,2,0]","[0,1,1,1,1,0,1,1,2,0]","[0,1,1,1,1,0,1,1,2,0]","[0,1,1,1,1,0,1,1,2,0]","[0,1,1,1,1,0,1,1,2,0]","[0,1,1,1,1,0,1,1,2,0]","[0,1,1,1,1,0,1,1,2,0]","[0,1,1,1,1,0,1,1,2,0]"] diff --git a/test/fixtures/HMM10-RMSMC.txt b/test/fixtures/HMM10-RMSMC.txt new file mode 100644 --- /dev/null +++ b/test/fixtures/HMM10-RMSMC.txt @@ -0,0 +1,1 @@ +[("[2,1,1,1,0,1,1,2,1,1]",2.4438034074800498e-8),("[1,1,1,1,1,2,1,1,1,0]",2.4438034074800498e-8),("[1,1,2,2,0,2,1,1,1,2]",2.4438034074800498e-8),("[1,1,2,2,0,2,1,1,1,2]",2.4438034074800498e-8),("[1,1,1,2,0,2,1,1,1,2]",2.4438034074800498e-8),("[1,1,2,2,0,2,1,1,1,2]",2.4438034074800498e-8),("[1,1,2,1,2,1,2,1,1,2]",2.4438034074800498e-8),("[1,1,2,1,2,1,2,1,1,2]",2.4438034074800498e-8),("[1,1,2,1,2,1,2,1,1,2]",2.4438034074800498e-8),("[1,2,1,1,2,2,0,1,1,1]",2.4438034074800498e-8)] diff --git a/test/fixtures/HMM10-SMC.txt b/test/fixtures/HMM10-SMC.txt new file mode 100644 --- /dev/null +++ b/test/fixtures/HMM10-SMC.txt @@ -0,0 +1,1 @@ +[("[1,1,0,1,1,2,1,1,1,2]",2.964810681340389e-9),("[1,1,0,1,1,2,1,1,1,2]",2.964810681340389e-9),("[1,1,0,1,1,2,1,1,1,2]",2.964810681340389e-9),("[1,2,0,2,1,2,1,1,1,0]",2.964810681340389e-9),("[1,2,0,2,1,2,1,1,1,0]",2.964810681340389e-9),("[1,1,1,1,0,1,1,1,1,1]",2.964810681340389e-9),("[1,1,1,1,0,1,1,1,1,1]",2.964810681340389e-9),("[1,1,1,1,0,1,1,1,1,1]",2.964810681340389e-9),("[1,1,1,1,1,0,2,0,1,2]",2.964810681340389e-9),("[1,1,1,1,1,0,2,0,1,2]",2.964810681340389e-9),("[1,1,1,1,1,1,2,0,1,1]",2.964810681340389e-9),("[1,1,2,1,1,1,2,0,1,1]",2.964810681340389e-9),("[1,1,2,1,1,1,2,0,1,1]",2.964810681340389e-9),("[1,1,1,1,1,1,1,0,1,1]",2.964810681340389e-9),("[1,1,1,1,1,1,1,0,1,1]",2.964810681340389e-9),("[1,1,1,1,1,1,1,0,1,1]",2.964810681340389e-9),("[1,1,1,1,2,1,2,1,1,2]",2.964810681340389e-9),("[1,1,1,1,2,1,2,1,1,2]",2.964810681340389e-9),("[1,1,1,1,2,1,2,1,1,2]",2.964810681340389e-9),("[1,1,1,1,1,2,2,1,1,0]",2.964810681340389e-9),("[1,1,1,1,1,2,2,1,1,0]",2.964810681340389e-9),("[1,1,1,1,1,2,2,1,1,0]",2.964810681340389e-9),("[1,1,1,1,1,2,2,1,1,2]",2.964810681340389e-9),("[1,1,1,1,1,2,2,1,1,2]",2.964810681340389e-9),("[1,1,1,1,1,2,2,1,1,2]",2.964810681340389e-9),("[1,2,0,1,1,1,2,1,2,0]",2.964810681340389e-9),("[1,2,0,1,1,1,2,1,2,0]",2.964810681340389e-9),("[1,2,1,1,0,2,2,1,2,0]",2.964810681340389e-9),("[1,2,1,1,0,2,2,1,2,0]",2.964810681340389e-9),("[1,1,1,1,0,2,2,1,2,0]",2.964810681340389e-9),("[1,2,2,1,1,1,1,1,2,0]",2.964810681340389e-9),("[1,2,2,1,1,1,1,1,2,0]",2.964810681340389e-9),("[1,1,1,1,1,1,2,1,1,0]",2.964810681340389e-9),("[1,1,1,2,1,0,0,1,1,0]",2.964810681340389e-9),("[1,1,1,2,1,0,0,1,1,0]",2.964810681340389e-9),("[1,1,1,2,1,0,0,1,1,0]",2.964810681340389e-9),("[1,1,1,1,2,0,1,1,1,0]",2.964810681340389e-9),("[1,1,1,1,2,0,1,1,1,0]",2.964810681340389e-9),("[1,1,1,1,1,2,0,1,2,2]",2.964810681340389e-9),("[1,1,1,1,1,2,0,1,2,2]",2.964810681340389e-9),("[1,1,1,1,1,2,0,1,1,1]",2.964810681340389e-9),("[2,1,1,1,1,0,1,1,1,1]",2.964810681340389e-9),("[1,1,1,1,1,0,1,1,1,1]",2.964810681340389e-9),("[1,1,1,1,1,2,2,0,1,2]",2.964810681340389e-9),("[1,1,1,1,1,2,2,0,1,2]",2.964810681340389e-9),("[1,1,1,1,1,2,2,0,1,2]",2.964810681340389e-9),("[1,1,1,1,1,2,2,0,1,2]",2.964810681340389e-9),("[1,1,1,1,2,1,2,0,1,2]",2.964810681340389e-9),("[2,1,1,1,2,1,2,0,1,2]",2.964810681340389e-9),("[1,1,1,2,0,2,1,2,1,0]",2.964810681340389e-9),("[1,1,1,2,0,1,1,1,1,2]",2.964810681340389e-9),("[1,1,1,2,0,1,1,1,1,2]",2.964810681340389e-9),("[1,1,1,1,0,0,1,1,1,1]",2.964810681340389e-9),("[1,1,1,1,0,0,1,1,1,1]",2.964810681340389e-9),("[1,1,1,1,0,0,1,1,1,1]",2.964810681340389e-9),("[1,1,1,1,1,1,1,2,1,0]",2.964810681340389e-9),("[1,2,0,1,1,1,1,2,1,0]",2.964810681340389e-9),("[1,2,0,1,1,1,1,2,1,0]",2.964810681340389e-9),("[1,1,1,1,2,1,2,1,1,1]",2.964810681340389e-9),("[1,1,2,1,1,1,1,1,2,2]",2.964810681340389e-9),("[1,1,2,1,1,1,1,1,2,2]",2.964810681340389e-9),("[1,1,2,1,1,1,1,2,1,1]",2.964810681340389e-9),("[1,1,2,1,1,1,1,2,1,1]",2.964810681340389e-9),("[1,2,1,1,2,1,1,1,2,0]",2.964810681340389e-9),("[1,2,1,1,2,1,1,1,2,0]",2.964810681340389e-9),("[1,2,1,1,2,1,1,1,2,0]",2.964810681340389e-9),("[1,1,1,1,2,1,1,1,2,0]",2.964810681340389e-9),("[1,1,0,1,0,1,0,1,1,2]",2.964810681340389e-9),("[1,1,0,1,0,1,0,1,1,2]",2.964810681340389e-9),("[1,1,0,1,0,1,0,1,1,2]",2.964810681340389e-9),("[0,1,1,1,1,0,1,1,2,0]",2.964810681340389e-9),("[1,1,1,1,1,0,1,1,2,0]",2.964810681340389e-9),("[1,1,2,1,2,2,0,1,1,1]",2.964810681340389e-9),("[1,1,1,1,0,1,1,1,1,0]",2.964810681340389e-9),("[1,1,1,1,0,1,1,1,1,0]",2.964810681340389e-9),("[1,1,1,1,2,1,0,0,1,1]",2.964810681340389e-9),("[1,1,1,1,2,1,0,0,1,1]",2.964810681340389e-9),("[1,1,2,1,2,2,1,2,1,2]",2.964810681340389e-9),("[1,1,2,1,2,2,1,2,1,2]",2.964810681340389e-9),("[1,1,1,1,2,2,1,2,1,2]",2.964810681340389e-9),("[1,1,1,1,2,2,1,2,1,2]",2.964810681340389e-9),("[1,1,1,1,1,1,2,2,1,2]",2.964810681340389e-9),("[1,1,1,1,1,1,2,2,1,2]",2.964810681340389e-9),("[1,1,1,1,1,1,2,2,1,2]",2.964810681340389e-9),("[1,1,1,1,1,2,0,1,1,2]",2.964810681340389e-9),("[1,1,1,2,2,2,0,1,1,2]",2.964810681340389e-9),("[1,1,1,2,2,2,0,1,1,2]",2.964810681340389e-9),("[1,1,1,2,2,2,0,1,1,2]",2.964810681340389e-9),("[1,1,1,1,2,2,0,1,1,2]",2.964810681340389e-9),("[1,1,1,1,2,2,0,1,1,2]",2.964810681340389e-9),("[1,1,1,1,1,1,2,1,2,0]",2.964810681340389e-9),("[1,1,1,1,1,1,2,1,2,0]",2.964810681340389e-9),("[1,1,1,1,1,1,2,1,2,0]",2.964810681340389e-9),("[1,1,1,1,1,2,1,2,1,0]",2.964810681340389e-9),("[1,1,1,1,1,2,1,2,1,0]",2.964810681340389e-9),("[1,2,1,1,1,2,1,2,1,0]",2.964810681340389e-9),("[2,1,1,1,2,1,1,2,1,0]",2.964810681340389e-9),("[1,1,1,1,1,1,0,2,1,0]",2.964810681340389e-9),("[1,1,1,1,1,1,0,2,1,0]",2.964810681340389e-9),("[2,2,2,1,1,1,1,1,2,1]",2.964810681340389e-9)] diff --git a/test/fixtures/LDA10-MH.txt b/test/fixtures/LDA10-MH.txt new file mode 100644 --- /dev/null +++ b/test/fixtures/LDA10-MH.txt @@ -0,0 +1,1 @@ +["(fromList [(\"topic1\",[(\"bear\",1.4089582472383573e-2),(\"wolf\",7.763677263154158e-2),(\"python\",0.694917073788123),(\"prolog\",0.21335657110795198)]),(\"topic2\",[(\"bear\",0.28727305543035053),(\"wolf\",0.35728080053205036),(\"python\",0.26593974632470524),(\"prolog\",8.950639771289397e-2)])],[(\"bear prolog prolog wolf prolog bear wolf bear bear prolog\",[(\"topic1\",3.801790281431827e-2),(\"topic2\",0.9619820971856817)]),(\"wolf prolog bear wolf wolf python bear bear wolf bear\",[(\"topic1\",4.693396178537035e-2),(\"topic2\",0.9530660382146297)]),(\"wolf prolog wolf wolf wolf wolf prolog python python bear\",[(\"topic1\",5.2449539316739855e-3),(\"topic2\",0.9947550460683261)]),(\"bear prolog prolog bear wolf bear python wolf prolog wolf\",[(\"topic1\",6.917861644240221e-2),(\"topic2\",0.9308213835575978)]),(\"bear bear 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diff --git a/test/fixtures/LR10-RMSMC.txt b/test/fixtures/LR10-RMSMC.txt new file mode 100644 --- /dev/null +++ b/test/fixtures/LR10-RMSMC.txt @@ -0,0 +1,1 @@ +[("5.333997036871341e-6",6.253483531321334e-5),("4.7394126422869915e-6",6.253483531321334e-5),("7.798412010176118e-6",6.253483531321334e-5),("3.6537314189667804e-3",6.253483531321334e-5),("2.8719951155583437e-3",6.253483531321334e-5),("8.106430574751586e-3",6.253483531321334e-5),("0.8083297132912659",6.253483531321334e-5),("0.3178833271596258",6.253483531321334e-5),("0.3487591395231385",6.253483531321334e-5),("2.027192522287899e-2",6.253483531321334e-5)] diff --git a/test/fixtures/LR10-SMC.txt b/test/fixtures/LR10-SMC.txt new file mode 100644 --- /dev/null +++ b/test/fixtures/LR10-SMC.txt @@ -0,0 +1,1 @@ +[("2.324831917751426e-5",8.615785653338886e-6),("4.0753397495054896e-8",8.615785653338886e-6),("7.274125904873279e-9",8.615785653338886e-6),("1.3743372716534289e-5",8.615785653338886e-6),("4.254983717992536e-6",8.615785653338886e-6),("1.2272127506266697e-6",8.615785653338886e-6),("1.214022726807993e-7",8.615785653338886e-6),("8.847449654106116e-8",8.615785653338886e-6),("1.6000818494452112e-3",8.615785653338886e-6),("2.0279043319035277e-3",8.615785653338886e-6),("3.5018249880037834e-5",8.615785653338886e-6),("0.16426780827561477",8.615785653338886e-6),("0.10773403426050324",8.615785653338886e-6),("0.3304703458482792",8.615785653338886e-6),("0.10913515995295375",8.615785653338886e-6),("3.8113707417415554e-7",8.615785653338886e-6),("1.1707029254682367e-4",8.615785653338886e-6),("2.047893831024706e-3",8.615785653338886e-6),("1.8725448138433734e-3",8.615785653338886e-6),("6.053601828693627e-2",8.615785653338886e-6),("0.1757594676547173",8.615785653338886e-6),("1.3511280746237259e-3",8.615785653338886e-6),("0.23723482733424164",8.615785653338886e-6),("0.16151469556914314",8.615785653338886e-6),("7.191080175022858e-3",8.615785653338886e-6),("1.6108325498387603e-7",8.615785653338886e-6),("1.6659054333722745e-7",8.615785653338886e-6),("4.28535218704211e-4",8.615785653338886e-6),("4.305836021545625e-4",8.615785653338886e-6),("4.7576965500979653e-4",8.615785653338886e-6),("4.4539756971784895e-4",8.615785653338886e-6),("3.96355147105004e-4",8.615785653338886e-6),("2.91792488057767e-3",8.615785653338886e-6),("0.1387157529569227",8.615785653338886e-6),("0.12679393576798442",8.615785653338886e-6),("0.23010548225976238",8.615785653338886e-6),("0.25223594655800285",8.615785653338886e-6),("6.97387528630698e-5",8.615785653338886e-6),("9.333831289852731e-5",8.615785653338886e-6),("8.375626668711192e-5",8.615785653338886e-6),("1.5213683176568195e-2",8.615785653338886e-6),("3.5712314627571923e-4",8.615785653338886e-6),("7.636217014509781e-4",8.615785653338886e-6),("2.0872090258618442e-4",8.615785653338886e-6),("5.196909883379355e-4",8.615785653338886e-6),("5.701798151154428e-4",8.615785653338886e-6),("5.093049208576314e-4",8.615785653338886e-6),("1.4278233878183234e-2",8.615785653338886e-6),("0.409063870280768",8.615785653338886e-6),("2.413899012911671e-2",8.615785653338886e-6),("4.9820455672153804e-2",8.615785653338886e-6),("2.3987373289798696e-3",8.615785653338886e-6),("2.3730997104438635e-3",8.615785653338886e-6),("1.5421674679073712e-2",8.615785653338886e-6),("6.127942201533583e-4",8.615785653338886e-6),("0.29100637723657274",8.615785653338886e-6),("6.466851911961999e-4",8.615785653338886e-6),("6.899429519546635e-4",8.615785653338886e-6),("6.796536628553891e-4",8.615785653338886e-6),("1.5687561944396283e-2",8.615785653338886e-6),("1.0114194783259966e-2",8.615785653338886e-6),("8.650936462496627e-4",8.615785653338886e-6),("8.659503706938266e-4",8.615785653338886e-6),("0.9866480964309671",8.615785653338886e-6),("0.9844641052458803",8.615785653338886e-6),("0.9877580766923669",8.615785653338886e-6),("0.3570814146622049",8.615785653338886e-6),("0.3333232242467457",8.615785653338886e-6),("0.28788395991944565",8.615785653338886e-6),("0.6235083846866266",8.615785653338886e-6),("2.9830083243998794e-2",8.615785653338886e-6),("0.6715098168079819",8.615785653338886e-6),("0.5092770566793119",8.615785653338886e-6),("0.14931145218944078",8.615785653338886e-6),("0.9476390701984468",8.615785653338886e-6),("0.19844654340805706",8.615785653338886e-6),("0.8692525556246279",8.615785653338886e-6),("0.2857288027412788",8.615785653338886e-6),("0.9128866108374706",8.615785653338886e-6),("0.5972931052418653",8.615785653338886e-6),("3.185136062093685e-2",8.615785653338886e-6),("0.7815143883956358",8.615785653338886e-6),("9.045285261453962e-4",8.615785653338886e-6),("1.0570963598552236e-4",8.615785653338886e-6),("0.9988704519081596",8.615785653338886e-6),("0.9983306238100842",8.615785653338886e-6),("0.999817180959221",8.615785653338886e-6),("0.999632323087958",8.615785653338886e-6),("0.9978593357863148",8.615785653338886e-6),("0.9932458970319142",8.615785653338886e-6),("0.9997633989820984",8.615785653338886e-6),("0.25474879877870016",8.615785653338886e-6),("0.12254684366442331",8.615785653338886e-6),("6.952221863096741e-2",8.615785653338886e-6),("0.38421927032809844",8.615785653338886e-6),("0.13255536658985864",8.615785653338886e-6),("0.1506084845751688",8.615785653338886e-6),("0.3502412842110343",8.615785653338886e-6),("1.28565002377979e-2",8.615785653338886e-6),("0.3782237084074611",8.615785653338886e-6)] diff --git a/test/fixtures/SSM-PMMH.txt b/test/fixtures/SSM-PMMH.txt new file mode 100644 --- /dev/null +++ b/test/fixtures/SSM-PMMH.txt @@ -0,0 +1,1 @@ +[[([74405.69500410178,143777.3515026691,195290.64675632896,483878.28639985673,600603.4104497777],1.0),([74405.69500410178,143777.3515026691,195290.64675632896,483878.28639985673,600603.4104497777],1.0),([74405.69500410178,143777.3515026691,195290.64675632896,483878.28639985673,600603.4104497777],1.0)],[([157620.04097610444,26661.523636563594,321204.4219216401,421274.0528523404,487363.3134055787],1.0),([157620.04097610444,26661.523636563594,321204.4219216401,421274.0528523404,487363.3134055787],1.0),([157620.04097610444,26661.523636563594,321204.4219216401,421274.0528523404,487363.3134055787],1.0)],[([-1.2600621067470811e67,-1.3171618074660135e67,3.55155213532486e66,-9.486041679240111e66,-1.4476178361450074e67],1.0),([-1.2600621067470811e67,-1.3171618074660135e67,3.55155213532486e66,-9.486041679240111e66,-1.4476178361450074e67],1.0),([-1.2600621067470811e67,-1.3171618074660135e67,3.55155213532486e66,-9.486041679240111e66,-1.4476178361450074e67],1.0)]] diff --git a/test/fixtures/SSM-RMSMC.txt b/test/fixtures/SSM-RMSMC.txt new file mode 100644 --- /dev/null +++ b/test/fixtures/SSM-RMSMC.txt @@ -0,0 +1,1 @@ +[([-2.660097878548362e12,4.2406657192899927e11,5.124397279021509e11,-1.5388049692223555e12,5.100591467413694e11],1.7934178371940385e-141),([85360.89249769927,82937.71043376798,236528.18865034508,184344.32920611685,257818.8194711436],1.7934178371940385e-141),([111456.98861817457,175718.5311026478,-123025.40752936345,-216315.66615773254,-216313.3788230968],1.7934178371940385e-141),([19634.90868499715,3982.228157420627,71064.25154723959,-61863.47069790381,-124170.21806752698],1.7934178371940385e-141),([-1.5475119433556266e13,7.505784271326075e13,1.8087989772377637e13,2.3121907140178836e13,6.957846697896459e13],1.7934178371940385e-141),([3.3114425601587117e13,-7.174858488587559e12,-5.3895766067097984e13,-5.574198391310134e13,-7.085806871739197e13],1.7934178371940385e-141),([1.7797637411011798e9,2.257078068208236e9,1.7822875201019692e9,-3.1059378475534713e8,-2.022387835329388e8],1.7934178371940385e-141),([-362.4859209624216,597.209862141266,354.2417236032639,699.0287190356412,-719.9079388224256],1.7934178371940385e-141),([-6962602.171312882,4072501.6094401204,-1935864.3227236385,6378383.05623946,2107530.9972696295],1.7934178371940385e-141),([535.0932822165735,229.4681249747279,-318.4034398226934,-425.6731795563692,-736.158075205745],1.7934178371940385e-141)] diff --git a/test/fixtures/SSM-RMSMCBasic.txt b/test/fixtures/SSM-RMSMCBasic.txt new file mode 100644 --- /dev/null +++ b/test/fixtures/SSM-RMSMCBasic.txt @@ -0,0 +1,1 @@ +[([-2.660097878548362e12,4.2406657192899927e11,5.124397279021509e11,-1.5388049692223555e12,5.100591467413694e11],1.7934178371940385e-141),([85360.89249769927,82937.71043376798,236528.18865034508,184344.32920611685,257818.8194711436],1.7934178371940385e-141),([111456.98861817457,175718.5311026478,-123025.40752936345,-216315.66615773254,-216313.3788230968],1.7934178371940385e-141),([19634.90868499715,3982.228157420627,71064.25154723959,-61863.47069790381,-124170.21806752698],1.7934178371940385e-141),([-1.5475119433556266e13,7.505784271326075e13,1.8087989772377637e13,2.3121907140178836e13,6.957846697896459e13],1.7934178371940385e-141),([3.3114425601587117e13,-7.174858488587559e12,-5.3895766067097984e13,-5.574198391310134e13,-7.085806871739197e13],1.7934178371940385e-141),([1.7797637411011798e9,2.257078068208236e9,1.7822875201019692e9,-3.1059378475534713e8,-2.022387835329388e8],1.7934178371940385e-141),([-362.4859209624216,597.209862141266,354.2417236032639,699.0287190356412,-719.9079388224256],1.7934178371940385e-141),([-6962602.171312882,4072501.6094401204,-1935864.3227236385,6378383.05623946,2107530.9972696295],1.7934178371940385e-141),([535.0932822165735,229.4681249747279,-318.4034398226934,-425.6731795563692,-736.158075205745],1.7934178371940385e-141)] diff --git a/test/fixtures/SSM-RMSMCDynamic.txt b/test/fixtures/SSM-RMSMCDynamic.txt new file mode 100644 --- /dev/null +++ b/test/fixtures/SSM-RMSMCDynamic.txt @@ -0,0 +1,1 @@ +[([61234.923743603955,79039.83817954235,354024.81636628765,225755.73057039993,-78843.37322818518],0.0),([61234.923743603955,-205024.66324964678,-438520.7645656072,-526045.6062936985,17959.08713788638],0.0),([61234.923743603955,130707.33129683959,260276.7204227042,538891.1815485102,432537.1717560617],0.0),([61234.923743603955,425968.16738967673,72802.89417099475,97062.29318414515,-90904.59187690681],0.0),([61234.923743603955,-80888.00179367141,122235.67304475381,48742.27626015559,-149682.32933231423],0.0),([61234.923743603955,43.833902800088254,-417728.0201965655,49565.634594935604,-303943.3354524304],0.0),([61234.923743603955,350501.69936972257,118986.06426751378,99950.78931739656,-60488.53431816819],0.0),([61234.923743603955,-117376.5868812376,116017.94360094423,378976.39475725644,74865.6296219704],0.0),([61234.923743603955,156368.9791422615,-586653.2615030725,-238480.82081038723,51581.15175237715],0.0),([61234.923743603955,-150776.59937461224,-30862.03908288705,200382.13919586508,-107135.36343350058],0.0)] diff --git a/test/fixtures/SSM-SMC.txt b/test/fixtures/SSM-SMC.txt new file mode 100644 --- /dev/null +++ b/test/fixtures/SSM-SMC.txt @@ -0,0 +1,1 @@ +[([-1.6946443595984358e8,-2.0398900541476977e8,5.988104418627801e8,5.186441087015647e7,-1.1107580460544899e9],3.747925572660412e-147),([-1.6946443595984358e8,1.762322765772586e8,1.3143034131110222e9,2.917359439754021e7,-4.678360689283452e8],3.747925572660412e-147),([-1.6946443595984358e8,-4.978125179866476e8,-6.568379081060445e8,-1.0039010467494124e9,-4.5194462919398534e8],3.747925572660412e-147),([-1.6946443595984358e8,-2.0398900541476977e8,6.65407483202134e8,-1.3610874802534976e9,1.7804869696064534e9],3.747925572660412e-147),([-1.6946443595984358e8,-4.978125179866476e8,-6.568379081060445e8,-1.0039010467494124e9,-4.5194462919398534e8],3.747925572660412e-147),([-1.6946443595984358e8,-7.848111477226721e8,-1.536250656089418e9,-1.2593852525318892e9,9.33478070563457e8],3.747925572660412e-147),([-1.6946443595984358e8,1.762322765772586e8,1.3143034131110222e9,2.917359439754021e7,-4.678360689283452e8],3.747925572660412e-147),([-1.6946443595984358e8,-4.978125179866476e8,-6.568379081060445e8,7.201669253635451e8,-6.528627637915363e8],3.747925572660412e-147),([-1.6946443595984358e8,-4.978125179866476e8,-6.568379081060445e8,7.201669253635451e8,-6.528627637915363e8],3.747925572660412e-147),([-1.6946443595984358e8,-7.848111477226721e8,-1.536250656089418e9,-1.2593852525318892e9,9.33478070563457e8],3.747925572660412e-147)] diff --git a/test/fixtures/SSM-SMC2.txt b/test/fixtures/SSM-SMC2.txt new file mode 100644 --- /dev/null +++ b/test/fixtures/SSM-SMC2.txt @@ -0,0 +1,1 @@ +[([([-9090.483553160731,-18364.240866577857,38447.317849110055,-3829.950678281628,-18689.938602553048],0.3333333333333341),([-9090.483553160731,-18364.240866577857,38447.317849110055,-3829.950678281628,-18689.938602553048],0.3333333333333341),([-9090.483553160731,-18364.240866577857,38447.317849110055,25131.836867847727,47603.03068211828],0.3333333333333341)],9.474658864966518e-180),([([-2.2418721864335723e9,2.4219211687208967e9,5.4463793547824545e9,7.074651672385337e8,2.595090695345872e8],0.3333333333333341),([-2.2418721864335723e9,2.4219211687208967e9,5.4463793547824545e9,7.074651672385337e8,2.595090695345872e8],0.3333333333333341),([-2.2418721864335723e9,2.4219211687208967e9,5.4463793547824545e9,7.074651672385337e8,2.595090695345872e8],0.3333333333333341)],9.474658864966518e-180)]