elynx-markov 0.8.0.0 → 0.9.0.0

raw patch · 6 files changed

+31/−16 lines, 6 filesdep ~basePVP ok

version bump matches the API change (PVP)

Dependency ranges changed: base

API changes (from Hackage documentation)

Files

• ChangeLog.md +6/−0
• README.md +5/−5
• elynx-markov.cabal +2/−2
• src/ELynx/MarkovProcess/AminoAcid.hs +1/−2
• src/ELynx/MarkovProcess/GammaRateHeterogeneity.hs +1/−1
• src/ELynx/Simulate/MarkovProcessAlongTree.hs +16/−6

@@ -5,6 +5,12 @@ ## Unreleased changes  +## Version 0.9.0.0++-   Toolchain update+-   Update to random version 1.3++ ## Version 0.8.0.0  -   Adapt to breaking changes in upstream libraries (`data-default`).

@@ -2,7 +2,7 @@  # The ELynx Suite -Version: 0.8.0.0.+Version: 0.9.0.0. Reproducible evolution made easy.  <p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>@@ -73,9 +73,9 @@     # OR: stack exec slynx -- --help     # OR: slynx --help -    ELynx Suite version 0.8.0.0.+    ELynx Suite version 0.9.0.0.     Developed by Dominik Schrempf.-    Compiled on October 27, 2024, at 07:14 am, UTC.+    Compiled on August 11, 2025, at 07:19 am, UTC.          Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]                  [-f|--force] [--no-elynx-file] COMMAND@@ -143,9 +143,9 @@     # OR: stack exec slynx -- simulate --help     # OR: slynx simulate --help -    ELynx Suite version 0.8.0.0.+    ELynx Suite version 0.9.0.0.     Developed by Dominik Schrempf.-    Compiled on October 27, 2024, at 07:14 am, UTC.+    Compiled on August 11, 2025, at 07:19 am, UTC.          Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]                           [-m|--mixture-model MODEL] [-n|--global-normalization]

@@ -1,6 +1,6 @@ cabal-version:      3.0 name:               elynx-markov-version:            0.8.0.0+version:            0.9.0.0 synopsis:           Simulate molecular sequences along trees description:   Examine, modify, and simulate molecular sequences in a reproducible way. Please see the README on GitHub at <https://github.com/dschrempf/elynx>.@@ -99,5 +99,5 @@   -- ghc-options:   hs-source-dirs:   bench   ghc-options:      -Wall -Wunused-packages-  build-depends:    base+  build-depends:    base <5   default-language: Haskell2010

@@ -127,8 +127,7 @@ pamlToAlphaMat m =   build     (n, n)-    ( \i j -> m ! alphaIndexToPamlIndex (round i) ! alphaIndexToPamlIndex (round j)-    )+    (\i j -> m ! alphaIndexToPamlIndex (round i) ! alphaIndexToPamlIndex (round j))  -- Lower triangular matrix of LG exchangeabilities in PAML order and in form of -- a list.

@@ -101,7 +101,7 @@     means =       V.fromList         [ integralAToB meanFunc (quantiles !! i) (quantiles !! (i + 1))-          | i <- [0 .. n - 2]+        | i <- [0 .. n - 2]         ]     -- The last category has to be calculated with an improper integration.     lastMean = integralAToInf meanFunc (quantiles !! (n - 1))

@@ -1,3 +1,4 @@+{-# LANGUAGE FlexibleContexts #-} {-# LANGUAGE ScopedTypeVariables #-}  -- |@@ -30,6 +31,7 @@ import Control.Concurrent import Control.Concurrent.Async import Control.Monad+import Control.Monad.IO.Class (MonadIO (liftIO)) import Data.Tree import qualified Data.Vector as V import ELynx.MarkovProcess.RateMatrix@@ -97,7 +99,7 @@  -- | See 'simulateAndFlatten', parallel version. simulateAndFlattenPar ::-  (RandomGen g) =>+  (SplitGen g) =>   Int ->   StationaryDistribution ->   ExchangeabilityMatrix ->@@ -216,17 +218,25 @@ -- requires benchmarks. I am just not sure if it makes sense to spend more time -- on this since the parallelization itself is a bit weird. Like so, we walk -- along separate trees in each process.-parComp :: (RandomGen g) => Int -> (Int -> IOGenM g -> IO b) -> IOGenM g -> IO [b]+parComp ::+  (FrozenGen g IO, SplitGen g, ThawedGen g IO) =>+  Int -> (Int -> MutableGen g IO -> IO b) -> MutableGen g IO -> IO [b] parComp num fun gen = do-  ncap <- getNumCapabilities+  ncap <- liftIO getNumCapabilities+  genF <- freezeGen gen   let chunks = getChunks ncap num-  rs <- replicateM ncap $ splitGenM gen-  gs <- mapM newIOGenM rs+      rs = splitGenN ncap genF+  gs <- mapM thawGen rs   mapConcurrently (uncurry fun) (zip chunks gs)+  where+    splitGenN :: (SplitGen g) => Int -> g -> [g]+    splitGenN n g+      | n < 1 = []+      | otherwise = let (g1, g2) = splitGen g in g1 : splitGenN (n - 1) g2  -- | See 'simulateAndFlattenMixtureModel', parallel version. simulateAndFlattenMixtureModelPar ::-  (RandomGen g) =>+  (SplitGen g) =>   Int ->   V.Vector Double ->   V.Vector StationaryDistribution ->