tlynx 0.6.0.0 → 0.6.1.0

raw patch · 19 files changed

+141/−30 lines, 19 filesdep +primitivePVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependencies added: primitive

API changes (from Hackage documentation)

Files

• ChangeLog.md +7/−0
• README.md +12/−6
• src/TLynx/Compare/Compare.hs +4/−1
• src/TLynx/Compare/Options.hs +3/−1
• src/TLynx/Connect/Connect.hs +3/−1
• src/TLynx/Connect/Options.hs +3/−1
• src/TLynx/Distance/Distance.hs +4/−1
• src/TLynx/Distance/Options.hs +3/−1
• src/TLynx/Examine/Examine.hs +4/−1
• src/TLynx/Examine/Options.hs +3/−1
• src/TLynx/Grabble.hs +41/−0
• src/TLynx/Options.hs +5/−7
• src/TLynx/Parsers.hs +3/−3
• src/TLynx/Shuffle/Options.hs +4/−1
• src/TLynx/Shuffle/Shuffle.hs +6/−1
• src/TLynx/Simulate/Options.hs +4/−1
• src/TLynx/Simulate/Simulate.hs +27/−1
• src/TLynx/TLynx.hs +2/−1
• tlynx.cabal +3/−1

@@ -5,6 +5,13 @@ ## Unreleased changes  +## Version 0.6.1.0++-   Split `ELynx.Tools` into separate modules because the package will be reduced.+-   Remove the following modules from `ELynx.Tools`: `Concurrent`,+    `LinearAlgebra`, `List`, `Misc`, and `Numeric`.++ ## Version 0.6.0.0  -   **elynx-tree:** remove parallel folds with layers (`parBranchFoldMapWithLayer`

@@ -69,13 +69,13 @@  # Get help -For example:--    slynx --help+    cabal exec slynx -- --help+    # OR: stack exec slynx -- --help+    # OR: slynx --help      ELynx Suite version 0.6.0.0.     Developed by Dominik Schrempf.-    Compiled on September 3, 2021, at 20:56 pm, UTC.+    Compiled on September 4, 2021, at 12:58 pm, UTC.          Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]                   [-f|--force] [--no-elynx-file] COMMAND@@ -113,6 +113,7 @@       - ProteinX (amino acids; including gaps)       - ProteinS (amino acids; including gaps, and translation stops)       - ProteinI (amino acids; including gaps, translation stops, and IUPAC codes)+         ELynx     -----     A Haskell library and tool set for computational biology. The goal of ELynx is@@ -126,6 +127,9 @@     tlynx     Analyze, modify, and simulate phylogenetic trees.     elynx     Validate and redo past analyses.     +    Get help for commands:+      slynx --help+         Get help for sub commands:       slynx examine --help @@ -134,11 +138,13 @@  The documentation of sub commands can be accessed separately: -    slynx simulate --help+    cabal exec slynx -- simulate --help+    # OR: stack exec slynx -- simulate --help+    # OR: slynx simulate --help      ELynx Suite version 0.6.0.0.     Developed by Dominik Schrempf.-    Compiled on September 3, 2021, at 20:56 pm, UTC.+    Compiled on September 4, 2021, at 12:58 pm, UTC.          Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]                            [-m|--mixture-model MODEL] [-e|--edm-file NAME] 

@@ -26,7 +26,10 @@ import qualified Data.Set as S import qualified Data.Text as T import qualified Data.Text.IO as T-import ELynx.Tools+import ELynx.Tools.ELynx+import ELynx.Tools.Environment+import ELynx.Tools.Logger+import ELynx.Tools.Options import ELynx.Tree import Graphics.Gnuplot.Simple import System.IO

@@ -17,7 +17,9 @@   ) where -import ELynx.Tools+import Data.Aeson+import ELynx.Tools.Reproduction+import GHC.Generics import Options.Applicative import TLynx.Parsers 

@@ -22,7 +22,9 @@ import qualified Data.ByteString.Lazy.Char8 as BL import Data.Default.Class import qualified Data.Set as S-import ELynx.Tools+import ELynx.Tools.ELynx+import ELynx.Tools.Environment+import ELynx.Tools.Logger import ELynx.Tree import System.IO import TLynx.Connect.Options

@@ -17,7 +17,9 @@   ) where -import ELynx.Tools+import Data.Aeson+import ELynx.Tools.Reproduction+import GHC.Generics import Options.Applicative import TLynx.Parsers 

@@ -33,7 +33,10 @@ import qualified Data.Text as T import qualified Data.Text.IO as T import qualified Data.Vector.Unboxed as V-import ELynx.Tools+import ELynx.Tools.ByteString+import ELynx.Tools.ELynx+import ELynx.Tools.Environment+import ELynx.Tools.Logger import ELynx.Tree import Statistics.Sample import System.IO

@@ -20,10 +20,12 @@   ) where +import Data.Aeson import qualified Data.Attoparsec.ByteString.Char8 as AC import qualified Data.ByteString.Char8 as BS-import ELynx.Tools+import ELynx.Tools.Reproduction import ELynx.Tree (Support (..), toSupportUnsafe)+import GHC.Generics import Options.Applicative import TLynx.Parsers import Text.Printf

@@ -22,7 +22,10 @@ import qualified Data.ByteString.Lazy.Char8 as BL import Data.Containers.ListUtils (nubOrd) import Data.List ((\\))-import ELynx.Tools+import ELynx.Tools.ByteString+import ELynx.Tools.ELynx+import ELynx.Tools.Environment+import ELynx.Tools.Logger import ELynx.Tree import System.IO   ( Handle,

@@ -17,7 +17,9 @@   ) where -import ELynx.Tools+import Data.Aeson+import ELynx.Tools.Reproduction+import GHC.Generics import Options.Applicative import TLynx.Parsers 

@@ -0,0 +1,41 @@+-- |+-- Module      :  TLynx.Grabble+-- Description :  Grabble a list+-- Copyright   :  (c) 2021 Dominik Schrempf+-- License     :  GPL-3.0-or-later+--+-- Maintainer  :  dominik.schrempf@gmail.com+-- Stability   :  experimental+-- Portability :  portable+--+-- Creation date: Mon Sep  6 09:39:16 2021.+module TLynx.Grabble+  ( grabble,+  )+where++import Control.Monad+import Control.Monad.Primitive+import Control.Monad.ST+import Data.Vector (Vector)+import qualified Data.Vector as V+import qualified Data.Vector.Mutable as M+import System.Random.MWC++-- | @grabble xs m n@ is /O(m*n')/, where @n' = min n (length xs)@. Choose @n'@+-- elements from @xs@, without replacement, and that @m@ times.+grabble :: PrimMonad m => [a] -> Int -> Int -> Gen (PrimState m) -> m [[a]]+grabble xs m n gen = do+  swapss <- replicateM m $+    forM [0 .. min (l - 1) n] $ \i -> do+      j <- uniformR (i, l) gen+      return (i, j)+  return $ map (V.toList . V.take n . swapElems (V.fromList xs)) swapss+  where+    l = length xs - 1++swapElems :: Vector a -> [(Int, Int)] -> Vector a+swapElems xs swaps = runST $ do+  mxs <- V.unsafeThaw xs+  mapM_ (uncurry $ M.unsafeSwap mxs) swaps+  V.unsafeFreeze mxs

@@ -11,14 +11,12 @@ -- Portability :  portable -- -- Creation date: Sat Sep  7 18:55:03 2019.-module TLynx.Options-  ( Arguments (..),-    CommandArguments (..),-    parseArguments,-  )-where+module TLynx.Options (CommandArguments (..)) where -import ELynx.Tools+import Data.Aeson+import ELynx.Tools.Options+import ELynx.Tools.Reproduction+import GHC.Generics import Options.Applicative import TLynx.Compare.Options import TLynx.Connect.Options

@@ -19,7 +19,7 @@ where  import Data.List-import ELynx.Tools+import ELynx.Tools.InputOutput import ELynx.Tree import Options.Applicative @@ -74,7 +74,7 @@             ++ "; default: Standard; for detailed help, see 'tlynx --help'"         )   where-    nwfs = map show (allValues :: [NewickFormat])+    nwfs = map show ([minBound ..] :: [NewickFormat])     nwlist = intercalate ", " (init nwfs) <> ", or " <> last nwfs  -- | Help for different 'NewickFormat's.@@ -82,7 +82,7 @@ newickHelp =   map     (toListItem . describeNewickFormat)-    (allValues :: [NewickFormat])+    ([minBound ..] :: [NewickFormat])     ++ ["- Nexus file including Newick trees"]   where     toListItem = ("- Newick " ++)

@@ -17,7 +17,10 @@   ) where -import ELynx.Tools+import Data.Aeson+import ELynx.Tools.Options+import ELynx.Tools.Reproduction+import GHC.Generics import Options.Applicative import TLynx.Parsers 

@@ -25,7 +25,11 @@ import Control.Monad.IO.Class (liftIO) import Control.Monad.Trans.Reader (ask) import qualified Data.ByteString.Lazy.Char8 as BL-import ELynx.Tools+import ELynx.Tools.Definitions+import ELynx.Tools.ELynx+import ELynx.Tools.Environment+import ELynx.Tools.Logger+import ELynx.Tools.Reproduction import ELynx.Tree import ELynx.Tree.Simulate.PointProcess   ( PointProcess (PointProcess),@@ -33,6 +37,7 @@   ) import System.IO (hClose) import System.Random.MWC (GenIO, initialize)+import TLynx.Grabble import TLynx.Parsers import TLynx.Shuffle.Options 

@@ -22,10 +22,13 @@   ) where +import Data.Aeson import Data.List import Data.Maybe-import ELynx.Tools+import ELynx.Tools.Options+import ELynx.Tools.Reproduction import ELynx.Tree.Simulate.PointProcess (TimeSpec (..))+import GHC.Generics import Options.Applicative  deriving instance Eq TimeSpec

@@ -1,4 +1,5 @@ {-# LANGUAGE OverloadedStrings #-}+{-# LANGUAGE ScopedTypeVariables #-} {-# LANGUAGE TemplateHaskell #-} {-# LANGUAGE TupleSections #-} @@ -31,6 +32,7 @@   ) import Control.Monad import Control.Monad.IO.Class+import Control.Monad.Primitive import Control.Monad.Trans.Reader hiding (local) import Control.Parallel.Strategies import qualified Data.ByteString.Builder as BB@@ -39,12 +41,36 @@ import Data.Maybe import qualified Data.Sequence as Seq import qualified Data.Set as Set-import ELynx.Tools+import qualified Data.Vector.Unboxed as VU+import Data.Word+import ELynx.Tools.ELynx+import ELynx.Tools.Environment+import ELynx.Tools.Logger+import ELynx.Tools.Reproduction import ELynx.Tree import qualified ELynx.Tree.Simulate.Coalescent as CS import qualified ELynx.Tree.Simulate.PointProcess as PP import System.Random.MWC+import TLynx.Grabble import TLynx.Simulate.Options++-- Split a generator.+splitGen :: PrimMonad m => Int -> Gen (PrimState m) -> m [Gen (PrimState m)]+splitGen n gen+  | n <= 0 = return []+  | otherwise = do+    seeds :: [VU.Vector Word32] <- replicateM (n -1) $ uniformVector gen 256+    fmap (gen :) (mapM initialize seeds)++-- For a given number of capabilities and number of calculations, get chunk+-- sizes. The chunk sizes will be as evenly distributed as possible and sum up+-- to the number of calculations.+getChunks :: Int -> Int -> [Int]+getChunks c n = ns+  where+    n' = n `div` c+    r = n `mod` c+    ns = replicate r (n' + 1) ++ replicate (c - r) n'  -- | Simulate phylogenetic trees using birth and death process. simulate :: ELynx SimulateArguments ()

@@ -15,7 +15,8 @@   ) where -import ELynx.Tools+import ELynx.Tools.ELynx+import ELynx.Tools.Options import TLynx.Compare.Compare import TLynx.Connect.Connect import TLynx.Distance.Distance

@@ -1,6 +1,6 @@ cabal-version:  2.2 name:           tlynx-version:        0.6.0.0+version:        0.6.1.0 synopsis:       Handle phylogenetic trees description:    Examine, compare, and simulate phylogenetic trees in a reproducible way. Please see the README on GitHub at <https://github.com/dschrempf/elynx>. category:       Bioinformatics@@ -31,6 +31,7 @@       TLynx.Distance.Options       TLynx.Examine.Examine       TLynx.Examine.Options+      TLynx.Grabble       TLynx.Options       TLynx.Parsers       TLynx.Shuffle.Options@@ -59,6 +60,7 @@     , mwc-random     , optparse-applicative     , parallel+    , primitive     , statistics     , text     , transformers