tlynx 0.7.2.2 → 0.8.0.0

raw patch · 9 files changed

+23/−18 lines, 9 filesdep +data-defaultdep −data-default-classPVP ok

version bump matches the API change (PVP)

Dependencies added: data-default

Dependencies removed: data-default-class

API changes (from Hackage documentation)

Files

• ChangeLog.md +5/−0
• README.md +5/−5
• src/TLynx/Connect/Connect.hs +1/−1
• src/TLynx/Distance/Distance.hs +1/−1
• src/TLynx/Examine/Examine.hs +2/−2
• src/TLynx/Grabble.hs +1/−1
• src/TLynx/Shuffle/Shuffle.hs +1/−1
• src/TLynx/Simulate/Simulate.hs +5/−5
• tlynx.cabal +2/−2

@@ -5,6 +5,11 @@ ## Unreleased changes  +## Version 0.8.0.0++-   Adapt to breaking changes in upstream libraries (`data-default`).++ ## Version 0.7.2.0  -   `slynx`: Allow global normalization of mixture models.

@@ -2,7 +2,7 @@  # The ELynx Suite -Version: 0.7.2.1.+Version: 0.8.0.0. 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 0.7.2.1.+    ELynx Suite version 0.8.0.0.     Developed by Dominik Schrempf.-    Compiled on June 15, 2023, at 19:54 pm, UTC.+    Compiled on October 27, 2024, at 07:14 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 0.7.2.1.+    ELynx Suite version 0.8.0.0.     Developed by Dominik Schrempf.-    Compiled on June 15, 2023, at 19:54 pm, UTC.+    Compiled on October 27, 2024, at 07:14 am, UTC.          Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]                           [-m|--mixture-model MODEL] [-n|--global-normalization]

@@ -19,7 +19,7 @@ import Control.Monad.IO.Class import Control.Monad.Trans.Reader (ask) import qualified Data.ByteString.Lazy.Char8 as BL-import Data.Default.Class+import Data.Default import qualified Data.Set as S import ELynx.Tools.ELynx import ELynx.Tools.Environment

@@ -43,7 +43,7 @@ import TLynx.Parsers import Text.Printf -median :: Ord a => [a] -> a+median :: (Ord a) => [a] -> a median xs = sort xs !! l2 where l2 = length xs `div` 2  pf :: String

@@ -46,7 +46,7 @@     v = BL.pack val  -- | Examine branches of a tree.-summarizeLengths :: HasLength e => Tree e a -> BL.ByteString+summarizeLengths :: (HasLength e) => Tree e a -> BL.ByteString summarizeLengths t =   BL.intercalate     "\n"@@ -73,7 +73,7 @@     g Nothing = Just 1     g (Just x) = Just $ x + 1 -examineTree :: HasName a => Handle -> Tree Phylo a -> IO ()+examineTree :: (HasName a) => Handle -> Tree Phylo a -> IO () examineTree h t = do   hPutStrLn h $ "Number of leaves: " ++ show (length lvs)   hPutStrLn h $ "Degree of root node: " ++ show (degree t)

@@ -23,7 +23,7 @@  -- | @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 :: StatefulGen g m => [a] -> Int -> Int -> g -> m [[a]]+grabble :: (StatefulGen g m) => [a] -> Int -> Int -> g -> m [[a]] grabble xs m n gen = do   swapss <- replicateM m $     forM [0 .. min (l - 1) n] $ \i -> do

@@ -76,7 +76,7 @@   liftIO $ hClose h  shuffleT ::-  StatefulGen g m =>+  (StatefulGen g m) =>   Int -> -- How many?   Length -> -- Stem length.   [Length] -> -- Coalescent times.

@@ -101,7 +101,7 @@   out "simulated trees" res ".tree"  bdSimulateNTreesConcurrently ::-  RandomGen g =>+  (RandomGen g) =>   Int ->   Double ->   Double ->@@ -120,7 +120,7 @@   return $ concat trss  coalSimulateNTreesConcurrently ::-  RandomGen g =>+  (RandomGen g) =>   Int ->   [Int] ->   [IOGenM g] ->@@ -133,7 +133,7 @@   return $ concat trss  bdSimulateAndSubSampleNTreesConcurrently ::-  RandomGen g =>+  (RandomGen g) =>   Int ->   Double ->   Double ->@@ -170,7 +170,7 @@   return $ map prune trs  coalSimulateAndSubSampleNTreesConcurrently ::-  RandomGen g =>+  (RandomGen g) =>   Int ->   Double ->   [Int] ->@@ -245,7 +245,7 @@   BB.intDec n <> BB.char8 ' ' <> BB.doubleDec (fromLength l) <> BB.char8 '\n'  -- Compute NChilSumStat for a phylogenetic tree.-toNChildSumStat :: HasLength e => Tree e a -> NChildSumStat+toNChildSumStat :: (HasLength e) => Tree e a -> NChildSumStat toNChildSumStat (Node br _ []) = [(getLength br, 1)] toNChildSumStat (Node br _ ts) = (getLength br, sumCh) : concat nChSS   where

@@ -1,6 +1,6 @@ cabal-version:      3.0 name:               tlynx-version:            0.7.2.2+version:            0.8.0.0 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>.@@ -53,7 +53,7 @@     , bytestring     , comonad     , containers-    , data-default-class+    , data-default     , elynx-tools     , elynx-tree     , gnuplot