slynx 0.7.0.1 → 0.7.1.0

raw patch · 10 files changed

+12/−11 lines, 10 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• ChangeLog.md +7/−0
• slynx.cabal +1/−1
• src/SLynx/Concatenate/Concatenate.hs +0/−1
• src/SLynx/Examine/Examine.hs +3/−3
• src/SLynx/Examine/Options.hs +1/−1
• src/SLynx/Filter/Filter.hs +0/−1
• src/SLynx/Simulate/Simulate.hs +0/−1
• src/SLynx/SubSample/SubSample.hs +0/−1
• src/SLynx/Tools.hs +0/−1
• src/SLynx/Translate/Translate.hs +0/−1

@@ -5,6 +5,13 @@ ## Unreleased changes  +## Version 0.7.1.0++-   Be less strict with quoted identifiers/names in phylogenetic trees.+-   Be less strict with FASTA identifiers.+-   Update tooling (GHC 9.2.4).++ ## Version 0.7.0.1  -   Random 1.2: Parallel functions now require an \`IOGenM\` random number

@@ -1,6 +1,6 @@ cabal-version:      3.0 name:               slynx-version:            0.7.0.1+version:            0.7.1.0 synopsis:           Handle molecular sequences description:   Examine, modify, and simulate molecular sequences in a reproducible way. Please see the README on GitHub at <https://github.com/dschrempf/elynx>.

@@ -1,5 +1,4 @@ {-# LANGUAGE OverloadedStrings #-}-{-# LANGUAGE TemplateHaskell #-}  -- | -- Module      :  Analyze.Analyze

@@ -1,5 +1,5 @@ {-# LANGUAGE OverloadedStrings #-}-{-# LANGUAGE TemplateHaskell #-}+{-# LANGUAGE TupleSections #-}  -- | --@@ -166,7 +166,7 @@ -- From https://stackoverflow.com/a/52602906/3536806. tuples :: [a] -> [(a, a)] tuples [] = []-tuples (x : xs) = map (\y -> (x, y)) xs ++ tuples xs+tuples (x : xs) = map (x,) xs ++ tuples xs  -- This is all ugly, but who cares. writeDivergenceMatrix :: Handle -> (Seq.Sequence, Seq.Sequence, MU.Matrix Int) -> IO ()@@ -183,7 +183,7 @@   let xys = tuples ss       ds = map (\(x, y) -> (x, y, either error id $ divergence x y)) xys   h <- outHandle "divergence matrices" ".div"-  sequence_ $ map (liftIO . writeDivergenceMatrix h) ds+  mapM_ (liftIO . writeDivergenceMatrix h) ds   liftIO $ hClose h  -- | Examine sequences.

@@ -65,4 +65,4 @@  filePathArg :: Parser FilePath filePathArg =-  strArgument $ metavar "INPUT-FILE" <> help "Read sequences from INPUT-FILE"+  strArgument $ metavar "INPUT-FILE" <> help "Read sequences from INPUT-FILE" <> action "file"

@@ -1,5 +1,4 @@ {-# LANGUAGE OverloadedStrings #-}-{-# LANGUAGE TemplateHaskell #-}  -- | -- Module      :  Analyze.Analyze

@@ -1,5 +1,4 @@ {-# LANGUAGE OverloadedStrings #-}-{-# LANGUAGE TemplateHaskell #-}  -- | -- Module      :  SLynx.Simulate.Simulate

@@ -1,5 +1,4 @@ {-# LANGUAGE OverloadedStrings #-}-{-# LANGUAGE TemplateHaskell #-}  -- | -- Module      :  Analyze.Analyze

@@ -1,5 +1,4 @@ {-# LANGUAGE OverloadedStrings #-}-{-# LANGUAGE TemplateHaskell #-}  -- | -- Module      :  SLynx.Tools

@@ -1,5 +1,4 @@ {-# LANGUAGE OverloadedStrings #-}-{-# LANGUAGE TemplateHaskell #-}  -- | -- Module      :  Analyze.Analyze