slynx 0.8.0.0 → 0.9.0.0
raw patch · 5 files changed
+19/−12 lines, 5 filesPVP ok
version bump matches the API change (PVP)
API changes (from Hackage documentation)
Files
- ChangeLog.md +6/−0
- README.md +5/−5
- slynx.cabal +1/−1
- src/SLynx/Examine/Examine.hs +3/−3
- src/SLynx/Simulate/Simulate.hs +4/−3
ChangeLog.md view
@@ -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`).
README.md view
@@ -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]
slynx.cabal view
@@ -1,6 +1,6 @@ cabal-version: 3.0 name: slynx-version: 0.8.0.0+version: 0.9.0.0 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>.
src/SLynx/Examine/Examine.hs view
@@ -127,9 +127,9 @@ pairwiseHamming = V.fromList [ either error normlz $ D.hamming x y- | x <- seqs,- y <- seqs,- x /= y+ | x <- seqs,+ y <- seqs,+ x /= y ] (hMean, hVar) = Sm.meanVariance pairwiseHamming hMin = V.minimum pairwiseHamming
src/SLynx/Simulate/Simulate.hs view
@@ -1,3 +1,4 @@+{-# LANGUAGE FlexibleContexts #-} {-# LANGUAGE OverloadedStrings #-} -- |@@ -90,7 +91,7 @@ -- Simulate a 'Alignment' for a given phylogenetic model, -- phylogenetic tree, and alignment length. simulateAlignment ::- (RandomGen g, HasLength e, HasName a) =>+ (SplitGen g, HasLength e, HasName a) => MP.PhyloModel -> Tree e a -> Int ->@@ -119,7 +120,7 @@ alph = A.all $ alphabetSpec code sequences = [ Seq.Sequence (fromName sName) "" code (U.fromList $ map (`Set.elemAt` alph) ss)- | (sName, ss) <- zip leafNames leafStates+ | (sName, ss) <- zip leafNames leafStates ] output = sequencesToFasta sequences logInfoS ""@@ -225,7 +226,7 @@ then concat [ BL.pack ("Component " ++ show i ++ ":") : summarizeMMComponent c- | (i, c) <- zip [1 :: Int ..] (V.toList $ MM.components m)+ | (i, c) <- zip [1 :: Int ..] (V.toList $ MM.components m) ] else []