tlynx 0.8.0.0 → 0.9.0.0

raw patch · 6 files changed

+16/−10 lines, 6 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• ChangeLog.md +6/−0
• README.md +5/−5
• src/TLynx/Compare/Compare.hs +1/−1
• src/TLynx/Distance/Distance.hs +2/−2
• src/TLynx/Shuffle/Shuffle.hs +1/−1
• tlynx.cabal +1/−1

@@ -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]

@@ -234,7 +234,7 @@             Just fn -> do               let compareCommonBps =                     [ (bpToBrLen1 M.! b, bpToBrLen2 M.! b)-                      | b <- S.toList bpCommon+                    | b <- S.toList bpCommon                     ]               liftIO $ epspdfPlot fn (plotBps compareCommonBps)               logInfoS

@@ -77,8 +77,8 @@   [(Int, Int, b)] pairwise dist trs =   [ (i, j, dist x y)-    | (i : is, x : xs) <- zip (tails [0 ..]) (tails trs),-      (j, y) <- zip is xs+  | (i : is, x : xs) <- zip (tails [0 ..]) (tails trs),+    (j, y) <- zip is xs   ]  -- | Compute distance functions between phylogenetic trees.

@@ -88,5 +88,5 @@   lss <- grabble ls n (length ls) gen   return     [ toReconstructedTree "" (PointProcess names times o)-      | (times, names) <- zip css lss+    | (times, names) <- zip css lss     ]

@@ -1,6 +1,6 @@ cabal-version:      3.0 name:               tlynx-version:            0.8.0.0+version:            0.9.0.0 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>.