elynx-tools 0.6.1.0 → 0.6.1.1

raw patch · 4 files changed

+24/−16 lines, 4 filesdep −textPVP ok

version bump matches the API change (PVP)

Dependencies removed: text

API changes (from Hackage documentation)

Files

• ChangeLog.md +7/−0
• README.md +14/−12
• elynx-tools.cabal +2/−3
• src/ELynx/Tools/InputOutput.hs +1/−1

@@ -5,6 +5,13 @@ ## Unreleased changes  +## Version 0.6.1.1++-   Remove plotting functionality (gnuplot incompatible with ghc921).+-   Read files strictly.+-   Refactor; flatten model hierarchy.++ ## Version 0.6.1.0  -   Split `ELynx.Tools` into separate modules because the package will be reduced.

@@ -2,7 +2,7 @@  # The ELynx Suite -Version: 0.6.0.0.+Version: 0.6.1.1. Reproducible evolution made easy.  <p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>@@ -69,15 +69,16 @@  # Get help -    cabal exec slynx -- --help+    cabal run slynx -- --help     # OR: stack exec slynx -- --help     # OR: slynx --help -    ELynx Suite version 0.6.0.0.+    Up to date+    ELynx Suite version 0.6.1.1.     Developed by Dominik Schrempf.-    Compiled on September 4, 2021, at 12:58 pm, UTC.+    Compiled on February 22, 2022, at 15:10 pm, UTC.     -    Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] +    Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]                  [-f|--force] [--no-elynx-file] COMMAND       Analyze, and simulate multi sequence alignments.     @@ -138,18 +139,19 @@  The documentation of sub commands can be accessed separately: -    cabal exec slynx -- simulate --help+    cabal run slynx -- simulate --help     # OR: stack exec slynx -- simulate --help     # OR: slynx simulate --help -    ELynx Suite version 0.6.0.0.+    Up to date+    ELynx Suite version 0.6.1.1.     Developed by Dominik Schrempf.-    Compiled on September 4, 2021, at 12:58 pm, UTC.+    Compiled on February 22, 2022, at 15:10 pm, UTC.     -    Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] -                          [-m|--mixture-model MODEL] [-e|--edm-file NAME] -                          [-p|--siteprofile-files NAMES] -                          [-w|--mixture-model-weights "[DOUBLE,DOUBLE,...]"] +    Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]+                          [-m|--mixture-model MODEL] [-e|--edm-file NAME]+                          [-p|--siteprofile-files NAMES]+                          [-w|--mixture-model-weights "[DOUBLE,DOUBLE,...]"]                           [-g|--gamma-rate-heterogeneity "(NCAT,SHAPE)"]                           (-l|--length NUMBER) [-S|--seed [INT]]       Simulate multi sequence alignments.

@@ -1,6 +1,6 @@-cabal-version:  2.2+cabal-version:  3.0 name:           elynx-tools-version:        0.6.1.0+version:        0.6.1.1 synopsis:       Tools for ELynx description:    Please see the README on GitHub at <https://github.com/dschrempf/elynx>. category:       Bioinformatics@@ -50,7 +50,6 @@     , mwc-random     , optparse-applicative     , template-haskell-    , text     , time     , transformers     , vector

@@ -100,7 +100,7 @@ parseFileOrIOWith :: Parser a -> Maybe FilePath -> IO a parseFileOrIOWith p mf = do   s <- maybe BL.getContents readGZFile mf-  return $ parseByteStringWith p s+  return $! parseByteStringWith p s  -- | Parse a 'String' and extract the result. parseStringWith :: Parser a -> String -> a