elynx 0.6.0.0 → 0.6.1.0

raw patch · 5 files changed

+30/−10 lines, 5 files

Files

• ChangeLog.md +7/−0
• README.md +12/−6
• app/Main.hs +6/−2
• app/Options.hs +4/−1
• elynx.cabal +1/−1

@@ -5,6 +5,13 @@ ## Unreleased changes  +## Version 0.6.1.0++-   Split `ELynx.Tools` into separate modules because the package will be reduced.+-   Remove the following modules from `ELynx.Tools`: `Concurrent`,+    `LinearAlgebra`, `List`, `Misc`, and `Numeric`.++ ## Version 0.6.0.0  -   **elynx-tree:** remove parallel folds with layers (`parBranchFoldMapWithLayer`

@@ -69,13 +69,13 @@  # Get help -For example:--    slynx --help+    cabal exec slynx -- --help+    # OR: stack exec slynx -- --help+    # OR: slynx --help      ELynx Suite version 0.6.0.0.     Developed by Dominik Schrempf.-    Compiled on September 3, 2021, at 20:56 pm, UTC.+    Compiled on September 4, 2021, at 12:58 pm, UTC.          Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]                   [-f|--force] [--no-elynx-file] COMMAND@@ -113,6 +113,7 @@       - ProteinX (amino acids; including gaps)       - ProteinS (amino acids; including gaps, and translation stops)       - ProteinI (amino acids; including gaps, translation stops, and IUPAC codes)+         ELynx     -----     A Haskell library and tool set for computational biology. The goal of ELynx is@@ -126,6 +127,9 @@     tlynx     Analyze, modify, and simulate phylogenetic trees.     elynx     Validate and redo past analyses.     +    Get help for commands:+      slynx --help+         Get help for sub commands:       slynx examine --help @@ -134,11 +138,13 @@  The documentation of sub commands can be accessed separately: -    slynx simulate --help+    cabal exec slynx -- simulate --help+    # OR: stack exec slynx -- simulate --help+    # OR: slynx simulate --help      ELynx Suite version 0.6.0.0.     Developed by Dominik Schrempf.-    Compiled on September 3, 2021, at 20:56 pm, UTC.+    Compiled on September 4, 2021, at 12:58 pm, UTC.          Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]                            [-m|--mixture-model MODEL] [-e|--edm-file NAME] 

@@ -1,6 +1,7 @@ {-# LANGUAGE OverloadedStrings #-} {-# LANGUAGE ScopedTypeVariables #-} {-# LANGUAGE TypeApplications #-}+{-# OPTIONS_GHC -Wno-deferred-type-errors #-}  -- | -- Module      :  Main@@ -24,7 +25,9 @@ import qualified Data.ByteString.Char8 as BS import Data.Maybe import Data.Version-import ELynx.Tools+import ELynx.Tools.InputOutput+import ELynx.Tools.Options+import ELynx.Tools.Reproduction import Options import Options.Applicative import Paths_elynx@@ -37,7 +40,8 @@ parseProgName :: Value -> J.Parser String parseProgName = withObject "progName" $ \o -> o .: "progName" --- TODO: Declaring program names here should not be necessary.+-- TODO: Create a data type collecting program names.+ parseAllR :: String -> Value -> J.Parser AllReproductions parseAllR "slynx" v =   S <$> (parseJSON v :: J.Parser (Reproduction (Arguments S.CommandArguments)))

@@ -22,7 +22,10 @@   ) where -import ELynx.Tools+import ELynx.Tools.InputOutput+import ELynx.Tools.Options+import ELynx.Tools.Reproduction+import GHC.Generics import Options.Applicative import qualified SLynx.Options as S import qualified TLynx.Options as T

@@ -1,6 +1,6 @@ cabal-version:  2.2 name:           elynx-version:        0.6.0.0+version:        0.6.1.0 synopsis:       Validate and (optionally) redo ELynx analyses description:    Please see the README on GitHub at <https://github.com/dschrempf/elynx>. category:       Bioinformatics