diff --git a/ChangeLog.md b/ChangeLog.md --- a/ChangeLog.md +++ b/ChangeLog.md @@ -4,6 +4,10 @@ ## Unreleased changes + +## Version 0.5.0.2 + +- Speed up mixture model simulation. - Improve rooting functions. - Improve `Topology` data type (but still a lot to do). - Various additions to the documentation. diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ # The ELynx Suite -Version: 0.5.0.1. +Version: 0.5.0.2. Reproducible evolution made easy.

@@ -73,9 +73,9 @@ slynx --help | head -n -16 - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] [--no-elynx-file] COMMAND @@ -90,7 +90,7 @@ Specify base name of output file -f,--force Ignore previous analysis and overwrite existing output files. - --no-elynx-file Do not write files for needed for reproducibility. + --no-elynx-file Do not write data required to reproduce an analysis. Available commands: concatenate Concatenate sequences found in input files. @@ -120,9 +120,9 @@ slynx concatenate --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE Concatenate sequences found in input files. @@ -141,9 +141,9 @@ slynx examine --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site] Examine sequences. If data is a multi sequence alignment, additionally analyze columns. @@ -163,9 +163,9 @@ slynx filter-rows --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH] [--shorter-than LENGTH] [--standard-characters] @@ -186,9 +186,9 @@ slynx filter-columns --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE [--standard-chars DOUBLE] @@ -210,9 +210,9 @@ slynx simulate --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] [-m|--mixture-model MODEL] [-e|--edm-file NAME] @@ -289,9 +289,9 @@ slynx sub-sample --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE (-n|--number-of-sites INT) @@ -319,9 +319,9 @@ slynx translate --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT) (-u|--universal-code CODE) @@ -344,9 +344,9 @@ tlynx --help | head -n -16 - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] [--no-elynx-file] COMMAND @@ -361,7 +361,7 @@ Specify base name of output file -f,--force Ignore previous analysis and overwrite existing output files. - --no-elynx-file Do not write files for needed for reproducibility. + --no-elynx-file Do not write data required to reproduce an analysis. Available commands: compare Compare two phylogenetic trees (compute distances and branch-wise differences). @@ -384,9 +384,9 @@ tlynx compare --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect] [-f|--newick-format FORMAT] NAMES @@ -413,9 +413,9 @@ tlynx examine --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT] Compute summary statistics of phylogenetic trees. @@ -437,9 +437,9 @@ tlynx simulate --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: tlynx simulate (-t|--nTrees INT) (-n|--nLeaves INT) PROCESS [-u|--sub-sample DOUBLE] [-s|--summary-statistics] @@ -474,9 +474,9 @@ elynx --help | head -n -16 - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: elynx COMMAND Validate and redo past ELynx analyses diff --git a/elynx-tools.cabal b/elynx-tools.cabal --- a/elynx-tools.cabal +++ b/elynx-tools.cabal @@ -1,6 +1,6 @@ cabal-version: 2.2 name: elynx-tools -version: 0.5.0.1 +version: 0.5.0.2 license: GPL-3.0-or-later license-file: LICENSE copyright: Dominik Schrempf (2020) @@ -44,25 +44,25 @@ default-language: Haskell2010 ghc-options: -Wall -Wunused-packages build-depends: - aeson >=1.5.4.1 && <1.6, - attoparsec >=0.13.2.4 && <0.14, + aeson >=1.5.5.1, + attoparsec >=0.13.2.5, base >=4.7 && <5, - base16-bytestring >=0.1.1.7 && <0.2, - bytestring >=0.10.10.0 && <0.11, - cryptohash-sha256 >=0.11.101.0 && <0.12, - deepseq >=1.4.4.0 && <1.5, - directory >=1.3.6.0 && <1.4, - fast-logger >=3.0.2 && <3.1, - hmatrix >=0.20.0.0 && <0.21, - monad-control >=1.0.2.3 && <1.1, - monad-logger >=0.3.35 && <0.4, - mwc-random >=0.14.0.0 && <0.15, - optparse-applicative >=0.15.1.0 && <0.16, - primitive >=0.7.1.0 && <0.8, - template-haskell >=2.16.0.0 && <2.17, - text >=1.2.3.2 && <1.3, - time >=1.9.3 && <1.10, - transformers >=0.5.6.2 && <0.6, - transformers-base >=0.4.5.2 && <0.5, - vector >=0.12.1.2 && <0.13, - zlib >=0.6.2.2 && <0.7 + base16-bytestring >=0.1.1.7, + bytestring >=0.10.12.0, + cryptohash-sha256 >=0.11.102.0, + deepseq >=1.4.4.0, + directory >=1.3.6.0, + fast-logger >=3.0.2, + hmatrix >=0.20.1, + monad-control >=1.0.2.3, + monad-logger >=0.3.36, + mwc-random >=0.14.0.0, + optparse-applicative >=0.15.1.0, + primitive >=0.7.1.0, + template-haskell >=2.16.0.0, + text >=1.2.4.1, + time >=1.9.3, + transformers >=0.5.6.2, + transformers-base >=0.4.5.2, + vector >=0.12.2.0, + zlib >=0.6.2.2 diff --git a/src/ELynx/Tools/Misc.hs b/src/ELynx/Tools/Misc.hs --- a/src/ELynx/Tools/Misc.hs +++ b/src/ELynx/Tools/Misc.hs @@ -14,7 +14,6 @@ ( -- * Weird stuff compose, allValues, - horizontalConcat, ) where @@ -25,11 +24,3 @@ -- | Get all values of a bounded enumerated type. allValues :: (Bounded a, Enum a) => [a] allValues = [minBound ..] - --- | A brain f***. As an example, let @xss@ be a list of alignments (i.e., a --- list of a list of a list of alleles). This function horizontally concatenates --- the sites. The number of species needs to be same in each alignment. No --- checks are performed! -horizontalConcat :: [[[a]]] -> [[a]] -horizontalConcat [xs] = xs -horizontalConcat xss = foldr1 (zipWith (++)) xss diff --git a/src/ELynx/Tools/Reproduction.hs b/src/ELynx/Tools/Reproduction.hs --- a/src/ELynx/Tools/Reproduction.hs +++ b/src/ELynx/Tools/Reproduction.hs @@ -230,7 +230,7 @@ writeELynxOpt :: Parser Bool writeELynxOpt = flag True False ( long "no-elynx-file" - <> help "Do not write files for needed for reproducibility." ) + <> help "Do not write data required to reproduce an analysis." ) -- | Random or fixed seed. data Seed = Random | Fixed (Vector Word32)