elynx-tools 0.5.0.1 → 0.5.0.2
raw patch · 5 files changed
+56/−61 lines, 5 filesdep ~aesondep ~attoparsecdep ~base16-bytestringPVP: major bump suggested
API removals or changes: PVP suggests a major version bump
Dependency ranges changed: aeson, attoparsec, base16-bytestring, bytestring, cryptohash-sha256, deepseq, directory, fast-logger, hmatrix, monad-control, monad-logger, mwc-random, optparse-applicative, primitive, template-haskell, text, time, transformers, transformers-base, vector, zlib
API changes (from Hackage documentation)
- ELynx.Tools: horizontalConcat :: [[[a]]] -> [[a]]
Files
- ChangeLog.md +4/−0
- README.md +29/−29
- elynx-tools.cabal +22/−22
- src/ELynx/Tools/Misc.hs +0/−9
- src/ELynx/Tools/Reproduction.hs +1/−1
ChangeLog.md view
@@ -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.
README.md view
@@ -2,7 +2,7 @@ # The ELynx Suite -Version: 0.5.0.1.+Version: 0.5.0.2. Reproducible evolution made easy. <p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>@@ -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
elynx-tools.cabal view
@@ -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
src/ELynx/Tools/Misc.hs view
@@ -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
src/ELynx/Tools/Reproduction.hs view
@@ -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)