elynx-nexus 0.6.1.1 → 0.7.0.1
raw patch · 5 files changed
+19/−13 lines, 5 filesPVP ok
version bump matches the API change (PVP)
API changes (from Hackage documentation)
Files
- ChangeLog.md +8/−1
- README.md +7/−8
- elynx-nexus.cabal +2/−2
- src/ELynx/Export/Nexus.hs +1/−1
- src/ELynx/Import/Nexus.hs +1/−1
ChangeLog.md view
@@ -5,9 +5,16 @@ ## Unreleased changes +## Version 0.7.0.1++- Random 1.2: Parallel functions now require an \`IOGenM\` random number+ generator.+- Fix splitting of the random number generator.++ ## Version 0.6.1.1 -- Remove plotting functionality (gnuplot incompatible with ghc921).+- Remove plotting functionality (gnuplot incompatible with ghc922). - Read files strictly. - Refactor; flatten model hierarchy.
README.md view
@@ -2,7 +2,7 @@ # The ELynx Suite -Version: 0.6.1.1.+Version: 0.7.0.0. Reproducible evolution made easy. <p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>@@ -74,9 +74,9 @@ # OR: slynx --help Up to date- ELynx Suite version 0.6.1.1.+ ELynx Suite version 0.7.0.0. Developed by Dominik Schrempf.- Compiled on February 22, 2022, at 15:10 pm, UTC.+ Compiled on July 10, 2022, at 08:48 am, UTC. Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] [--no-elynx-file] COMMAND@@ -144,16 +144,16 @@ # OR: slynx simulate --help Up to date- ELynx Suite version 0.6.1.1.+ ELynx Suite version 0.7.0.0. Developed by Dominik Schrempf.- Compiled on February 22, 2022, at 15:10 pm, UTC.+ Compiled on July 10, 2022, at 08:48 am, 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,...]"] [-g|--gamma-rate-heterogeneity "(NCAT,SHAPE)"]- (-l|--length NUMBER) [-S|--seed [INT]]+ (-l|--length NUMBER) [-S|--seed INT] Simulate multi sequence alignments. Available options:@@ -175,8 +175,7 @@ -g,--gamma-rate-heterogeneity "(NCAT,SHAPE)" Number of gamma rate categories and shape parameter -l,--length NUMBER Set alignment length to NUMBER- -S,--seed [INT] Seed for random number generator; list of 32 bit- integers with up to 256 elements (default: random)+ -S,--seed INT Seed for random number generator (default: random) -h,--help Show this help text Substitution models:
elynx-nexus.cabal view
@@ -1,6 +1,6 @@ cabal-version: 3.0 name: elynx-nexus-version: 0.6.1.1+version: 0.7.0.1 synopsis: Import and export Nexus files description: Examine, modify, and simulate molecular sequences in a reproducible way. Please see the README on GitHub at <https://github.com/dschrempf/elynx>. category: Bioinformatics@@ -8,7 +8,7 @@ bug-reports: https://github.com/dschrempf/elynx/issues author: Dominik Schrempf maintainer: dominik.schrempf@gmail.com-copyright: Dominik Schrempf (2021)+copyright: 2021 Dominik Schrempf license: GPL-3.0-or-later license-file: LICENSE build-type: Simple
src/ELynx/Export/Nexus.hs view
@@ -3,7 +3,7 @@ -- | -- Module : ELynx.Export.Nexus -- Description : Nexus types and classes--- Copyright : (c) Dominik Schrempf 2021+-- Copyright : 2021 Dominik Schrempf -- License : GPL-3 -- -- Maintainer : dominik.schrempf@gmail.com
src/ELynx/Import/Nexus.hs view
@@ -3,7 +3,7 @@ -- | -- Module : ELynx.Import.Nexus -- Description : Nexus types and classes--- Copyright : (c) Dominik Schrempf 2021+-- Copyright : 2021 Dominik Schrempf -- License : GPL-3 -- -- Maintainer : dominik.schrempf@gmail.com