slynx 0.6.1.0 → 0.6.1.1
raw patch · 18 files changed
+67/−61 lines, 18 filessetup-changedPVP ok
version bump matches the API change (PVP)
API changes (from Hackage documentation)
Files
- ChangeLog.md +7/−0
- README.md +14/−12
- Setup.hs +0/−3
- slynx.cabal +2/−2
- src/SLynx/Concatenate/Concatenate.hs +2/−2
- src/SLynx/Concatenate/Options.hs +1/−1
- src/SLynx/Examine/Examine.hs +5/−5
- src/SLynx/Examine/Options.hs +1/−1
- src/SLynx/Filter/Filter.hs +3/−3
- src/SLynx/Filter/Options.hs +1/−1
- src/SLynx/Options.hs +1/−1
- src/SLynx/Simulate/PhyloModel.hs +7/−7
- src/SLynx/Simulate/Simulate.hs +11/−11
- src/SLynx/SubSample/Options.hs +1/−1
- src/SLynx/SubSample/SubSample.hs +2/−2
- src/SLynx/Tools.hs +3/−3
- src/SLynx/Translate/Options.hs +2/−2
- src/SLynx/Translate/Translate.hs +4/−4
ChangeLog.md view
@@ -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.
README.md view
@@ -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.
− Setup.hs
@@ -1,3 +0,0 @@-import Distribution.Simple--main = defaultMain
slynx.cabal view
@@ -1,6 +1,6 @@-cabal-version: 2.2+cabal-version: 3.0 name: slynx-version: 0.6.1.0+version: 0.6.1.1 synopsis: Handle molecular sequences 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
src/SLynx/Concatenate/Concatenate.hs view
@@ -18,8 +18,8 @@ where import Control.Monad.Trans.Reader-import qualified ELynx.Data.Sequence.Sequence as S-import ELynx.Export.Sequence.Fasta+import ELynx.Sequence.Export.Fasta+import qualified ELynx.Sequence.Sequence as S import ELynx.Tools.ELynx import ELynx.Tools.Environment import SLynx.Concatenate.Options
src/SLynx/Concatenate/Options.hs view
@@ -19,7 +19,7 @@ import Control.Applicative import Data.Aeson-import ELynx.Data.Alphabet.Alphabet+import ELynx.Alphabet.Alphabet import ELynx.Tools.Reproduction import GHC.Generics import Options.Applicative
src/SLynx/Examine/Examine.hs view
@@ -22,11 +22,11 @@ import qualified Data.ByteString.Lazy.Char8 as BL import qualified Data.Set as S import qualified Data.Vector.Unboxed as V-import qualified ELynx.Data.Alphabet.Alphabet as A-import qualified ELynx.Data.Alphabet.Character as C-import qualified ELynx.Data.Sequence.Alignment as M-import qualified ELynx.Data.Sequence.Distance as D-import qualified ELynx.Data.Sequence.Sequence as Seq+import qualified ELynx.Alphabet.Alphabet as A+import qualified ELynx.Alphabet.Character as C+import qualified ELynx.Sequence.Alignment as M+import qualified ELynx.Sequence.Distance as D+import qualified ELynx.Sequence.Sequence as Seq import ELynx.Tools.ByteString import ELynx.Tools.ELynx import ELynx.Tools.Environment
src/SLynx/Examine/Options.hs view
@@ -18,7 +18,7 @@ where import Data.Aeson-import ELynx.Data.Alphabet.Alphabet+import ELynx.Alphabet.Alphabet import ELynx.Tools.Reproduction import GHC.Generics import Options.Applicative
src/SLynx/Filter/Filter.hs view
@@ -22,9 +22,9 @@ import Control.Monad.Trans.Reader import qualified Data.ByteString.Lazy.Char8 as BL import Data.Maybe (fromMaybe)-import qualified ELynx.Data.Sequence.Alignment as M-import qualified ELynx.Data.Sequence.Sequence as S-import ELynx.Export.Sequence.Fasta+import qualified ELynx.Sequence.Alignment as M+import ELynx.Sequence.Export.Fasta+import qualified ELynx.Sequence.Sequence as S import ELynx.Tools.ELynx import ELynx.Tools.Environment import ELynx.Tools.Logger
src/SLynx/Filter/Options.hs view
@@ -21,7 +21,7 @@ import Control.Applicative import Data.Aeson-import ELynx.Data.Alphabet.Alphabet+import ELynx.Alphabet.Alphabet import ELynx.Tools.Reproduction import GHC.Generics import Options.Applicative
src/SLynx/Options.hs view
@@ -14,7 +14,7 @@ module SLynx.Options (CommandArguments (..)) where import Data.Aeson-import ELynx.Data.Alphabet.Alphabet+import ELynx.Alphabet.Alphabet import ELynx.Tools.Options import ELynx.Tools.Reproduction import GHC.Generics
src/SLynx/Simulate/PhyloModel.hs view
@@ -23,16 +23,16 @@ import Data.Either (rights) import Data.Maybe import qualified Data.Vector as V-import ELynx.Data.MarkovProcess.AminoAcid-import ELynx.Data.MarkovProcess.CXXModels-import qualified ELynx.Data.MarkovProcess.MixtureModel as M-import ELynx.Data.MarkovProcess.Nucleotide-import qualified ELynx.Data.MarkovProcess.PhyloModel as P-import ELynx.Data.MarkovProcess.RateMatrix-import qualified ELynx.Data.MarkovProcess.SubstitutionModel as S import ELynx.Import.MarkovProcess.EDMModelPhylobayes ( EDMComponent, )+import ELynx.MarkovProcess.AminoAcid+import ELynx.MarkovProcess.CXXModels+import qualified ELynx.MarkovProcess.MixtureModel as M+import ELynx.MarkovProcess.Nucleotide+import qualified ELynx.MarkovProcess.PhyloModel as P+import ELynx.MarkovProcess.RateMatrix+import qualified ELynx.MarkovProcess.SubstitutionModel as S import ELynx.Tools.Equality import ELynx.Tools.InputOutput import Numeric.LinearAlgebra
src/SLynx/Simulate/Simulate.hs view
@@ -30,19 +30,19 @@ import qualified Data.Vector as V import qualified Data.Vector.Storable as VS import qualified Data.Vector.Unboxed as U-import ELynx.Data.Alphabet.Alphabet as A-import qualified ELynx.Data.MarkovProcess.AminoAcid as MA-import ELynx.Data.MarkovProcess.GammaRateHeterogeneity-import qualified ELynx.Data.MarkovProcess.MixtureModel as MM-import qualified ELynx.Data.MarkovProcess.PhyloModel as MP-import qualified ELynx.Data.MarkovProcess.RateMatrix as MR-import qualified ELynx.Data.MarkovProcess.SubstitutionModel as MS-import qualified ELynx.Data.Sequence.Sequence as Seq hiding- ( name,- )-import ELynx.Export.Sequence.Fasta+import ELynx.Alphabet.Alphabet as A import ELynx.Import.MarkovProcess.EDMModelPhylobayes import ELynx.Import.MarkovProcess.SiteprofilesPhylobayes+import qualified ELynx.MarkovProcess.AminoAcid as MA+import ELynx.MarkovProcess.GammaRateHeterogeneity+import qualified ELynx.MarkovProcess.MixtureModel as MM+import qualified ELynx.MarkovProcess.PhyloModel as MP+import qualified ELynx.MarkovProcess.RateMatrix as MR+import qualified ELynx.MarkovProcess.SubstitutionModel as MS+import ELynx.Sequence.Export.Fasta+import qualified ELynx.Sequence.Sequence as Seq hiding+ ( name,+ ) import ELynx.Simulate.MarkovProcessAlongTree import ELynx.Tools.ByteString import ELynx.Tools.Definitions
src/SLynx/SubSample/Options.hs view
@@ -23,7 +23,7 @@ import qualified Data.Text.Lazy as LT import qualified Data.Text.Lazy.Builder as LT import qualified Data.Text.Lazy.Builder.Int as LT-import ELynx.Data.Alphabet.Alphabet+import ELynx.Alphabet.Alphabet import ELynx.Tools.Options import ELynx.Tools.Reproduction import GHC.Generics
src/SLynx/SubSample/SubSample.hs view
@@ -20,8 +20,8 @@ import Control.Monad import Control.Monad.IO.Class import Control.Monad.Trans.Reader (ask)-import qualified ELynx.Data.Sequence.Alignment as M-import ELynx.Export.Sequence.Fasta+import qualified ELynx.Sequence.Alignment as M+import ELynx.Sequence.Export.Fasta import ELynx.Tools.ELynx import ELynx.Tools.Environment import ELynx.Tools.Logger
src/SLynx/Tools.hs view
@@ -22,9 +22,9 @@ where import Control.Monad.IO.Class-import ELynx.Data.Alphabet.Alphabet-import ELynx.Data.Sequence.Sequence-import ELynx.Import.Sequence.Fasta+import ELynx.Alphabet.Alphabet+import ELynx.Sequence.Import.Fasta+import ELynx.Sequence.Sequence import ELynx.Tools.InputOutput import ELynx.Tools.Logger import Options.Applicative
src/SLynx/Translate/Options.hs view
@@ -19,8 +19,8 @@ import Data.Aeson import Data.List-import ELynx.Data.Alphabet.Alphabet-import ELynx.Data.Character.Codon+import ELynx.Alphabet.Alphabet+import ELynx.Character.Codon import ELynx.Tools.Reproduction import GHC.Generics import Options.Applicative
src/SLynx/Translate/Translate.hs view
@@ -18,10 +18,10 @@ where import Control.Monad.Trans.Reader-import ELynx.Data.Character.Codon-import ELynx.Data.Sequence.Sequence-import ELynx.Data.Sequence.Translate-import ELynx.Export.Sequence.Fasta+import ELynx.Character.Codon+import ELynx.Sequence.Export.Fasta+import ELynx.Sequence.Sequence+import ELynx.Sequence.Translate import ELynx.Tools.ELynx import ELynx.Tools.Environment import ELynx.Tools.Logger