elynx-markov 0.6.0.0 → 0.6.1.0

raw patch · 7 files changed

+25/−13 lines, 7 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• ChangeLog.md +7/−0
• README.md +12/−6
• elynx-markov.cabal +1/−1
• test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs +1/−1
• test/ELynx/Data/MarkovProcess/NucleotideSpec.hs +1/−1
• test/ELynx/Import/MarkovProcess/EDMModelPhylobayesSpec.hs +1/−1
• test/ELynx/Import/MarkovProcess/SiteprofilesPhylobayesSpec.hs +2/−3

@@ -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 +1,6 @@ cabal-version:  2.2 name:           elynx-markov-version:        0.6.0.0+version:        0.6.1.0 synopsis:       Simulate molecular sequences along trees 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

@@ -17,7 +17,7 @@ import ELynx.Data.MarkovProcess.AminoAcid import qualified ELynx.Data.MarkovProcess.RateMatrix as R import qualified ELynx.Data.MarkovProcess.SubstitutionModel as S-import ELynx.Tools+import ELynx.Tools.Equality import Numeric.LinearAlgebra import Test.Hspec 

@@ -17,7 +17,7 @@ import ELynx.Data.MarkovProcess.Nucleotide import ELynx.Data.MarkovProcess.RateMatrix import ELynx.Data.MarkovProcess.SubstitutionModel-import ELynx.Tools+import ELynx.Tools.Equality import Test.Hspec  stationaryDist :: StationaryDistribution

@@ -14,7 +14,7 @@ where  import ELynx.Import.MarkovProcess.EDMModelPhylobayes-import ELynx.Tools+import ELynx.Tools.InputOutput import Numeric.LinearAlgebra (fromList) import Test.Hspec 

@@ -15,10 +15,9 @@  import qualified Data.Vector.Storable as V import ELynx.Import.MarkovProcess.EDMModelPhylobayes-  ( EDMComponent,-  ) import ELynx.Import.MarkovProcess.SiteprofilesPhylobayes-import ELynx.Tools+import ELynx.Tools.Equality+import ELynx.Tools.InputOutput import Test.Hspec  fn :: FilePath