cabal-version:      3.0
name:               elynx-markov
version:            0.8.0.0
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
homepage:           https://github.com/dschrempf/elynx#readme
bug-reports:        https://github.com/dschrempf/elynx/issues
author:             Dominik Schrempf
maintainer:         dominik.schrempf@gmail.com
copyright:          2021 Dominik Schrempf
license:            GPL-3.0-or-later
license-file:       LICENSE
build-type:         Simple
extra-source-files:
  ChangeLog.md
  data/EDMDistsIQTREE.nex
  data/EDMDistsPhylobayes.txt
  data/HSSPMany.siteprofiles
  data/HSSPSingle.siteprofiles
  README.md

source-repository head
  type:     git
  location: https://github.com/dschrempf/elynx

library
  exposed-modules:
    ELynx.Import.MarkovProcess.EDMModelPhylobayes
    ELynx.Import.MarkovProcess.SiteprofilesPhylobayes
    ELynx.MarkovProcess.AminoAcid
    ELynx.MarkovProcess.CXXModels
    ELynx.MarkovProcess.CXXModelsData
    ELynx.MarkovProcess.GammaRateHeterogeneity
    ELynx.MarkovProcess.MixtureModel
    ELynx.MarkovProcess.Nucleotide
    ELynx.MarkovProcess.PhyloModel
    ELynx.MarkovProcess.RateMatrix
    ELynx.MarkovProcess.SubstitutionModel
    ELynx.Simulate.MarkovProcess
    ELynx.Simulate.MarkovProcessAlongTree

  other-modules:    Paths_elynx_markov
  autogen-modules:  Paths_elynx_markov
  hs-source-dirs:   src
  ghc-options:      -Wall -Wunused-packages
  build-depends:
    , async
    , attoparsec
    , base            >=4.7 && <5
    , bytestring
    , containers
    , elynx-seq
    , hmatrix
    , integration
    , math-functions
    , mwc-random
    , random
    , statistics
    , vector

  default-language: Haskell2010

test-suite markov-test
  type:             exitcode-stdio-1.0
  main-is:          Spec.hs
  other-modules:
    ELynx.Import.MarkovProcess.EDMModelPhylobayesSpec
    ELynx.Import.MarkovProcess.SiteprofilesPhylobayesSpec
    ELynx.MarkovProcess.AminoAcidSpec
    ELynx.MarkovProcess.NucleotideSpec
    ELynx.MarkovProcess.RateMatrixSpec
    ELynx.Simulate.MarkovProcessAlongTreeSpec
    Paths_elynx_markov

  autogen-modules:  Paths_elynx_markov
  hs-source-dirs:   test
  ghc-options:      -Wall -Wunused-packages
  build-depends:
    , base          >=4.7 && <5
    , containers
    , elynx-markov
    , elynx-tools
    , hmatrix
    , hspec
    , random
    , vector

  default-language: Haskell2010

benchmark markov-bench
  type:             exitcode-stdio-1.0
  main-is:          Bench.hs

  -- other-modules:
  -- autogen-modules:
  -- ghc-options:
  hs-source-dirs:   bench
  ghc-options:      -Wall -Wunused-packages
  build-depends:    base
  default-language: Haskell2010