cabal-version:      2.2
name:               elynx-markov
version:            0.5.1.1
license:            GPL-3.0-or-later
license-file:       LICENSE
copyright:          Dominik Schrempf (2021)
maintainer:         dominik.schrempf@gmail.com
author:             Dominik Schrempf
homepage:           https://github.com/dschrempf/elynx#readme
bug-reports:        https://github.com/dschrempf/elynx/issues
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
build-type:         Simple
extra-source-files:
    README.md
    ChangeLog.md
    data/EDMDistsIQTREE.nex
    data/EDMDistsPhylobayes.txt
    data/HSSPMany.siteprofiles
    data/HSSPSingle.siteprofiles

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

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

    hs-source-dirs:   src
    other-modules:    Paths_elynx_markov
    autogen-modules:  Paths_elynx_markov
    default-language: Haskell2010
    ghc-options:      -Wall -Wunused-packages
    build-depends:
        async >=2.2.3,
        attoparsec >=0.13.2.5,
        base >=4.7 && <5,
        bytestring >=0.10.12.0,
        containers >=0.6.2.1,
        elynx-seq >=0.5.1.1,
        hmatrix >=0.20.2,
        integration >=0.2.1,
        math-functions >=0.3.4.2,
        mwc-random >=0.15.0.1,
        primitive >=0.7.1.0,
        statistics >=0.15.2.0,
        vector >=0.12.3.0

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

    default-language: Haskell2010
    ghc-options:      -Wall -Wunused-packages
    build-depends:
        base >=4.7 && <5,
        containers >=0.6.2.1,
        elynx-markov -any,
        elynx-tools >=0.5.1.1,
        hmatrix >=0.20.2,
        hspec >=2.7.10,
        mwc-random >=0.15.0.1,
        vector >=0.12.3.0

benchmark markov-bench
    type:             exitcode-stdio-1.0
    main-is:          Bench.hs
    hs-source-dirs:   bench
    default-language: Haskell2010
    ghc-options:      -Wall -Wunused-packages
    build-depends:    base >=4.14.1.0