cabal-version:      2.2
name:               elynx-markov
version:            0.5.0.1
license:            GPL-3.0-or-later
license-file:       LICENSE
copyright:          Dominik Schrempf (2020)
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 >=2.2.2 && <2.3,
        attoparsec >=0.13.2.4 && <0.14,
        base >=4.7 && <5,
        bytestring >=0.10.10.0 && <0.11,
        containers >=0.6.2.1 && <0.7,
        elynx-seq >=0.5.0.1 && <0.6,
        hmatrix >=0.20.0.0 && <0.21,
        integration >=0.2.1 && <0.3,
        math-functions >=0.3.4.1 && <0.4,
        mwc-random >=0.14.0.0 && <0.15,
        parallel >=3.2.2.0 && <3.3,
        primitive >=0.7.1.0 && <0.8,
        statistics >=0.15.2.0 && <0.16,
        vector >=0.12.1.2 && <0.13

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 && <0.7,
        elynx-markov -any,
        elynx-tools >=0.5.0.1 && <0.6,
        hmatrix >=0.20.0.0 && <0.21,
        hspec >=2.7.4 && <2.8,
        mwc-random >=0.14.0.0 && <0.15,
        vector >=0.12.1.2 && <0.13