cabal-version: 1.12
name: elynx-seq
version: 0.1.0
license: GPL-3
license-file: LICENSE
copyright: Dominik Schrempf (2019)
maintainer: dominik.schrempf@gmail.com
author: Dominik Schrempf
homepage: https://github.com/dschrempf/elynx#readme
bug-reports: https://github.com/dschrempf/elynx/issues
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
build-type: Simple
extra-source-files:
    README.md
    ChangeLog.md

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

library
    exposed-modules:
        ELynx.Data.Alphabet.Alphabet
        ELynx.Data.Alphabet.Character
        ELynx.Data.Alphabet.DistributionDiversity
        ELynx.Data.Character.AminoAcid
        ELynx.Data.Character.AminoAcidI
        ELynx.Data.Character.AminoAcidS
        ELynx.Data.Character.AminoAcidX
        ELynx.Data.Character.BoundaryMutation
        ELynx.Data.Character.Character
        ELynx.Data.Character.Codon
        ELynx.Data.Character.Nucleotide
        ELynx.Data.Character.NucleotideI
        ELynx.Data.Character.NucleotideX
        ELynx.Data.MarkovProcess.AminoAcid
        ELynx.Data.MarkovProcess.CXXModels
        ELynx.Data.MarkovProcess.CXXModelsData
        ELynx.Data.MarkovProcess.EDMModel
        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.Data.Sequence.Alignment
        ELynx.Data.Sequence.Defaults
        ELynx.Data.Sequence.Sequence
        ELynx.Data.Sequence.Translate
        ELynx.Export.Sequence.CountsFile
        ELynx.Export.Sequence.Fasta
        ELynx.Import.MarkovProcess.EDMModelPhylobayes
        ELynx.Import.MarkovProcess.SiteprofilesPhylobayes
        ELynx.Import.Sequence.Fasta
        ELynx.Simulate.MarkovProcess
        ELynx.Simulate.MarkovProcessAlongTree
    hs-source-dirs: src
    other-modules:
        Paths_elynx_seq
    default-language: Haskell2010
    ghc-options: -Wall -O2
    build-depends:
        async >=2.2.2 && <2.3,
        base >=4.12.0.0 && <4.13,
        bytestring >=0.10.8.2 && <0.11,
        containers >=0.6.0.1 && <0.7,
        data-memocombinators >=0.5.1 && <0.6,
        elynx-tools >=0.1.0 && <0.2,
        elynx-tree >=0.1.0 && <0.2,
        hmatrix >=0.20.0.0 && <0.21,
        integration >=0.2.1 && <0.3,
        math-functions >=0.3.2.1 && <0.4,
        matrices >=0.5.0 && <0.6,
        megaparsec >=7.0.5 && <7.1,
        mwc-random >=0.14.0.0 && <0.15,
        optparse-applicative >=0.14.3.0 && <0.15,
        parallel >=3.2.2.0 && <3.3,
        primitive >=0.6.4.0 && <0.7,
        statistics >=0.15.0.0 && <0.16,
        transformers >=0.5.6.2 && <0.6,
        vector >=0.12.0.3 && <0.13,
        vector-th-unbox >=0.2.1.6 && <0.3,
        word8 >=0.1.3 && <0.2

test-suite seq-test
    type: exitcode-stdio-1.0
    main-is: Spec.hs
    hs-source-dirs: test
    other-modules:
        ELynx.Data.Alphabet.DistributionDiversitySpec
        ELynx.Data.MarkovProcess.AminoAcidSpec
        ELynx.Data.MarkovProcess.NucleotideSpec
        ELynx.Data.Sequence.AlignmentSpec
        ELynx.Data.Sequence.SequenceSpec
        ELynx.Data.Sequence.TranslateSpec
        ELynx.Export.Sequence.FastaSpec
        ELynx.Import.MarkovProcess.EDMModelPhylobayesSpec
        ELynx.Import.MarkovProcess.SiteprofilesPhylobayesSpec
        ELynx.Import.Sequence.FastaSpec
        ELynx.Simulate.MarkovProcessAlongTreeSpec
        Files
        Paths_elynx_seq
    default-language: Haskell2010
    ghc-options: -Wall -O2 -eventlog -threaded -rtsopts
                 -with-rtsopts=-N
    build-depends:
        async >=2.2.2 && <2.3,
        base >=4.12.0.0 && <4.13,
        bytestring >=0.10.8.2 && <0.11,
        containers >=0.6.0.1 && <0.7,
        data-memocombinators >=0.5.1 && <0.6,
        elynx-seq -any,
        elynx-tools >=0.1.0 && <0.2,
        elynx-tree >=0.1.0 && <0.2,
        hmatrix >=0.20.0.0 && <0.21,
        hspec >=2.7.1 && <2.8,
        hspec-megaparsec >=2.0.1 && <2.1,
        integration >=0.2.1 && <0.3,
        math-functions >=0.3.2.1 && <0.4,
        matrices >=0.5.0 && <0.6,
        megaparsec >=7.0.5 && <7.1,
        mwc-random >=0.14.0.0 && <0.15,
        optparse-applicative >=0.14.3.0 && <0.15,
        parallel >=3.2.2.0 && <3.3,
        primitive >=0.6.4.0 && <0.7,
        statistics >=0.15.0.0 && <0.16,
        transformers >=0.5.6.2 && <0.6,
        vector >=0.12.0.3 && <0.13,
        vector-th-unbox >=0.2.1.6 && <0.3,
        word8 >=0.1.3 && <0.2