cabal-version:      2.2
name:               elynx-tree
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:           Handle phylogenetic trees
description:
    Examine, compare, and simulate phylogenetic trees 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/ConnectA.tree
    data/ConnectB.tree
    data/ConnectConstraints.tree
    data/Many.trees
    data/MicrospoEDM32.tree
    data/MicrospoEDM64.tree
    data/MicrospoPoisson.tree
    data/Multifurcating.tree
    data/NewickConstraint.tree
    data/NewickRevBayes.tree
    data/NewickRooted.tree
    data/Newick.tree
    data/RevBayes.trees
    data/SimpleTree.nex
    data/TreeDist.trees
    data/UltraMetric.tree

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

library
    exposed-modules:
        ELynx.Topology
        ELynx.Topology.Phylogeny
        ELynx.Topology.Rooted
        ELynx.Tree
        ELynx.Tree.Bipartition
        ELynx.Tree.Distance
        ELynx.Tree.Length
        ELynx.Tree.Name
        ELynx.Tree.Parallel
        ELynx.Tree.Partition
        ELynx.Tree.Phylogeny
        ELynx.Tree.Rooted
        ELynx.Tree.Splittable
        ELynx.Tree.Support
        ELynx.Tree.Zipper
        ELynx.Tree.Distribution.BirthDeath
        ELynx.Tree.Distribution.BirthDeathCritical
        ELynx.Tree.Distribution.BirthDeathCriticalNoTime
        ELynx.Tree.Distribution.BirthDeathNearlyCritical
        ELynx.Tree.Distribution.CoalescentContinuous
        ELynx.Tree.Distribution.TimeOfOrigin
        ELynx.Tree.Distribution.TimeOfOriginNearCritical
        ELynx.Tree.Distribution.Types
        ELynx.Tree.Export.Newick
        ELynx.Tree.Export.Nexus
        ELynx.Tree.Import.Newick
        ELynx.Tree.Import.Nexus
        ELynx.Tree.Simulate.Coalescent
        ELynx.Tree.Simulate.PointProcess

    hs-source-dirs:   src
    other-modules:    Paths_elynx_tree
    autogen-modules:  Paths_elynx_tree
    default-language: Haskell2010
    ghc-options:      -Wall -Wunused-packages
    build-depends:
        aeson >=1.5.4.1 && <1.6,
        attoparsec >=0.13.2.4 && <0.14,
        base >=4.14.1.0 && <4.15,
        bytestring >=0.10.10.0 && <0.11,
        comonad >=5.0.6 && <5.1,
        containers >=0.6.2.1 && <0.7,
        deepseq >=1.4.4.0 && <1.5,
        double-conversion >=2.0.2.0 && <2.1,
        elynx-nexus >=0.5.0.1 && <0.6,
        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

test-suite tree-test
    type:             exitcode-stdio-1.0
    main-is:          Spec.hs
    hs-source-dirs:   test
    other-modules:
        ELynx.Topology.RootedSpec
        ELynx.Tree.Arbitrary
        ELynx.Tree.BipartitionSpec
        ELynx.Tree.DistanceSpec
        ELynx.Tree.PartitionSpec
        ELynx.Tree.PhylogenySpec
        ELynx.Tree.RootedSpec
        ELynx.Tree.SupportSpec
        ELynx.Tree.Export.NewickSpec
        ELynx.Tree.Export.NexusSpec
        ELynx.Tree.Import.NewickSpec
        ELynx.Tree.Import.NexusSpec
        Paths_elynx_tree

    default-language: Haskell2010
    ghc-options:      -Wall -Wunused-packages
    build-depends:
        QuickCheck >=2.13.2 && <2.14,
        attoparsec >=0.13.2.4 && <0.14,
        base >=4.14.1.0 && <4.15,
        bytestring >=0.10.10.0 && <0.11,
        containers >=0.6.2.1 && <0.7,
        elynx-tools >=0.5.0.1 && <0.6,
        elynx-tree -any,
        hspec >=2.7.4 && <2.8

benchmark tree-bench
    type:             exitcode-stdio-1.0
    main-is:          Bench.hs
    hs-source-dirs:   bench
    other-modules:
        Length
        Lens
        Paths_elynx_tree

    default-language: Haskell2010
    ghc-options:
        -Wall -Wunused-packages -threaded -rtsopts -with-rtsopts=-N

    build-depends:
        base >=4.7 && <5,
        criterion >=1.5.7.0 && <1.6,
        elynx-tools >=0.5.0.1 && <0.6,
        elynx-tree -any,
        microlens >=0.4.11.2 && <0.5,
        mwc-random >=0.14.0.0 && <0.15,
        parallel >=3.2.2.0 && <3.3