cabal-version:  2.2
name:           elynx-tree
version:        0.4.1
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
homepage:       https://github.com/dschrempf/elynx#readme
bug-reports:    https://github.com/dschrempf/elynx/issues
author:         Dominik Schrempf
maintainer:     dominik.schrempf@gmail.com
copyright:      Dominik Schrempf (2020)
license:        GPL-3.0-or-later
license-file:   LICENSE
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.Phylogeny
      ELynx.Topology.Rooted
      ELynx.Tree
      ELynx.Tree.Bipartition
      ELynx.Tree.Distance
      ELynx.Tree.Measurable
      ELynx.Tree.Named
      ELynx.Tree.Parallel
      ELynx.Tree.Partition
      ELynx.Tree.Phylogeny
      ELynx.Tree.Rooted
      ELynx.Tree.Splittable
      ELynx.Tree.Supported
      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
  other-modules:
      Paths_elynx_tree
  autogen-modules:
      Paths_elynx_tree
  hs-source-dirs:
      src
  ghc-options: -Wall
  build-depends:
      aeson
    , attoparsec
    , base >=4.7 && <5
    , bytestring
    , comonad
    , containers
    , deepseq
    , double-conversion
    , elynx-nexus
    , math-functions
    , mwc-random
    , parallel
    , primitive
    , statistics
  default-language: Haskell2010

test-suite tree-test
  type: exitcode-stdio-1.0
  main-is: Spec.hs
  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.SupportedSpec
      ELynx.Tree.Export.NewickSpec
      ELynx.Tree.Export.NexusSpec
      ELynx.Tree.Import.NewickSpec
      ELynx.Tree.Import.NexusSpec
      Paths_elynx_tree
  hs-source-dirs:
      test
  ghc-options: -Wall
  build-depends:
      QuickCheck
    , attoparsec
    , base >=4.7 && <5
    , bytestring
    , containers
    , elynx-tools
    , elynx-tree
    , hspec
  default-language: Haskell2010

benchmark tree-bench
  type: exitcode-stdio-1.0
  main-is: Bench.hs
  other-modules:
      Paths_elynx_tree
  hs-source-dirs:
      bench
  ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
  -- ghc-options: -Wall
  build-depends:
      base >=4.7 && <5
    , bytestring
    , criterion
    , deepseq
    , elynx-tools
    , elynx-tree
    , mwc-random
    , parallel
  default-language: Haskell2010