cabal-version:      3.0
name:               elynx-tree
version:            0.7.2.0
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:          2021 Dominik Schrempf
license:            GPL-3.0-or-later
license-file:       LICENSE
build-type:         Simple
extra-source-files:
  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/Newick.tree
  data/NewickConstraint.tree
  data/NewickRevBayes.tree
  data/NewickRooted.tree
  data/RevBayes.trees
  data/SimpleTree.nex
  data/TreeDist.trees
  data/UltraMetric.tree
  README.md

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.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.Length
    ELynx.Tree.Mrca
    ELynx.Tree.Name
    ELynx.Tree.Parallel
    ELynx.Tree.Partition
    ELynx.Tree.Phylogeny
    ELynx.Tree.Rooted
    ELynx.Tree.Simulate.Coalescent
    ELynx.Tree.Simulate.PointProcess
    ELynx.Tree.Splittable
    ELynx.Tree.Support
    ELynx.Tree.Zipper

  other-modules:    Paths_elynx_tree
  autogen-modules:  Paths_elynx_tree
  hs-source-dirs:   src
  ghc-options:      -Wall -Wunused-packages
  build-depends:
    , aeson
    , attoparsec
    , base
    , bytestring
    , comonad
    , containers
    , data-default-class
    , deepseq
    , elynx-nexus
    , math-functions
    , parallel
    , random
    , statistics

  default-language: Haskell2010

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

  autogen-modules:  Paths_elynx_tree
  hs-source-dirs:   test
  ghc-options:
    -Wall -Wunused-packages -threaded -rtsopts -with-rtsopts=-N

  build-depends:
    , attoparsec
    , base
    , bytestring
    , containers
    , data-default
    , elynx-tools
    , elynx-tree
    , hspec
    , QuickCheck
    , quickcheck-classes

  default-language: Haskell2010

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

  autogen-modules:  Paths_elynx_tree
  hs-source-dirs:   bench
  ghc-options:
    -Wall -Wunused-packages -threaded -rtsopts -with-rtsopts=-N

  build-depends:
    , base         >=4.7 && <5
    , criterion
    , elynx-tools
    , elynx-tree
    , microlens
    , parallel
    , random

  default-language: Haskell2010