name:           Forestry
version:        0.0.0.1
author:         Christian Hoener zu Siederdissen, Sarah Berkemer, 2017
copyright:      Christian Hoener zu Siederdissen, 2017
homepage:       https://github.com/choener/Forestry
bug-reports:    https://github.com/choener/Forestry/issues
maintainer:     choener@bioinf.uni-leipzig.de
category:       Formal Languages, Bioinformatics
license:        BSD3
license-file:   LICENSE
build-type:     Simple
stability:      experimental
cabal-version:  >= 1.10.0
tested-with:    GHC == 8.0.2
synopsis:       Comparison of trees and forests.
description:
                Wikipedia on forestry: "the science and craft of creating,
                managing, using, conserving, and repairing forests and
                associated resources."
                .
                This is a modest starting point and provides just:
                .
                * forest alignments
                * tree alignments
                .
                Build this library and executable with GHC-8.0.2
                .
                To enable @RNAforestry@, use @cabal new-build -frnaforestry@ or
                @cabal new-configure -w compiler-path -frnaforestry && cabal
                new-build@. We suggest using @cabal@ with the nix-style local
                build options.



Extra-Source-Files:
  changelog.md
  README.md



flag rnaforestry
  description: build the RNAforestry example application
  default:     False
  manual:      True



library
  build-depends: base                   >= 4.7      &&  < 5.0
               , containers
               , lens                   >= 4.0
               , log-domain             >= 0.11
               , text                   >= 1.0
               , vector                 >= 0.10
               --
               , ADPfusion              == 0.5.2.*
               , ADPfusionForest        == 0.0.0.*
               , BiobaseNewick          == 0.0.0.*
               , BiobaseTypes           == 0.1.3.*
               , ForestStructures       == 0.0.0.*
               , FormalGrammars         == 0.3.1.*
               , PrimitiveArray         == 0.8.0.*
               , PrimitiveArray-Pretty  == 0.0.0.*
  exposed-modules:
    Data.Forest.Static.Align.Affine
    Data.Forest.Static.Align.Linear
  default-language:
    Haskell2010
  default-extensions: BangPatterns
                    , UnicodeSyntax
                    , TemplateHaskell
                    , QuasiQuotes
                    , TypeOperators
                    , DataKinds
                    , MultiParamTypeClasses
                    , TypeFamilies
                    , OverloadedStrings
                    , FlexibleContexts
  ghc-options:
    -- TODO switch to O2 again!
    -O2 -funbox-strict-fields



executable RNAforestry
  if flag(rnaforestry)
    buildable:
      True
    build-depends: base
                 , cmdargs                >= 0.10
                 , containers
                 , filepath
                 , lens
                 , log-domain             >= 0.10
                 , streaming              >= 0.1
                 , streaming-bytestring   >= 0.1
                 , streaming-utils        >= 0.1
                 , text
                 , vector
                 --
                 , BiobaseNewick          == 0.0.0.*
                 , ForestStructures
                 , PrimitiveArray
                 , PrimitiveArray-Pretty
                 , Forestry
                 , ViennaRNA-extras       == 0.0.0.*
                 , BiobaseXNA             == 0.10.0.*
                 , BiobaseTypes
  else
    buildable:
      False
  hs-source-dirs:
    src
  main-is:
    RNAforestry.hs
  default-language:
    Haskell2010
  default-extensions: BangPatterns
                    , DataKinds
                    , DeriveDataTypeable
                    , FlexibleContexts
                    , GADTs
                    , MultiParamTypeClasses
                    , OverloadedStrings
                    , QuasiQuotes
                    , RecordWildCards
                    , TemplateHaskell
                    , TypeFamilies
                    , TypeOperators
                    , UnicodeSyntax
  ghc-options:
    -O2
    -funbox-strict-fields



test-suite properties
  type:
    exitcode-stdio-1.0
  main-is:
    properties.hs
  ghc-options:
    -threaded -rtsopts -with-rtsopts=-N -O2 -funbox-strict-fields
  hs-source-dirs:
    tests
  default-language:
    Haskell2010
  default-extensions: BangPatterns
                    , UnicodeSyntax
  build-depends: base
               , QuickCheck
               , tasty                        >= 0.11
               , tasty-quickcheck             >= 0.8
               , tasty-th                     >= 0.1
               --
               , Forestry



benchmark benchmark
  default-extensions: BangPatterns
                    , UnicodeSyntax
  build-depends:  base
               ,  criterion         >=  1.0.2
               --
               ,  Forestry
  default-language:
    Haskell2010
  hs-source-dirs:
    tests
  main-is:
    benchmark.hs
  type:
    exitcode-stdio-1.0
  ghc-options:
    -O2



source-repository head
  type: git
  location: git://github.com/choener/Forestry