zsyntax.cabal

cabal-version:  2.4
name:           zsyntax
version:        0.2.0.1
description:    An automated theorem prover for Zsyntax, a
                logical calculus for molecular biology inspired by linear logic,
                that can be used to automatically verify biological
                pathways expressed as logical sequents.

                The prover implements automatic proof search for the
                Zsyntax sequent calculus (ZBS), a logical calculus for
                a context-sensitive fragment of multiplicative linear
                logic where sequents are decorated so to account for
                the biochemical constraints.

                The theory behind the Zsyntax sequent calculus and its
                proof search procedure is developed in F. Sestini,
                S. Crafa, Proof-search in a context-sensitive logic
                for molecular biology, Journal of Logic and
                Computation, 2018
                (<https://doi.org/10.1093/logcom/exy028>).

category:       Logic, Theorem Provers, Bioinformatics
synopsis:       Automated theorem prover for the Zsyntax biochemical calculus
homepage:       https://github.com/fsestini/zsyntax#readme                 
bug-reports:    https://github.com/fsestini/zsyntax/issues
author:         Filippo Sestini
maintainer:     sestini.filippo@gmail.com
copyright:      2018 Filippo Sestini
license:        BSD-3-Clause
license-file:   LICENSE
build-type:     Simple

extra-source-files:
    README
    CHANGELOG.md

source-repository head
  type: git
  location: https://github.com/fsestini/zsyntax

library

  exposed-modules:
      Zsyntax
      Zsyntax.Formula
      Zsyntax.ReactionList

      Zsyntax.Labelled.Rule
      Zsyntax.Labelled.Formula
      Zsyntax.Labelled.DerivationTerm

      Zsyntax.Labelled.Rule.BipoleRelation
      Zsyntax.Labelled.Rule.Frontier
      Zsyntax.Labelled.Rule.Interface

      Otter
      Otter.Rule
      Otter.SearchRes
      Otter.Internal.Search
      Otter.Internal.Structures

  default-extensions:
      LambdaCase
      TupleSections
  hs-source-dirs: src
  ghc-options:
      -Wall
      -Wcompat
      -Wincomplete-record-updates
      -Wincomplete-uni-patterns
      -Wredundant-constraints
      -Wno-unticked-promoted-constructors
      -- -Werror
  build-depends:
      base >=4.7 && <5
    , constraints >= 0.10.1 && < 0.13.5
    , containers >= 0.6.0 && < 0.7
    , multiset >= 0.3.4 && < 0.4
    , mtl >= 2.2.2 && < 2.3
    , composition >= 1.0.2 && < 1.1
    , microlens-platform >= 0.3.11 && < 0.4.4
    , extra >= 1.6.13 && < 1.7.14
    , bifunctors
    , text
  default-language: Haskell2010

test-suite zsyntax-test
  type:             exitcode-stdio-1.0
  hs-source-dirs:   test
  build-depends:    base >=4.7 && <5
                  , zsyntax
                  , containers >= 0.6.0 && < 0.7
                  , multiset >= 0.3.4 && < 0.4
                  , mtl >= 2.2.2 && < 2.3
                  , text
                  , hspec
                  , QuickCheck
  main-is:          Main.hs
  default-language: Haskell2010

benchmark zsyntax-benchmark
  type:             exitcode-stdio-1.0
  hs-source-dirs:   benchmark
  build-depends:    base >=4.7 && <5
                  , zsyntax
                  , containers >= 0.6.0 && < 0.7
                  , multiset >= 0.3.4 && < 0.4
                  , mtl >= 2.2.2 && < 2.3
                  , text
                  , criterion
  main-is:          Main.hs
  default-language: Haskell2010