Cabal revisions of ADPfusion-0.5.2.0
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-name: ADPfusion-version: 0.5.2.0-author: Christian Hoener zu Siederdissen, 2011-2016-copyright: Christian Hoener zu Siederdissen, 2011-2016-homepage: https://github.com/choener/ADPfusion-bug-reports: https://github.com/choener/ADPfusion/issues-maintainer: choener@bioinf.uni-leipzig.de-category: Algorithms, Data Structures, Bioinformatics, Formal Languages-license: BSD3-license-file: LICENSE-build-type: Simple-stability: experimental-cabal-version: >= 1.10.0-tested-with: GHC == 7.8.4, GHC == 7.10.3, GHC == 8.0.1-synopsis: Efficient, high-level dynamic programming.-description:- <http://www.bioinf.uni-leipzig.de/Software/gADP/ generalized Algebraic Dynamic Programming>- .- ADPfusion combines stream-fusion (using the stream interface- provided by the vector library) and type-level programming to- provide highly efficient dynamic programming combinators.- .- ADPfusion allows writing dynamic programs for single- and- multi-tape problems. Inputs can be sequences, or sets. New- input types can be defined, without having to rewrite this- library thanks to the open-world assumption of ADPfusion.- .- The library provides the machinery for Outside and Ensemble- algorithms as well. Ensemble algorithms combine Inside and- Outside calculations.- .- Starting with version 0.4.1 we support writing multiple- context-free grammars (interleaved syntactic variables). Such- grammars have applications in bioinformatics and linguistics.- .- The homepage provides a number of tutorial-style examples, with- linear and context-free grammars over sequence and set inputs.- .- The formal background for generalized algebraic dynamic- progrmaming and ADPfusion is described in a number of papers.- These can be found on the gADP homepage and in the README.- .----Extra-Source-Files:- README.md- changelog.md----flag examples- description: build the examples- default: False- manual: True--flag debug- description: dump intermediate Core files- default: False- manual: True--flag spectest- description: build the spec-ctor test case- default: False- manual: True--flag devel- description: build additional tests- default: False- manual: True--flag btstruc- description: performance test for backtracking structures- default: False- manual: True----library- build-depends: base >= 4.7 && < 5.0- , bits >= 0.4 && < 0.6- , containers- , mmorph >= 1.0 && < 1.1- , mtl >= 2.0 && < 2.3- , primitive >= 0.5.4 && < 0.7- , QuickCheck >= 2.7 && < 2.9- , strict >= 0.3 && < 0.4- , template-haskell >= 2.0 && < 3.0- , th-orphans >= 0.12 && < 0.14- , transformers >= 0.3 && < 0.6- , tuple >= 0.3 && < 0.4- , vector >= 0.11 && < 0.12- --- , DPutils == 0.0.0.*- , OrderedBits == 0.0.1.*- , PrimitiveArray == 0.7.1.*-- exposed-modules:- -- multi imports- ADP.Fusion.Core- ADP.Fusion.Point- ADP.Fusion.Unit- -- core system- ADP.Fusion.Core.Apply- ADP.Fusion.Core.Classes- ADP.Fusion.Core.Multi- ADP.Fusion.Core.TH- ADP.Fusion.Core.TH.Backtrack- ADP.Fusion.Core.TH.Common- ADP.Fusion.Core.TyLvlIx- ADP.Fusion.SynVar.Array- ADP.Fusion.SynVar.Array.Type- ADP.Fusion.SynVar.Axiom- ADP.Fusion.SynVar.Backtrack- ADP.Fusion.SynVar.Fill- ADP.Fusion.SynVar.Indices.Classes- ADP.Fusion.SynVar.Recursive.Type- ADP.Fusion.SynVar.Split.Type- ADP.Fusion.SynVar.TableWrap- ADP.Fusion.Term.Chr.Type- ADP.Fusion.Term.Deletion.Type- ADP.Fusion.Term.Edge.Type- ADP.Fusion.Term.Epsilon.Type- ADP.Fusion.Term.PeekIndex.Type- ADP.Fusion.Term.Strng.Type- -- Point- ADP.Fusion.Core.Point- ADP.Fusion.SynVar.Indices.Point- ADP.Fusion.SynVar.Recursive.Point- ADP.Fusion.Term.Chr.Point- ADP.Fusion.Term.Deletion.Point- ADP.Fusion.Term.Epsilon.Point- ADP.Fusion.Term.Strng.Point- -- Unit- ADP.Fusion.Core.Unit- ADP.Fusion.SynVar.Indices.Unit- ADP.Fusion.Term.Deletion.Unit- ADP.Fusion.Term.Epsilon.Unit- -- tutorials- ADP.Fusion.Tutorial.NeedlemanWunsch-- default-extensions: BangPatterns- , ConstraintKinds- , CPP- , DataKinds- , DefaultSignatures- , FlexibleContexts- , FlexibleInstances- , GADTs- , KindSignatures- , MultiParamTypeClasses- , RankNTypes- , RecordWildCards- , ScopedTypeVariables- , StandaloneDeriving- , TemplateHaskell- , TupleSections- , TypeFamilies- , TypeOperators- , TypeSynonymInstances- , UndecidableInstances-- default-language:- Haskell2010- ghc-options:- -O2 -funbox-strict-fields----test-suite properties- type:- exitcode-stdio-1.0- main-is:- properties.hs- other-modules:- QuickCheck.Common- QuickCheck.Point- ghc-options:- -threaded -rtsopts -with-rtsopts=-N- hs-source-dirs:- tests- default-language:- Haskell2010- default-extensions: BangPatterns- , CPP- , FlexibleContexts- , FlexibleInstances- , MultiParamTypeClasses- , ScopedTypeVariables- , TemplateHaskell- , TypeFamilies- , TypeOperators- , TypeSynonymInstances- cpp-options:- -DADPFUSION_TEST_SUITE_PROPERTIES- build-depends: base- , ADPfusion- , bits- , OrderedBits- , PrimitiveArray- , QuickCheck- , strict- , test-framework >= 0.8 && < 0.9- , test-framework-quickcheck2 >= 0.3 && < 0.4- , test-framework-th >= 0.2 && < 0.3- , vector------ Very simple two-sequence alignment.--executable NeedlemanWunsch-- if flag(examples)- buildable:- True- build-depends: base- , ADPfusion- , PrimitiveArray- , template-haskell- , vector- else- buildable:- False- hs-source-dirs:- src- main-is:- NeedlemanWunsch.hs- default-language:- Haskell2010- default-extensions: BangPatterns- , FlexibleContexts- , FlexibleInstances- , MultiParamTypeClasses- , RecordWildCards- , TemplateHaskell- , TypeFamilies- , TypeOperators- ghc-options:- -O2- -funbox-strict-fields- -funfolding-use-threshold1000- -funfolding-keeness-factor1000- if flag(debug)- ghc-options:- -ddump-to-file- -ddump-simpl- -dsuppress-all------ Very simple two-sequence alignment.--executable spectest-- if flag(spectest)- buildable:- True- build-depends: base- , ADPfusion- , PrimitiveArray- , template-haskell- , vector- else- buildable:- False- hs-source-dirs:- src- main-is:- SpecTest.hs- default-language:- Haskell2010- default-extensions: BangPatterns- , FlexibleContexts- , FlexibleInstances- , MultiParamTypeClasses- , RecordWildCards- , TemplateHaskell- , TypeFamilies- , TypeOperators- ghc-options:- -O2- -funbox-strict-fields- -funfolding-use-threshold1000- -funfolding-keeness-factor1000- if flag(debug)- ghc-options:- -ddump-to-file- -ddump-simpl- -dsuppress-all----benchmark TestBacktrackingStructures- type:- exitcode-stdio-1.0-- if flag(btstruc)- buildable:- True- build-depends: base- , template-haskell- , fmlist >= 0.9 && < 0.10- , vector- , criterion >= 1.1 && < 1.2- else- buildable:- False- hs-source-dirs:- tests- main-is:- BacktrackingStructures.hs- default-language:- Haskell2010- default-extensions: BangPatterns- , FlexibleContexts- , FlexibleInstances- , MultiParamTypeClasses- , RecordWildCards- , TemplateHaskell- , TypeFamilies- , TypeOperators- ghc-options:- -O2- -funfolding-use-threshold1000- -funfolding-keeness-factor1000----source-repository head- type: git- location: git://github.com/choener/ADPfusion-+name: ADPfusion +version: 0.5.2.0 +x-revision: 1 +author: Christian Hoener zu Siederdissen, 2011-2016 +copyright: Christian Hoener zu Siederdissen, 2011-2016 +homepage: https://github.com/choener/ADPfusion +bug-reports: https://github.com/choener/ADPfusion/issues +maintainer: choener@bioinf.uni-leipzig.de +category: Algorithms, Data Structures, Bioinformatics, Formal Languages +license: BSD3 +license-file: LICENSE +build-type: Simple +stability: experimental +cabal-version: >= 1.10.0 +tested-with: GHC == 7.8.4, GHC == 7.10.3, GHC == 8.0.1 +synopsis: Efficient, high-level dynamic programming. +description: + <http://www.bioinf.uni-leipzig.de/Software/gADP/ generalized Algebraic Dynamic Programming> + . + ADPfusion combines stream-fusion (using the stream interface + provided by the vector library) and type-level programming to + provide highly efficient dynamic programming combinators. + . + ADPfusion allows writing dynamic programs for single- and + multi-tape problems. Inputs can be sequences, or sets. New + input types can be defined, without having to rewrite this + library thanks to the open-world assumption of ADPfusion. + . + The library provides the machinery for Outside and Ensemble + algorithms as well. Ensemble algorithms combine Inside and + Outside calculations. + . + Starting with version 0.4.1 we support writing multiple + context-free grammars (interleaved syntactic variables). Such + grammars have applications in bioinformatics and linguistics. + . + The homepage provides a number of tutorial-style examples, with + linear and context-free grammars over sequence and set inputs. + . + The formal background for generalized algebraic dynamic + progrmaming and ADPfusion is described in a number of papers. + These can be found on the gADP homepage and in the README. + . + + + +Extra-Source-Files: + README.md + changelog.md + + + +flag examples + description: build the examples + default: False + manual: True + +flag debug + description: dump intermediate Core files + default: False + manual: True + +flag spectest + description: build the spec-ctor test case + default: False + manual: True + +flag devel + description: build additional tests + default: False + manual: True + +flag btstruc + description: performance test for backtracking structures + default: False + manual: True + + + +library + build-depends: base >= 4.7 && < 5.0 + , bits >= 0.4 + , containers + , mmorph >= 1.0 + , mtl >= 2.0 + , primitive >= 0.5.4 + , QuickCheck >= 2.7 + , strict >= 0.3 + , template-haskell >= 2.0 + , th-orphans >= 0.12 + , transformers >= 0.3 + , tuple >= 0.3 + , vector >= 0.11 + -- + , DPutils >= 0.0.0.0 + , OrderedBits == 0.0.1.* + , PrimitiveArray == 0.7.1.* + + exposed-modules: + -- multi imports + ADP.Fusion.Core + ADP.Fusion.Point + ADP.Fusion.Unit + -- core system + ADP.Fusion.Core.Apply + ADP.Fusion.Core.Classes + ADP.Fusion.Core.Multi + ADP.Fusion.Core.TH + ADP.Fusion.Core.TH.Backtrack + ADP.Fusion.Core.TH.Common + ADP.Fusion.Core.TyLvlIx + ADP.Fusion.SynVar.Array + ADP.Fusion.SynVar.Array.Type + ADP.Fusion.SynVar.Axiom + ADP.Fusion.SynVar.Backtrack + ADP.Fusion.SynVar.Fill + ADP.Fusion.SynVar.Indices.Classes + ADP.Fusion.SynVar.Recursive.Type + ADP.Fusion.SynVar.Split.Type + ADP.Fusion.SynVar.TableWrap + ADP.Fusion.Term.Chr.Type + ADP.Fusion.Term.Deletion.Type + ADP.Fusion.Term.Edge.Type + ADP.Fusion.Term.Epsilon.Type + ADP.Fusion.Term.PeekIndex.Type + ADP.Fusion.Term.Strng.Type + -- Point + ADP.Fusion.Core.Point + ADP.Fusion.SynVar.Indices.Point + ADP.Fusion.SynVar.Recursive.Point + ADP.Fusion.Term.Chr.Point + ADP.Fusion.Term.Deletion.Point + ADP.Fusion.Term.Epsilon.Point + ADP.Fusion.Term.Strng.Point + -- Unit + ADP.Fusion.Core.Unit + ADP.Fusion.SynVar.Indices.Unit + ADP.Fusion.Term.Deletion.Unit + ADP.Fusion.Term.Epsilon.Unit + -- tutorials + ADP.Fusion.Tutorial.NeedlemanWunsch + + default-extensions: BangPatterns + , ConstraintKinds + , CPP + , DataKinds + , DefaultSignatures + , FlexibleContexts + , FlexibleInstances + , GADTs + , KindSignatures + , MultiParamTypeClasses + , RankNTypes + , RecordWildCards + , ScopedTypeVariables + , StandaloneDeriving + , TemplateHaskell + , TupleSections + , TypeFamilies + , TypeOperators + , TypeSynonymInstances + , UndecidableInstances + + default-language: + Haskell2010 + ghc-options: + -O2 -funbox-strict-fields + + + +test-suite properties + type: + exitcode-stdio-1.0 + main-is: + properties.hs + other-modules: + QuickCheck.Common + QuickCheck.Point + ghc-options: + -threaded -rtsopts -with-rtsopts=-N + hs-source-dirs: + tests + default-language: + Haskell2010 + default-extensions: BangPatterns + , CPP + , FlexibleContexts + , FlexibleInstances + , MultiParamTypeClasses + , ScopedTypeVariables + , TemplateHaskell + , TypeFamilies + , TypeOperators + , TypeSynonymInstances + cpp-options: + -DADPFUSION_TEST_SUITE_PROPERTIES + build-depends: base + , ADPfusion + , bits + , OrderedBits + , PrimitiveArray + , QuickCheck + , strict + , test-framework >= 0.8 && < 0.9 + , test-framework-quickcheck2 >= 0.3 && < 0.4 + , test-framework-th >= 0.2 && < 0.3 + , vector + + + +-- Very simple two-sequence alignment. + +executable NeedlemanWunsch + + if flag(examples) + buildable: + True + build-depends: base + , ADPfusion + , PrimitiveArray + , template-haskell + , vector + else + buildable: + False + hs-source-dirs: + src + main-is: + NeedlemanWunsch.hs + default-language: + Haskell2010 + default-extensions: BangPatterns + , FlexibleContexts + , FlexibleInstances + , MultiParamTypeClasses + , RecordWildCards + , TemplateHaskell + , TypeFamilies + , TypeOperators + ghc-options: + -O2 + -funbox-strict-fields + -funfolding-use-threshold1000 + -funfolding-keeness-factor1000 + if flag(debug) + ghc-options: + -ddump-to-file + -ddump-simpl + -dsuppress-all + + + +-- Very simple two-sequence alignment. + +executable spectest + + if flag(spectest) + buildable: + True + build-depends: base + , ADPfusion + , PrimitiveArray + , template-haskell + , vector + else + buildable: + False + hs-source-dirs: + src + main-is: + SpecTest.hs + default-language: + Haskell2010 + default-extensions: BangPatterns + , FlexibleContexts + , FlexibleInstances + , MultiParamTypeClasses + , RecordWildCards + , TemplateHaskell + , TypeFamilies + , TypeOperators + ghc-options: + -O2 + -funbox-strict-fields + -funfolding-use-threshold1000 + -funfolding-keeness-factor1000 + if flag(debug) + ghc-options: + -ddump-to-file + -ddump-simpl + -dsuppress-all + + + +benchmark TestBacktrackingStructures + type: + exitcode-stdio-1.0 + + if flag(btstruc) + buildable: + True + build-depends: base + , template-haskell + , fmlist >= 0.9 && < 0.10 + , vector + , criterion >= 1.1 && < 1.2 + else + buildable: + False + hs-source-dirs: + tests + main-is: + BacktrackingStructures.hs + default-language: + Haskell2010 + default-extensions: BangPatterns + , FlexibleContexts + , FlexibleInstances + , MultiParamTypeClasses + , RecordWildCards + , TemplateHaskell + , TypeFamilies + , TypeOperators + ghc-options: + -O2 + -funfolding-use-threshold1000 + -funfolding-keeness-factor1000 + + + +source-repository head + type: git + location: git://github.com/choener/ADPfusion +