PrimitiveArray

Efficient multidimensional arrays https://github.com/choener/PrimitiveArray

Latest on Hackage:0.8.0.1

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BSD3 licensed by Christian Hoener zu Siederdissen, 2011-2016

Build Status

PrimitiveArray

generalized Algebraic Dynamic Programming Homepage

PrimitiveArray provides operations on multi-dimensional arrays. Internally, the representation is based on the vector library, while the multi-dimensional indexing follows repa.

Primitive arrays are designed to be used together with ADPfusion.

Contact

Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany
choener@bioinf.uni-leipzig.de
http://www.bioinf.uni-leipzig.de/~choener/

Changes

0.8.0.1

  • PointL delays inlining to phase 0 for table filling. This is part of the close-to-C optimization effort for linear languages.
  • disabling smallcheck until I fix how things are generated

0.8.0.0

  • renamed Interface (Iter) to Boundary (Boundary)
  • Typeable instances for Dense primitive arrays
  • EdgeBoundary index structure
  • changes and fixes to quickcheck/smallcheck
  • added ScoreMatrix module with simple score and distance matrix structure (requires log-domain)

0.7.2.0

  • JSONKey (To/From) for index types.

0.7.1.0

  • minor updates to dependencies
  • tasty framework
  • Subword/upper triangular indexing provided by DPutils

0.7.0.1

  • Data.PrimitiveArray.Checked to capture index out-of-bounds problems

0.7.0.0

  • vector <= 0.11 support; including compatibility layer
  • redesigned Index structures (for dealing with Inside/Outside/Complement)

0.6.1.1

  • Hashable instances for all index structures
  • Hashable instances for Unboxed and Boxed arrays. These require Hashable instances for vectors, which are not available by default

0.6.1.0

  • OrderedBits < 0.0.1
  • travis.yml update

0.6.0.0

  • moved primitive array classes to Data.PrimitiveArray.Class
  • added from / to lenses
  • Field1 .. Field6 lenses for indices (Z:.a:.b...) (with Z being Field0) - lens stuff currently commented out; aiming to have an extra package [lens is fairly heavy]
  • FillTables should work now (with PointL, Subword)
  • freezing of whole stacks of (Z:.mutarr:.mutarr:. ...) tables
  • explicit 'Shape Subword'; this allows for simpler code in a number of places and is especially useful for CYK-style algorithms that have a single-dimensional upper-triangular matrix.
  • rangeStream of Extshape is new and used by the FillTables module
  • Binary, Cereal, Aeson instances for indices and immutable tables
  • orphan instances of Binary, Cereal, Aeson for Z, and (:.)
  • topmostIndex returns the final index position for CYK-style (bottom to top) parsing
  • removed Data.Array.Repa.Index.Point (we have PointL, PointR in Points.hs)
  • added Data.Array.Repa.Index.Set (for sets with an interface, used by Hamiltonian path problems)
  • Data.Array.Repa.Index.Outside is now just a newtype wrapped around other Index types. We want to be able to say "a Subword, but for Outside algorithms"
  • travis-ci integration

0.5.4.0

  • actually implemented PointR

  • added the rather important strictness annotation for mutable arrays in .Zero

0.5.3.0

  • fixed vector-th-unbox problem
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