v0.3.0

Changes from v0.2.2:

• CLI updates
  • gambit query now accepts query signatures from a signature file.
  • New command group gambit signatures with info and create subcommands.
  • New debug command group (hidden).
• Performance enhancements
  • Signature calculation for multiple sequence files can be run in parallel.
  • Signature calculation with large k much faster.
  • Benchmarks for signature calculation.
• Documentation
  • Installation instructions
  • More complete CLI docs
• API and internals
  • Major refactor to gambit.kmers and gambit.signatures
    • find_kmers() renamed to calc_signature() and moved to gambit.signatures.calc, related
      functions also renamed and moved.
    • Refactored k-mer search into new find_kmers() function, which finds locations of prefix
      matches in sequence.
    • Several other classes and functions moved from gambit.kmers to gambit.signatures submodules.
    • Rearrangement of stuff within gambit.signatures.
    • Added required kmerspec attribute to AbstractKmerArray.
    • Renamed some KmerSpec attributes
    • Rename gambit.kmers.reverse_complement() -> revcomp()
  • Refactor of Jaccard functions
    • Removed _sparse from function names
    • Array and matrix functions now calculate distance only, renamed from jaccard_* to jaccarddist_*
  • New features
    • Most functions which take DNA sequences now accept str, bytes, or Bio.Seq.Seq.
    • Convert signatures between compatible KmerSpecs.
    • HDF5Signatures close() method and context manager.
  • Other
    • Updated Cython kmers code.
    • Many updates/improvements to tests.