v0.4.0

Changes from 0.3.0:

New features

• Result reporting
  • Results include list of closest reference genomes. This is only reported in JSON-based
    output formats.
  • New "next_taxon" attribute, indicating the next most specific taxon for which the
    threshold was not met.

CLI

• signatures info subcommand uses current reference DB by default.

Documentation

• Some improvements to API docs.

API and internals

• calc_signature() function can take multiple sequences as input.
• Remove calc_signature_parse() function.
• Refactoring
  • Rename GAMBITDatabase -> ReferenceDatabase, gambit.db.gambitdb -> .refdb
  • Rename gambit.signatures -> gambit.sigs.
  • Merge gambit.sigs.array, gambit.sigs.meta -> gambit.sigs.base
  • Rename gambit.io.export -> gambit.results
  • Move generic sequence code from gambit.kmers to gambit.seq.
  • Merge gambit.io.seq -> gambit.seq.
  • Rename load_database* funcs -> load_db*.
  • Move gambit.io.json -> gambit.util.json, gambit.io.util -> gambit.util.io,
    remove gambit.io.
  • Moved some other stuff between modules.
• Improvements to gambit.sigs.hdf5.HDF5Signatures
  • Improvements to .create() method.
  • Support compression.
• Format-independent functions for reading/writing signature data.
• jaccarddist_pairwise() function.
• Add more tree-based methods to Taxon.
• gambit.metric changes
  • jaccarddist_array and jaccarddist_matrix functions now accept any sequence type (e.g.
    list) for the refs argument, but with diminished performance.