v1.0.1

• Significant documentation updates.
• Better error reporting:
  • When database files cannot be found (in CLI and API).
  • On attempting to open an invalid signatures file.
• Misc
  • Run tests on Python 3.11 and 3.12.
  • Minor changes to output of gambit signatures info.

v1.0.0

New features

• tree command for generating hierarchical clustering trees from distance matrices.

General

• Preferred extensions for genome database files and signatures files have been changed from .db and .h5 to .gdb and .gs.

Performance improvements

• Use process-based parallelism by default for parsing multiple sequence files (much faster).
• Speed up gambit dist with -s option applied.

CLI

• Strip directory and extension from input file IDs. This applies to CSV output for querying distance calculation and IDs in generated signature files.
• -k and --prefix parameters now default to values used RefSeq database.
• Add option to specify number of cores to use.
• Add option to disable progress bar printing.

v0.5.1

Minor edits to project README and metadata.

v0.5.0

New features

• gambit dist command for calculating distance matrices.

CLI

• Sequence file input
  • Explicitly restrict input to FASTA format only.
  • Files may be gzipped.
  • Read input file lists from text files.
• Minor changes to options of subcommands in signatures group.

API

• gambit.db subpackage:
  • Database-loading funcs moved to class methods of ReferenceDatabase.
  • Additional taxonomy tree methods.
  • Some additional internal reorganization/refactoring.

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.

0.4.0b1

v0.4.0b1

Update version to 0.4.0b1

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.

v0.2.2

Changes from v0.2.1:

• Replace testdb_210126 with testdb_210818. Small enough to include all files, including reference signatures and query sequences, in version control.
• Store pre-calculated query results for tests.
• Some other minor test improvements and bug fixes.

v0.2.1

Changes from v0.2.0:

• Added license
• Add setuptools to runtime dependencies
• Minor docstring edits

v0.2.0

Changes from 0.1.0:

• User-facing
  • Rework JSON results format to be simpler and hide internal details
  • Add CSV results format (default)
  • Display progress while querying
  • Increase query performance and decrease memory usage
• Internal
  • Major redesign of GAMBITDatabase and query funcs
    • GAMBITDatabase stores indices of reference signatures instead of loading them all up front
    • Read reference signatures in chunks when calculating distance matrix
    • Maintain reference to SQLAlchemy Session object on GAMBITDatabase.
  • strict classification parameter
    • Enables new behavior of finding and reconciling all matching taxa
    • Defaults to off, which results old behavior of using only closest match
  • Fix bug in consensus_taxon() and add tests
  • Flexible, generic progress monitoring API
    • Add to long-running functions like querying, distance matrix calculation, and k-mer finding
  • "archive" export format for saving full result data.
  • Lots of test improvements
  • More type annotations
  • Update API docs