v1.1.0

• Command line interface:
  • Better error reporting when database file(s) not found
  • Add more details to output of gambit signatures info command
• Major overhaul of internal Python API and tests (see below)
  • Many fixes to API documentation
• Increase minimum Python version to 3.9
• Make compatible with SQLAlchemy 2.0

Internal

• Changed project structure to src/ layout
• Build system:
  • Fix issues with package data not being properly included (only affected building distributions archives/wheels)
  • Build with Cython 3
  • Remove build-time dependency on Numpy
• Removed some unnecessary or outdated modules/code:
  • gambit.util.typing
  • gambit.util.dev
  • gambit.sigs.convert (sparse_to_dense and dese_to_sparse functions moved to gambit.sigs.calc)
  • gambit.db.migrate
• Moved modules containing test-oriented code out of gambit package and into tests/:
  • gambit.test
  • gambit.sigs.test
  • gambit.results.test
  • gambit.cli.test
• Remove use of deprecated Python/library features:
  • typing aliases to collection types
• Other internal API changes:
  • Convert gambit.results subpackage to module
  • Move functions for comparison query result objects to tests/results.py
  • Significant restructuring of classes used to represent query results
  • Removed SequenceFile class, replaced most occurrences with Path / "path-like" (compressed FASTA files are not detected and handled automatically).
• Tests:
  • Structure as package (add __init__.py files)
  • Simplify test file names (no longer need to be unique due to previous item)
  • Added type annotations throughout
  • Rewrote several test files to remove overly complicated Pytest fixtures
• Other:
  • Added (hidden) --pretty flag to query subcommand to prettify JSON output
  • Improvements to GitHub CI pipeline
  • HDF5 file format version no

v1.1.0pre1

Fix CI setup

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.