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• Removed some unnecessary or outdated modules/code: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