Release v1.1.0 · jlumpe/gambit

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Removed some unnecessary or outdated modules/code: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