- Support for Python 3.8 through 3.11
- [pre-commit](https://pre-commit.com) added to repo and code sanitized
- GitHub Action automated testing with `pytest`
- GitHub Action based wheel for PyPi support following the CPython EOL model. See https://devguide.python.org/versions/
- Documentation added using [Sphinx](https://www.sphinx-doc.org/en/master/index.html) and [MyST](https://myst-parser.readthedocs.io/en/latest/) Markdown
- Documentation updates for missing example content and style.
- Documentation build on version tag using GitHub Action workflow in `update-docs.yml`
- docstrings updated
- Updated `LICENSE.md` copyright for 2023
- Added `sse2neon.h` macro for arm64 support
- Project url updated in `setup.py`.
- Made paths platform independent in `setup.py`
- removed SSW Library java and demo data files for clarity since they are unused. Updated `Makefile` to remove java build
- Code updated with warnings for deprecated camelCase methods for snake_case migration.
- Test coverage added for deprecation warnings
- Tests updated to check `Alignment` named tuples
- `ssw-py-ci-github-action.yml` github action workflow added for automated CI
- `sswpy.pyx` renamed to `alignmentmgr.pyx` and `SSW` class is now `AlignmentMgr`.
- `alignmenttuple.py` module for result tuple datastructure added
- `ssw/__init__.py` aliases `AlignmentMgr` to `SSW` for deprecated support
- `.github/workflows/build-wheels-pypi.yml` added
- `README.md` updated for completion including badges
- Added `BitwiseAlignmentFlag` class and `bitwise_flag`, `distance_cutoff`, and `score_cutoff` arguments to `AlignmentMgr.align` to enable more SSW upstream features.
- Updated `test_ssw.py` to test `bitwise_flag` and `score_filter` and `distance_filter`
- Added `MANIFEST.in` and `setup.package_data` updated for completion.
- `ssw.alignmentmgr.AlignmentMgr.align_c` runs `nogil` now.
- PyPI builds using `build-wheels-pypi.yml` GitHub Action workflow on version tag