Changelog

Version 1.0.0 (March 13, 2023)

  • Support for Python 3.8 through 3.11

  • pre-commit 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 and MyST 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