v0.5.0-a1

Changed

• Store Database sequences using shared_ptr for fast slicing and extraction of a database subset.
• Use templates to generate platform-specific Cython files.

Fixed

• SSE2 not being detected on x86-64, where it is mandatory.
• Mark Opal search functions as noexcept in Cython to avoid exception checks.

Added

• Support for compiling and running package on Windows.
• Support for Python 3.12.

v0.4.1

Fixed

• FullResult.__repr__ not returning a roundtripping string (#4, by @valentynbez).
• Database.search overflowing for long sequences with non-sw algorithms (#3).

Changed

• Make Database.search raise an OverflowError instead of a RuntimeError on score overflow.

v0.4.0

Changed

• Bumped Cython dependency to v3.0.

Fixed

• PyPy 3.9 builds failing on missing PyInterpreterState_GetID.

v0.3.0

Added

• Database.extract method to subset a database given a sequence of indices.
• Database.mask method to subset a database given a boolean mask.

Changed

• Replaced cpu-features library with archspec Python package for runtime detection of CPU features.

Fixed

• Segmentation fault in alignment reconstruction code for Needleman-Wunsch algorithm (#1).
• Erroneous error message in Database.search on invalid overflow value (#2).

v0.2.0

Added

• query_length and target_length properties to FullResult to the lenghts of the complete query and target sequences.
• FullResult.coverage method to compute the coverage of the alignment using either the query or the target as the reference.

Changed

• Compile Cython extension with binding=False to fix rendering of documentation.

Fixed

• Insertion & deletion symbols being inverted in FullResult.cigar strings.

v0.1.1

Added

• Buffer protocol implementation to pyopal.ScoreMatrix.
• Sphinx documentation hosted on ReadTheDocs.

Fixed

• Docstring now showing in the main pyopal module.
• Database.insert potentially crashing when given negative indexes.
• Database.search not listing the right return type.

v0.1.0

Initial release.