v0.4.0

Added

• BaseTrimmer.backend property to get the backend used by a trimmer object.
• Zero-copy slicing for AlignmentSequences and AlignmentResidues objects.
• noduplicateseqs method for AutomaticTrimmer objects.
• OverlapTrimmer class to perform overlap trimming with SSE-accelerated implementation.
• AutomaticTrimmer.METHODS attribute to expose all supported automatic trimming methods.
• __repr__ implementation to all trimmer classes.

Fixed

• Missing deallocation code for standalone AlignmentResidues objects.
• Alignment.load not working properly in PyPy environments.
• Alignment constructor sometimes crashing when not given any sequence.

Changed

• Use aligned memory for some temporary buffers used in SIMD code.
• Enable loop unrolling when supported by the compiler.
• Skip letter validation when creating an Alignment object with sequences from an AlignmentSequences object.

Removed

• consistency_threshold and consistency_window arguments of ManualTrimmer.

v0.3.0

Added

• Support for loading an Alignment from a file-like object for certain formats.
• Generic optimized backend using caching optimizations from inab/trimal#66.

Fixed

• Compilation of code for OSX platforms in Python 3.10.
• File not being closed on error when loading a FASTA alignment.

Changed

• Add tests for loading an Alignment without requiring importlib.resources.

v0.2.2

Added

• Keyword arguments to specify the half-window sizes in manual trimmer.
• Alignment.dump and Alignment.dumps function to write an alignment to a file, file-like object, or string.
• Optimized implementation of Similarity::calculateVectors.

Changed

• Use faster implementation of SSE2 horizontal sum based on _mm_sad_epu8.

v0.2.1

Fixed

• Missing SSE2 files in source distribution.

v0.2.0

Added

• Vendored cpu_features library to perform runtime detection of CPU features.
• SIMD implementation of the similarity statistic code with SSE2 instructions.

Fixed

• Compilation on platforms without OpenMP by adding an empty omp.h header file.

v0.1.2

Added

• Python constructor and buffer protocol support for SimilarityMatrix.
• SimilarityMatrix.similarity method to get the similarity between two characters instead.

Fixed

• Source compilation failing because of source files in the pytrimal folder.

v0.1.1

Added

• Type annotations for all classes of the pytrimal extension module.

Fixed

• Cython header files not being included in source distribution.

v0.1.0

Initial release.