v0.8.0

Changed

• Update vendored trimAl to d89ffc3 (2.0_RC).
• Use scoring-matrices package to get a base for the SimilarityMatrix class.
• Rename backend to platform for all trimmer classes.
• Use trimAl platform-specific code to accelerate computations.
• Migrate documentation to pydata-sphinx-theme.

Fixed

• Missing trimmer classes in API documentation.
• Pin supported versions of scoring-matrices package to ~=0.2.0.

Removed

• Outdated platform-specific code.
• archspec dependency (replaced by cpu_features used internally in trimAl).

v0.8.0-alpha1

Changed

• Update vendored trimAl to d89ffc3 (2.0_RC).
• Use scoring-matrices package to get a base for the SimilarityMatrix class.
• Rename backend to platform for all trimmer classes.
• Use trimAl platform-specific code to accelerate computations.

Fixed

• Missing trimmer classes in API documentation.

Removed

• Outdated platform-specific code.
• archspec dependency (replaced by cpu_features used internally in trimAl).

v0.7.0

Changed

• Bumped Cython dependency to v3.0.

v0.6.0

Fixed

• Overflow in calculateSpuriousVector for certain sequence block sizes.
• MMX backend never being used unless explicitly required even when being the best supported backend.

Changed

• Use archspec Python package instead of cpu-features library for CPU feature detection at runtime.
• Use importlib.resources.files to load package data in pytrimal.tests.

v0.5.5

Fixed

• calculateSpuriousVector method of SIMD implementations not being declared override.

Changed

• Replaced aligned_alloc with posix_memalign for compatibility with MacOS.

v0.5.4

Added

• AVX2 and MMX implementations of the SIMD statistics computation.
• Tests for all SIMD implementations supported on the local machine.

Changed

• Refactor SIMD code using C++ templates and generic implementation.

Fixed

• Broken rendering of function signatures in Sphinx documentation.
• residues_mask and sequences_mask attributes of TrimmedAlignment not being documented (#1).

v0.5.3

Fixed

• SimilarityMatrix.nt inverting the degenerated argument value.

v0.5.2

Changed

• Replace NEON horizontal sums with implementations using vaddvq on Aarch64 and vpaddl on Armv7.
• Remove one layer of table lookup in all Similarity::CalculateVectors implementations.
• Make all SIMD code use local buffers and deallocate early.

Fixed

• Invalid operator being used in Cython code to deallocate C++ arrays.

Added

• SSE2 and NEON implementations for the Gaps statistic.

v0.5.1

Fixed

• Build of cpu_features for platforms without hardware detection support.

v0.5.0

Added

• pytrimal.RepresentativeTrimmer class to trim by maximum identity or fixed number of cluster representatives.
• pickle protocol support for all trimmer classes.
• Conversion methods to convert an Alignment from and to Biopython or PyHMMER objects.
• Arm NEON implementation of the statistics computation algorithm, with speed-up similar to that of the SSE implementation.

Fixed

• std::streambuf implementation based on the readinto Python method not working on Arm because of char being used to read ASCII.

Removed

• Support for Python 3.5, due to Cython compatibility issues.