Added

• Sequence data validation against Aligner.scoring_matrix.alphabet.
• Compilation of Limited API wheels for Python 3.11 and later.

Changed

• Support scoring matrices with alphabets that are subsets of FAMSA_ALPHABET.
• Avoid unneeded copy in Sequence.__init__ and GappedSequence.__init__.

Fixed

• Incorrect handling of extra symbols in Sequence and Aligner.

Added

• PFASUM31, PFASUM43 and PFASUM60 scoring matrices as pyfamsa constants.

Changed

• Update FAMSA to v2.4.1.
• Change default scoring matrix from MIQS to PFASUM41.
• Drop support for Python 3.7 due to outdated manylinux setup.`

Fixed

• Extra key in pyproject.toml causing build issues with version 0.11.0 of scikit-build-core.

Added

• Support for Python 3.13.

Changed

• Use scikit-build-core to build package.

Removed

• Support for Python 3.6.

Fixed

• Unit tests failing on missing on missing optional importlib-resources dependency.

Added

• Constructor to GappedSequence class, taking an identifier and a sequence as bytes objects.
• Constructor to Alignment class, taking an iterable of GappedSequence object.
• Alignment.copy implementation.
• Slicing implementation to Alignment.
• Aligner.align_profiles function to align two profiles (#5).

Fixed

• Pin supported versions of scoring-matrices package to ~=0.2.0.

Changed

• Use C++ shared_ptr in GappedSequence and Alignment to avoid copying data when possible.
• Migrate documentation to pydata-sphinx-theme.

Added

• scoring-matrices dependency to handle alternative scoring matrices.
• scoring_matrix argument to Aligner constructor to use a non-default matrix (#3).

Fixed

• Use of outdated importlib.resources interface in pyfamsa.tests package.
• Missing defines for compilation of NEON code on non-Aarch64 Arm platforms.

Added

• pickle protocol support for Sequence objects.

Fixed

• Disable creation of empty Sequence objects to prevent segmentation faults in FAMSA (#2).

Fixed

• Disable use of memory-monotonic allocations to fix multithreading errors (#1).

Changed

• Bumped Cython dependency to v3.0.

Fixed

• PyPy builds failing on missing PyInterpreterState_GetID.