pyfamsa

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• Use of outdated importlib.resources interface in pyfamsa.tests package.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.

Added

• pyfamsa.famsa_info function to get version information about the embedded FAMSA version.
• Explicit support for Python 3.11.
• Wheel distributions for MacOS Aarch64 platforms.

Changed

• Bumped vendored FAMSA to v2.2.2.

Fixed

• Aligner.build_tree and Aligner.align now accept inputs containing less than two sequences.

Added

• MyPy Type stubs for the pyfamsa._famsa Cython extension.
• Documentation for the Aligner.build_tree method.

Fixed

• Missing header files for compilation on older platforms.
• Missing define macros for Windows build target.

Initial release.