Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

v0.6.2 - 2026-01-05

Fixed

• std::fill and std::vector C++ algorithm functions changing signatures in latest Cython version.

• Patch segmentation fault in profile-profile alignments (#8, refresh-bio/FAMSA#61).

• Ensure build in debug mode on ReadTheDocs.

v0.6.1 - 2025-10-02

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.

v0.6.0 - 2025-08-13

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• Drop support for Python 3.7 due to outdated manylinux setup.`

v0.5.3-post1 - 2025-03-04

Fixed

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

v0.5.3 - 2024-11-05

Added

• Support for Python 3.13.

Changed

• Use scikit-build-core to build package.

Removed

• Support for Python 3.6.

v0.5.2 - 2024-09-19

Changed

• Update to FAMSA v2.2.3.

v0.5.1 - 2024-08-28

Fixed

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

v0.5.0 - 2024-08-28

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.

v0.4.0 - 2024-05-06

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• Use of outdated importlib.resources interface in pyfamsa.tests package.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

v0.3.2 - 2024-01-27

Added

• pickle protocol support for Sequence objects.

Fixed

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

v0.3.1 - 2023-01-14

Fixed

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

v0.3.0 - 2023-07-21

Changed

• Bumped Cython dependency to v3.0.

Fixed

• PyPy builds failing on missing PyInterpreterState_GetID.

v0.2.0 - 2022-11-22

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.

v0.1.1 - 2022-08-06

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.

v0.1.0 - 2022-08-05

Initial release.