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 #

v0.5.1 - 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Use of outdated importlib.resources interface in pyfamsa.tests package.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.