CHANGELOG.md

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 - 2024-02-20

Added

• Pre-compiled wheels for Python 3.12 and PyPy 3.10.

Fixed

• Use NEON and SSE2 unconditionally on platforms where they are available by default.

v0.5.0 - 2023-07-22

Changed

• Bump Cython dependency to v3.0.

Fixed

• Add missing signature of Sketch.index to type stubs.
• PyPy builds failing on missing PyInterpreterState_GetID function.

v0.4.1 - 2022-08-20

Changed

• Use lists instead of arrays to store state of Minimizers when pickling.
• Skip serialization of minimizer index to reduce total state size.
• Make Mapper.query_draft and Mapper.query_genome return hits sorted by identity in descending order.

v0.4.0 - 2022-08-04

Added

• Multi-threaded computation of fragment mapping in Mapper.query_draft and Mapper.query_genome.

Fixed

• NEON-specific compile flags in setup.py for Aarch64 target platforms.
• Broken compilation for Arm platforms because of missing header guards.

v0.3.1 - 2022-07-22

Added

• Slightly improve documentation in some classes.
• Sphinx documentation for the project hosted on ReadTheDocs.
• Links and instructions to install package from the Bioconda channel.

v0.3.0 - 2022-07-17

Added

• pickle protocol implementation to Mapper and Sketch via __getstate__ and __setstate__.
• Minimizers class to access the minimizers of a Sketch or Mapper object.

Changed

• Make Sketcher and Mapper final.
• Prevent direct instantiation of Mapper objects.
• Update Mapper._query_draft to recycle memory between fragments.
• Vendor Boost::math headers (v1.79) to allow compiling without depdendencies.

Fixed

• Broken compilation of _fastani extension module as universal2 binaries on MacOS.

v0.2.1 - 2021-06-20

Fixed

• Missing header files in the tar.gz distribution, preventing compilation of the wheel from source.

v0.2.0 - 2021-06-20

Added

• Sketch.clear method to remove all sequences currently in a Sketch and reset the list of minimizers.
• SIMD code to read and reverse-complement the input sequences efficiently on supported platforms (x86-64 with SSE2 or SSSE3, and ARM with NEON).

Changed

• Split the Sketch type in two depending on whether the object is at the sketching stage (Sketch) or at the querying stage (Mapper).
• Sketch.add_genome, Sketch.add_draft, Mapper.query_genome and Mapper.query_draft can now be passed a Unicode string for the sequence.

Fixed

• Integer underflow causing minimizers out of the block window to be added to the final minimizers list.

v0.1.2 - 2021-06-15

Changed

• Querying functions now release GIL to allow efficient parallel querying.

v0.1.1 - 2021-06-13

Fixed

• Source distribution missing Cython and C++ sources, thus preventing compilation.

v0.1.0 - 2021-06-13

Initial release.