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#

[v0.1.0-alpha.5] - 2025-11-04#

Added#

  • Hash implementation for all Serial objects based on ASN serialization.

  • __rich_repr__ implementations for several classes.

  • Type hints to pyncbitk.object.seqset.

  • descriptions and length properties to BioSeqHandle proxy class.

  • WIP extension pyncbitk.objects.taxon providing a client to the NCBI Taxonomy service.

Changed#

  • Pin required pyncbitk-runtime to 29.6 and later.

  • Make pyncbitk.algo a package and move BLAST API to pyncbitk.algo.blast.

Fixed#

  • Typo for MacOS cibuildwheel configuration in pyproject.toml

  • Type name changes in pyncbitk.objects.seq.

[v0.1.0-alpha.4] - 2025-10-30#

Added#

  • Flag to skip parsing FASTA record IDs in FASTAReader.

Changed#

  • Reorganized wheel distribution to redistribute ncbi-cxx-toolkit-public runtime libraries in a separate pyncbitk-runtime wheel.

  • Removed unused Conan configuration file from main pyncbitk package.

  • Update readthedocs.yaml configuration to build the package from source on new commits.

Fixed#

  • Compilation issues on MacOS related to $RPATH management for Python extensions.

  • Uninitialized variable in AlignMap.__getitem__ causing crashes in debug mode only.

v0.1.0-alpha.3 - 2025-10-28#

Added#

  • Setters for percent_identity and culling_limit to Blast.

  • Getters for gaps in SeqAlign and individual AlignRow.

  • GeneralId.db_tag property to access the DBTag of a GeneralId.

Changed#

  • Update cibuildwheel configuration to strip wheels before uploading to PyPI.

v0.1.0-alpha.2 - 2025-10-26#

Added#

  • Buffer protocol support to NcbiEAaData.

  • Encoding constructor to all SeqData subclasses.

  • Options to configure the BlastP word size and word threshold.

  • New general class DBTag storing a database cross-reference.

  • New pyncbitk.objects.seqdesc module with some sequence description classes.

  • descriptions keyword argument to BioSeq constructor allowing to set the sequence descriptions.

Changed#

  • Make Blast.run copy the current options to avoid race conditions.

  • Bump NCBI C++ Toolkit to v29.6.0.

  • Improve NCBIptb build system integration to support editable installs.

  • Update Docker image with build artifacts.

  • Build wheels in Limited API for Python 3.11 and later.

Fixed#

  • Issue in Blast.run with arbitrary query iterable not setting the query vector.

  • Issue in Blast.run on empty subject vector.

  • Compilation issues with Conan.

  • DatabaseReader.keys() iteration not incrementing the underlying C++ iterator.

  • Recent versions of scikit-build-core-conan not supporting Python 3.8.

v0.1.0-alpha.1 - 2024-12-12#

Initial release.