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#

v0.3.2 - 2024-11-05#

Added#

  • Support for Python 3.13.

Changed#

  • Use scikit-build-core to build the project.

  • Use CMake to detect availability of qsort_r / qsort_s on the current platform.

  • Use thread-local storage to support parallelism on platforms without qsort_r.

Removed#

  • Support for Python 3.6.

v0.3.1 - 2024-07-18#

Changed#

  • Migrate documentation to pydata-sphinx-theme.

  • Make Hit.evalue and Hit.log_evalue release the GIL when possible.

Fixed#

  • Signatures of __init__ methods missing from all Cython types after the v3.0 update.

v0.3.0 - 2024-06-11#

Added#

  • Slicing for Template, Molecule and Jess objects.

Fixed#

  • Typing for chain_id property of TemplateAtom.

  • Query.__next__ ignores and raises a warning on NaN matrices caused by planar molecule coordinates.

Changed#

  • Make Jess generic over the internal template class to allow Template subclasses as inputs and Hit outputs attribute.

  • Make Molecule.conserved return an instance of the caller class rather than a Molecule object.

v0.2.1 - 2024-05-30#

Fixed#

  • Type hints for Molecule.load and Template.load not marked as accepting paths.

  • Thread-unsafe use of qsort in Jess code, replaced with qsort_r or qsort_s to allow multithreading.

v0.2.0 - 2024-05-24#

Added#

  • best_match argument to Jess.query to only return the best match to each template for a query molecule.

  • id argument to Molecule.load and Molecule.loads to allow overriding the PDB ID stored in the file.

  • ignore_endmdl argument to Molecule.load and Molecule.loads to control whether the parser should stop at the first model in a file.

Changed#

  • Make Molecule.load stop at the first model when parsing a PDB file.

Fixed#

  • Invalid pointer assignments in TessAtom.c causing compilation errors on stricter compilers.

v0.1.1 - 2024-04-18#

Added#

  • Support for passing filenames to Template.load and Molecule.load directly.

  • Default initialization of empty Jess objects from an empty iterable.

  • Make Jess implement the Sized abstract base class interface.

Changed#

  • Skip displaying default attribute values in repr implementation of Atom and TemplateAtom.

  • Make Jess.query optional parameters keyword-only.

v0.1.0 - 2024-04-18#

Initial release.