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spyrmsd CHANGELOG

Version 0.Y.Z

Date: DD/MM/YYYY Contributors: @RMeli

Added

  • Python 3.13 and 3.14 in CI [PR #147 | @RMeli]
  • Optional dependencies for testing (test), development (dev), and parallelization (parallel) in pyproject.toml [PR #152 | @copilot]

Changed

  • Migrated all package configuration from setup.cfg and setup.py to pyproject.toml [PR #XXX | @RMeli]
  • Workflows to use pip install -e . instead of python setup.py develop [PR #XXX | @RMeli]

Removed

  • support for Open Babel [PR #151 | @RMeli]
  • Python 3.9 and 3.10 from CI [PR #147 | @RMeli]
  • setup.cfg file in favour of pyproject.toml [PR #XXX | @RMeli]
  • setup.py file in favour of pyproject.toml [PR #XXX | @RMeli]
  • .coveragerc file in favour of pyproject.toml [PR #XXX | @RMeli]

Version 0.9.0

Date: 07/05/2025 Contributors: @RMeli, @Jnelen, @frgoe003

Added

  • --version CLI option [PR #131 | @RMeli]
  • prmsdwrapper, a first implementation of a multicore version of rmsdwrapper. It also supports a timeout functionality. [PR #113 | @Jnelen]
  • return_best_isomorphism option for symmrmsd calculation [PR #143 | @frgoe003]

Version 0.8.0

Date: 28/05/2024 Contributors: @RMeli

Added

  • Warnings filter for tests of multiple backends [PR #118 | @RMeli]
  • Parametrized fixture to run tests with all available backends [PR #118 | @RMeli]

Improved

  • Test IDs [PR #117 | @RMeli]

Changed

  • the default backend for pip installations to rustworkx [PR#122 | @RMeli]
  • pre-commit versions [PR #120 | @RMeli]
  • Versions of several GitHub Actions [PR #120 | @RMeli]
  • Location of backend tests to standalone file [PR #118 | @RMeli]

Removed

  • Many CI configurations in favour of running tests for all available backends [PR #118 | @RMeli]
  • tests/molecule.py in favour of fixtures [PR #118 | @RMeli]

Version 0.7.0

Date: 05/04/2024 Contributors: @RMeli, @takluyver, @Jnelen

Added

  • Support for rustworkx graph library [PR #111 | @RMeli]
  • Functionality to manually select the backend from CLI [PR #108 | @RMeli]
  • Functionality to manually select the backend [PR #107 | @Jnelen]
  • Python 3.12 to CI [PR #102 | @RMeli]
  • macOS M1 (macoOS-14) to CI [PR #102 | @RMeli]

Changed

  • Molecular graphs cache to cache by backend [PR #107 | @Jnelen]
  • Python build system to use flit_core directly [PR #103 | @takluyver]
  • Minimum version of Python to 3.9 (to reduce CI matrix) [PR #102 | @RMeli]

Fixed

  • Failing tests with pytest=8.0.0 [PR #101 | @RMeli]

Improved

  • Messages for NotImplementedError exceptions [PR #90 | @RMeli]

Removed

  • .gitattributes and .lgtm.yaml stale files
  • versioneer [PR #91 | @RMeli]

Version 0.6.0

Date: 08/09/2023 Contributors: @RMeli

Improved

  • Documentation on loading RDKit and Open Babel molecules [PR #77 | @RMeli]

Changed

  • Versions of pre-commit hooks tools [PR #85 | @RMeli]
  • Version of several GitHub actions [PR #76 | @RMeli]
  • Versioneer to 0.28 [PR #76 | @RMeli]
  • Minimum Python version to 3.7 to match CI [PR #76 | @RMeli]
  • Code according to black==23.3.0 [PR #76 | @RMeli]

Added

  • pre-commit CI action [PR #85 | @RMeli]
  • extras_require to setup.py for RDKit and Open Babel [PR #84 | @RMeli]
  • Error message when spyrmsd is used as module but neither OpenBabel nor RDKit are installed [PR #81 | @RMeli]
  • Pin to sphinx<7 to avoid compatibility with RTD theme [PR #77 | @RMeli]

Removed

  • ubuntu-latest-3.7-rdkit-gt configuration from CI due to continuous failures [PR #84 | @RMeli]
  • Outdated information about RDKit from the documentation [PR #84 | @RMeli]
  • Support for Open Babel 2 [PR #84 | @RMeli]
  • LGTM badge and code annotations [PR #76 | @RMeli]

Version 0.5.2

Date: 23/02/2022 Contributors: @RMeli

Fixed

  • Inconsistent number of nodes with graph-tool for disconnected graphs [PR #61 | @RMeli]

Improved

  • Support for more types of node properties (including strings) with graph-tool [PR #64 | @RMeli]

Changed

  • ValueError exception into NonIsomorphicGraphs(ValueError) exception [PR #65 | @RMeli]

Added

  • Warning for disconnected graphs [PR #61| @RMeli]

Version 0.5.1

Date: 21/09/2021 Contributors: @RMeli

Fixed

  • Wrong covalent radius in graph.adjacency_matrix_from_atomic_coordinates() [PR #58 | @RMeli]

Added

  • pre-commit configuration file [PR #57 | @RMeli]
  • Support for gzip-compressed files (.gz) [PR #56 | @RMeli]

Removed

  • Dependency QCElemental [PR #58 | @RMeli]

Version 0.5.0

Date: 21/06/2021

Contributors: @RMeli

Added

  • molecule.Molecule constructor from RDKit molecule [PR #50 | @RMeli]
  • molecule.Molecule constructor from Open Babel molecule [PR #50 | @RMeli]
  • --n-tests option for pytest [PR #44 | @RMeli]

Improved

  • spyrmsd.rmsdwrapper to deal with single molecule [PR #51 | @RMeli]
  • Issue template [PR #46 | @RMeli]
  • Speed of computation of squared pairwise distances [PR #45 | @RMeli]

Changed

  • spyrmsd standalone tool now invoked with python -m spyrmsd -h [PR #52 | @RMeli]
  • Moved spyrmsd.coords_from_molecule to molecule module [PR #52 | @RMeli]
  • Moved spyrmsd.rmsdwrapper to rmsd module [PR #52 | @RMeli]
  • Long tests no longer run in CI [PR #44 | @RMeli]

Removed

  • spyrmsd module [PR #52 | @RMeli]
  • Travis CI and AppVeyor bindings [PR #44 | @RMeli]
  • --long option for pytest [PR #44 | @RMeli]