v0.8.0

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]

v0.7.0

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]

v0.6.0

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• Outdated information about RDKit from the documentation [PR #84 | @RMeli]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]

v0.5.2

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]

v0.5.1

Version 0.5.1

Date: 21/09/2021
Contributors: @RMeli

Fixed

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

Added

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

Removed

• Removed dependency QCElemental [PR #58 | @RMeli]

v0.5.0

Version 0.5.0

Date: 21/06/2021
Contributors: @RMeli

Added

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

Improved

• Improved spyrmsd.rmsdwrapper to deal with single molecule [PR #51 | @RMeli]
• Improved issue template [PR #46 | @RMeli]
• Improved 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

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

0.4.0

Increase robustness of spyrmsd, especially for small systems that can be superimposed perfectly by the QCP method.

0.3.5

spyrmsd: symmetry-corrected RMSD calculations in Python

Duecredit

Added references via duecredit

CI Fixes

Fix CI after changes in conda URL.