Releases | Open Source Science

spyrmsd - v0.9.0

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]

- Python
Published by RMeli 10 months ago

spyrmsd - 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]

- Python
Published by RMeli almost 2 years ago

spyrmsd - 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]

- Python
Published by RMeli almost 2 years ago

spyrmsd - 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]

- Python
Published by RMeli over 2 years ago

spyrmsd - 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]

- Python
Published by RMeli about 4 years ago

spyrmsd - 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]

- Python
Published by RMeli over 4 years ago

spyrmsd - 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]