Spyrmsd

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` [PR122 | 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]

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]

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* Outdated information about RDKit from the documentation [PR 84 | RMeli]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]

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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]

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Date: 21/09/2021
Contributors: RMeli

Fixed

* Wrong covalent radius in `graph.adjacency_matrix_from_atomic_coordinates()` [PR 58 | RMeli]

Added

* [pre-commit](https://pre-commit.com/) configuration file [PR #57 | RMeli]
* Support for gzip-compressed files (`.gz`) [PR 56 | RMeli]

Removed

* Dependency `QCElemental` [PR 58 | RMeli]

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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]

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