Version 0.5.1

This new release of NAGL fixes a bug in which charges could not be applied to some large molecules and includes some developer-facing tooling and automation improvements.

What's Changed

• Do not use defaults channel in environments by @mattwthompson in #162
• Add patch for long inchis by @lilyminium in #165
• Switch back to using pyproject.toml to build by @mattwthompson in #169
• Update RTD config by @mattwthompson in #172
• Update/fix docs builds by @mattwthompson in #176
• Finalize 0.5.1 release notes by @mattwthompson in #175

Full Changelog: v0.5.0...v0.5.1

Version 0.5.0

This new release of NAGL adds support for single-atoms and ions, fixes some normalization issues, and swaps the order of validating molecules so that a lookup table is checked before any validation.

Warning: this will change the behaviour of previous models, as previous molecules that would have been broken (e.g. C=[Cl+]) are now found in the lookup table.

What's Changed

• Code cleanup by @lilyminium in #132
• [DNM] Add general linear fit target by @lilyminium in #131
• Update zenodo setup by @mattwthompson in #135
• Add multiple molecule support by @lilyminium in #137
• Fix Pylint check by @lilyminium in #141
• Run examples on Ubuntu only by @lilyminium in #140
• Check lookup tables for values before ChemicalDomains by @lilyminium in #145
• Add ion capabilities by @lilyminium in #146
• Fix nightly tests by @lilyminium in #142
• Fix CI warnings by @lilyminium in #147
• Add base tests by @lilyminium in #150
• Fix normalization by @lilyminium in #149
• Diagnose and fix methane charging by @lilyminium in #153
• Fix optional postprocess layer by @lilyminium in #156
• Update changelog for 0.5.0 by @lilyminium in #157

Full Changelog: v0.4.0...v0.5.0

Version 0.4.0

This version adds lookup tables to GNNModels. This version should be backwards-compatible with previous NAGL models constructed without a lookup table.

What's Changed

• Fix CI by @j-wags in #117
• Add CHANGELOG to rendered docs by @mattwthompson in #116
• Fix dev CI by @lilyminium in #120
• Fix remaining problems in CI by @j-wags in #123
• Add lookup tables by @lilyminium in #122
• Remove Python 3.12 exclusions from CI by @lilyminium in #125
• Unpin RDKit by @mattwthompson in #128
• Update ci versions by @lilyminium in #127
• Add a couple more tests for lookup tables by @lilyminium in #129
• Update changelog for v0.4.0 by @lilyminium in #126

New Contributors

• @j-wags made their first contribution in #117

Full Changelog: v0.3.8...v0.4.0

Version 0.3.8

This version drops pyarrow and rich as core dependencies. It also removes Python 3.9 support.

What's Changed

• Pin snappy<1.2 by @lilyminium in #107
• Revert "Add back 3.9 support" by @mattwthompson in #105
• Switch to plain importlib by @lilyminium in #109
• Add unprocessed methods by @lilyminium in #111
• Remove dgl config by @lilyminium in #110
• Revert "Pin snappy<1.2 (#107)" by @lilyminium in #112
• Make pyarrow optional by @lilyminium in #113
• Update changelog for 0.3.8 by @lilyminium in #114
• Remove rich library by @lilyminium in #115

Full Changelog: v0.3.7...v0.3.8

Version 0.3.7

This version improves performance of inference on larger molecules, both with and without DGL installed.

What's Changed

• Remove Binder tooling by @mattwthompson in #99
• Add tests and clean things up by @lilyminium in #100
• Improve explosions in memory and time during inference by @lilyminium in #102
• update changelog for v0.3.7 by @lilyminium in #104

Full Changelog: v0.3.6...v0.3.7

Version 0.3.6

This patch release fixes a typing error when generating conformers with RDKit.

What's Changed

• Remove oe from examples ci by @lilyminium in #97

Full Changelog: v0.3.5...v0.3.6

Version 0.3.5

This patch release adds fixes to documentation.

What's Changed

• Fixes to docs and an example by @Yoshanuikabundi in #73
• Remove exclusion of dgl with py3.12, and move python info step by @lilyminium in #94
• Add examples CI by @lilyminium in #93
• Update changelog with current commits by @lilyminium in #95

Full Changelog: v0.3.4...v0.3.5

Version 0.3.4

This patch release fixes typing and compatibility with DGL 2.0, as well as adding in support for SLURM workers in batch distribution.

What's Changed

• Start new CHANGELOG past v0.3.3 by @lilyminium in #77
• Fix typing for DGL 2.0 by @lilyminium in #79
• Fix batch distribution for other worker types by @lilyminium in #82
• Update versioneer by @mattwthompson in #86
• Add 3.12 to test matrix by @lilyminium in #87
• Add nightly builds by @lilyminium in #88
• Add back 3.9 support by @lilyminium in #89
• Fix CUDA launch error by @lilyminium in #83
• Update changelog with current commits by @lilyminium in #90

Full Changelog: v0.3.3...v0.3.4

Version 0.3.3

This is a patch release to fix Issue #69, where the OpenEye toolkit was still being called despite not being available.

What's Changed

• Fix bug report template imports by @IAlibay in #70
• Add install from source instructions by @lilyminium in #72
• Fixes openeye/rdkit conversion by @lilyminium in #71
• Remove binder links from docs by @lilyminium in #74
• Update changelog for 0.3.3 by @lilyminium in #75
• add Irfan to changelog by @lilyminium in #76

New Contributors

• @IAlibay made their first contribution in #70

Full Changelog: v0.3.2...v0.3.3

Version 0.3.2

This minor patch version fixes an issue where using NAGL ignored warnings globally (Issue #64), and also turns off warnings capture in general now that the OpenFF toolkit version 0.14.4 no longer generates spurious warnings.

What's Changed

• Remove warnings filter by @lilyminium in #65
• Update README.md by @lilyminium in #66
• Update CHANGELOG for v0.3.2 by @lilyminium in #68

Full Changelog: v0.3.1...v0.3.2