openff-nagl - v0.5.3

This patch release of openff-nagl works around a bug/behavior change in OpenEye Toolkits 2025.1.1/OEChem 4.2.

What's Changed

• Constrain torchdata<=0.10.0 by @mattwthompson in https://github.com/openforcefield/openff-nagl/pull/189
• Use new runner actions by @mattwthompson in https://github.com/openforcefield/openff-nagl/pull/196
• Drop testing on Python 3.10 by @mattwthompson in https://github.com/openforcefield/openff-nagl/pull/197
• Update a test for large InChI support by @mattwthompson in https://github.com/openforcefield/openff-nagl/pull/200
• Bump omsf/start-aws-gha-runner from 1.0.0 to 1.1.0 by @dependabot[bot] in https://github.com/openforcefield/openff-nagl/pull/204
• Bump actions/checkout from 4 to 5 by @dependabot[bot] in https://github.com/openforcefield/openff-nagl/pull/208
• Fix aromaticity? perception? changes? in OpenEye 2025.1.1 by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/210

New Contributors

• @dependabot[bot] made their first contribution in https://github.com/openforcefield/openff-nagl/pull/204

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.5.2...v0.5.3

- Python
Published by j-wags 7 months ago

openff-nagl - Version 0.5.2

This patch release of NAGL fixes an incompatibility with PyTorch 2.6+ where the default arguments for loading a model were changed. In addition, some developer-facing tooling was added.

What's Changed

• Add GPU-enabled CI by @mattwthompson in https://github.com/openforcefield/openff-nagl/pull/170
• add weights_only=False by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/183
• Add release notes for v0.5.2 by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/185

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.5.1...v0.5.2

- Python
Published by lilyminium about 1 year ago

openff-nagl - 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 https://github.com/openforcefield/openff-nagl/pull/162
• Add patch for long inchis by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/165
• Switch back to using pyproject.toml to build by @mattwthompson in https://github.com/openforcefield/openff-nagl/pull/169
• Update RTD config by @mattwthompson in https://github.com/openforcefield/openff-nagl/pull/172
• Update/fix docs builds by @mattwthompson in https://github.com/openforcefield/openff-nagl/pull/176
• Finalize 0.5.1 release notes by @mattwthompson in https://github.com/openforcefield/openff-nagl/pull/175

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.5.0...v0.5.1

- Python
Published by mattwthompson about 1 year ago

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

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.4.0...v0.5.0

- Python
Published by lilyminium over 1 year ago

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

New Contributors

• @j-wags made their first contribution in https://github.com/openforcefield/openff-nagl/pull/117

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.3.8...v0.4.0

- Python
Published by lilyminium over 1 year ago

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

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.3.7...v0.3.8

- Python
Published by lilyminium almost 2 years ago

openff-nagl - 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 https://github.com/openforcefield/openff-nagl/pull/99
• Add tests and clean things up by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/100
• Improve explosions in memory and time during inference by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/102
• update changelog for v0.3.7 by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/104

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.3.6...v0.3.7

- Python
Published by lilyminium almost 2 years ago

openff-nagl - 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 https://github.com/openforcefield/openff-nagl/pull/97

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.3.5...v0.3.6

- Python
Published by lilyminium almost 2 years ago

openff-nagl - Version 0.3.5

This patch release adds fixes to documentation.

What's Changed

• Fixes to docs and an example by @Yoshanuikabundi in https://github.com/openforcefield/openff-nagl/pull/73
• Remove exclusion of dgl with py3.12, and move python info step by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/94
• Add examples CI by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/93
• Update changelog with current commits by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/95

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.3.4...v0.3.5

- Python
Published by lilyminium almost 2 years ago

openff-nagl - 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 https://github.com/openforcefield/openff-nagl/pull/77
• Fix typing for DGL 2.0 by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/79
• Fix batch distribution for other worker types by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/82
• Update versioneer by @mattwthompson in https://github.com/openforcefield/openff-nagl/pull/86
• Add 3.12 to test matrix by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/87
• Add nightly builds by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/88
• Add back 3.9 support by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/89
• Fix CUDA launch error by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/83
• Update changelog with current commits by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/90

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.3.3...v0.3.4

- Python
Published by lilyminium almost 2 years ago

openff-nagl - 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 https://github.com/openforcefield/openff-nagl/pull/70
• Add install from source instructions by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/72
• Fixes openeye/rdkit conversion by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/71
• Remove binder links from docs by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/74
• Update changelog for 0.3.3 by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/75
• add Irfan to changelog by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/76

New Contributors

• @IAlibay made their first contribution in https://github.com/openforcefield/openff-nagl/pull/70

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.3.2...v0.3.3

- Python
Published by lilyminium about 2 years ago

openff-nagl - 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 https://github.com/openforcefield/openff-nagl/pull/65
• Update README.md by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/66
• Update CHANGELOG for v0.3.2 by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/68

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.3.1...v0.3.2

- Python
Published by lilyminium over 2 years ago

openff-nagl - Version 0.3.1

This version is a minor update that removes all top-level OpenFF toolkit imports to avoid recursion errors when adding NAGL to the toolkit GLOBALTOOLKITREGISTRY.

What's Changed

• Install dgl from conda-forge by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/55
• Guard toolkit imports by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/61
• update changelog for v0.3.1 by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/62

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.3.0...v0.3.1

- Python
Published by lilyminium over 2 years ago

openff-nagl - v0.3.0

What's Changed

• Update codecov action version by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/43
• Pin pydantic < 2.0 by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/41
• Run pytest as a module by @mattwthompson in https://github.com/openforcefield/openff-nagl/pull/44
• Refactor to use arrow by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/45
• Pydantic v1 and v2 compatibility by @mattwthompson in https://github.com/openforcefield/openff-nagl/pull/46
• update changelog by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/47
• Rename targets to align with labels by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/48
• Remove unused, old, or redundant code by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/49
• Remove offmolecule and uncomment test by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/50
• Fix doc badge by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/51
• Fix examples env and links by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/52
• Add domains, versioning, and tests by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/54

New Contributors

• @mattwthompson made their first contribution in https://github.com/openforcefield/openff-nagl/pull/44

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.2.3...v0.3.0

- Python
Published by lilyminium over 2 years ago

openff-nagl - Version 0.3.0, release candidate 1

This is a major release with API breaks from version 0.2.x. This release introduces: * creation of GNNModels and the training set up (TrainingGNNModel, DataConfig, OptimizerConfig) from configuration classes that can be read from YAML * more specific creation that requires each layer to be specified fully * multiple-objective losses, with pre-defined targets for charge RMSE, dipole moments, and ESPs * metric options, e.g. RMSE, MAE * lazy loading of data for data that's too large to fit into memory * library-agnostic data in the form of Arrow datasets * additional labelling functions to create Arrow datasets

What's Changed

• Update codecov action version by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/43
• Pin pydantic < 2.0 by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/41
• Run pytest as a module by @mattwthompson in https://github.com/openforcefield/openff-nagl/pull/44
• Refactor to use arrow by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/45
• Pydantic v1 and v2 compatibility by @mattwthompson in https://github.com/openforcefield/openff-nagl/pull/46
• update changelog by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/47
• Rename targets to align with labels by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/48
• Remove unused, old, or redundant code by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/49
• Remove offmolecule and uncomment test by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/50
• Fix doc badge by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/51
• Fix examples env and links by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/52

New Contributors

• @mattwthompson made their first contribution in https://github.com/openforcefield/openff-nagl/pull/44

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.2.3...v0.3.0rc1

- Python
Published by lilyminium over 2 years ago

openff-nagl - Version 0.2.3

This is a minor update of 0.2.2 with additional documentation and fixing Versioneer.

What's Changed

• Add link to OpenFF install guide by @Yoshanuikabundi in https://github.com/openforcefield/openff-nagl/pull/37
• Prepare notebooks for central examples by @Yoshanuikabundi in https://github.com/openforcefield/openff-nagl/pull/40
• remove quotes from prefix by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/42

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.2.2...v0.2.3

- Python
Published by lilyminium over 2 years ago

openff-nagl - Version 0.2.2

Warning: This is working scientific code that is not production-ready. The API is unstable and likely to change in the future.

This release fixes a bug from v0.2.1 where different architectures gave different results in model inference. It also adds documentation and save/load functions.

What's Changed

• Fix versioneer prefix by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/25
• Expand GNNModel arguments and add load function by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/26
• Fix warnings showing up in inference by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/27
• Add save function to GNNModel by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/29
• More docstrings! by @Yoshanuikabundi in https://github.com/openforcefield/openff-nagl/pull/33
• Expose base classes and hide metaclasses by @Yoshanuikabundi in https://github.com/openforcefield/openff-nagl/pull/32
• Fix edge ordering by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/34
• Migrate from pkgresources to importlibresources by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/35
• New NAGL docs take 2 by @Yoshanuikabundi in https://github.com/openforcefield/openff-nagl/pull/21
• Document creation of custom features by @Yoshanuikabundi in https://github.com/openforcefield/openff-nagl/pull/36

New Contributors

• @Yoshanuikabundi made their first contribution in https://github.com/openforcefield/openff-nagl/pull/33

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.2.0...v0.2.2

- Python
Published by lilyminium almost 3 years ago

openff-nagl - Version 0.2.1

This is a patch release version for 0.2.1.

What's Changed

• Fix versioneer prefix by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/25
• Expand GNNModel arguments and add load function by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/26
• Fix warnings showing up in inference by @lilyminium in https://github.com/openforcefield/openff-nagl/pull/27

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.2.0...v0.2.1

- Python
Published by lilyminium about 3 years ago

openff-nagl - v0.2.0

What's Changed

• Minor bug fixes
• Non-user-facing modules made private
• Refactored so that DGL is not necessary for model inference

Warning: This is working scientific code that is not production-ready. The API is unstable and likely to change in the future.

Full Changelog: https://github.com/openforcefield/openff-nagl/compare/v0.1.0...v0.2.0

- Python
Published by lilyminium about 3 years ago

openff-nagl - v0.2.0-alpha.1

Changes: - adds some client utilities - adds some unit tests - adds a GIN structure

Warning: This is working scientific code that is not production-ready. The API is unstable and likely to change in the future.

Full Changelog: https://github.com/openforcefield/openff-nagl/commits/v0.2.0-alpha.1

- Python
Published by lilyminium about 3 years ago