Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

v0.5.0 – 2024-11-06

Authors

Added

  • General linear fit target and example (PR #131)

  • Support for multiple molecules (PR #137, Issue #136)

Changed

  • Removed unused, undocumented code paths, and updated docs (PR #132)

Fixed

  • Fixed molecule normalization issues (Issue #119, PR #149)

  • Check lookup tables for allowed molecules before ChemicalDomain for forbidden ones (PR #145, Issue #144)

  • Add support for single atoms (PR #146, Issue #138)

  • Fixed optionality for PostProcessLayers (PR #156, Issue #155)

v0.4.0 – 2024-07-18

This version adds support for lookup tables.

Authors

Added

  • Added lookup table support (openff.nagl.lookups.AtomPropertiesLookupTable) (PR #122, #129)

  • Pins to DGL for compatibility (PR #117)

v0.3.8 – 2024-04-11

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

Authors

What’s Changed

  • Switch to plain importlib (PR #109)

  • Add unprocessed methods(PR #111)

  • Remove dgl config (PR #110)

  • Make pyarrow optional (PR #113)

  • Remove rich library (PR #115)

v0.3.7 – 2024-04-05

Authors

Fixed

  • Refactored resonance enumeration to avoid generating whole molecules with itertools.product where possible (PR #102, Issue #101)

  • Refactored NXMolGraph.in_edges to use np.where to speed code up (PR #102, Issue #101)

  • Removed Binder tooling (PR #99)

v0.3.6 – 2024-03-22

Authors

Fixed

  • Fixed typing of conformer generation from RDKit (PR #97)

v0.3.5 – 2024-03-21

Authors

Fixed

  • Fixes to docs and examples (Issue #92, PR #73)

v0.3.4 – 2024-02-15

Authors

Fixed

  • Fixed CUDA launch error (Issue #81, PR #83)

  • Updated versioneer (PR #86)

  • Fixed batch distribution hardcoding (Issue #80, PR #82)

  • Fixed node and edge typing, adding DGL 2.0 compatibility (Issue #78, PR #79)

v0.3.3 - 2023-12-22

Authors

Fixed

  • Fixed OpenFF molecule conversion with toolkit wrappers (Issue #69, PR #71)

  • Bug report templates

v0.3.2 - 2023-10-26

Authors

Changed

  • Added documentation link in README (PR #66, Issue #63)

  • Removed capture_toolkit_warnings usage in Molecule creation as OpenFF Toolkit v0.14.4 no longer needs it, and removed warnings filter from method (PR #65, Issue #64)

v0.3.1 - 2023-09-08

Authors

Changed

  • Guarded openff.toolkit imports (PR #61, Issue #56)

v0.3.0 - 2023-08-29

Authors

Reviewers

Added

  • Codecov coverage (PR #43)

  • Multiple target objectives and configuratin files (PR #45)

  • Support for pydantic v2 (PR #46)

  • Added ChemicalDomain and model versioning (PR #54)

Fixed

  • pytest runs (PR #44)

  • documentation badge and links (PR #51, #52)

Changed

  • Major refactor to move to using Arrow databases (PR #45, PR #48)

  • Removed importing OFFMolecule in favour of Molecule (PR #50, Issue #13)

Removed

  • Old _app and _cli utilities that were not well tested are not supported in refactor (PR #49)

v0.2.3 - 2023-07-05

Authors

Reviewers

Added

  • Link to OpenFF install guide (PR #37)

Fixed

  • Versioneer version prefix (PR #42)

Changed

  • Update examples for central examples page (PR #40)

v0.2.2 - 2023-03-29

Authors

Reviewers

Added

  • GNNModel.load (PR #26)

  • GNNModel.save function (PR #29)

  • General documentation (PR #21, PR #33)

  • Documentation of creation of custom features (PR #36)

Fixed

  • Fix edge ordering in NXMol graph (Issue #28, PR #34)

Changed

  • Migrate away from pkg_resources to importlib_resources (PR #35)

  • Expose base classes and hide metaclasses (PR #32)

  • Update examples for central examples page (PR #40)

v0.2.1 - 2023-03-02

Authors

Reviewers

Added

  • GNNModel.load function (PR #26)

  • convolution_dropout and readout_dropout keywords to GNNModel (PR #26)

Fixed

  • Versioneer __version__ string (PR #25)

v0.2.0 - 2023-02-05

Authors

Added

  • New toolkit wrappers (PR #14, PR #16)

Fixed

Changed

  • Refactored code so DGL is not required for install or model inference (PR #23)

Deprecated

Removed