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CHANGELOG.md

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Changelog

All notable changes to the project are documented in this file.

The format follows Common Changelog, and the project adheres to Semantic Versioning.

Unreleased

0.4.1 - 2024-01-03

Changed

  • Relax protobuf version requirement (#62)

Fixed

  • Fix hydrogen handling in scaffolds with explicit attachment points (#70)
  • Avoid memory leaks and other tensorflow issues (#68)

0.4.0 - 2023-06-16

Added

  • Add an option for decode to return the entire generation trace (#51)

Changed

  • Reformat with black==23.1.0 and pin it in CI to avoid further unexpected updates (#50)

Fixed

  • Remove deprecated numpy types to make molecule_generation work with numpy>=1.24.0 (#49)
  • Patch GetSSSR for compatibility with rdkit>=2022.09.1 (#58)

0.3.0 - 2022-10-18

Added

  • Add support for fine-tuning a pretrained model on new data (#30)
  • Add a __version__ attribute to make the package version easily accessible at runtime (#35)

Changed

  • Drop the exact version requirements for python and tensorflow to support entire ranges of versions (#35)

Removed

  • Drop unused GraphMultitaskModel which ended up in the open-source release by accident (#34)

Fixed

  • Make the inference server check the status of child processes every 10 seconds, so that it can exit gracefully in case of errors instead of hanging (#33)

0.2.0 - 2022-07-01

Added

  • Add MoLeRGenerator, which uses the MoLeR decoder (without the encoder) as an autoregressive policy (#6)
  • Add load_model_from_directory, which can load any model by automatically picking the right wrapper class (#24)
  • Implement an option for encode to return not only the mean latent code but also the variance (#26)

Changed

  • Improve how the MoLeR visualisers handle node selection steps (#10)
  • Refactor how MoLeR keeps track of generation steps during decoding and include partial molecules in the step info classes (#27)

Fixed

  • Fix one-off errors in the latent-based visualisation mode (#10)
  • Constrain protobuf version to avoid pulling in a breaking release (#25)

0.1.0 - 2022-04-11

🌱 First public release, matching what was used for the original paper.

Added

  • Add full implementation of MoLeR as introduced in the paper
  • Add reference implementation of CGVAE, not yet supported by the high-level model API