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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

Changed

Fixed

0.5.0 - 2024-11-28

Changed

Added

  • Reuse search results when given a partially filled directory (#98) (@kmaziarz)
  • Expose stop_on_first_solution as a CLI flag (#100) (@kmaziarz)
  • Add an option to set time limit for route extraction (#104) (@kmaziarz)
  • Extend single-step evaluation with stereo-agnostic results (#102) (@kmaziarz)

Fixed

  • Install torch_scatter from conda instead of pip (#110) (@kmaziarz)
  • Remove dependency on typing_extensions for Python 3.8+ (#107) (@austint)
  • Pin further Chemformer dependencies to avoid torch reinstallation (#108) (@kmaziarz)
  • Shift the pandas dependency to the external model packages (#94) (@kmaziarz)
  • Fix constructor arguments in ParallelReactionModel (#96) (@kmaziarz)

0.4.1 - 2024-05-04

Fixed

  • Fix incorrectly uploaded RetroKNN weights (#91) (@kmaziarz)
  • Fix GLN weights and issues in its model wrapper (#92) (@kmaziarz)

0.4.0 - 2024-04-10

Changed

  • Merge reaction and reaction model base classes in search and reaction_prediction (#63, #67, #73, #74, #76, #84) (@austint, @kmaziarz)
  • Make reaction models return Sequence[Reaction] instead of PredictionList objects (#61) (@austint)
  • Suppress the remaining noisy logs and warnings coming from single-step models (#53) (@kmaziarz)
  • Improve efficiency and logging of retro* algorithm (#62) (@austint)
  • Improve error handling in single-step evaluation and allow CLI to use the default checkpoints (#75) (@kmaziarz)
  • Make basic classes from interface importable from top-level (#81) (@austint)

Added

  • Integrate the Graph2Edits model (#65, #66) (@kmaziarz)
  • Improve the docs and add tutorials (#54, #77, #78, #79, #82) (@kmaziarz, @austint)
  • Add random search algorithm as a simple baseline (#83) (@austint)
  • Add optional argument limit_graph_nodes to base search algorithm class to stop search after the search graph exceeds a certain number of nodes (#85) (@austint)

Fixed

  • Fix small issues in Chemformer, MEGAN and RootAligned (#80) (@kmaziarz)
  • Get all single-step models to work on CPU (#57) (@kmaziarz)
  • Make the data loader class work with relative paths (#69) (@kmaziarz)

0.3.0 - 2023-12-19

Changed

  • Simplify single-step model setup (#41, #48) (@kmaziarz)
  • Refactor single-step evaluation script and move it to cli/ (#43) (@kmaziarz)
  • Return model predictions as dataclasses instead of pydantic models (#47) (@kmaziarz)
  • Make the package compatible with PyPI (#50) (@kmaziarz)

Added

0.2.0 - 2023-11-21

Changed

  • Select search hyperparameters depending on which algorithm and single-step model are used (#30) (@kmaziarz)
  • Improve the heuristic used for estimating diversity (#22, #28) (@kmaziarz)

Added

  • Add code for PDVN MCTS and extracting training data for policies and value functions (#8) (@austint, @fiberleif)
  • Add a top-level CLI for running end-to-end search (#26) (@kmaziarz)
  • Release single-step evaluation framework and wrappers for several model types (#14, #15, #20, #32, #35) (@kmaziarz)
  • Release checkpoints for all supported single-step model types (#21) (@kmaziarz)
  • Support *.csv and *.smi formats for the single-step evaluation data (#33) (@kmaziarz)
  • Implement node evaluators commonly used in MCTS and Retro* (#23, #27) (@kmaziarz)
  • Add option to terminate search when the first solution is found (#13) (@austint)
  • Add code to extract routes in order found instead of by minimum cost (#9) (@austint)
  • Declare support for type checking (#4) (@kmaziarz)
  • Add method to extract precursors from SynthesisGraph objects (#36) (@austint)

Fixed

0.1.0 - 2023-05-25

🌱 Initial public release, containing several multi-step search algorithms and a minimal interface for single-step models.