syntheseus 0.4.0

This release largely simplifies the interaction between reaction prediction and search, merging the duplicated abstractions. It also significantly improves docs and tutorials, and integrates a new Graph2Edits model class.

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])