Aizynthfinder

Trivial changes

- Updated pinned versions of route_distances, jinja2 and tensorflow

Features

- Support for Retro* tree search
- Support for breadth-first exhaustive tree search
- Support for depth-first proof-number tree search
- Possible to save concatenated reaction trees to separate file

Bugfixes

- RouteCostScorer fix for rare routes

Features

- Profiling feature enabled in search trees
- New, customizable configuration of training pre-processing tools
- Generic post-processing support in aizynthcli
- Introduce short aliases for filter policies
- Reaction shape support in GraphViz visualisation of routes

Features

- ReactantsCountFiler (Github issue 42) to filter reactions with incompatible number of reactants
- ForwardRegenerationFiler to filter reactions where the forward reaction is incompatible
- Possible to skip quick Keras filter for specific policies
- Possible to select more than one policy in the GUI application
- Reaction classes has a hash function
- Possible to extract sub trees from ReactionTree objects
- RDKit can be used instead of RDChiral for expansions

Bugfixes

- Possible to use more than depth 6 in the GUI application
- Fix failure in MctsNode class when expansion policy return no molecules

Trivial changes

- Update type hints to be compatible with latest numpy release
- Update route-distances dependency

Features

- Generalized expansion and filter policies - policies no longer need to be Keras models
- Updated image generation for synthesis routes
- Improved code to prune "regeneration reactions" in MCTS (Github issue 38)
- Reactants are sorted in output from ReactionTree class
- New arguments to the "aizynthcli" tool
- Introduce option to return all solved routes from a TreeAnalysis class

Breaking changes

- Package structure re-factorization
- Behaviour of RetroReaction, FilterPolicy and ExpansionPolicy classes has been changed
- Configuration class holding search tree settings is no longer loading settings from yaml-file on instantiation

Deprecations

- Removed MCTS-specific routines in the TreeAnalysis class
- Removed code for identifying cycles in ReactionTree
- Remove JSON interface to AiZynthFinder class

Bugfixes

- Fixed property assignment when converting MCTS node to ReactionTree

Trivial changes

- Documentation updates
- Extensive re-factoring of test cases

Features

- Add `AiZynthExpander` class as public interface to single-step reactions
- Route distance calculations and clustering is now dependent on package `route-distances`
- Route distance calculations with ML model is now supported
- Reaction tree objects now has property `is_branched`