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CHANGELOG.md

@@ -1,5 +1,41 @@
 # CHANGELOG
 
+## Version 4.0.0 2023-11-30
+
+### Features
+
+- `Configuration` now supports a `rescale_prior` property which rescales the priors in `TemplateBasedExpansionStrategy`.
+- Functionality of `ScorerCollection` has been extended.
+- Pricing is now supported in `InMemoryInchiKeyQuery`.
+- Reward scorer has been added to Configuration scorers as `search_reward` item.
+- `MaxTransformScorerer` and `FractionInStockScorer` have been created to separate scores in `StateScorer`.
+- Reaction routes are scored with all reward scorers after the search is complete.
+- `StockAvailabilityScorer` and `ReactionClassMembershipScorer` have been added to the scorers.
+- Atom mapping existing in target molecule can be inherited.
+- A caching feature has been add to the expansion strategies.
+- Degenerate states can now be grouped in the MCTS algorithm.
+- `ChemformerBasedExpansionStrategy` and `ModelZooExpansionStrategy` can be found under plugins and used as additional expansion strategies.
+- Support for the stereocenter model has been added with to support chiral fingerprints for molecules and reactions.
+- The `Configuration` format has been entirely revamped to a more easy-to-use format.
+- A `MolbloomFilterQuery` has been created as a stock query class.
+
+### Trivial changes
+
+- Python version requirements have been updated to versions 3.9 - 3.11.
+- `MoleculeCost` has been moved from aizynthfinder.context.cost.collection to the Retro* package.
+
+### Deprecations
+
+- Graphviz has been removed from aizynthfinder.utils.image.
+- `Reaction` class has been removed from aizynthfinder.chem.reaction.
+- aizynthfinder.context.cost package has been removed.
+
+### Bug-fixes
+
+- Fixed an issue with `max_transforms` to ensure only the given number of maximum depth is considered.
+- Pinned Jupyter notebook version to ^6.5.3 to avoid errors when displaying widgets.
+- Rollout child has been removed from the MCTS search algorithm.
+
 ## Version 3.7.0 2023-06-01 (2023-04-11)
 
 ### Features
@@ -23,7 +59,7 @@
 
 - Fixing an issue when concatenating JSON data files.
 
-## Version 3.6.0 2022-11-28 (2022-11-25)
+## Version 3.6.0 2022-11-25
 
 ### Features
 
@@ -36,20 +72,35 @@
 - Graphviz dependency for route drawing is removed, pure python implementation is used instead
 - Dependencies reworked so that a minimal package can be installed
 - Extra dependencies are related to route distances, clustering, training, MongoDB and external models
-- Downloaded files are now the latest USPTO and Ringbreaker models
+- (AZ) support for template lookup is removed
 
 ### Trivial changes
 
 - RDKit and route-distances package now installed from pypi
 - Documentation updated and extended
 
-## Version 3.5.0 2022-11-28 (2022-07-21)
+## Version 3.5.2 2022-07-27
+
+### Trivial changes
+
+- Fix dependency for route-distances
+- Update Seldon environment
+
+## Version 3.5.1 2022-07-22
+
+### Bug-fixes
+
+- Fix atom-mapping inheritence for atoms only in reactants
+
+## Version 3.5.0 2022-07-21
 
 ### Features
 
+- All Seldon models now uses version 0.5.0 of aizynthfinder_models (Reaction connect models july 2022)
 - Atom-mapping is tracked from product to reactant
 - Support loading of template library from (gzipped) CSV file
 - Support of saving aizynthcli output to (gzipped) JSON file
+- DeepRetrosynthesis model now returns a field called "mapped_reaction_smiles"
 - AiZynthExpander now tracks non-applicable templates
 
 ### Bug-fixes
@@ -58,37 +109,38 @@
 ### Trival changes
 - Silent progress bar when utilizing local Keras model
 
+
 ## Version 3.4.0 2022-04-28
 
 ### Features
 
+- Deep retrosynthesis Seldon model
 - Gracefully fail predictions with aizynthcli if target is unsanitizable (Github issue 66)
 
 ### Trivial changes
 - Update version of Sphinx, scikit-learn and Black
 - Remove usage of depracted Pandas function append (Github issue 63)
 - Correct documentation of aizynthcli (Github issue 67)
 
-## Version 3.3.1 2022-03-09
-
-### Trivial changes
-
-- Updated pinned versions of route_distances, jinja2 and tensorflow
-
-## Version 3.3.0 2022-02-24
+## Version 3.3.0 2022-02-14
 
 ### 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
 
+### Trivial changes
+
+- Retro* search algorithm moved to public package
+
+## Version 3.2.1 2022-01-17
+
 ### Bugfixes
 
 - RouteCostScorer fix for rare routes
 
-## Version 3.2.0 2022-02-24
+## Version 3.2.0 2022-01-11
 
 ### Features
 
@@ -98,10 +150,12 @@
 - Introduce short aliases for filter policies
 - Reaction shape support in GraphViz visualisation of routes
 
-## Version 3.1.0 2021-12-21
+## Version 3.1.0 2021-11-09
 
 ### Features
 
+- Reaction connect API is updated for version 2.0
+- Filter to remove unreasonable expansions (when the template remove most of the molecule)
 - 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
@@ -118,13 +172,23 @@
 ### Trivial changes
 
 - Update type hints to be compatible with latest numpy release
-- Update route-distances dependency
+
+## Version 3.0.1 2021-08-31
+
+### Trivial changes
+
+- REST and GRPC Tensorflow clients now using named input vectors when provided 
+
+### Bugfixes
+
+- Correct input vectors provided to REST and GRPC tensorflow clients for filter policy
 
 ## Version 3.0.0  2021-07-26
 
 ### Features
 
 - Generalized expansion and filter policies - policies no longer need to be Keras models
+- ReactionConnect-based expansion policy and stock query
 - 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
@@ -141,7 +205,6 @@
 
 - Removed MCTS-specific routines in the TreeAnalysis class
 - Removed code for identifying cycles in ReactionTree
-- Remove JSON interface to AiZynthFinder class
 
 ### Bugfixes
 
@@ -152,7 +215,7 @@
 - Documentation updates
 - Extensive re-factoring of test cases
 
-## Version 2.6.0 - 2021-06-11 (2021-05-03)
+## Version 2.6.0 - 2021-05-03
 
 ### Features
 
@@ -161,12 +224,17 @@
 - Route distance calculations with ML model is now supported
 - Reaction tree objects now has property `is_branched`
 
+### Trivial changes
 
-## Version 2.5.0 - 2021-06-11 (2021-03-30)
+- `scikit-learn` is now imported before `tensorflow`, according to Github issue 30
+
+## Version 2.5.0 - 2021-03-30
 
 ### Features
 
 - Introduce an interface for search algorithm working on AND/OR trees
+- Add a reference implementation of the Retro* algorithm in the az sub-package
+- Improved AiZynthExpander model to group predictions with the same precursors
 - The progress bar is now removed upon completion of the tree search
 - Move `ReactionTree` class to a new module (this will not brake backwards compatibility)
 
@@ -176,10 +244,9 @@
 
 ### Trivial changes
 
-- `scikit-learn` is now imported before `tensorflow`, according to Github issue 30
-
-## Version 2.4.0 - 2021-02-22 (2021-02-22)
+- Use pylint as the code linter
 
+## Version 2.4.0 - 2021-02-22
 
 ### Features
 
@@ -192,45 +259,67 @@
 - Update of black version causing some re-formatting
 - Small changes to documentation
 
-## Version 2.3.0 - 2021-02-22 (2021-01-20)
+## Version 2.3.0 - 2021-01-20
 
 ### Features
 
 - Add option to timeout distance calculation of route collections
-
-## Version 2.2.1 - 2020-12-18
+- Add option to perform clustering in Seldon AiZynthFinder model
+- Add new Seldon model AiZynthExpander encapsulating expansion policies
 
 ### Bugfixes
 
-- Include templates for producing routes in package
+- Jinja templates are now packaged with the python package
+
+## Version 2.2.1 - 2020-12-01
 
-## Version 2.2.0 - 2020-12-14 (2020-11-23)
+### Bug fixes
+
+- Fix price and amount function in AiZynth MongoDB stock query
+
+### Trivial changes
+
+- Introduce caching of fingerprints in template info class
+
+## Version 2.2.0 - 2020-11-23
 
 ### Features
 
 - Add support for clustering of routes
 - Add new scorers for total price and route score
 - Add support for adding stop criteria to all stocks
 - Add stop criteria UI for Jupyter notebook
+- Enable the applicability filtered-expansion model in Seldon model
+- Improved memory management for template look-up
 
 ### Trivial changes
 
 - Refactor handling of MongoDB instances
 - Refactor code to connect with REST and gRPC servers
+- Refactor AiZynth buyables query class
 
 
-## Version 2.1.0 - 2020-12-07 (2020-11-03)
+## Version 2.1.1 - 2020-11-08
+
+### Bugfixes
+
+- Matching names of policies and scorers in Seldon model
+
+## Version 2.1.0 - 2020-11-03
 
 ### Features
 
 - Possibility to extract a combined tree for all predicted routes
 - New classes to use Tensorflow servers as policies
+- Add an internal stock query class to use on the AiZynth platform
+- Enable use of the tool as a Seldon server
 
 ### Trivial changes
 
+- Reduced memory consumption for average product similarity scorer
 - Improved code for route visualizaition
 
-## Version 2.0.0 - 2020-11-24 (2020-09-29)
+## Version 2.0.0 - 2020-09-29
 
 ### Breaking changes
 
@@ -252,32 +341,35 @@
 - Catch exceptions from RDChiral more gracefully
 
 
-## Version 1.2.0 - 2020-11-24 (2020-09-04)
+## Version 1.2.0 - 2020-09-04
 
 ### Features
 
 - Add score "number of pre-cursors"
 - Add score "number of pre-cursors in stock"
+- Add a stock query to use the AiZynth Buyable API
 - Enable the loading of MCTS configuration from dict
 
 ### Bugfixes
 
 - Fix bug in State score for branched reaction trees
 - Fix bug in "Number of reaction" score for branched MCTS trees
+- Fix bug in "Average template occurence" score for trees with no reactions
 - Fix bug in Jupyter GUI when selecting policies of several available
 
 ### Trivial changes
 
 - Update python requirement specifications
 
-## Version 1.1.0 - 2020-11-24 (2020-06-30)
+## Version 1.1.0 - 2020-06-30
 
 ### Features
 
 - Introduce a route scoring framework
 - Flag repetetive patterns in routes so they can be hidden
 - Enable possibility to use more than one rollout policy
 - Add --nproc argument to aizynthcli to enable trivial multiprocessing
+- Add tool to download publicly released data
 
 ### Bugfixes
 
@@ -287,6 +379,58 @@
 
 - Add consistency check between rollout neural network and template list
 
-## Version 1.0.0 - 2020-06-11
+## Version 1.0.0 - 2020-06-01
+
+### Breaking changes
+
+- The tree search algorithm now breaks down any target molecule in stock by default
+
+### Features
+
+- Add option to break down target molecules that are in stock
+- Add a GUI extension and API to lookup reactions in Reaxys and Pistachio
+- Metadata is added to reactions and to the output
+
+### Bugfixes
+
+- Fix issue with tree search when all children are rejected 
+
+### Trivial changes
+
+- Improved documentation
+- Improved test coverage
+- Interface to graphviz is entirely within the package, not with third-party library
+
+## Version 0.3.0 - 2020-04-14
+
+### Features
+
+- Add tools to train rollout policy model
+- Add tools to create stock from SMILES
+- Introduced the RouteCollection class for easy analysis of routes
+- Introduced possibility to use external Keras model
+
+### Bugfixes
+
+- Fix recreation of reaction tree from dict for certain types of routes
+
+
+## Version 0.2.0 - 2020-03-16
+
+### Features
+
+- Moved internal tree search classes to aizynthfinder.mcts package
+- Removed concept of runaway nodes, now exhaustively look through all actions
+- Add auto-selecting of stocks and policy in aizynthcli tool
+- Add support for custom stock class in aizynthcli tool
+- Add support for MongoDB stock lookup
+
+### Bugfixes
+
+- Fix cut-off of predictions in Policy class based on threshold and minimum number
+
+## Version 0.1.0 - 2020-02-18
 
-- First public version
+- Re-factored codebase
+- Provide route visualization in Jupyter Notebooks
+- Provide command to run predictions in batch