Prepare release v.0.0.2

Changelog v0.0.2

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Highlights

New Features & Enhancements

Moving Source Code from SynUtils

• Refactored and moved the source code from SynUtils to SynKit.
• Reorganized the subpackages and removed the "Syn-" prefix for better clarity and consistency.

Rule Composition

• Migrated the rule composition code from SynTemp to SynKit, with added test cases.
• Developed the MoleculeRule class, which converts a molecule to a transformation rule (G → G), making it compatible with rule composition.
• Introduced the ReactorRule class, which applies transformation rules using rule composition, allowing backward predictions with a single structure.

Rebalancing Using Rule Composition

• Added a new function to rebalance reactions if the transformation rules are already known.

Reactor Subpackage Refactoring

• Refactored the Reactor subpackage by removing unnecessary files such as rule_apply.py and inference.py.
• Created the ReactorEngine class, which performs rule applications while retaining AAM reactions and handling reagents.
• Enhanced handling of multi-step reactions for better flexibility.

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Known Limitations

BatchCluster

• The processing speed of BatchCluster is slower compared to GraphCluster. There may be an internal issue affecting performance.

Reactor

• The ReactorEngine currently only works with balanced reactions.

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