Syntemp

Maintenance
- **Resolved Pytorch version conflict**: Kept version 2.2.0 for consistency across the codebase.
- **Updated the mapper version**: Note that the reproducibility of the paper cannot be guaranteed with the latest version. For reproducibility, please refer to version 0.0.6 and below.
- **Removed `MØD`** from this version for improved functionality.
- **Replaced `synutility` with `synkit`**: This update ensures consistency and better integration across the modules.

Deprecated
- **Deprecation Warning**: The following features will be removed in version 1.0.1:
- The `SynUtils`, `SynComp`, and `SynChemistry` modules have been moved to the `synutility` repository.
- `ITSConstruction` will be removed, as it has been moved to `synutility`.

Additional Notes
- Users are encouraged to transition to the updated modules and take note of upcoming removals to ensure smooth upgrades in future versions.

Added
- **New feature**: Added `ITSArbitrary` to generate all possible ITS Graphs from AAM (Atom-Atom Mapping).
- **Note**: This feature is still under development and may experience slow performance and potential memory issues when the number of combinations exceeds 8! (i.e., 40,320).

- **Dependencies split**: Separate lightweight installation options:
- `pip install syntemp`: Installs the basic version (without Atom-Atom Mapping tools).
- `pip install syntemp[all]`: Installs the full set of dependencies, including tools for Atom-Atom Mapping (`rxnmapper`, `localmapper`, and `graphormermapper`).

Changed
- **Enhanced rule clustering**: Improved rule clustering functionality to handle batch processing and mitigate the combinatorial explosion problem.
- **Note**: This change does not yet integrate with Hierarchical Clustering.

- **Improved Isomorphic Filter**: Integrated a new graph signature filter, reducing the ITS clustering time from 78 minutes to just 2 minutes.

- **Hydrogen Inference Refactor**:
- Refactored the hydrogen inference function for better readability and efficiency.
- Integrated graph signature to reduce isomorphism checks, improving processing time by 50%.
- Removed the `timeout` option (planned for removal in version 0.0.10 due to redundancy).
- **Issue**: The process remains slow, and there may be potential memory explosion if the number of combinations exceeds 8! (i.e., 40,320).

- **ITSExtraction refactor**: Removed redundant `deepcopy` calls, resulting in a 50% reduction in processing time.

- **Code Cleanup**:
- Removed redundant Python functions, which have now been moved to the `synutility` repository.
- Removed unused variables in the `syntemp` command-line interface (CLI).

Deprecated
- **Deprecation Warning**: The following features will be removed in version 0.0.10:
- `SynUtils` and `SynChemistry` modules have been moved to the `synutility` repository.
- `ITSConstruction` will also be removed as it has been moved to `synutility`.

Fixed
- **Memory Usage & Performance**: Improved memory management and processing performance in several functions, especially in hydrogen inference and ITS extraction.

Security
- No security updates in this release.

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