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Add Gaussian noise 3D transform and augmentation#50

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tonyzamyatin wants to merge 22 commits intomainfrom
feature/ts-gaussian-noise
Draft

Add Gaussian noise 3D transform and augmentation#50
tonyzamyatin wants to merge 22 commits intomainfrom
feature/ts-gaussian-noise

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Summary

What problem does this PR solve, and what is the user-visible outcome?

Fixes # (optional)

Type of change

  • Feature
  • Bug fix
  • Documentation
  • Refactor / Maintenance
  • CI / Build
  • Tests
  • Other: ___

Changes

  • Bullet the key changes (1–5 bullets)
  • Keep it concise but specificg

Breaking changes

  • None
  • Yes (describe impact and migration notes):

How I tested this

  • Unit tests pass
  • Integration / e2e checks
  • Docs build locally
  • Manual verification (brief steps):

Checklist

Before PR:

  • Branch name follows policy (feature/bugfix/hotfix/docs/chore/ci/tests/perf/build)
  • Ran test locally and ALL tests pass
  • Updated or added tests covering new behavior (if applicable)
  • Updated configuration defaults (if applicable).

PR:

  • This pull request has a clear but concise title (prefixed with a git commit emoji, use:emoji_name: to select an emoji)
  • Relevant labels added
  • If this PR introduces breaking changes it is labelled with breaking-change and provides a migration guide

- Update DimeNet model implementation in `dimenet.py` to use new embed() method.
- Add DimeReaction
- Update 3d representation to also use reactant xyz file
- Updated imports and config files after renaming
- Deleted the optimal model configuration file for DimeNet++
…taset to data module; Add support for multiple test loaders
…improve logging for training and validation steps
- Add `data_module` config file
- Updat data loading configurations to use `dataloader_factory` instead of `dataloader` for consistency across YAML files.
- Add Hydra configuration to disable automatic logging and set output directory to the current directory for all benchmark models.
- Introduce a new configuration file for `dimereaction` model
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