chore: Set ruff compatibility check to py39

[jdeschamps]

Description

ruff was enforcing compatibility with py38, which we don't support anymore. Updating the pre-commit env to py39 caused all the from typing import Dict, List, Tuple to cause errors.

This PR removes all such imports and replace them with the annotation dict, tuple or list.

Changes Made

• Modified: Almost all files.

Related Issues

• Resolves Linter (ruff) enforces py38 although we dropped support #301

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Please ensure your PR meets the following requirements:

• Code builds and passes tests locally, including doctests
• New tests have been added (for bug fixes/features)
• Pre-commit passes
• PR to the documentation exists (for bug fixes / features)