linting: change linter to ruff

[gcroci2]

Due to the broken change of python extension in vscode, we have to reset linter and formatter used in this project.

Ruff is both a linter and formatter, providing an all-in-one solutions with surprising performance(see here1 and here2). Ruff replaces prospector, and it has also isort functionalities.

⚠️ Note that developers have to reset their dev env by installing ruff and updating vscode extensions.

Inspired by @CunliangGeng

• Blocked by feat: improve Trainer and DeeprankDataset logic for production testing #515, feature: separate max edge distance from interaction radius throughout #504, refactor: unify buildgraph.py and build_graph functions for atom and residue level graphs #507
• Run ruff as checker and formatter on the entire code-base, and fix issues
• Go through the ignore checks in the toml file, and evaluate which ones to remove (and fix the code accordingly)
• As mentioned here, we should add mypy as a complement to Ruff (for typing rules).

[github-actions]

This PR is stale because it has been open for 14 days with no activity.

[DaniBodor]

replaced by #554