Integrating ruff precommit

[Abellegese]

Thank you for taking your time to contribute to Ersilia, just a few checks before we proceed

• Have you followed the guidelines in our Contribution Guide
• Have you written new tests for your core changes, as applicable?
• Have you successfully ran tests with your changes locally?

Refactoring Overview

This PR integrate ruff and precommit-hook based linting. Also refactors the codebase to comply with the specified ruff linting and formatting rules. Below is a checklist of the key changes made:

• Line Length: Updated to a maximum of 88 characters for better readability.

• Indentation: Standardized indentation width to 4 spaces.

• Target Python Version: Refactored code to align with Python 3.10 features and standards.

• Selected Rules: Enabled checks for:

  • D101, D102: Require docstrings for public classes and methods.
  • E4, E9, F: Address common syntax, logic, and runtime errors.
  • I: Import formatting and ordering.
  • W: Address warnings for improved code quality.

• Ignored Rules: Excluded:

  • D104: Missing docstring in packages.
  • D105: Missing docstring in magic methods.
  • D107: Missing docstring in init.

• Fixable Rules: Applied automated fixes for all applicable rules.

• Dummy Variables: Standardized naming for unused variables with the regex ^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$.

• Docstring Style: Adopted NumPy-style docstrings for consistency.

• Formatting: Ensured:

  • Double quotes for string literals.
  • Spaces for indentation.
  • Consistent handling of trailing commas.
  • Automatic detection of line endings.
  • Proper formatting for code examples in docstrings (line length = 50 characters).

Results

• On github action
  
• On local
  

Related to #1417

[DhanshreeA]

@Abellegese could you please resolve conflicts here?

[Abellegese]

Yes @DhanshreeA I will.