Touch up several parts of the repository

[CasperWA]

Closes #290
Closes #289
Closes #288

Temp.: Still updating CI/CD

AI Summary

This pull request modernizes and streamlines the repository's Python packaging, CI/CD workflows, and dependency management. The main changes include upgrading to Python 3.12, switching to PEP 621/Flit-based packaging, simplifying dependency files, and updating CI/CD steps for improved maintainability and reliability.

Python version and tooling upgrades:

• Migrated the entire codebase and CI/CD workflows from Python 3.11 to Python 3.12, including updating Dockerfile, .pre-commit-config.yaml, and all workflow files to use Python 3.12 and relevant pre-commit hook arguments. [1] [2] [3] [4] [5] [6]

Packaging and dependency management:

• Replaced legacy setup.py and requirements files with a modern pyproject.toml using Flit for packaging and dependency management, including moving development dependencies to [project.optional-dependencies] and removing requirements_dev.txt. [1] [2] [3]
• Added a minimal requirements file for CI (.github/utils/requirements_ci.txt) to centralize CI dependencies.

CI/CD workflow improvements:

• Updated GitHub Actions to use the latest versions of actions/checkout and actions/setup-python, and switched changelog generation to github-changelog-generator Docker image for more robust release notes. [1] [2]
• Refactored install steps in CI workflows to use the new requirements file and removed redundant code for installing pre-commit. [1] [2]
• Improved release tagging and version update logic in .github/utils/update_version.sh for clarity and maintainability.

Pre-commit and linting changes:

• Updated .pre-commit-config.yaml to match new Python version, removed the local pylint hook, and adjusted hook arguments for compatibility.
• Removed the pylint-safety job from CI, simplifying linting and safety checks.

Other updates:

• Updated copyright year in LICENSE.

These changes collectively modernize the repository, reduce maintenance overhead, and improve CI/CD robustness.