Feature/cleanup and fix issues

[JulienGrv]

What has been done:

• update GitHub actions
• use editable install, requirements are placed in the setup.py and it is not required to repeat them anywhere else
• use python -m build in place of the deprecated python setup.py
• shell snippets are POSIX compliant now
• update pre-commit hooks
• remove version: 3.8 in .readthedocs.yml because it does not work
• add VSCode recommended extensions to work on the project
• add developer instructions in CONTRIBUTING.md
• update README.md
• format markdown, yaml and toml files
• remove deprecated setup.cfg, pylint.cfg and pre_commit.bat
• align ruff and black settings between direct usage and pre-commit usage
• always install decode and export extra dependencies for gui extra
• fix issue where python builtins were deleted and overriden, which caused python internals to fail when looking for the eval function. Unfortunately, fixing this issue introduced another one for the gui. However, as a general rule of thumb, we should not mess with python builtins or else we can break python itself. Hopefully we can find a better implementation in the future.
• remove fastpath argument to pandas Series as it is long deprecated and causes warnings when running pytest
• tox.ini settings are simplified as well thanks to new canonical requirements.txt files and gui extras installation

[danielhrisca]

Let me know when it is ready

[JulienGrv]

Hi @danielhrisca , it's ready now. However there is still issues in the CI tests that need to be fixed but the situation is slightly improved with this PR. I have listed what has been done in this PR. Good luck fixing the issues with numpy 2.0!

[danielhrisca]

thank you Julien!