Improve linting and code formatting

We now format our code to be 88 symbols per line, which is quite old recommendation. E.g. PyCharm now draw vertical line to guide you at 120 symbols. I think, we should use this across our code.

In some places in bindings I still would like to have our original formatting, so I placed // clang-format off // clang-format on guards around them

We now also uses ruff for both formatting and linting

And we go for prek instead of pre-commit

We fix the issues identified by the linter (additional checks added).