Add type hints to function signatures and fix linting errors

[jrom99]

Hello, I've added the type hints to function signatures, and removed the setup.py file in favor of pyproject.toml. I then fixed all linting errors that were raised by basedpyright basic type checking mode.

One of the tests was not passing because the regex was case sensitive, so I also updated the regex.

I've made some QOL improvements so that plotTree can now autoscale to its contents and use strings for x_attr and y_attr. And renameTips can reuse the old names when they are missing (so you can rename specified tips and reticulations).

The decimalDate function seemed to assume multiple things about the input data format (single char separator, same separator for all items, dates are stored left-to-right), so I added support for extracting and using each separator from the format string.

I used f-strings instead of the older format method, and r-escaped some of the regex to remove the warnings.

Overall, there were no backward-incompatible changes to the API itself, but the type annotations require python >= 3.9 (was 3.8 before).