Use pyproject.toml to manage all configurations

[elmq0022]

Move the configurations to the pyproject.toml for all tools that support it. This would put all our development tool settings into a single location.

A list of tools that support pyproject.toml can be found at awesome pyproject.toml

We use isort, pylint, and pytest. We also have a single setup.cfg with settings for flake8 and coverage. I'm not sure if these are in use or should be moved at this time.

This change could be done in a single or multiple pull requests.