Move flake8, black, and pytest configs to pyproject.toml #1013
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Consolidating tooling configs here is neater and helps avoid fragmented options (like how flake8 was set to 100 line length but black was set to 88).
This also updates these tools to their latest versions.
If you would rather use a different line length like 88 (the black default) or 79 (the flake8 default) or something else, this PR can be edited. I just used 100 since it was already configured in the flake8 config file.