chore: Apply whitespace fixes from hooks

- Remove trailing whitespace
- Correct single newline at end of files (skip for json)
- Update to formatting in a few places due to black

pyproject.toml

@@ -5,5 +5,5 @@ build-backend = "setuptools.build_meta"
 line-length = 120
 [tool.isort]
 # make it compatible with black
-profile = "black" 
+profile = "black"
 skip_gitignore = true