Sadly, atom-python-isort hasn't been maintained for over three years now. There's more than a dozen unaddressed issues and a few open pull requests that are going nowhere. I've been maintaining atom-isort for the last year. I've fixed the long standing bugs and made a number of enhancements such as:
Integration with Atom's linter
Error handling and reporting via Atom's notification manager
A small but growing spec test suite to avoid future regressions
Plus I'm still actively developing and improving this package. I have a plans to refactor some parts of the codebase for performance and usability. I also want to migrate the codebase to ES6 and improve the README documentation.