updated parser to clap 3.0 / added option groups

[epi052]

closes #112

Landing a Pull Request (PR)

Long form explanations of most of the items below can be found in the CONTRIBUTING guide.

Branching checklist

• There is an issue associated with your PR (bug, feature, etc.. if not, create one)
• Your PR description references the associated issue (i.e. fixes #123456)
• Code is in its own branch
• Branch name is related to the PR contents
• PR targets main

Static analysis checks

• All rust files are formatted using cargo fmt
• All clippy checks pass when running cargo clippy --all-targets --all-features -- -D warnings -A clippy::mutex-atomic
• All existing tests pass

Documentation

• New code is documented using doc comments
• Documentation about your PR is included in the README, as needed

Additional Tests

• New code is unit tested
• New code is integration tested, as needed
• New tests pass