CLI:
- Improve help page for command line tool
- Switch to argparse
- Rename tests to match names in the preprint and to avoid double negative ambiguity
- Bug fix: could not load config from user provided file
- Bug fix: full_report option not useful for short report output format
Clash tests:
- Option to ignore hydrogens if present in ligand
InChI tests:
- Better error messages when InChI generation fails
Internal energy test:
- Better error messages when conformation generation fails