v0.3.0 Finalizing Steps

[iblacksand]

Because of some important changes, v0.3.0 should be pushed fairly soon.

Checklist

• Fix CLI to be useful
• Improve README installation instructions
• Make peptide mapping files created by default
• Update documentation
  • New outputs
  • Improved input
• Double check google colab example is up-to-date
• Update pyproject.toml to have updated version number