Reproducibility and Documentation

[ChristopherMancuso]

• fix the unit tests
• add good example gene sets
• update all documentation, can two versions of documentation be up on ReadtheDocs
• check all examples run, including CLI
• add latest version of python to all tests
• update comments/doc strings in functions
• update Zenodo to detail the correct license agreements
• update logger outputs
• change test to res (for results)