Finish unit tests for current version of the code

[wllgrnt]

Current code coverage is poor for everything except the Database class, and the unit tests don't test many of the possible networks I can generate e.g. atomic networks.

[wllgrnt]

Left to do generally:

• Finish unit tests for the treeFileToNestedLists function
• Add tests for atomic networks
• Add AFG tests (and proper handling of AFG code in general)

• 7 (Unit test for chainref)

Network:

• init() with chainref param
• extractAtomicData() with chainref param

Database:

• Check the behaviour when a request is made for multiple records
• Check that headers are successfully removed
• Check that all methods handle the "chainref" param properly
• Check SuperNetwork methods
• Check Mapping methods

Partition:

• Some AFG tests
• PlotStripeDiagram
• GetPFAMArray
• PlotPymolStructure

SuperNetwork

• Literally everything

[wllgrnt]

Currently the database, Infomap, and matplotlib are mocked, such that failures there can't be tested properly. Is bad!