Subject Cleanup

[sneakers-the-rat]

Subject is one of our many beloved superfund sites. meta issue to track what needs to be done

• Expose history table and all other stored data in a uniform way. it should be trivial to browse the structure of the hdf file.
• separate some of the ungodly long methods
• use private and public methods so it's not so polluted
• use properties instead of trying to maintain attribute state very brittle-ly
• Fish out code that determines file structure out into separate objects.
• Following ^, clean up assign_protocol so it's clearer what we expect (pending a fuller restructuring of protocols in general)
• Smooth out some of the edge cases in prepare_run and data_thread that make unpredictable and untestable behavior.

[sneakers-the-rat]

Got started on this https://github.com/wehr-lab/autopilot/blob/7a8c561d2a94c1ce5f69f621dd1c40be3e7e1ef7/autopilot/core/subject.py#L40-L217