clean up / simplify code to wrap up semester

[rmarren1]

• refactored the data structure so that less information needs to passed between functions (all data for a subject / trial is stored within one data struct, indexed by meaningful keywords) - a08089563bc71ca17dead96459b97ce307188678

• take away user options (but keep functionality so we can use it for fast testing). - 30703c50862498bed1619fcfb835d74112e0be4d

• hard-code the 'best' options into the configuration of the pipeline - 34ddfac096273dac2517b2fa362282dfc8b3d2bb

• simplify docker set up to make standing up service easy - a08089563bc71ca17dead96459b97ce307188678

[rmarren1]

^ explain how to set up the development version in the git README.md, forgot to for presentation

[rmarren1]

done ^^