Refactor to use AnnData

[jvivian]

Not sure if when we'll do this, but had a thought going to bed last night that we could simplify the model input and clean up the code by decoupling things like factor specification from the inputs (i.e. why are factors hardcoded ? What if someone else wants to use different factors without needing to use the python package directly and override factors when calling the model? What if they have different data? Etc)

We'd do this by converting the input into an Anndata object:

https://anndata.readthedocs.io/en/latest/

X - Matrix contains numeric data
obs matrix contains info like Time, State for each observation
var matrix contains information about variables, such as alternate name, factor assignment, etc.)

So the input could be generalized to that input (or for general users), 2-3 Excel files, one for each matrix.

[jvivian]

Going to try and implement this today if I can. This will almost assuredly cause merge conflicts for anyone working on code that touches processing.py or Dashboard.py.