TODO list for a v1.0 tag

[mattkinsey]

There's definitely more than just this list (I'll keep expanding it) but here's a starting point for the things we need to do before we tag a 1.0 release:

• [x] rename output columns to match the tex document
• [x] add the sections from the latex to the sphinx docs (things like the input param description, output description, high level model overview, etc)
  • [x] param file
  • [x] output columns
  • [x] model description
  • [x] make sure readable_col_names exactly matches the tex table
• [ ] finish up the function level docs
• [x] replace all print() with logging (there's only a few left)
• [x] cleanup logging output (e.g. viz.plot defaults to INFO, there's a warning when falling back to numpy in postprocess that should be info, etc)
• [x] add some descriptions to the (many) tqdm bars so the user knows what's being progressed
• [x] I renamed the columns in the csse historical file to 'cumulative_reported_cases' and 'cumulative_deaths' (from 'Confirmed' and 'Deaths'. I think I cleaned up everywhere that matters but we need to test that this didn't break anything downstream.
• [ ] add something like scripts/ and include all the run scripts?
• [x] move some of the hardcoded params around things like doubling time and case reporting estimation to param file
  • [ ] we moved the "main" ones but things related to the mpert distributions still need to be moved over
• [ ] lint everything and setup github actions and commit hooks
  • [x] isort
  • [x] black
  • [x] flake8
  • [ ] pylint (this might be too much...)
  • [x] add support for storing Aij as a sparse matrix for when you can't spare the mem

[mattkinsey]

closing to switch over to making this a GH milestone