Update README.md

[nrweir]

Update README.md

We need to read through the README carefully and see what is deprecated going from the "old" master to v3/dev. For example, the paths to some of the scripts referenced in the readme have changed, I'm not sure if the cli remains as it's described, etc.

Other tasks:

• include install instructions relevant to 4.0.0
• include links to readthedocs when that's live
• include a "version history" section where we can indicate what has changed between releases (? this can also be done as its own .txt file in the repo if it will be too unwieldy)
• probably more I'm not thinking of right now