So I want to thank everyone that reviewed my original messy PR. I took a hint from Bjorn and redid them all to be absolutely minimal and just what they involve. I hope you now approve of these.
They're dependent. 3--bases-on-->2--bases-on-->1, need to be merged in that order. There was no other way to do it, I only did #1 and #2 because I couldn't do #3 without them. So much stuff was old and broken it snowballed. I did not put the PyTest conversion in these PRs - I will have to do that at the Hackathon maybe.
So if you get a chance, I would really appreciate it if we could try to get these in by Thursday - a big ask I know - for the Hackathon. If we could do a v0.8.5 release Thursday that would be optimal. The new README, updated docs and motif finding tutorial will help people get onboarded much faster. If not, that's okay, I can just point them to my docs branch but it won't be serving the formatted docs... so yeah.