These are chat archives for dereneaton/ipyrad
Check out the docs, I put some serious work into them tonight. I think it's best to push all of the API stuff to after the CLI descriptions. Probably best to explain it as an analysis method, but then say, hey, you could also assemble your data using it to.
I agree here too. In terms of organization, I like the way msprime has it set up, and I also like the way you have the docs for pyrad set up. The full tutorial is basically the first thing you see after the dl link, then all the more complicated stuff is below it (operating on the assumption that API users are going to be more comfortable digging for information, and lowering the barrier to entry for noobs).
nbconvert --to-rst(or something like that) function to convert them. This way we can quickly rebuild the tutorials even if we change the data or program.
.......... Saving assembly
[.......] saving, which also could make it more clear if a job stopped and saved before it was finished.