Msprime: Clean up mutations/models docs

[jeromekelleher]

1409 made a small update to the mutations part of the docs. There's a few updates that we need to make to bring the "models" section up to date:

• Make sure we use sim_mutations and sim_ancestry in all the examples
• Update the examples to use jupyter code blocks (see the ancestry.md page for examples to follow here) and delete the old images from the repo

[awohns]

Happy to address this! I happened to be working with the new mutation models this week anyway

[awohns]

The msprime.SLiMMutationModel example includes a parameter called allow_ancestral. I can't find where this is documented, does it not exist anymore?

[petrelharp]

See https://github.com/tskit-dev/msprime/issues/1206#issuecomment-768562378 for the proposal on this (and documentation).

[awohns]

Ah great, thanks @petrelharp

[awohns]

Another point: the SVG and the text of "Infinite Alleles Mutation Models" don't match up. The text seems to indicate that there are multiple copies of the same allele. Maybe I'm missing something fundamental about this example, but the point of Infinite Alleles is that each allele is new?

[petrelharp]

I meant that five of the samples inherited allele 13, etcetera.

[awohns]

Don't 8 samples inherit allele 13?
Edit, ah sorry peter, was being dense and didn't see that it's a single site so there's overwriting

[petrelharp]

Heh, this is exactly why I put that sentence in, to make the reader notice things like it being a single site. =) But, clearly it needs to say what's going on a bit more explicitly.