Jerome Kelleher

This would allow us to exactly track where ancestral material passed through all individuals in the pedigree, which would be useful for explanatory purposes and also probably helpful for some...

Experimental yaml input format

7

This is an experiment to see what a yaml/json input format (building on demes) would look like. It mostly works I think, except for the basic confusion about the direction...

We should be able to implement models of (independent) codon sequence evolution following the approaches of [Arenas and Posada 2007](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-458) It's not entirely satisfactory that we'll end up with independent...

Decouple trajectory from sweeps

1

I'm finding the time and population size conversions in the sweeps model super confusing, and I would *really* like to decouple the trajectory simulation from the sweep definition. I don't...

Initial outline for Trajectory refactoring

4

Here's a rough outline for what I'm thinking the low-level C will look like. I think it's worth getting things right here in the Python version before looking at the...

"Sandbox violation" with meson 0.57

3

Looks like our C library build is broken by meson 0.57. The recommended approach for now is to make sure you have an older version installed: ``` python3 -m pip...

Msprime slow for long genomes

17

Msprime is much slower than MaCS when simulating long genomes/lots of recombination, as we've seen with the BosTau model in stdpopsim. There may be some low-hanging fruit in making this...

Add RateMap.zip(other1, other2,...) method

6

It would be useful to have a method that would combine two or more RateMaps and return an iterator over the distinct intervals at the rates. So, in usage, it...

that was added in #1524

Tidy up benchmarking docs

2

There's some typos in the commands, and ``asv run HEAD^!`` works better for me than the first command given.