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Simulate genealogical trees and genomic sequence data using population genetic models
Initial draft for changes discussed in #2158 to enable simulating beyond local roots.
[sims.ipynb.zip](https://github.com/tskit-dev/msprime/files/13653216/sims.ipynb.zip) Above is a Notebook describing the issue in more detail. The summary is that: when running basic selective sweeps using algorithms.py's framework, there is some illogical output. The sweep_pop_sizes...
Draft intended to expose some of the issues to @agushin101 as discussed in #2242.
A few different people have been asking about how we keep more information about sweeps in the SweepGenicSelection. It's not entirely clear to me how we do this, but here...
Looks like all other dep updates are good, but stdpopsim is failing: `AttributeError: 'DemographicModel' object has no attribute 'population_configurations'`
We have temporarily pinned `stdpopsim` to version `0.1.2` until we can fix the tests in `test_demography.py` so they are compatible with the latest `stdpopsim` release.
As discussed in #2232, we could easily extent the current `log_arg_likelihood` such that we also return the correct likelihood when the ARG simulation was stopped early. This means we need...
Removed argument of `DemographicEvent.get_ll_representation()`. Solves #1037 as this is no longer used by stdpopsim. The [`TestLowLevelRepresentation`](https://github.com/GertjanBisschop/msprime/blob/7db7dce6aec6e605eff366b7e602315cc55b13ca/tests/test_demography.py#L560) test suite is marked as containing tests that were only needed to ensure compatibility...
In #2157 we decided to add a boolean flag ``stop_at_local_mrca`` which states whether we should keep simulating the ancestry of genome segments after an mrca has been reached. We also...
Elevated mutation rates at CpG dinucleotides are one of the major contributors to mutation rate variation in mammals. These can't easily be simulated by `sim_mutations`, but there are probably reasonable...
