msprime
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tskit-dev
Simulate genealogical trees and genomic sequence data using population genetic models
Version 1.3.2 was intended to be a hotfix release that put recent fixes for packaging etc on the stable code. However, some of the SMC K change that we were...
Bring SMC k logic together in one place as part of #2294
Currently we store the head of the segment chain to represent a lineage in both the Python and C versions. This is getting increasingly unwieldly. Replace with an object representing...
A population can have an activation time that is greater than zero -- for example, to sample ancient individuals. When using the demography debugger's `coalescence_rate_trajectory()` function, specifying lineages from that...
Hi all, I'm running into a "TSK_ERR_MUTATION_TIME_OLDER_THAN_PARENT_NODE" error when trying to recapitate a truncated tree sequence. I've attached [some code and a tree sequence](https://github.com/user-attachments/files/16788184/Archive.zip) to walk through the issue. The...
The last step to allow demographies to be instantiated from provenance entries. We exceptionally allow a `demography.Population` object to be created with an existing ID, but only if generated when...
In ancestry.md, we say "Although this is obviously not a common ancestor event, note that for both of these models each node has to carry at least one of these...
Ran across this bug (?) while writing some tests-- consider a two-population island model, both populations of size $N$, with a mass migration event at time 0 where 50% of...
The test `tests/test_mutations.py::TestMatrixMutationModel::test_TPM[0.5-0.25-50-500]` fails under Windows with recent numpy. Line https://github.com/tskit-dev/msprime/blob/main/msprime/mutations.py#L395 finds the values in matrix `S` that are close to 1. Under linux this array is: `[ 1.00000000e+00 9.99652651e-01...
