Changelog#

[1.1.0] - 2026-06-10#

Add the joint (multi-population) site-frequency spectrum via jsfs().
Add the two-locus site-frequency spectrum under recombination via sfs2(), with support for multiple-merger coalescents.
Add summary statistics: Hudson’s fst(), Patterson’s f-statistics (f2(), f3(), f4()), Tajima’s tajimas_d() with the theta_pi() and theta_w() estimators, and cross-locus linkage via the correlation of coalescence times.
Accelerate state-space construction with numba, which is now a required dependency.
Compute moments of large state spaces from the sparse action of the matrix exponential (threaded over epochs), controlled by expm_action_min_dim.
Validate the new statistics against msprime/tskit ground truth, including within the scenario-comparison workflow (Kingman and multiple-merger models, and beyond the two-lineage case).
Use the spawn start method for the worker pool on macOS to avoid fork/numba deadlocks.
Documentation: add a dedicated Spectra & summary statistics reference page and drop the exponentiation-backend page.

Speed up single population single locus Kingman coalescent SFS computations by flattening block counting state space.
Rescale rate matrix instead of recomputing it for new epochs in the one population, one locus case.
Relocate phase-type settings to Settings class.