.. _modules.changelog: Changelog ========= [1.2.0] - 2026-06-13 ^^^^^^^^^^^^^^^^^^^^ - Add the cross-locus correlation of the two-locus SFS via :meth:`TwoLocusSFSDistribution.corr() `. - Build large rate matrices sparsely with an explicit state-space size cap (:attr:`Settings.dense_rate_matrix_max_states `, :attr:`Settings.max_state_space_size `). - Evaluate the final unbounded epoch in closed form by default and batch the per-bin spectrum solves, substantially speeding up SFS/jSFS/2-SFS moments (:attr:`Settings.closed_form_last_epoch `). - Compute the single-population standard-coalescent SFS flattening weights in closed form, avoiding the partition-sized block-counting state space, so large-``n`` SFS (and SFS-based inference) is much faster. - Raise a clear error for demographies that never absorb (isolated demes or blocked migration) instead of returning a meaningless value. [1.1.1] - 2026-06-10 ^^^^^^^^^^^^^^^^^^^^ - Relax the ``numpy`` upper bound (``>=1.26.4``) to allow numpy 2, so phasegen can coexist with current, numpy-2-built msprime/tskit. [1.1.0] - 2026-06-10 ^^^^^^^^^^^^^^^^^^^^ - Add the joint (multi-population) site-frequency spectrum via :meth:`Coalescent.jsfs() `. - Add the two-locus site-frequency spectrum under recombination via :meth:`Coalescent.sfs2() `, with support for multiple-merger coalescents. - Add summary statistics: Hudson's :meth:`Coalescent.fst() `, Patterson's f-statistics (:meth:`Coalescent.f2() `, :meth:`Coalescent.f3() `, :meth:`Coalescent.f4() `), Tajima's :meth:`UnfoldedSFSDistribution.tajimas_d() ` with the :meth:`UnfoldedSFSDistribution.theta_pi() ` and :meth:`UnfoldedSFSDistribution.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 :attr:`Settings.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. [1.0.2] - 2025-07-14 ^^^^^^^^^^^^^^^^^^^^ - 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 :class:`~phasegen.settings.Settings` class. [1.0.1] - 2025-02-17 ^^^^^^^^^^^^^^^^^^^^ - Minor improvements in logging and first release archived in Zenodo. [1.0.0] - 2024-08-05 ^^^^^^^^^^^^^^^^^^^^ - First stable release