1.3.2

Bug fixes

Three related bugs that caused hangs or out-of-memory crashes when the Gibbs sampler for mu drives the mutation rate to extremely small values (observed on datasets with very few or zero mutations, e.g., WCSS 04_free_exp_pop/sims/sim_048):

• Fix infinite loop in sample_mutational_history when mu*T is tiny — Floating-point cancellation in log(p_0/(1-p_1)) caused the no-delta sampling loop to run forever. Fixed with a Taylor expansion for small mu*T and a skip guard.
• Cap root displace proposal scale in inner_node_displace_move — With tiny mu, the Gaussian proposal scale became ~330 million years, causing the coalescent prior to allocate GiB of grid cells. Capped delta_scale to the tree span.
• Cap subtree slide proposal scale in subtree_slide_move — Same issue as above but in a different move type. Capped delta_scale to the tree span.

Diagnostics

• Warning in ensure_space — The coalescent prior's grid allocator now logs a warning to stderr when allocating more than 10,000 new cells, making similar issues easier to detect in the future.

1.3.1

Bug fix

• BEAST log output: consistent calendar-aware time conversion. The BEAST X and BEAST 2 log output in beasty_output.cpp mixed two conventions for converting internal times (days since 2020-01-01) to years: to_linear_year (calendar-aware, accounts for leap years) for age(root), but simple / 365 division for rootHeight and age(TIP). This introduced a systematic error of ~2 days over multi-year spans for datasets in 2025, a small but perceptible delta that will only grow in the future. All absolute time and time-delta conversions in BEAST log output now use to_linear_year / delta_linear_years. Rate and magnitude conversions (* 365 / / 365) and Newick tree branch lengths are unchanged.

1.3.0

New Features

• Flexible prior on mutation rate (mu): Configurable Gamma(alpha, beta) prior via --v0-mu-prior-alpha/--v0-mu-prior-beta or --v0-mu-prior-mean/--v0-mu-prior-stddev. Default recovers the existing uniform prior. Initial mu defaults to the prior mean when a proper prior is specified.

• Flexible prior on population size (n0): Configurable Inverse-Gamma(alpha, beta) prior via --v0-pop-n0-prior-alpha/--v0-pop-n0-prior-beta or mean/stddev variants. Default recovers the existing Jeffreys (1/x) prior.

• Flexible prior on growth rate (g): Configurable Laplace prior with adjustable location, scale, and optional bounds via --v0-pop-g-prior-* options. Includes an exponential distribution shorthand (--v0-pop-g-prior-exponential-with-mean).

• Flexible prior on Skygrid N_bar: Configurable Inverse-Gamma prior on the geometric-mean effective population size across Skygrid knots via --v0-skygrid-nbar-prior-* options. Conjugate with the coalescent likelihood, preserving exact Gibbs sampling.

• Skygrid knot date control: New --v0-skygrid-first-knot-date and --v0-skygrid-last-knot-date options for explicit control over the Skygrid time range.

• --v0-steps 0 and --v0-steps 1 now work: Useful for inspecting the initial state or quick smoke tests.

Performance

• 2x speedup on datasets with missing data: Replaced the slow_elements coroutine with direct interval-level iteration, eliminating per-site suspend/resume overhead (34% fewer CPU cycles).

• Integrity checks now opt-in in release builds: Previously always-on checks consuming ~23% of runtime are now gated behind --v0-paranoid.

Bug Fixes

• Fixed undefined behaviour in SPR move branch_info handling.
• Abort with a descriptive error when output files cannot be opened (previously silent failure).
• Print version and help instead of crashing when invoked without arguments.

Other

• Population quantities (n0, g, N_bar, gamma_k) now displayed in year units.
• All new priors are serialized in FlatBuffers and exported to BEAST 2.6.2, 2.7.7, and X XML formats.
• Updated Google Colab notebooks.
• Added Codecov integration.

1.2.2

Release 1.2.2

* Tweaking GitHub CI to automatically create working release artifacts

1.2.1

Release 1.2.1

* Testing GitHub CI's ability to automatically create release artifacts

1.2.0

• Change license to MIT

1.1.6

• Export posterior support in delphy_mcc
• Improve handling of sites with no data at all in MAPLE files

1.1.5

• Fix compilation issues on macos and Ubuntu 22.02

1.1.4

• Efficiency improvements for Skygrid

Release 1.1.3

• Add support for exporting BEAST2 2.7.7 input XML and output log files
• Bugfix for BEAST X 10.5.0 input XML export: fix needless loss of precision in dates