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Changelog

All notable changes to this project (since 2026-02-19) are documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]​

Added​

  • New flag --data-augmentation (see tpplc --help for details)
  • Added math functions, distribution types and functions, and tree types and functions to the library. The code is in separate library files (math.tppl, distributions.tppl and trees.tppl) in the src/lib/ directory.
  • Added diversification model example for the birth-death diffusion (BDD) model, version 2 (analogous to ClaDS2).
  • Added diversification model versions with hard-coded delayed sampling.
  • Added constant-rate birth-death (CRBD) model using weights based on analytical likelihood rather than simulation.
  • Python interface: Introduced CompileArguments and RunArguments classes for handling compile and run arguments. RunArguments can now be serialized to and deserialized from JSON files for easier reuse and reproducibility.

Changed​

  • Moved the functions exp, log, sqrt, minInt, maxInt, floor, ceil, round from the standard.tppl library file to math.tppl.
  • Python interface: Compile arguments now mirrors the arguments used by tpplc for improved consistency and alignment between interfaces.

Deprecated​

Removed​

  • Removed the Tree type from the standard.tppl library file. An identical type, called ClockTree, is now in the trees.tppl library file. This change allows a more convenient interface, in that a user can synonymize a local custom Tree type with ClockTree, or any other tree type in the standard library that is appropriate for the model script.
  • Jupyter interface: Removed legacy syntax highlighting support that was only compatible with older Jupyter Notebook versions.

Fixed​

  • Changed the rho parameter (leaf sampling probability) in the data files for the diversification model scripts from 2.0 to 0.5.

Security​

v0.3​

Added​

  • New flag --infer-time (see tpplc --help for details)
  • Add a changelog to the webside

Changed​

  • The debug statement now accepts multiple arguments

Deprecated​

Removed​

Fixed​

  • Using debug to print strings no longer crashes

Security​