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

Changed

Deprecated

Removed

Fixed

Security

v0.4.1

Added

Changed

Deprecated

Removed

Fixed

• (treeppl-python#23) Added missing import of importlib.resources, which would be implicitly imported on some machines, but not all.

Security

v0.4

Added

• (dppl#223, treeppl#147, dppl#230, treeppl#150, treeppl#151) New flag --data-augmentation (see tpplc --help for details)
• (treeppl#138) Added some distribution functions for manual updates via conjugate priors
• (treeppl#138) Added diversification model example for the birth-death diffusion (BDD) model, version 2 (analogous to ClaDS2).
• (treeppl#138) Added diversification model versions with hard-coded delayed sampling.
• (treeppl#138) Added constant-rate birth-death (CRBD) model using weights based on analytical likelihood rather than simulation.
• (treeppl-python#18) 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.
• (dppl#231) Added previous weight and proposal weight to output of --debug-mcmc
• (miking#986, dppl#234, dppl#236, treeppl#155) Experimental new inference method -m mcmc-graph
• (treeppl#149) Models included with the compiler can now be referenced in imports or as arguments to tpplc via, e.g., treeppl::models/diversification/crbd.tppl

Changed

• (dppl#229) Inference methods using alignment now crash if no aligned assumes were found.
• (dppl#238) SMC-based inference methods now refuse to compile if no observe or weights are found.
• (treeppl-python#18) Python interface: Compile arguments now mirrors the arguments used by tpplc for improved consistency and alignment between interfaces.
• (miking#984, treeppl#135) Command line flags are now split into categories, and some parameters can be given to a compiled model
• (treeppl#143) The debug statement now prints literal strings as-is, while variables are pretty-printed.
• (miking#999) Incompatible flags are reported as such, rather than unrecognized.

Deprecated

Removed

• (treeppl#153) 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.
• (treeppl-python#18) Jupyter interface: Removed legacy syntax highlighting support that was only compatible with older Jupyter Notebook versions.

Fixed

• (treeppl#138) Changed the rho parameter (leaf sampling probability) in the data files for the diversification model scripts from 2.0 to 0.5.
• (dppl#228) Running multiple sweeps with -m mcmc now resets state properly between the runs
• (miking#981) The debug statement now properly handles printing strings
• (treeppl#157) Bug in the code generation for pigeons related flags.

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