From 2f4ac61cc5d2667a98045856d8f9dee344c9b7de Mon Sep 17 00:00:00 2001 From: Jan Kudlicka Date: Wed, 29 Apr 2026 16:06:02 +0200 Subject: [PATCH] Update changelog (related to update of the Python interface). --- docs/changelog.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/changelog.md b/docs/changelog.md index c14dbc9..33c6ca0 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -19,16 +19,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - 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