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Update changelog (related to update of the Python interface). #52

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3 changes: 3 additions & 0 deletions docs/changelog.md
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Expand Up @@ -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

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