From 6b104a1420cbfd7e0e2de54ca9a7b459c21c978c Mon Sep 17 00:00:00 2001 From: Fredrik Ronquist Date: Thu, 26 Mar 2026 15:32:12 +0100 Subject: [PATCH 1/4] Changed changelog so that it is based on the latest release Rebasing to include recent additions to changelog. --- docs/changelog.md | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/docs/changelog.md b/docs/changelog.md index c2d62fe..4d7f8f2 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -14,6 +14,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added +- 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`). +- 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. + ### Changed ### Deprecated @@ -44,3 +49,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Using `debug` to print strings no longer crashes ### 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 + From 4eba6517d03352f769162fc32e466ab150b4a3ff Mon Sep 17 00:00:00 2001 From: Fredrik Ronquist Date: Thu, 26 Mar 2026 16:16:24 +0100 Subject: [PATCH 2/4] Added more info about the changes in the divmodels pull request --- docs/changelog.md | 25 +++++-------------------- 1 file changed, 5 insertions(+), 20 deletions(-) diff --git a/docs/changelog.md b/docs/changelog.md index 4d7f8f2..0617a71 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -14,39 +14,24 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added -- 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`). +- 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. ### Changed -### Deprecated - -### Removed - -### Fixed - -### 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 +- Moved the functions `exp`, `log`, `sqrt`, `minInt`, `maxInt`, `floor`, `ceil`, `round` from the `standard.tppl` library file to `math.tppl`. ### 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. + ### Fixed -- Using `debug` to print strings no longer crashes +- Changed the `rho` parameter (leaf sampling probability) in the data files for the diversification model scripts from `2.0` to `0.5`. ### Security From f5458be08f198ed43f6115c5f75ff80b89ebaec3 Mon Sep 17 00:00:00 2001 From: Fredrik Ronquist Date: Fri, 27 Mar 2026 04:30:46 +0100 Subject: [PATCH 3/4] Added comment about the import of math.tppl in model files --- docs/changelog.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/changelog.md b/docs/changelog.md index 0617a71..70bd24e 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed - Moved the functions `exp`, `log`, `sqrt`, `minInt`, `maxInt`, `floor`, `ceil`, `round` from the `standard.tppl` library file to `math.tppl`. +- Added import of `math.tppl` where needed to example model files. ### Deprecated From 865cae18f4932651d1317d6cb43d9881e43f42b5 Mon Sep 17 00:00:00 2001 From: Viktor Palmkvist Date: Thu, 23 Apr 2026 15:21:09 +0200 Subject: [PATCH 4/4] Remove mention of math imports, implied by other comments and a bit too much internal detail --- docs/changelog.md | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/changelog.md b/docs/changelog.md index 70bd24e..0617a71 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -22,7 +22,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed - Moved the functions `exp`, `log`, `sqrt`, `minInt`, `maxInt`, `floor`, `ceil`, `round` from the `standard.tppl` library file to `math.tppl`. -- Added import of `math.tppl` where needed to example model files. ### Deprecated