From 3b47a8b6a44b674428bd1daaff7cadb7f95a7fbe Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Fri, 14 Aug 2026 10:58:35 +0200 Subject: [PATCH] Update changelog --- CHANGELOG.md | 46 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fe7be354..7af446cd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,51 @@ # PEtab changelog +## 0.9 series + +### 0.9.0 + +This release will require Python>=3.12 and numpy>=2.1. + +**Fixes** +* Fixed the mean of residuals and added an option to choose between + normalized and unnormalized errors in `plot_goodness_of_fit` + (by @plakrisenko in https://github.com/PEtab-dev/libpetab-python/pull/473) +* Made `scipy` a lazy import, so it is no longer required unless + probability distributions are actually used + (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/486) +* Fixed `PetabStrPrinter` for non-integer rational exponents + (by @wshlavacek in https://github.com/PEtab-dev/libpetab-python/pull/489) +* Fixed spurious `nan`-related warnings in `Subplot.from_df` + (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/496) +* Fixed a missing `return` in the noise distribution merge of + `petab1to2`, which caused `noiseDistribution` to always be `NaN` after + conversion + (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/502) +* Fixed the PEtab v2 extension config model + (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/506) +* Fixed SBML math parsing by using `sbmlmath` instead of + `sympy.sympify` + (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/509) + +**Features** +* Added support for PEtab SciML problems, including a dedicated linter + (by @BSnelling, @m-philipps and @dilpath in https://github.com/PEtab-dev/libpetab-python/pull/482 + https://github.com/PEtab-dev/libpetab-python/pull/505, + https://github.com/PEtab-dev/libpetab-python/pull/499, + https://github.com/PEtab-dev/libpetab-python/pull/498, + https://github.com/PEtab-dev/libpetab-python/pull/511, and + https://github.com/PEtab-dev/libpetab-python/pull/513) +* Added support for BNGL models + (by @wshlavacek in https://github.com/PEtab-dev/libpetab-python/pull/508) +* Added linting of the mapping table, and allowed pure annotation-only + mapping entries + (by @m-philipps and @BSnelling in + https://github.com/PEtab-dev/libpetab-python/pull/480 and + https://github.com/PEtab-dev/libpetab-python/pull/500) +* Minor improvements to the v1-to-v2 converter: warn when dropping + `parameterScale`/`initializationPriorType`/`initializationPriorParameters`, + and use the experiments table column order suggested by the PEtab format + (by @m-philipps in https://github.com/PEtab-dev/libpetab-python/pull/479) ## 0.8 series