PEtab-dev/libpetab-python: libpetab-python v0.9.0

Zenodo (CERN European Organization for Nuclear Research)

Abstract

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, https://github.com/PEtab-dev/libpetab-python/pull/513, and https://github.com/PEtab-dev/libpetab-python/pull/516) 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)

Authors 21

1. Daniel Weindl

   University of Bonn

   Affiliation as printed

   University of Bonn // @ICB-DCM

2. Yannik Schaelte
3. Dilan Pathirana
4. Polina Lakrisenko

   University of Bonn

   Affiliation as printed

   University of Bonn

5. Fabian Fröhlich

   The Francis Crick Institute

   Affiliation as printed

   The Francis Crick Insitute

6. Simon Merkt
7. Carolin Loos
   Affiliation as printed

   @ICB-DCM

8. ErikaDudkin
9. Maren Philipps
10. Paul L. Stapor
    Affiliation as printed

    TNG, Technology Consulting GmbH

11. Jan Hasenauer
12. BSnelling
13. Paul Jonas Jost
14. Lorenzo Contento
    Affiliation as printed

    @PumasAI

15. DantongWang
16. Elba Raimundez
17. Frank Bergmann

    Heidelberg University

    Affiliation as printed

    Heidelberg University

18. Jakob Vanhoefer

    University of Bonn

    Affiliation as printed

    IRU Biomathematics @ Uni Bonn

19. Bill Hlavacek

    Los Alamos National Laboratory

    Affiliation as printed

    Los Alamos National Laboratory

20. Charles Tapley Hoyt Aachen

    RWTH Aachen University

    Affiliation as printed

    RWTH Aachen University

21. LaraFuhrmann