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Add `src/python/v1_v2.py`, which converts the v1 problems without a v2 encoding with `petab1to2(reparametrize="all")` (requires libpetab-python#539), and its output for 32 problems. `Froehlich_CellSystems2018` is skipped, because the generated condition table is huge. The existing v2 encodings of `Boehm_JProteomeRes2014` and `Schwen_PONE2014` are kept. These conversions are a starting point for testing v2 tools; refinement follows separately. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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src/python/v1_v2.pyand its output: mechanical PEtab v2 conversions of all v1 problems that don't have a v2 encoding yet, generated withpetab1to2(reparametrize="all")from PEtab-dev/libpetab-python#539. All estimated log-scaled parameters are reparametrized aslog10_<id>/log_<id>, except where that isn't possible (e.g., parameters used as placeholder overrides). The existing hand-refined encodings ofBoehm_JProteomeRes2014andSchwen_PONE2014are kept.Froehlich_CellSystems2018is skipped, because the generated condition table is huge.This is meant as a starting point for testing v2 tools. Refinement of the individual problems follows separately.
For all converted problems except the large ones (
Chen_MSB2009,Lang_PLOSComputBiol2024,Smith_BMCSystBiol2013,SalazarCavazos_MBoC2020), log-likelihood and gradient computed with AMICI agree between v1 and v2 (relative llh difference ≤ 2e-8, gradient difference ≤ 4e-4 relative to the largest gradient entry, at nominal and at shifted parameters).Known issues:
bmp-petablintfails forFujita_SciSignal2010andGiordano_Nature2020due to unused conditions, which are only a warning. Fixed in Don't failpetablintfor PEtab v2 problems with only warnings PEtab-dev/libpetab-python#569 (petablintfails for PEtab v2 problems with only warnings PEtab-dev/libpetab-python#567), requires a new libpetab release.Brannmark_JBC2010andIsensee_JCB2018, the pre-existingexperimentIdcolumn of the v1 measurement table is renamed to a randomexperiment_id_<uuid>column, so re-running the conversion changes the files (petab1to2: random column name for pre-existingexperimentIdcolumn PEtab-dev/libpetab-python#568).Supersedes #270.
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