PEtab v2 import #2974
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PEtab v2 import #2974
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Codecov Report❌ Patch coverage is
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## main #2974 +/- ##
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+ Coverage 76.71% 77.38% +0.67%
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Files 309 311 +2
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Branches 1497 1500 +3
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- Misses 4621 4648 +27
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FFroehlich
approved these changes
Nov 7, 2025
| # compile amici model | ||
| if case.startswith("0006") and not jax: | ||
| # TODO: petab.flatten_timepoint_specific_output_overrides(problem) | ||
| # petab.flatten_timepoint_specific_output_overrides(problem) |
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Other tests suggest this is now supported
| # TODO: So far, PEtab can only upgrade file-based problems, | ||
| # not petab.v1.Problem objects. | ||
| raise NotImplementedError( | ||
| "Only `petab.v2.Problem` is currently supported. " |
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should this error message explicitly mention incompatibility with file based problems to avoid confusion?
| ): | ||
| target_entity.value = expr | ||
| else: | ||
| # if the target is not an expression, it must be an |
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TODO: would be more efficient to convert this into a multi-model problem, but who knows whether we will ever get around to implementing that.
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Experimental import of SBML- and PySB-based PEtab v2 problems.
Not particularly performant or feature-complete yet - to be extended.
Closes #2662.
👀 https://amici--2974.org.readthedocs.build/en/2974/examples/example_petab/petab_v2.html
👀 https://amici--2974.org.readthedocs.build/en/2974/generated/amici.petab.petab_importer.html#module-amici.petab.petab_importer