Support valid AMICI noise distributions that are invalid in PEtab #1157
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❗ Your organization needs to install the Codecov GitHub app to enable full functionality. @@ Coverage Diff @@
## develop #1157 +/- ##
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- Coverage 88.16% 84.35% -3.82%
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Files 79 148 +69
Lines 5257 11681 +6424
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+ Hits 4635 9853 +5218
- Misses 622 1828 +1206
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dweindl
reviewed
Oct 25, 2023
pypesto/petab/importer.py
Outdated
| @@ -280,7 +281,7 @@ def create_model( | |||
| logger.info( | |||
| f"Compiling amici model to folder " f"{self.output_folder}." | |||
| ) | |||
| self.compile_model(**kwargs) | |||
| self.compile_model(validate=self.validate_petab, **kwargs) | |||
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This fails for pysb models. Pass validate only if from petab.models import MODEL_TYPE_SBML; petab_problem.model.type_id == MODEL_TYPE_SBML. Requires petab>=0.1.27
FFroehlich
approved these changes
Oct 26, 2023
This was referenced Nov 15, 2023
Merged
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The PEtab importer will throw "invalid PEtab" errors if a user requests e.g. a negative binomial noise distribution. The user can skip the validation check with
PetabImporter(..., validate_petab=False). However, AMICI will still complain about the invalid PEtab [1], becausevalidate_petabisn't passed to AMICI. This PR fixes this, s.t. users can use any AMICI noise distribution [2].[1] https://github.com/AMICI-dev/AMICI/blob/3c5e997df3655c26dde35705ef25b2a0f419fe8b/python/sdist/amici/petab_import.py#L565
[2] https://github.com/AMICI-dev/AMICI/blob/3c5e997df3655c26dde35705ef25b2a0f419fe8b/python/sdist/amici/import_utils.py#L182-L188