Support for PEtab SciML in jax #2614
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #2614 +/- ##
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+ Coverage 76.48% 77.25% +0.76%
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Files 308 309 +1
Lines 19540 19804 +264
Branches 1499 1500 +1
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+ Hits 14945 15299 +354
+ Misses 4582 4492 -90
Partials 13 13
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dweindl
reviewed
Oct 29, 2025
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Please add to python_examples.rst
| ignore:Conservation laws for non-constant species in models with RateRules are currently not supported and will be turned off.:UserWarning | ||
| ignore:Conservation laws for non-constant species in models with Species-AssignmentRules are currently not supported and will be turned off.:UserWarning | ||
| ignore:Conservation laws for non-constant species in combination with parameterized stoichiometric coefficients are not currently supported and will be turned off.:UserWarning | ||
| ignore:PEtab v2.0.0 mapping tables are only partially supported:UserWarning |
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Still relevant? I couldn't see that warning anywhere.
| allow_reinit_fixpar_initcond: bool | None = True, | ||
| generate_sensitivity_code: bool | None = True, | ||
| model_name: str | None = "model", | ||
| hybridisation: dict | None = None, |
| Parses the hybridisation information and updates the model accordingly | ||
| :param hybridization: | ||
| hybridization information |
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This could be more informative 😅
Is this documented in petab-sciml? Add reference?
| } | ||
| if len(outputs.keys()) != len(net["output_vars"]): | ||
| raise ValueError( | ||
| f"Could not find all output variables for neural network {net_id}" |
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Include the missing ones in the message?
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| True | ||
| if p | ||
| in set(self._parameter_mappings[sc].map_sim_var.keys()) | ||
| else False |
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Suggested change
| True | |
| if p | |
| in set(self._parameter_mappings[sc].map_sim_var.keys()) | |
| else False | |
| p in set(self._parameter_mappings[sc].map_sim_var.keys()) |
| } | ||
| for net_id, net_config in config["neural_nets"].items() | ||
| } | ||
| if not jax or petab_problem.model.type_id == MODEL_TYPE_PYSB: |
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Suggested change
| if not jax or petab_problem.model.type_id == MODEL_TYPE_PYSB: | |
| if not jax or petab_problem.model.type_id != MODEL_TYPE_SBML: |
More future-proof.
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| # for backwards compatibility | ||
| import_model = import_model_sbml |
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Suggested change
| # for backwards compatibility | |
| import_model = import_model_sbml |
This has been removed in main, I guess it's an unintentional merge leftover.
| self.sbml_doc.validateSBML | ||
| )() | ||
| _check_lib_sbml_errors(self.sbml_doc, self.show_sbml_warnings) | ||
| # _check_lib_sbml_errors(self.sbml_doc, self.show_sbml_warnings) |
| # the SBMLError log in the sbml document. Thus, it is sufficient to | ||
| # check the error log just once after all conversion/validation calls. | ||
| _check_lib_sbml_errors(self.sbml_doc, self.show_sbml_warnings) | ||
| # _check_lib_sbml_errors(self.sbml_doc, self.show_sbml_warnings) |
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