Execution of multiple event assignments from the same event about amici

[FFroehlich]

AMICI/python/sdist/amici/sbml_import.py

Lines 1670 to 1673 in da19a55

	# else the species was affected by an event assignment,
	# hence the updated value should be updated further.
	else:
	species_value = bolus[state_vector.index(species_sym)]

I'd say, in the else case, that assignment should be ignored.

Example: Assuming a model with a concentration-based species S in compartment C, and an event with two event assignments – EA_S assigning to S and EA_C assigning to C. In this case, S should only change due to EA_S, but not due to the volume change caused by EA_C. Currently, first EA_S is applied, then EA_C.

Correct?

Yes, sounds correct.

[dweindl]

Might have been correct before. I don't quite understand why, yet. But changing that leads to failures in:

• https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01779/01779-model.m
• https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01780/01780-model.m
• https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic/01506/01506-model.m

[dweindl]

From elsewhere in the SBML spec (sec 4.6.8):

There is one exception: if
the species’ quantity is determined by an AssignmentRule, RateRule, AlgebraicRule, or an EventAssignment
and the species has the attribute value hasOnlySubstanceUnits=“false”, it means that the concentration
is assigned by the rule or event; in that case, the amount must be calculated when the compartment size
changes.

It's not exactly intuitive and quite possibly a common source of error, but the present implementation is correct.