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sbmlteam / sbml-test-suite

The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML support provided in a software package.
https://sbml.org/software/sbml-test-suite/
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tests with compartment volume assignments #90

Closed FFroehlich closed 1 year ago

FFroehlich commented 1 year ago

Thanks to https://github.com/AMICI-dev/AMICI/issues/2062 we just realised there are a couple of edge cases with volume assignment rules that we did not handle adequately in AMICI. As we are passing all test cases that do not contain any features that we explicitly do not support (we do not support a subset of compartment assignments via events), we have reason to believe the test-suite currently does not sufficiently cover concentration changes due to volume changes.

luciansmith commented 1 year ago

You closed this--if I'm reading the issue correctly, the problem is not the SBML file itself, but re-setting the initial conditions of a model after the SBML is read? And thus wouldn't be covered by the SBML test suite?

It could be covered by a SED-ML test suite with some ModelChanges, I think; I'll keep that in mind if we get to create such a beast.

FFroehlich commented 1 year ago

You closed this--if I'm reading the issue correctly, the problem is not the SBML file itself, but re-setting the initial conditions of a model after the SBML is read? And thus wouldn't be covered by the SBML test suite?

Yes, that's correct. It's still relevant for systems where compartments (and potentially also species) are assigned via events, but there likely already are tests for that already and we simply currently don't support those events.

luciansmith commented 1 year ago

Thanks!