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Adds a check to prevent rate rule conversion when species from different compartments appear in the same rate rule. This change ensures that the converter correctly handles models with multiple compartments and avoids generating invalid or unexpected results. Also, adds example models for testing.
particularly useful given that std::list it does not exist in older versions
fbergmann
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Dec 29, 2025
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Thank you so much, I've tested with BioMD 299, and it worked as expected.
While I think that speciesFromMultipleCompartmentsInSameRateRule looks way more complicated than it should (6 levels of indentation), it's fine. No need to change to a hash_map for simpler access.
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Description
Ratel to reaction conversion will only fail with multiple compartments if the species referred to in a given rate rule come from different compartments
Motivation and Context
Types of changes
Checklist:
Testing