Fixes for named stoichiometries#1312
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luciansmith merged 13 commits intodevelopfrom Mar 24, 2026
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The stoichiometry branch was failing all over the place; try to recreate the changes one by one instead.
It would work if we sent 'regenerateModel' the current SBML... but that breaks other things.
The fix has to go in LLVMModelGenerator.cpp, and the now-uncommented code has to go earlier.
Last time I got this close to working, calling steadyState twice didn't work. Now it does!
* Put stubs for init stoichiometries * Throw error on variable stoichiometries * Put stoichiometry names in ID list. * Allow 'init(n)' to set/get initial stoichiometries (which are actually unchanging: setting 'init' or not does the same thing) * Drop the function that claimed to set multiple stoichiometries, since it actually did not. * Add convenience function to get a particular stoichiometry id (either its name or "stoich(sp, rxn)") * Stoichiometry seletion record names fixed.
SAVE_STATE_21 was simply incorrect: it never should have worked. Technically, the test suite models that have an assignment rule that never changes will 'work' in roadrunner, but only coincidentally: the assignment rule is never evaluated in an context other than as an effective initial assignment. Model 1121 was another model like that; just switch to 1122 instead for the test (which wasn't supposed to be 'about' assigned stoichiometries anyway.)
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The stoichiometry branch was failing all over the place; try to recreate the changes one by one instead.