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Update version number for minor release.
…e strings. Also, don't log errors and then throw that same error; that's redundant.
Hopefully fix for sbmlteam/python-libsbml#40 , since at least one of the linked issues claims that the underlying swig bug is 'fixed'. Hopefully this means 'with 4.4.1'.
Update swig version.
As a first pass at fixing named stoichiometries, throw on invalid name strings.
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.)
We're getting github complaints about node20 vs. node24.
Fixes for named stoichiometries
It turns out 'r.n' didn't actually work. This hopefully fixes it! Also, update the version number.
In python, r['n'] was working, but not r.model['n']. Hopefully this fixes the latter.
… imitate getConservedMoietyIds.
The python bindings were getting 'n' from r.model['n'], which didn't work. This was because I was calling 'getStoichiometry' wrong in LLVMExecutableModel. Added tests for this on the C++ side.
Fixes using a stoichiometry name as an ID on a roadrunner object.
Try re-enabling python tests on mac.
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