Handle reserved names in PEtab parameter mapping #2461
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@FFroehlich : Do you see a problem with keeping the original IDs as parameter/state/... IDs and only using the prefixes in the sympy / C++ symbols? This would anyways be more convenient for users. |
sounds good! |
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Note for implementation: This will require moving the reserved-names handling from SbmlImporter to DEModel or DEExporter. This would anyways be a good idea. In particular, in the context of potentially extracting SBML to ODE conversion from AMICI into a separate package in the future. |
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Avoid symbolic replacements for handling reserved symbols in amici. Instead, only handle them during code printing. This has the advantage that users won't be bothered by changed IDs. This, however, makes it a breaking change for anybody currently relying on "amici_*" entity IDs. I don't expect this to be much of a problem, since probably most users would have renamed their model entities to avoid this "amici_"-prefixing. Fixes AMICI-dev#2461.
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Some model entity IDs are replaced by
amici_{actual_id}during model import, but the current PEtab parameter mapping generated byamici.petab.parameter_mapping.create_parameter_mappingwill contain the original IDs instead of the amici-model-IDs. This needs to be changed.See ICB-DCM/pyPESTO#1418
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