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ICB-DCM / pyPESTO

python Parameter EStimation TOolbox
https://pypesto.readthedocs.io
BSD 3-Clause "New" or "Revised" License
216 stars 47 forks source link

Decouple PEtab and AMICI #1301

Open dilpath opened 7 months ago

dilpath commented 7 months ago

Currently, the PEtab importer depends on AMICI, so I have to install AMICI to use it. However, I use PEtab+pyPESTO in a few applications that do not involve AMICI. Using the PEtab importer to create the pyPESTO problem is convenient, and I supply a custom (non-AMICI) objective to PetabImporter.create_problem(objective=custom_objective). Having it default to using an AMICI objective is fine, but then the imports etc need to handled properly when AMICI is not available.

PaulJonasJost commented 7 months ago

Agreed. Will need to adjust this for me as well for integrating roadrunner. Will have a look at it.