Decouple PEtab and AMICI

Open dilpath opened this issue 2 years ago • 1 comments

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.

Feb 01 '24 16:02 dilpath

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

Feb 02 '24 10:02 PaulJonasJost