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Decouple PEtab and AMICI #1301

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dilpath opened this issue Feb 1, 2024 · 1 comment · Fixed by #1442
Open

Decouple PEtab and AMICI #1301

dilpath opened this issue Feb 1, 2024 · 1 comment · Fixed by #1442
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enhancement New feature or request

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@dilpath
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dilpath commented Feb 1, 2024

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.

@dilpath dilpath added the enhancement New feature or request label Feb 1, 2024
@PaulJonasJost PaulJonasJost self-assigned this Feb 2, 2024
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PaulJonasJost commented Feb 2, 2024

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

@dweindl dweindl linked a pull request Sep 9, 2024 that will close this issue
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