2456 showed that we need the parameter table for proper PEtab import, but there is no option to pass the parameter table as individual file (since in the early days, we didn't (think we'd) need it). To avoid any surprises and wrong gradients there, I'd suggest to remove this functionality as part of fixing #2455.
Independent of this specific issue, I think it would be good to allow removing deprecated functionality not only in major releases, but also in minor releases after a certain transition period (maybe 1y after the first release containing the deprecation warning? after 3 minor releases? ...? See also, for example, numpy's policy). Opinions? @FFroehlich?
Remove deprecated functionality for PEtab import from individual files instead of petab.Problem:
https://github.com/AMICI-dev/AMICI/blob/3fbb90be64a1aafd8d0ed61404a60f867a42a584/python/sdist/amici/petab/sbml_import.py#L32-L37
2456 showed that we need the parameter table for proper PEtab import, but there is no option to pass the parameter table as individual file (since in the early days, we didn't (think we'd) need it). To avoid any surprises and wrong gradients there, I'd suggest to remove this functionality as part of fixing #2455.
There has been a DeprecationWarning in place for almost 2 years (https://github.com/AMICI-dev/AMICI/pull/1810) and I think this isn't used anyways.
Independent of this specific issue, I think it would be good to allow removing deprecated functionality not only in major releases, but also in minor releases after a certain transition period (maybe 1y after the first release containing the deprecation warning? after 3 minor releases? ...? See also, for example, numpy's policy). Opinions? @FFroehlich?