AMICI
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AMICI-dev
Advanced Multilanguage Interface to CVODES and IDAS
Add downstream tests of tools that depend on AMICI and for which we want to ensure near-continuous compatibility (e.g. pyPESTO). These tests are not expected to pass, but can inform...
This implements a proof of concept for the PEtab [multi-language proposal](https://github.com/PEtab-dev/PEtab/pull/538). Handles PySB-PEtab problems using the recent PEtab model abstraction (https://github.com/PEtab-dev/libpetab-python/pull/145). Should remove the need for the current `PysbPetabProblem` and...
this has not been tested thoroughly yet and might fail
- Throw warning if specified observable is not contained in model expressions
Currently, `import_petab_problem` checks for an importable model with the given name and skips import if it finds one. It's the user's responsibility to ensure re-import if anything changed. It would...
Was removed in #1498 due to erroneous implementation. - parameters are now scaled within `simulate_petab` - added FD checks, essentially copied from `pypesto.objective.ObjectiveBase.check_grad{_multi_eps}` [1] - added a test case: a...
When trying to execute a PETab problem with a model with initial events via ``` petab_problem = petab.Problem.from_yaml(yaml_file) model = import_petab_problem(petab_problem) simulate_petab(petab_problem, model) ``` I get the following errors ```...
This one is to replace #1245. However, it seems like in the long time of divergence, there were changes to functions from sbml_import, that may be not captured, as these...