Maren Philipps
PetabImporter does not check for existing amici models in location specified by output_folder arg.
**Bug description** When using the `PetabImporter` the amici model is re-compiled although it is already available at the location specified by the `output_folder` argument. Before compiling the amici model the...
**Bug description** `visualize.parameters` fails with `ValueError` when some of the optimization starts failed, i.e. `result.optimize_result[i]['x']` is `None`: ``` ---> 17 pypesto.visualize.parameters( 18 results=result, 19 start_indices="all", 20 reference=reference, 21 ) File...
- Switch from no longer maintained `pyjulia` to `juliacall` package (#1397) - Update example; switch to using `ForwardDiff`
The Julia objective makes use of the `pyjulia` package to call Julia code from Python. According to their website, "Ongoing development of the Python/Julia interface has transitioned to [PythonCall.jl/juliacall](https://github.com/JuliaPy/PythonCall.jl)". The...
For the paper https://doi.org/10.1186/s12918-016-0319-7 the Journal is BMC Systems Biology and the proper ISO 4 abbreviation is `BMC Syst. Biol.`.
- add a documentation example for performing gradient checks (closes #1481) - fix #1494 I'd be happy about suggestions on the "Best practices" and "How to fix my gradients".
Gradient check for an `AmiciObjective` ```python pypesto_problem.objective.check_gradients_match_finite_differences( x=startpoints[0], ) ``` invokes an error: ``` Traceback (most recent call last): File "", line 1, in File "/home/maren/pyPESTO/pypesto/objective/amici/amici.py", line 665, in check_gradients_match_finite_differences...
The test for [`PetabImportTest.test_check_gradients`](https://github.com/ICB-DCM/pyPESTO/blob/58c7b5fcdcc54690f80f8d4e3e407e39420560b9/test/petab/test_petab_import.py#L117-L136) asserts that the gradients are `False`, in contrast to the description in L119.
**Checklist for the submission of new PEtab problems** - [ ] The PEtab problem is based on a model that is peer-reviewed and published - [ ] The problem ID...
Yuhong's publication on oncolyte virus therapy in zebrafish has a model in PEtab format, at the moment in the preprint phase.