-
A 1-line python API to the linter would be nice, basically calling petablint::main with arguments.
-
**Feature description**
Currently we have several different (rather redundant) gradient checking routines, which only have slightly different functionalities, which in my opinion do not all justify b…
-
Implement parameter priors
(How to prevent over-weighting in mini-batch optimization?)
-
specifying 'noiseFormula' as 'lambda reg' will make
https://github.com/ICB-DCM/AMICI/blob/16e3d762a94a35d21825f904d9d4381f82d117ab/python/amici/petab_import.py#L502
fail since `sp.sympify('lam…
-
If in the visualization table, the column XValues is not provided, it is inferred:
- if in measurement file measurement time is not constant, then XValues = 'time' ->plot time course
- if its const…
-
At the moment, there can be `NaN`s (after `pd.read_csv`) in optional PEtab string columns, such as `observableNames`, that, if interpreted as a string, are converted to the string literal `'nan'`.
``…
-
I'd suggest: At some point, https://github.com/icb-dcm/petab should be run automatically as a test and used to check every new model before adding it to the official list of models, or essentially eve…
-
**Bug description**
Many of these messages in the log file, possibly every function evaluation during optimization.
```
Using existing amici model in folder /.../amici_models/icg_body.
```
**Ex…
-
Reported by @plakrisenko
The measurements and simulation are almost identical.
Comparing the data [1] and simulation [2] from the original benchmark collection.
- [1] seems to correspond with …
-
When petab problem is imported in pypesto would be good to update parameter names according to the scale: `lin`, `log` or `log10`.
In case being `lin` leave as it is. In case any of the others change…