Moritz E. Beber
Moritz E. Beber
In your notebook, you load the model successfully. Did you try to write it to SBML it without modifying the reactions' annotation attribute?
Okay, I think we need to implement a better solution here. Probably, a wrapper that can upgrade old JSON versions to the newer format.
No idea, if it's still alive tbh. It's probably not worth the effort but I feel personally responsible for the current JSON reading mess.
@Hemant27031999 I am really glad for all the work that you're putting into cobrapy. Some of the changes that you propose are quite far reaching. I assume that this work...
In a far future we should get redGEM and lumpGEM from Hatzimanikati's lab in Python but this is a good start indeed!
Another option is to transform it to a string since Python is perfectly capable of parsing `float("inf")`, `float("-inf")`, or even `float("nan")`.
The rumors are true :laughing: https://github.com/opencobra/cobrapy/blob/374ebfed7345eef6b32d8b7e6311676cb6232b17/cobra/io/json.py#L141 The current JSON schema desperately needs an update anyway in order to accommodate groups and compartments. So it wouldn't be a problem to change...
The reason I set `allow_nan=False` at the time is that it is not part of the official JSON spec. Since the JSON format is used by more tools than just...
> However, there is a potential caveat here. Basically if your zero tolerance is stricter than your solver tolerance you get nonsense. We should throw a warning in that case....
> There is already one Model class that is "a faithful Python representation of an SBML model", that is the SBML model class from the libsbml API. Anything else we...