Christian Diener
Christian Diener
Not sure if it helps, but I have seen similar issues if you have sympy installed within a conda environment and via the normal non-conda pip as well. Uninstalling the...
Good idea. We already have rich as a dependency, so would be better to use rich.progress.track for that. There should also be a toggle to turn that on and off,...
OSQP is not a good solver for linear problems. GLPK - or CPLEX/Gurobi for larger models - will perform better here.
Alternatively, you can try to lower the tolerance, and it might converge by doing: ``` merged_model.solver = "osqp" merged_model.tolerance = 1e-4 solution =cobra.flux_analysis.pfba(merged_model) return solution ```
Yep, unfortunately not supported yet. There is current work to bring it to SBML and JSON (see the respective PR). MAT is on the horizon but will probably still take...
The newer discussion is in #1240 and the previous PR is in #996.
A JSON object is not the same as an object in Python but rather a something like a dict (https://restfulapi.net/json-objects/). @zakandrewking when you said that the JSON schema allows annotations...
This looks good to me and has the advantage that is already valid under the current schema which makes it backwards compatible.
Oh I see so the problem is that loading it does not throw an error because it should not pass the schema.
@Hemant27031999 yeah I saw the the same thing. I think this is due to schema validation being really slow and reading JSON is currently really fast. Also most validation is...