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PySCeS / pysces

The official PySCeS project source code repository.
https://pysces.github.io
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SBML translation of log #53

Closed bgoli closed 3 years ago

bgoli commented 3 years ago

Should fix #45

jmrohwer commented 3 years ago

I picked up another issue with the L3 formula parsing, i.e. && which should be replaced with and. Fixed in 4e7254e. The test models in https://github.com/PySCeS/pyscesdev/tree/main/sbml_test_models now all covert to PSC without error. All except 235 also execute and give the correct answers when compared to the curation data on BioModels. Model 860 gives some error in the SBML conversion about units not being able to be interpreted correctly, but the model runs and gives the correct numeric answer.

Model 235 executes the simulation correctly but fails in the end during REq evaluation. Not sure if this should be pursued further, this is a gene regulatory network model, maybe it fails because there are no fluxes?

Jupyter notebook with execution results for all the models uploaded to pyscesdev/sbml_test_models as well.

jmrohwer commented 3 years ago

Why are you adding all the PSC files to psc when they are already in pscmodels? They are duplicated. Seems like a remnant from an improper in-place install or executing the python interpreter from the source directory. :confused:

bgoli commented 3 years ago

I use a developer mode installation so run everything in-place I'll add that folder to .gitignore