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matthiaskoenig / fbc_curation

FROG analysis in python for the reproducibility of FBC models
https://runfrog.de
GNU Lesser General Public License v3.0
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fbc_curation does not set the solver and metadata can be misleading #63

Open glucksfall opened 2 years ago

glucksfall commented 2 years ago

Hello,

I tried fbc_curation for a couple of models using a system installation. Because results using cobrapy and cameo were different (fva/gene KO's) I decided to install the software in a virtual environment. I didn't install gurobipy in the virtual environment, while the system has it installed. Unexpectedly, the results from system vs venv installations differed even more.

I checked the code and the solver glpk is not set explicitly. So, metadata (line 39 in cobrapy_curator.py and line 47 in cameo_curator.py) misleads if gurobipy is installed in the python path and selected by cobrapy as the solver.

Best,