Because of some issue with the propagation of the metabolite ids with
optlang and gurobipy (opencobra/cobrapy#819)
the reconstruct_scoGEM.py doesn't work with gurobi as the solver.
Therefore, glpk is used as solver in the reconstruction of ScoGEM, these
changes are incorporated into reconstruct_scoGEM.py
Additionally, this revealed an issue that was adressed but not solved properly in
fix_iKS1317_issues.py, but solved in fix_issue33_annotation_bugs.py.
This was very confusing. Thus, this issue is now sorted out completely
in fix_iKS1317_issues.py, and removed from
fix_issue33_annotation_bugs.py.
Finally, I've upgraded cobrapy to 0.14.2 in the requirements, as this
was wrongly suggested to cause the issued described above (see also PR
73)
I've rerun the model reconstruction and exported the model files.
Because of some issue with the propagation of the metabolite ids with optlang and gurobipy (opencobra/cobrapy#819) the
reconstruct_scoGEM.pydoesn't work with gurobi as the solver. Therefore, glpk is used as solver in the reconstruction of ScoGEM, these changes are incorporated intoreconstruct_scoGEM.pyAdditionally, this revealed an issue that was adressed but not solved properly in
fix_iKS1317_issues.py, but solved infix_issue33_annotation_bugs.py. This was very confusing. Thus, this issue is now sorted out completely infix_iKS1317_issues.py, and removed fromfix_issue33_annotation_bugs.py.Finally, I've upgraded cobrapy to 0.14.2 in the requirements, as this was wrongly suggested to cause the issued described above (see also PR
73)
I've rerun the model reconstruction and exported the model files.
develas a target branch (top left drop-down menu)