├── .gitattributes ├── .github ├── style.yapf ├── update_version.py └── workflows │ ├── CI-test.yml │ └── python-publish.yml ├── .gitignore ├── .readthedocs.yaml ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.rst ├── Update_version.md ├── conda-recipe └── meta.yaml ├── docs ├── Makefile ├── doc_requirements.txt ├── logo.png ├── logo.svg ├── make.bat ├── puzzle.svg ├── snapshot.png └── source │ ├── 9_cnapy_integration.rst │ ├── api_reference.rst │ ├── conf.py │ ├── examples │ ├── JN_01_solver.ipynb │ ├── JN_02_analysis.ipynb │ ├── JN_03_plotting.ipynb │ ├── JN_04_strain_design_introduction.ipynb │ ├── JN_05_strain_design_mcs.ipynb │ ├── JN_06_strain_design_nested.ipynb │ ├── JN_07_network_design.ipynb │ ├── JN_08_compression.ipynb │ └── movie.gif │ ├── img │ ├── SmallExample.svg │ ├── SmallExample_mcs1.svg │ ├── SmallExample_mcs2.svg │ ├── e_coli_core.svg │ ├── e_coli_core_SUCP.svg │ ├── e_coli_core_dGCP.svg │ ├── e_coli_core_pGCP.svg │ ├── e_coli_core_wGCP.svg │ └── optcouple.jpg │ └── index.rst ├── environment.yml ├── requirements.txt ├── setup.py ├── straindesign ├── __init__.py ├── compute_strain_designs.py ├── cplex_interface.py ├── efmtool.jar ├── efmtool.py ├── glpk_interface.py ├── gurobi_interface.py ├── indicatorConstraints.py ├── lptools.py ├── names.py ├── networktools.py ├── parse_constr.py ├── pool.py ├── scip_interface.py ├── solver_interface.py ├── strainDesignMILP.py ├── strainDesignModule.py ├── strainDesignProblem.py └── strainDesignSolutions.py └── tests ├── __init__.py ├── conftest.py ├── custom.py ├── iMLcore.xml ├── model_gpr.xml ├── model_small_example.xml ├── model_weak_coupling.xml ├── test_01_load_models_and_solvers.py ├── test_02_lp_optimization.py ├── test_03_plots.py ├── test_04_preprocessing.py ├── test_05_straindesign.py └── test_06_multiprocessing.py /.gitattributes: -------------------------------------------------------------------------------- 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