├── .gitattributes ├── .github └── workflows │ └── python-package.yml ├── .gitignore ├── .travis.yml ├── CLAI ├── LICENSE.txt ├── MANIFEST.in ├── README.rst ├── data ├── README.rst └── thermo_data.thermodb ├── doc ├── .gitignore ├── Makefile ├── autodoc.sh ├── conf.py ├── index.rst ├── integrating_metabolomics.rst ├── make.bat ├── model.rst ├── quickstart.rst ├── requirements.txt ├── solver.rst └── thermoDB.rst ├── docker ├── .bashrc ├── .dockerignore ├── .gitattributes ├── .gitignore ├── Dockerfile ├── README.md ├── build ├── build.bat ├── mplimporthook.py ├── requirements.txt ├── run ├── run.bat ├── solvers │ └── instructions.txt ├── src │ └── add_your_external_packages_here ├── utils │ ├── activate_gurobi.sh │ ├── gurobi.lic.template │ ├── install_cplex.sh │ └── install_gurobi.sh └── work │ └── This_is_your_shared_space.txt ├── models ├── .gitattributes ├── README.rst ├── glycolysis.mat ├── iJO1366.json ├── iJO1366 │ ├── compartment_data.json │ └── lexicon.csv ├── small_ecoli.mat └── small_ecoli │ ├── compartment_data.json │ └── lexicon.csv ├── pytfa ├── __init__.py ├── analysis │ ├── __init__.py │ ├── chebyshev.py │ ├── manipulation.py │ ├── sampling.py │ └── variability.py ├── core │ ├── __init__.py │ └── model.py ├── io │ ├── __init__.py │ ├── base.py │ ├── dict.py │ ├── enrichment.py │ ├── json.py │ ├── plotting.py │ └── viz.py ├── optim │ ├── __init__.py │ ├── config.py │ ├── constraints.py │ ├── debugging.py │ ├── meta.py │ ├── reformulation.py │ ├── relaxation.py │ ├── utils.py │ └── variables.py ├── redgem │ ├── __init__.py │ ├── debugging.py │ ├── lumpgem.py │ ├── network_expansion.py │ ├── redgem.py │ └── utils.py ├── thermo │ ├── __init__.py │ ├── equilibrator.py │ ├── metabolite.py │ ├── reaction.py │ ├── std.py │ ├── tmodel.py │ └── utils.py └── utils │ ├── __init__.py │ ├── logger.py │ ├── numerics.py │ └── str.py ├── requirements.txt ├── setup.cfg ├── setup.py ├── tests ├── .gitignore ├── lpdiff.py ├── pytest.ini ├── redgem_params.yml ├── 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