├── .coveragerc ├── .github └── workflows │ ├── python-package.yml │ └── python-publish.yml ├── .gitignore ├── LICENSE ├── NEWS.md ├── README.rst ├── docs ├── Makefile ├── api.rst ├── api │ ├── balancecheck.rst │ ├── bayesian.rst │ ├── bayesian_util.rst │ ├── command.rst │ ├── database.rst │ ├── datasource_context.rst │ ├── datasource_entry.rst │ ├── datasource_kegg.rst │ ├── datasource_modelseed.rst │ ├── datasource_native.rst │ ├── datasource_reaction.rst │ ├── datasource_sbml.rst │ ├── expression_affine.rst │ ├── expression_boolean.rst │ ├── fastcore.rst │ ├── fastgapfill.rst │ ├── fluxanalysis.rst │ ├── fluxcoupling.rst │ ├── formula.rst │ ├── gapfill.rst │ ├── gapfilling.rst │ ├── graph.rst │ ├── importer.rst │ ├── lpsolver_cplex.rst │ ├── lpsolver_generic.rst │ ├── lpsolver_glpk.rst │ ├── lpsolver_gurobi.rst │ ├── lpsolver_lp.rst │ ├── lpsolver_qsoptex.rst │ ├── manual_curation.rst │ ├── mapmaker.rst │ ├── massconsistency.rst │ ├── metabolicmodel.rst │ ├── moma.rst │ ├── randomsparse.rst │ ├── reaction.rst │ ├── translate_id.rst │ └── util.rst ├── commands.rst ├── conf.py ├── development.rst ├── extensions │ └── doilinks.py ├── faq.rst ├── file_format.rst ├── index.rst ├── install.rst ├── overview.rst ├── references.rst ├── tutorial.rst └── tutorial │ ├── 01-entireEcoli.dot.png │ ├── 02-elementP.dot.png │ ├── 03-combine1.dot.png │ ├── 04-combine2.dot.png │ ├── 05-cpt.dot.png │ ├── 06-cptToy.png │ ├── 07-subsetRxn.dot.png │ ├── 08-subsetCpd.dot.png │ ├── 09-color.dot.png │ ├── 10-details.dot.png │ ├── 11-fba.dot.png │ ├── 12-fva.dot.png │ ├── 13-hideEdges.dot.png │ ├── 14-imagesize.dot.png │ ├── 15-nofpp.dot.png │ ├── 16-array2.dot.png │ ├── Pathway.png │ ├── Robustness_chart.png │ ├── applying_supplemental_data.rst │ ├── constraint_based.rst │ ├── curation.rst │ ├── fpp.rst │ ├── generating_models.rst │ ├── import_export.rst │ ├── modelmapping.rst │ └── psamm-install.rst ├── psamm ├── __init__.py ├── balancecheck.py ├── bayesian.py ├── bayesian_util.py ├── command.py ├── commands │ ├── __init__.py │ ├── chargecheck.py │ ├── console.py │ ├── duplicatescheck.py │ ├── excelexport.py │ ├── fastgapfill.py │ ├── fba.py │ ├── fluxcheck.py │ ├── fluxcoupling.py │ ├── formulacheck.py │ ├── fva.py │ ├── gapcheck.py │ ├── gapfill.py │ ├── genedelete.py │ ├── gimme.py │ ├── masscheck.py │ ├── model_mapping.py │ ├── primarypairs.py │ ├── psammotate.py │ ├── randomsparse.py │ ├── robustness.py │ ├── sbmlexport.py │ ├── search.py │ ├── tableexport.py │ ├── tmfa.py │ └── vis.py ├── database.py ├── datasource │ ├── __init__.py │ ├── context.py │ ├── entry.py │ ├── kegg.py │ ├── modelseed.py │ ├── native.py │ ├── reaction.py │ └── sbml.py ├── expression │ ├── __init__.py │ ├── affine.py │ └── boolean.py ├── external-data │ ├── biomass_compound_descriptions.tsv │ ├── biomass_reaction_descriptions.tsv │ ├── chebi_pH7_3_mapping.tsv │ ├── tcdb_families.tsv │ └── tcdb_substrates.tsv ├── fastcore.py ├── fastgapfill.py ├── findprimarypairs.py ├── fluxanalysis.py ├── fluxcoupling.py ├── formula.py ├── gapfill.py ├── gapfilling.py ├── generate_biomass.py ├── generate_model.py ├── graph.py ├── importer.py ├── importers │ ├── __init__.py │ ├── cobrajson.py │ ├── matlab.py │ └── sbml.py ├── lpsolver │ ├── __init__.py │ ├── cplex.py │ ├── generic.py │ ├── glpk.py │ ├── gurobi.py │ ├── lp.py │ └── qsoptex.py ├── manual_curation.py ├── mapmaker.py ├── massconsistency.py ├── metabolicmodel.py ├── moma.py ├── randomsparse.py ├── reaction.py ├── tests │ ├── __init__.py │ ├── test_balancecheck.py │ ├── test_bayesian.py │ ├── test_command.py │ ├── test_database.py │ ├── test_datasource_entry.py │ ├── test_datasource_kegg.py │ ├── test_datasource_native.py │ ├── test_datasource_reaction.py │ ├── test_datasource_sbml.py │ ├── test_expression_affine.py │ ├── test_expression_boolean.py │ ├── test_fastcore.py │ ├── test_fastgapfill.py │ ├── test_findprimarypairs.py │ ├── test_fluxanalysis.py │ ├── test_fluxcoupling.py │ ├── test_formula.py │ ├── test_gapfill.py │ ├── test_gapfilling.py │ ├── test_gimme.py │ ├── test_graph.py │ ├── test_importer.py │ ├── test_lpsolver_cplex.py │ ├── test_lpsolver_generic.py │ ├── test_lpsolver_lp.py │ ├── test_manual_curation.py │ ├── test_mapmaker.py │ ├── test_massconsistency.py │ ├── test_metabolicmodel.py │ ├── test_model-generation.py │ ├── test_moma.py │ ├── test_psammotate.py │ ├── test_randomsparse.py │ ├── test_reaction.py │ ├── test_robustness.py │ ├── test_tmfa.py │ ├── test_translate_id.py │ ├── test_util.py │ └── test_vis.py ├── translate_id.py └── util.py ├── setup.cfg └── setup.py /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zhanglab/psamm/HEAD/.coveragerc -------------------------------------------------------------------------------- /.github/workflows/python-package.yml: -------------------------------------------------------------------------------- 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