INSTALL.rst
LICENSE
MANIFEST.in
README.rst
pyproject.toml
setup.cfg
setup.py
src/cobra/__init__.py
src/cobra/exceptions.py
src/cobra.egg-info/PKG-INFO
src/cobra.egg-info/SOURCES.txt
src/cobra.egg-info/dependency_links.txt
src/cobra.egg-info/requires.txt
src/cobra.egg-info/top_level.txt
src/cobra.egg-info/zip-safe
src/cobra/core/__init__.py
src/cobra/core/configuration.py
src/cobra/core/dictlist.py
src/cobra/core/formula.py
src/cobra/core/gene.py
src/cobra/core/group.py
src/cobra/core/metabolite.py
src/cobra/core/model.py
src/cobra/core/object.py
src/cobra/core/reaction.py
src/cobra/core/singleton.py
src/cobra/core/solution.py
src/cobra/core/species.py
src/cobra/flux_analysis/__init__.py
src/cobra/flux_analysis/deletion.py
src/cobra/flux_analysis/fastcc.py
src/cobra/flux_analysis/gapfilling.py
src/cobra/flux_analysis/geometric.py
src/cobra/flux_analysis/helpers.py
src/cobra/flux_analysis/loopless.py
src/cobra/flux_analysis/moma.py
src/cobra/flux_analysis/parsimonious.py
src/cobra/flux_analysis/phenotype_phase_plane.py
src/cobra/flux_analysis/reaction.py
src/cobra/flux_analysis/room.py
src/cobra/flux_analysis/variability.py
src/cobra/io/__init__.py
src/cobra/io/dict.py
src/cobra/io/json.py
src/cobra/io/mat.py
src/cobra/io/sbml.py
src/cobra/io/schema_v1.json
src/cobra/io/yaml.py
src/cobra/io/web/__init__.py
src/cobra/io/web/abstract_model_repository.py
src/cobra/io/web/bigg_models_repository.py
src/cobra/io/web/biomodels_repository.py
src/cobra/io/web/load.py
src/cobra/manipulation/__init__.py
src/cobra/manipulation/annotate.py
src/cobra/manipulation/delete.py
src/cobra/manipulation/modify.py
src/cobra/manipulation/validate.py
src/cobra/medium/__init__.py
src/cobra/medium/annotations.py
src/cobra/medium/boundary_types.py
src/cobra/medium/minimal_medium.py
src/cobra/sampling/__init__.py
src/cobra/sampling/achr.py
src/cobra/sampling/hr_sampler.py
src/cobra/sampling/optgp.py
src/cobra/sampling/sampling.py
src/cobra/summary/__init__.py
src/cobra/summary/metabolite_summary.py
src/cobra/summary/model_summary.py
src/cobra/summary/reaction_summary.py
src/cobra/summary/summary.py
src/cobra/test/__init__.py
src/cobra/test/conftest.py
src/cobra/test/test_manipulation.py
src/cobra/test/test_medium.py
src/cobra/test/data/JSON_with_inf_bounds.json
src/cobra/test/data/annotation.xml
src/cobra/test/data/e_coli_core.xml
src/cobra/test/data/example_notes.xml
src/cobra/test/data/fbc_ex1.xml
src/cobra/test/data/fbc_ex2.xml
src/cobra/test/data/iJO1366.pickle
src/cobra/test/data/iJO1366.xml.gz
src/cobra/test/data/invalid0.xml
src/cobra/test/data/invalid1.xml
src/cobra/test/data/invalid2.xml
src/cobra/test/data/invalid_annotation_format.json
src/cobra/test/data/mini.json
src/cobra/test/data/mini.mat
src/cobra/test/data/mini.pickle
src/cobra/test/data/mini.yml
src/cobra/test/data/mini_cobra.xml
src/cobra/test/data/mini_fbc1.xml
src/cobra/test/data/mini_fbc2.xml
src/cobra/test/data/mini_fbc2.xml.bz2
src/cobra/test/data/mini_fbc2.xml.gz
src/cobra/test/data/raven.mat
src/cobra/test/data/raven.pickle
src/cobra/test/data/salmonella.genes
src/cobra/test/data/salmonella.media
src/cobra/test/data/salmonella.pickle
src/cobra/test/data/salmonella.xml
src/cobra/test/data/textbook.xml.gz
src/cobra/test/data/textbook_fva.json
src/cobra/test/data/textbook_pfba_fva.json
src/cobra/test/data/textbook_solution.pickle
src/cobra/test/data/update_pickles.py
src/cobra/test/data/valid_annotation_format.json
src/cobra/test/data/valid_annotation_output.xml
src/cobra/test/data/validation.xml
src/cobra/util/__init__.py
src/cobra/util/array.py
src/cobra/util/context.py
src/cobra/util/solver.py
src/cobra/util/util.py