15.1.1.6.1.2. cobra.test.test_flux_analysis

15.1.1.6.1.2.1. Module Contents

cobra.test.test_flux_analysis.construct_ll_test_model()

cobra.test.test_flux_analysis.ll_test_model(request)

cobra.test.test_flux_analysis.construct_room_model()

cobra.test.test_flux_analysis.construct_room_solution()

cobra.test.test_flux_analysis.construct_geometric_fba_model()

cobra.test.test_flux_analysis.captured_output()

A context manager to test the IO summary methods.

class cobra.test.test_flux_analysis.TestCobraFluxAnalysis

Test the simulation functions in cobra.flux_analysis.

test_pfba_benchmark(large_model, benchmark, solver)

test_pfba(model, solver)

test_geometric_fba_benchmark(model, benchmark, solver)

test_geometric_fba(solver)

test_single_gene_deletion_fba_benchmark(model, benchmark, solver)

test_single_gene_deletion_fba(model, solver)

test_single_gene_deletion_moma_benchmark(model, benchmark, solver)

test_single_gene_deletion_linear_moma_benchmark(model, benchmark, solver)

test_moma_sanity(model, solver)

Test optimization criterion and optimality.

test_single_gene_deletion_moma(model, solver)

test_single_gene_deletion_moma_reference(model, solver)

test_linear_moma_sanity(model, solver)

Test optimization criterion and optimality.

test_single_gene_deletion_linear_moma(model, solver)

test_single_gene_deletion_benchmark(model, benchmark, solver)

test_single_gene_deletion_room_benchmark(model, benchmark, solver)

test_single_gene_deletion_linear_room_benchmark(model, benchmark, solver)

test_room_sanity(model, solver)

test_linear_room_sanity(model, solver)

test_single_reaction_deletion_room(solver)

test_single_reaction_deletion_room_linear(solver)

test_single_reaction_deletion(model, solver)

compare_matrices(matrix1, matrix2, places=3)

test_double_gene_deletion_benchmark(large_model, benchmark)

test_double_gene_deletion(model)

test_double_reaction_deletion(model)

test_double_reaction_deletion_benchmark(large_model, benchmark)

test_flux_variability_benchmark(large_model, benchmark, solver)

test_flux_variability_loopless_benchmark(model, benchmark, solver)

test_pfba_flux_variability(model, pfba_fva_results, fva_results, solver)

test_flux_variability(model, fva_results, solver)

test_flux_variability_loopless(model, solver)

test_fva_data_frame(model)

test_fva_infeasible(model)

test_fva_minimization(model)

test_find_blocked_reactions_solver_none(model)

test_essential_genes(model)

test_essential_reactions(model)

test_find_blocked_reactions(model, solver)

test_loopless_benchmark_before(benchmark)

test_loopless_benchmark_after(benchmark)

test_loopless_solution(ll_test_model)

test_loopless_solution_fluxes(model)

test_add_loopless(ll_test_model)

test_gapfilling(salmonella)

check_line(output, expected_entries, pattern=compile)

Ensure each expected entry is in the output.

check_in_line(output, expected_entries, pattern=compile)

Ensure each expected entry is contained in the output.

test_model_summary_previous_solution(model, opt_solver, names)

test_model_summary(model, opt_solver, names)

test_model_summary_with_fva(model, opt_solver, fraction)

test_metabolite_summary_previous_solution(model, opt_solver, met)

test_metabolite_summary(model, opt_solver, met, names)

test_metabolite_summary_with_fva(model, opt_solver, fraction, met)

class cobra.test.test_flux_analysis.TestCobraFluxSampling

Tests and benchmark flux sampling.

test_single_achr(model)

test_single_optgp(model)

test_multi_optgp(model)

test_wrong_method(model)

test_validate_wrong_sample(model)

test_fixed_seed(model)

test_equality_constraint(model)

test_inequality_constraint(model)

setup_class()

test_achr_init_benchmark(model, benchmark)

test_optgp_init_benchmark(model, benchmark)

test_sampling()

test_achr_sample_benchmark(benchmark)

test_optgp_sample_benchmark(benchmark)

test_batch_sampling()

test_variables_samples()

test_inhomogeneous_sanity(model)

Test whether inhomogeneous sampling gives approximately the same standard deviation as a homogeneous version.

test_reproject()

test_complicated_model()

Difficult model since the online mean calculation is numerically unstable so many samples weakly violate the equality constraints.

test_single_point_space(model)

Model where constraints reduce the sampling space to one point.

class cobra.test.test_flux_analysis.TestProductionEnvelope

Test the production envelope.

test_envelope_one(model)

test_envelope_multi_reaction_objective(model)

test_multi_variable_envelope(model, variables, num)

test_envelope_two(model)

class cobra.test.test_flux_analysis.TestReactionUtils

Test the assess_ functions in reactions.py.

test_assess(model, solver)