17.37. test_sbml

Testing SBML functionality based on libsbml.

17.37.1. Module Contents

17.37.1.1. Classes

TestCobraIO

Tests the read and write functions.

17.37.1.2. Functions

test_validate(trial, data_directory)

Test validation function.

io_trial(request, data_directory)

test_filehandle(data_directory, tmp_path)

Test reading and writing to file handle.

test_from_sbml_string(data_directory)

Test reading from SBML string.

test_model_history(tmp_path)

Testing reading and writing of ModelHistory.

test_groups(data_directory, tmp_path)

Testing reading and writing of groups

test_missing_flux_bounds1(data_directory)

test_missing_flux_bounds2(data_directory)

test_validate(trial, data_directory)

Test validation function.

test_validation_warnings(data_directory)

Test the validation warnings.

test_infinity_bounds(data_directory, tmp_path)

Test infinity bound example.

test_boundary_conditions(data_directory)

Test infinity bound example.

test_gprs(data_directory, tmp_path)

Test that GPRs are written and read correctly

test_identifiers_annotation()

test_smbl_with_notes(data_directory, tmp_path)

Test that NOTES in the RECON 2.2 style are written and read correctly

test_sbml.config[source]
test_sbml.jsonschema[source]
test_sbml.IOTrial[source]
test_sbml.trials[source]
test_sbml.trial_names[source]
test_sbml.test_validate(trial, data_directory)[source]

Test validation function.

class test_sbml.TestCobraIO[source]

Tests the read and write functions.

classmethod compare_models(cls, name, model1, model2)[source]
classmethod extra_comparisons(cls, name, model1, model2)[source]
test_read_1(self, io_trial)[source]
test_read_2(self, io_trial)[source]
test_write_1(self, io_trial)[source]
test_write_2(self, io_trial)[source]
test_sbml.io_trial(request, data_directory)[source]
test_sbml.test_filehandle(data_directory, tmp_path)[source]

Test reading and writing to file handle.

test_sbml.test_from_sbml_string(data_directory)[source]

Test reading from SBML string.

test_sbml.test_model_history(tmp_path)[source]

Testing reading and writing of ModelHistory.

test_sbml.test_groups(data_directory, tmp_path)[source]

Testing reading and writing of groups

test_sbml.test_missing_flux_bounds1(data_directory)[source]
test_sbml.test_missing_flux_bounds2(data_directory)[source]
test_sbml.test_validate(data_directory)[source]

Test the validation code.

test_sbml.test_validation_warnings(data_directory)[source]

Test the validation warnings.

test_sbml.test_infinity_bounds(data_directory, tmp_path)[source]

Test infinity bound example.

test_sbml.test_boundary_conditions(data_directory)[source]

Test infinity bound example.

test_sbml.test_gprs(data_directory, tmp_path)[source]

Test that GPRs are written and read correctly

test_sbml.test_identifiers_annotation()[source]
test_sbml.test_smbl_with_notes(data_directory, tmp_path)[source]

Test that NOTES in the RECON 2.2 style are written and read correctly