17.1.1.7.1.2.1.7. cobra.test.test_io.test_sbml

Testing SBML functionality based on libsbml.

17.1.1.7.1.2.1.7.1. Module Contents

17.1.1.7.1.2.1.7.1.1. Classes

TestCobraIO

Tests the read and write functions.

17.1.1.7.1.2.1.7.1.2. 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

cobra.test.test_io.test_sbml.config

cobra.test.test_io.test_sbml.jsonschema

cobra.test.test_io.test_sbml.IOTrial

cobra.test.test_io.test_sbml.trials

cobra.test.test_io.test_sbml.trial_names

cobra.test.test_io.test_sbml.test_validate(trial, data_directory)

Test validation function.

class cobra.test.test_io.test_sbml.TestCobraIO

Tests the read and write functions.

classmethod compare_models(cls, name, model1, model2)

classmethod extra_comparisons(cls, name, model1, model2)

test_read_1(self, io_trial)

test_read_2(self, io_trial)

test_write_1(self, io_trial)

test_write_2(self, io_trial)

cobra.test.test_io.test_sbml.io_trial(request, data_directory)

cobra.test.test_io.test_sbml.test_filehandle(data_directory, tmp_path)

Test reading and writing to file handle.

cobra.test.test_io.test_sbml.test_from_sbml_string(data_directory)

Test reading from SBML string.

cobra.test.test_io.test_sbml.test_model_history(tmp_path)

Testing reading and writing of ModelHistory.

cobra.test.test_io.test_sbml.test_groups(data_directory, tmp_path)

Testing reading and writing of groups

cobra.test.test_io.test_sbml.test_missing_flux_bounds1(data_directory)

cobra.test.test_io.test_sbml.test_missing_flux_bounds2(data_directory)

cobra.test.test_io.test_sbml.test_validate(data_directory)

Test the validation code.

cobra.test.test_io.test_sbml.test_validation_warnings(data_directory)

Test the validation warnings.

cobra.test.test_io.test_sbml.test_infinity_bounds(data_directory, tmp_path)

Test infinity bound example.

cobra.test.test_io.test_sbml.test_boundary_conditions(data_directory)

Test infinity bound example.

cobra.test.test_io.test_sbml.test_gprs(data_directory, tmp_path)

Test that GPRs are written and read correctly

cobra.test.test_io.test_sbml.test_identifiers_annotation()

cobra.test.test_io.test_sbml.test_smbl_with_notes(data_directory, tmp_path)

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