def test_parse_limits_table_file(self):
path = self.write_model_file(
'limits_1.tsv', '\n'.join([
'# comment', '', 'rxn_1', 'rxn_2\t-100', 'rxn_3\t-\t3e-1',
'rxn_4\t-1000\t-100 # line comment'
]))
limits = list(native.parse_limits_file(path))
self.assertEqual(limits[0], ('rxn_1', None, None))
self.assertEqual(limits[1], ('rxn_2', -100, None))
self.assertEqual(limits[2][0], 'rxn_3')
self.assertEqual(limits[2][1], None)
self.assertAlmostEqual(limits[2][2], 3e-1)
self.assertEqual(limits[3], ('rxn_4', -1000, -100))
def test_parse_limits_yaml_file(self):
path = self.write_model_file(
'limits_1.yaml', '\n'.join([
'- include: limits_2.yml', '- reaction: rxn_3',
' lower: -1000', '- reaction: rxn_4', ' fixed: 10'
]))
self.write_model_file(
'limits_2.yml', '\n'.join([
'- reaction: rxn_1', ' lower: -1', ' upper: 25.5',
'- reaction: rxn_2'
]))
limits = list(native.parse_limits_file(path))
self.assertEqual(limits, [('rxn_1', -1, 25.5), ('rxn_2', None, None),
('rxn_3', -1000, None), ('rxn_4', 10, 10)])
def test_parse_limits_table_file(self):
path = self.write_model_file('limits_1.tsv', '\n'.join([
'# comment',
'',
'rxn_1',
'rxn_2\t-100',
'rxn_3\t-\t3e-1',
'rxn_4\t-1000\t-100 # line comment'
]))
limits = list(native.parse_limits_file(path))
self.assertEqual(limits[0], ('rxn_1', None, None))
self.assertEqual(limits[1], ('rxn_2', -100, None))
self.assertEqual(limits[2][0], 'rxn_3')
self.assertEqual(limits[2][1], None)
self.assertAlmostEqual(limits[2][2], 3e-1)
self.assertEqual(limits[3], ('rxn_4', -1000, -100))
def test_parse_limits_yaml_file(self):
path = self.write_model_file('limits_1.yaml', '\n'.join([
'- include: limits_2.yml',
'- reaction: rxn_3',
' lower: -1000',
'- reaction: rxn_4',
' upper: 0'
]))
self.write_model_file('limits_2.yml', '\n'.join([
'- reaction: rxn_1',
' lower: -1',
' upper: 25.5',
'- reaction: rxn_2'
]))
limits = list(native.parse_limits_file(path))
self.assertEqual(limits, [
('rxn_1', -1, 25.5),
('rxn_2', None, None),
('rxn_3', -1000, None),
('rxn_4', None, 0)
])
def test_parse_limits_table_file_too_many_fields(self):
path = self.write_model_file('limits.tsv', '\n'.join([
'rxn_1\t-\t100\ttext']))
with self.assertRaises(native.ParseError):
list(native.parse_limits_file(path))
def test_parse_limits_table_file_too_many_fields(self):
path = self.write_model_file('limits.tsv',
'\n'.join(['rxn_1\t-\t100\ttext']))
with self.assertRaises(native.ParseError):
list(native.parse_limits_file(path))
