def test_script_lookup_table_check_non_existing_tag_ignored(caplog, tmp_path):
"""Check non-existing metadata tags are ignored"""
LOGGER.info('Testing custom lookup tables, for command line script\n')
tmp_path = str(tmp_path)
model_name = 'beeler_reuter_model_1977'
model_file = os.path.join(CELLML_FOLDER, model_name + '.cellml')
assert os.path.isfile(model_file)
outfile = os.path.join(tmp_path, 'beeler_reuter_model_1977_lookup_tables.cpp')
# Call commandline script
testargs = ['chaste_codegen', '--skip-singularity-fixes', model_file, '--opt', '-o', outfile,
'--lookup-table', 'membrane_voltage', '-150.0001', '199.9999', '0.01',
'--lookup-table', 'cytosolic_calcium_concentration', '0.00001', '30.00001', '0.0001',
'--lookup-table', 'non_existing_tag', '-150.0001', '199.9999', '0.01']
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
assert 'WARNING' in caplog.text
assert "A lookup table was specified for non_existing_tag but it is not tagged in the model, skipping!" \
in caplog.text
# Check output
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models', 'Opt')
compare_file_against_reference(os.path.join(reference, 'beeler_reuter_model_1977_lookup_tables.hpp'),
os.path.join(tmp_path, 'beeler_reuter_model_1977_lookup_tables.hpp'))
compare_file_against_reference(os.path.join(reference, 'beeler_reuter_model_1977_lookup_tables.cpp'),
os.path.join(tmp_path, 'beeler_reuter_model_1977_lookup_tables.cpp'))
def test_script_data_clamp_opt(tmp_path):
"""Convert code with data clamp opt"""
LOGGER.info('Testing multiple models\n')
tmp_path = str(tmp_path)
model_name = 'grandi_pasqualini_bers_2010_ss'
model_file = os.path.join(CELLML_FOLDER, model_name + '.cellml')
assert os.path.isfile(model_file)
target = os.path.join(tmp_path, model_name + '.cellml')
shutil.copyfile(model_file, target)
testargs = ['chaste_codegen', '--use-model-factory', '--skip-singularity-fixes', '--cvode-data-clamp', '--opt',
target]
# Call commandline script
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models')
reference_opt = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models')
compare_file_against_reference(os.path.join(reference, 'CVODE_DATA_CLAMP',
model_name + 'CvodeDataClamp.hpp'),
os.path.join(tmp_path, model_name + 'CvodeDataClamp.hpp'))
compare_file_against_reference(os.path.join(reference, 'CVODE_DATA_CLAMP',
model_name + 'CvodeDataClamp.cpp'),
os.path.join(tmp_path, model_name + 'CvodeDataClamp.cpp'))
compare_file_against_reference(os.path.join(reference_opt, 'CVODE_DATA_CLAMP_OPT',
model_name + 'CvodeDataClampOpt.hpp'),
os.path.join(tmp_path, model_name + 'CvodeDataClampOpt.hpp'))
compare_file_against_reference(os.path.join(reference_opt, 'CVODE_DATA_CLAMP_OPT',
model_name + 'CvodeDataClampOpt.cpp'),
os.path.join(tmp_path, model_name + 'CvodeDataClampOpt.cpp'))
def test_script_opt(tmp_path):
"""Convert an optimised normal model type"""
# If using --opt with no output file and not dynamic it will generate both non-opt and opt models
# this version does not have the ModelFactory stuff
LOGGER.info('Testing model with options --normal --opt and -o for command line script\n')
tmp_path = str(tmp_path)
model_name = 'aslanidi_Purkinje_model_2009'
model_file = os.path.join(CELLML_FOLDER, model_name + '.cellml')
assert os.path.isfile(model_file)
target = os.path.join(tmp_path, model_name + '.cellml')
shutil.copyfile(model_file, target)
# Call commandline script
testargs = ['chaste_codegen', '--skip-singularity-fixes', target, '--normal', '--opt', '--use-modifiers']
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
# Check output
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models')
compare_file_against_reference(os.path.join(reference, 'Opt', 'non_dynamic_aslanidi_Purkinje_model_2009.hpp'),
os.path.join(tmp_path, 'aslanidi_Purkinje_model_2009Opt.hpp'))
compare_file_against_reference(os.path.join(reference, 'Opt', 'non_dynamic_aslanidi_Purkinje_model_2009.cpp'),
os.path.join(tmp_path, 'aslanidi_Purkinje_model_2009Opt.cpp'))
compare_file_against_reference(os.path.join(reference, 'Normal', 'non_dynamic_aslanidi_Purkinje_model_2009.hpp'),
os.path.join(tmp_path, 'aslanidi_Purkinje_model_2009.hpp'))
compare_file_against_reference(os.path.join(reference, 'Normal', 'non_dynamic_aslanidi_Purkinje_model_2009.cpp'),
os.path.join(tmp_path, 'aslanidi_Purkinje_model_2009.cpp'))
def test_script_RL_labview(tmp_path):
"""Convert a RushLarsen model type in labview output"""
LOGGER.info('Testing model with options --rush-larsen-labview\n')
tmp_path = str(tmp_path)
model_name = 'aslanidi_Purkinje_model_2009'
model_file = os.path.join(CELLML_FOLDER, model_name + '.cellml')
assert os.path.isfile(model_file)
outfile = os.path.join(tmp_path, 'aslanidi_atrial_model_2009.txt')
# Call commandline script
testargs = ['chaste_codegen', model_file, '--rush-larsen-labview', '-o', outfile]
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
# Check output
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models', 'RL_labview')
compare_file_against_reference(os.path.join(reference, 'aslanidi_atrial_model_2009.txt'),
os.path.join(tmp_path, 'aslanidi_atrial_model_2009.txt'))
def test_script_CVODE_DATA_CLAMP_modifiers(tmp_path):
"""Convert a CVODE with data clamp and modifiers model type with modifiers"""
LOGGER.info('Testing model CVODE with data clamp , for command line script\n')
tmp_path = str(tmp_path)
model_name = 'shannon_wang_puglisi_weber_bers_2004'
model_file = os.path.join(CELLML_FOLDER, model_name + '.cellml')
assert os.path.isfile(model_file)
outfile = os.path.join(tmp_path, 'Shannon2004_with_modifiers.cpp')
# Call commandline script
testargs = ['chaste_codegen', '--use-model-factory', '--skip-singularity-fixes', model_file, '--cvode-data-clamp',
'-o', outfile, '--use-modifiers']
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
# Check output
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models', 'CVODE_DATA_CLAMP')
compare_file_against_reference(os.path.join(reference, 'Shannon2004_with_modifiers.hpp'),
os.path.join(tmp_path, 'Shannon2004_with_modifiers.hpp'))
compare_file_against_reference(os.path.join(reference, 'Shannon2004_with_modifiers.cpp'),
os.path.join(tmp_path, 'Shannon2004_with_modifiers.cpp'))
def test_script_GRL2Opt(tmp_path):
"""Convert a Generalised RushLarsen First Order Opt model type"""
LOGGER.info('Testing model Generalised RushLarsen First Order Opt , for command line script\n')
tmp_path = str(tmp_path)
model_name = 'viswanathan_model_1999_epi'
model_file = os.path.join(CELLML_FOLDER, model_name + '.cellml')
assert os.path.isfile(model_file)
outfile = os.path.join(tmp_path, 'dynamic_viswanathan_model_1999_epi.cpp')
# Call commandline script
testargs = ['chaste_codegen', '--use-model-factory', '--skip-singularity-fixes', model_file, '--grl2',
'--opt', '-o', outfile, '--dynamically-loadable']
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
# Check output
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models', 'GRL2Opt')
compare_file_against_reference(os.path.join(reference, 'dynamic_viswanathan_model_1999_epi.hpp'),
os.path.join(tmp_path, 'dynamic_viswanathan_model_1999_epi.hpp'))
compare_file_against_reference(os.path.join(reference, 'dynamic_viswanathan_model_1999_epi.cpp'),
os.path.join(tmp_path, 'dynamic_viswanathan_model_1999_epi.cpp'))
def test_script_dynamic_RL(tmp_path):
"""Convert a RushLarsen model type"""
LOGGER.info('Testing model with options --rush-larsen, and --dynamically-loadable for command line script\n')
tmp_path = str(tmp_path)
model_name = 'livshitz_rudy_2007'
model_file = os.path.join(CELLML_FOLDER, model_name + '.cellml')
assert os.path.isfile(model_file)
outfile = os.path.join(tmp_path, 'dynamic_livshitz_rudy_2007.cpp')
# Call commandline script
testargs = ['chaste_codegen', '--skip-singularity-fixes', model_file, '--rush-larsen', '-o', outfile,
'--dynamically-loadable']
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
# Check output
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models', 'RL')
compare_file_against_reference(os.path.join(reference, 'dynamic_livshitz_rudy_2007.hpp'),
os.path.join(tmp_path, 'dynamic_livshitz_rudy_2007.hpp'))
compare_file_against_reference(os.path.join(reference, 'dynamic_livshitz_rudy_2007.cpp'),
os.path.join(tmp_path, 'dynamic_livshitz_rudy_2007.cpp'))
def test_script_dynamic_BEopt(tmp_path):
"""Convert a BackwardsEuler model type"""
LOGGER.info('Testing model with options --backward-euler, --dynamically-loadable, --opt for command line script\n')
tmp_path = str(tmp_path)
model_name = 'courtemanche_ramirez_nattel_1998'
model_file = os.path.join(CELLML_FOLDER, model_name + '.cellml')
assert os.path.isfile(model_file)
outfile = os.path.join(tmp_path, 'dynamic_courtemanche_ramirez_nattel_1998.cpp')
# Call commandline script
testargs = ['chaste_codegen', '--use-model-factory', '--skip-singularity-fixes', model_file, '--backward-euler',
'--opt', '-o', outfile, '--dynamically-loadable']
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
# Check output
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models', 'BEopt')
compare_file_against_reference(os.path.join(reference, 'dynamic_courtemanche_ramirez_nattel_1998.hpp'),
os.path.join(tmp_path, 'dynamic_courtemanche_ramirez_nattel_1998.hpp'))
compare_file_against_reference(os.path.join(reference, 'dynamic_courtemanche_ramirez_nattel_1998.cpp'),
os.path.join(tmp_path, 'dynamic_courtemanche_ramirez_nattel_1998.cpp'))
def test_script_cvode_jacobian(tmp_path):
"""Convert a CVODE model type with jacobian"""
LOGGER.info('Testing model with options --cvode and -o for command line script\n')
tmp_path = str(tmp_path)
model_name = 'shannon_wang_puglisi_weber_bers_2004'
model_file = os.path.join(CELLML_FOLDER, model_name + '.cellml')
assert os.path.isfile(model_file)
outfile = os.path.join(tmp_path, 'dynamic_Shannon2004.cpp')
# Call commandline script
testargs = ['chaste_codegen', '--use-model-factory', '--skip-singularity-fixes', model_file, '--cvode',
'-o', outfile, '--use-analytic-jacobian', '--dynamically-loadable']
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
# Check output
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models', 'Cvode_with_jacobian')
compare_file_against_reference(os.path.join(reference, 'dynamic_Shannon2004.hpp'),
os.path.join(tmp_path, 'dynamic_Shannon2004.hpp'))
compare_file_against_reference(os.path.join(reference, 'dynamic_Shannon2004.cpp'),
os.path.join(tmp_path, 'dynamic_Shannon2004.cpp'))
def test_script_cvode(tmp_path):
"""Convert a CVODE model type"""
LOGGER.info('Testing model with options -t CVODE and -o for command line script\n')
tmp_path = str(tmp_path)
model_name = 'mahajan_shiferaw_2008'
model_file = os.path.join(CELLML_FOLDER, model_name + '.cellml')
assert os.path.isfile(model_file)
outfile = os.path.join(tmp_path, 'dynamic_mahajan_shiferaw_2008.cpp')
# Call commandline script
testargs = ['chaste_codegen', '--skip-singularity-fixes', model_file, '--cvode', '-o', outfile,
'--dynamically-loadable']
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
# Check output
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models', 'Cvode')
compare_file_against_reference(os.path.join(reference, 'dynamic_mahajan_shiferaw_2008.hpp'),
os.path.join(tmp_path, 'dynamic_mahajan_shiferaw_2008.hpp'))
compare_file_against_reference(os.path.join(reference, 'dynamic_mahajan_shiferaw_2008.cpp'),
os.path.join(tmp_path, 'dynamic_mahajan_shiferaw_2008.cpp'))
def test_script_class_convtype_output_dll_loadable(tmp_path):
"""Convert a normal model with a given class name and dynamicly loadable via command line script"""
LOGGER.info('Testing model with options --normal -c --dynamically-loadable and -o for command line script\n')
tmp_path = str(tmp_path)
model_name = 'noble_model_1998'
model_file = os.path.join(CELLML_FOLDER, model_name + '.cellml')
assert os.path.isfile(model_file)
outfile = os.path.join(tmp_path, 'output_class.c')
# Call commandline script
testargs = ['chaste_codegen', '--use-model-factory', '--skip-singularity-fixes', model_file, '-c', 'Chaste_CG',
'--normal', '-o', outfile, '--dynamically-loadable']
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
# Check output
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models', 'Normal')
compare_file_against_reference(os.path.join(reference, 'output_class.h'),
os.path.join(tmp_path, 'output_class.h'))
compare_file_against_reference(os.path.join(reference, 'output_class.c'),
os.path.join(tmp_path, 'output_class.c'))
def test_V_not_state_mparam(caplog, tmp_path):
"""Test V parameter"""
LOGGER.info('Testing V as parameter\n')
tmp_path = str(tmp_path)
model_name = 'test_V_not_state_mparam'
model_file = os.path.join(CELLML_FOLDER, '..', '..', model_name + '.cellml')
assert os.path.isfile(model_file)
outfile = os.path.join(tmp_path, 'test_V_not_state_mparam.cpp')
# Call commandline script
testargs = ['chaste_codegen', model_file, '-o', outfile]
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
# Check output
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models', 'Normal')
compare_file_against_reference(os.path.join(reference, 'test_V_not_state_mparam.hpp'),
os.path.join(tmp_path, 'test_V_not_state_mparam.hpp'))
compare_file_against_reference(os.path.join(reference, 'test_V_not_state_mparam.cpp'),
os.path.join(tmp_path, 'test_V_not_state_mparam.cpp'))
def test_script_cvode_opt(tmp_path):
"""Convert an optimised cvode model type"""
# If using --opt with an output and/or dynamicly loadable file it will generate only the opt model
LOGGER.info('Testing model with options --normal --opt and -o for command line script\n')
tmp_path = str(tmp_path)
model_name = 'aslanidi_Purkinje_model_2009'
model_file = os.path.join(CELLML_FOLDER, model_name + '.cellml')
assert os.path.isfile(model_file)
outfile = os.path.join(tmp_path, 'dynamic_aslanidi_Purkinje_model_2009.cpp')
# Call commandline script
testargs = ['chaste_codegen', '--use-model-factory', '--skip-singularity-fixes', model_file, '--cvode', '--opt',
'-o', outfile, '--dynamically-loadable', '--use-modifiers']
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
# Check output
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models', 'Cvode_opt')
compare_file_against_reference(os.path.join(reference, 'dynamic_aslanidi_Purkinje_model_2009.hpp'),
os.path.join(tmp_path, 'dynamic_aslanidi_Purkinje_model_2009.hpp'))
compare_file_against_reference(os.path.join(reference, 'dynamic_aslanidi_Purkinje_model_2009.cpp'),
os.path.join(tmp_path, 'dynamic_aslanidi_Purkinje_model_2009.cpp'))
def test_piecewise_handling(caplog, tmp_path):
"""Test piecewise handling"""
LOGGER.info('Testing piecewise handling\n')
tmp_path = str(tmp_path)
model_name = 'test_piecewises_be'
model_file = os.path.join(CELLML_FOLDER, '..', '..', model_name + '.cellml')
assert os.path.isfile(model_file)
outfile = os.path.join(tmp_path, 'test_piecewises_be.cpp')
# Call commandline script
testargs = ['chaste_codegen', model_file, '--backward-euler', '-o', outfile]
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
# Check output
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models', 'BE')
compare_file_against_reference(os.path.join(reference, 'test_piecewises_be.hpp'),
os.path.join(tmp_path, 'test_piecewises_be.hpp'))
compare_file_against_reference(os.path.join(reference, 'test_piecewises_be.cpp'),
os.path.join(tmp_path, 'test_piecewises_be.cpp'))
def test_script_lookup_table(tmp_path):
"""Convert a model with custom lookup table"""
LOGGER.info('Testing custom lookup tables, for command line script\n')
tmp_path = str(tmp_path)
model_name = 'beeler_reuter_model_1977'
model_file = os.path.join(CELLML_FOLDER, model_name + '.cellml')
assert os.path.isfile(model_file)
outfile = os.path.join(tmp_path, 'beeler_reuter_model_1977_lookup_tables.cpp')
# Call commandline script
testargs = ['chaste_codegen', '--skip-singularity-fixes', model_file, '--opt', '-o', outfile,
'--lookup-table', 'membrane_voltage', '-150.0001', '199.9999', '0.01',
'--lookup-table', 'cytosolic_calcium_concentration', '0.00001', '30.00001', '0.0001']
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
# Check output
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models', 'Opt')
compare_file_against_reference(os.path.join(reference, 'beeler_reuter_model_1977_lookup_tables.hpp'),
os.path.join(tmp_path, 'beeler_reuter_model_1977_lookup_tables.hpp'))
compare_file_against_reference(os.path.join(reference, 'beeler_reuter_model_1977_lookup_tables.cpp'),
os.path.join(tmp_path, 'beeler_reuter_model_1977_lookup_tables.cpp'))
def test_script_convert_quiet(caplog, tmp_path):
"""Convert a normal model via command line script in quiet mode"""
caplog.set_level(logging.INFO, logger='chaste_codegen')
LOGGER.info('Testing regular model conversion for command line script in quiet mode\n')
tmp_path = str(tmp_path)
model_name = 'fox_mcharg_gilmour_2002'
model_file = os.path.join(CELLML_FOLDER, model_name + '.cellml')
assert os.path.isfile(model_file)
target = os.path.join(tmp_path, model_name + '.cellml')
shutil.copyfile(model_file, target)
testargs = ['chaste_codegen', '--skip-singularity-fixes', target, '--quiet']
# Call commandline script
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
assert "The model has no capacitance tagged." not in caplog.text
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models', 'Normal')
compare_file_against_reference(os.path.join(reference, model_name + '_console_script.hpp'),
os.path.join(tmp_path, model_name + '.hpp'))
compare_file_against_reference(os.path.join(reference, model_name + '_console_script.cpp'),
os.path.join(tmp_path, model_name + '.cpp'))
def test_script_RLopt(tmp_path):
"""Convert a RushLarsen model type"""
LOGGER.info('Testing model with options --rush-larsen --opt, for command line script\n')
tmp_path = str(tmp_path)
model_name = 'bondarenko_szigeti_bett_kim_rasmusson_2004_apical'
model_file = os.path.join(CELLML_FOLDER, model_name + '.cellml')
assert os.path.isfile(model_file)
outfile = os.path.join(tmp_path, 'dynamic_bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp')
# Call commandline script
testargs = ['chaste_codegen', '--use-model-factory', '--skip-singularity-fixes', model_file, '--rush-larsen',
'--opt', '-o', outfile, '--dynamically-loadable']
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
# Check output
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models', 'RLopt')
compare_file_against_reference(os.path.join(reference,
'dynamic_bondarenko_szigeti_bett_kim_rasmusson_2004_apical.hpp'),
os.path.join(tmp_path,
'dynamic_bondarenko_szigeti_bett_kim_rasmusson_2004_apical.hpp'))
compare_file_against_reference(os.path.join(reference,
'dynamic_bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp'),
os.path.join(tmp_path,
'dynamic_bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cpp'))
def test_range_and_capacitance_units(caplog, tmp_path):
"""Test range"""
LOGGER.info('Testing range specs and capacitance incompatible units warning\n')
tmp_path = str(tmp_path)
model_name = 'test_luo_rudy_1991_with_range_cap_dimensionless'
model_file = os.path.join(CELLML_FOLDER, '..', '..', model_name + '.cellml')
assert os.path.isfile(model_file)
outfile = os.path.join(tmp_path, 'test_luo_rudy_1991_with_range_cap_dimensionless.cpp')
# Call commandline script
testargs = ['chaste_codegen', model_file, '--opt', '-o', outfile]
with mock.patch.object(sys, 'argv', testargs):
chaste_codegen()
# check capacitance units warning
assert 'WARNING' in caplog.text
assert "luo_rudy_1991 The model has capacitance in incompatible units." in caplog.text
# Check output
reference = os.path.join(os.path.join(TESTS_FOLDER), 'chaste_reference_models', 'Normal')
compare_file_against_reference(os.path.join(reference, 'test_luo_rudy_1991_with_range_cap_dimensionless.hpp'),
os.path.join(tmp_path, 'test_luo_rudy_1991_with_range_cap_dimensionless.hpp'))
compare_file_against_reference(os.path.join(reference, 'test_luo_rudy_1991_with_range_cap_dimensionless.cpp'),
os.path.join(tmp_path, 'test_luo_rudy_1991_with_range_cap_dimensionless.cpp'))
