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Cleanup: Delete or ignore temporary model files #1393

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Merged
FFroehlich merged 1 commit into from
Jan 30, 2021
Merged

Cleanup: Delete or ignore temporary model files #1393

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46 changes: 23 additions & 23 deletions python/tests/test_sbml_import.py
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Original file line number Diff line number Diff line change
Expand Up @@ -325,33 +325,33 @@ def test_sympy_exp_monkeypatch():
importer = amici.SbmlImporter(urlopen(url).read().decode('utf-8'),
from_file=False)
module_name = 'BIOMD0000000529'
outdir = 'BIOMD0000000529'

importer.sbml2amici(module_name, outdir)
model_module = amici.import_model_module(module_name=module_name,
module_path=outdir)
with TemporaryDirectory() as outdir:
importer.sbml2amici(module_name, outdir)
model_module = amici.import_model_module(module_name=module_name,
module_path=outdir)

model = model_module.getModel()
model.setTimepoints(np.linspace(0, 8, 250))
model.requireSensitivitiesForAllParameters()
model.setAlwaysCheckFinite(True)
model.setParameterScale(amici.parameterScalingFromIntVector([
amici.ParameterScaling.none
if re.match(r'n[0-9]+$', par_id)
else amici.ParameterScaling.log10
for par_id in model.getParameterIds()
]))

model = model_module.getModel()
model.setTimepoints(np.linspace(0, 8, 250))
model.requireSensitivitiesForAllParameters()
model.setAlwaysCheckFinite(True)
model.setParameterScale(amici.parameterScalingFromIntVector([
amici.ParameterScaling.none
if re.match(r'n[0-9]+$', par_id)
else amici.ParameterScaling.log10
for par_id in model.getParameterIds()
]))

solver = model.getSolver()
solver.setSensitivityMethod(amici.SensitivityMethod.forward)
solver.setSensitivityOrder(amici.SensitivityOrder.first)
solver = model.getSolver()
solver.setSensitivityMethod(amici.SensitivityMethod.forward)
solver.setSensitivityOrder(amici.SensitivityOrder.first)

rdata = amici.runAmiciSimulation(model, solver)
rdata = amici.runAmiciSimulation(model, solver)

# print sensitivity-related results
assert rdata['status'] == amici.AMICI_SUCCESS
check_derivatives(model, solver, None, assert_fun, atol=1e-2, rtol=1e-2,
epsilon=1e-3)
# print sensitivity-related results
assert rdata['status'] == amici.AMICI_SUCCESS
check_derivatives(model, solver, None, assert_fun, atol=1e-2, rtol=1e-2,
epsilon=1e-3)


def normal_nllh(m, y, sigma):
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2 changes: 1 addition & 1 deletion sonar-project.properties
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ sonar.organization=icb-dcm
sonar.projectKey=ICB-DCM_AMICI

sonar.sources=.
sonar.exclusions=build/**,ThirdParty/**,doc/**,models/**,python/sdist/amici/**,**/*.html,**/*.m,model_*/**
sonar.exclusions=build/**,ThirdParty/**,doc/**,models/**,python/sdist/amici/**,**/*.html,**/*.m,model_*/**,**/sbml_test_models/**

sonar.sourceEncoding=UTF-8

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