skip_on_valgrind

python/tests/petab/test_petab_problem.py

@@ -1,7 +1,9 @@
 from amici.petab.petab_problem import PetabProblem
 from benchmark_models_petab import get_problem
+from amici.testing import skip_on_valgrind
 
 
+@skip_on_valgrind
 def test_amici_petab_problem_pregenerate():
     """PetabProblem with pre-generated ExpDatas"""
     # any example is fine - the only assumption is that we don't have
@@ -29,6 +31,7 @@ def test_amici_petab_problem_pregenerate():
         assert edata.parameters[0] == 0.12345
 
 
+@skip_on_valgrind
 def test_amici_petab_problem_on_demand():
     """PetabProblem with on-demand ExpDatas"""
     # any example is fine - the only assumption is that we don't have
@@ -64,6 +67,7 @@ def test_amici_petab_problem_on_demand():
     )
 
 
+@skip_on_valgrind
 def test_amici_petab_problem_pregenerate_equals_on_demand():
     """Check that PetabProblem produces the same ExpDatas
     independent of the `store_edatas` parameter."""

python/tests/test_antimony_import.py

@@ -2,8 +2,10 @@
 import numpy as np
 from amici.antimony_import import antimony2amici
 from amici.testing import TemporaryDirectoryWinSafe as TemporaryDirectory
+from amici.testing import skip_on_valgrind
 
 
+@skip_on_valgrind
 def test_antimony_example():
     """If this example requires changes, please also update documentation/python_interface.rst."""
     ant_model = """

python/tests/test_compare_conservation_laws_sbml.py

@@ -5,6 +5,7 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose, assert_array_equal
+from amici.testing import skip_on_valgrind
 
 
 @pytest.fixture
@@ -123,6 +124,7 @@ def get_results(
     return amici.runAmiciSimulation(model, solver, edata)
 
 
+@skip_on_valgrind
 def test_compare_conservation_laws_sbml(models, edata_fixture):
     # first, create the model
     model_with_cl, model_without_cl = models
@@ -288,6 +290,7 @@ def test_adjoint_pre_and_post_equilibration(models, edata_fixture):
             assert_allclose(raa_cl["sllh"], raa["sllh"], 1e-5, 1e-5)
 
 
+@skip_on_valgrind
 def test_get_set_model_settings(models):
     """test amici.(get|set)_model_settings cycles for models with and without
     conservation laws"""

python/tests/test_cxxcodeprinter.py

@@ -1,8 +1,10 @@
 import sympy as sp
 from amici.cxxcodeprinter import AmiciCxxCodePrinter
 from sympy.codegen.rewriting import optims_c99
+from amici.testing import skip_on_valgrind
 
 
+@skip_on_valgrind
 def test_optimizations():
     """Check that AmiciCxxCodePrinter handles optimizations correctly."""
     try:

python/tests/test_de_model.py

@@ -1,8 +1,10 @@
 import sympy as sp
 from amici.de_model import Event
 from amici.import_utils import amici_time_symbol
+from amici.testing import skip_on_valgrind
 
 
+@skip_on_valgrind
 def test_event_trigger_time():
     e = Event(
         sp.Symbol("event1"), "event name", amici_time_symbol - 10, sp.Float(0)

python/tests/test_ode_export.py

@@ -93,6 +93,7 @@ def test_csc_matrix_vector():
     assert str(sparse_matrix) == "Matrix([[0], [da2_db_1]])"
 
 
+@skip_on_valgrind
 def test_match_deriv():
     from amici.de_export import DERIVATIVE_PATTERN as pat
 

python/tests/test_pandas.py

@@ -5,6 +5,8 @@
 import amici
 import numpy as np
 import pytest
+from amici.testing import skip_on_valgrind
+
 
 # test parameters for test_pandas_import_export
 combos = itertools.product([(10, 5), (5, 10), ()], repeat=3)
@@ -18,6 +20,7 @@
 ]
 
 
+@skip_on_valgrind
 @pytest.mark.parametrize("case", cases)
 def test_pandas_import_export(sbml_example_presimulation_module, case):
     """TestCase class for testing csv import using pandas"""

python/tests/test_petab_objective.py

@@ -10,6 +10,7 @@
 import pytest
 from amici.petab.petab_import import import_petab_problem
 from amici.petab.simulations import SLLH, simulate_petab
+from amici.testing import skip_on_valgrind
 
 # Absolute and relative tolerances for finite difference gradient checks.
 ATOL: float = 1e-3
@@ -29,6 +30,7 @@ def lotka_volterra() -> petab.Problem:
     )
 
 
+@skip_on_valgrind
 def test_simulate_petab_sensitivities(lotka_volterra):
     petab_problem = lotka_volterra
     amici_model = import_petab_problem(petab_problem)

python/tests/test_rdata.py

@@ -4,6 +4,7 @@
 import pytest
 from amici.numpy import evaluate
 from numpy.testing import assert_almost_equal, assert_array_equal
+from amici.testing import skip_on_valgrind
 
 
 @pytest.fixture(scope="session")
@@ -19,6 +20,7 @@ def rdata_by_id_fixture(sbml_example_presimulation_module):
     return model, rdata
 
 
+@skip_on_valgrind
 def test_rdata_by_id(rdata_by_id_fixture):
     model, rdata = rdata_by_id_fixture
 
@@ -42,6 +44,7 @@ def test_rdata_by_id(rdata_by_id_fixture):
     )
 
 
+@skip_on_valgrind
 def test_evaluate(rdata_by_id_fixture):
     # get IDs of model components
     model, rdata = rdata_by_id_fixture

python/tests/test_sbml_import.py

@@ -654,6 +654,7 @@ def _test_set_parameters_by_dict(model_module):
     assert model.getParameters() == old_parameter_values
 
 
+@skip_on_valgrind
 @pytest.mark.parametrize("extract_cse", [True, False])
 def test_code_gen_uses_cse(extract_cse):
     """Check that code generation honors AMICI_EXTRACT_CSE"""
@@ -675,6 +676,7 @@ def test_code_gen_uses_cse(extract_cse):
         os.environ = old_environ
 
 
+@skip_on_valgrind
 def test_code_gen_uses_lhs_symbol_ids():
     """Check that code generation uses symbol IDs instead of plain array
     indices"""
@@ -691,6 +693,7 @@ def test_code_gen_uses_lhs_symbol_ids():
     assert "dobservable_x1_dx1 = " in dwdx
 
 
+@skip_on_valgrind
 def test_hardcode_parameters(simple_sbml_model):
     """Test model generation works for model without observables"""
     sbml_doc, sbml_model = simple_sbml_model