Merge branch 'develop' into fix/citations2

pyproject.toml

@@ -197,6 +197,8 @@ extend-select = [
     "YTT",           # flake8-2020
     "TID252",        # relative-imports
     "S101",          # to identify use of assert statement
+    "PT027",         # remove unittest style assertion
+    "PT009",         # Use pytest.raises instead of unittest-style
 ]
 ignore = [
     "E741",        # Ambiguous variable name

tests/integration/test_models/test_full_battery_models/test_lithium_ion/test_compare_outputs.py

@@ -4,11 +4,10 @@
 
 import pybamm
 import numpy as np
-import unittest
 from tests import StandardOutputComparison
 
 
-class TestCompareOutputs(unittest.TestCase):
+class TestCompareOutputs:
     def test_compare_outputs_surface_form(self):
         # load models
         options = [
@@ -142,12 +141,3 @@ def test_compare_narrow_size_distribution(self):
         # compare outputs
         comparison = StandardOutputComparison(solutions)
         comparison.test_all(skip_first_timestep=True)
-
-
-if __name__ == "__main__":
-    print("Add -v for more debug output")
-    import sys
-
-    if "-v" in sys.argv:
-        debug = True
-    unittest.main()

tests/integration/test_models/test_submodels/test_interface/test_butler_volmer.py

@@ -2,15 +2,15 @@
 # Tests for the electrode-electrolyte interface equations
 #
 
+import pytest
 import pybamm
 from tests import get_discretisation_for_testing
 
-import unittest
 import numpy as np
 
 
-class TestButlerVolmer(unittest.TestCase):
-    def setUp(self):
+class TestButlerVolmer:
+    def setup_method(self):
         self.delta_phi_s_n = pybamm.Variable(
             "surface potential difference [V]",
             ["negative electrode"],
@@ -73,7 +73,7 @@ def setUp(self):
             "reaction source terms [A.m-3]": 1,
         }
 
-    def tearDown(self):
+    def teardown_method(self):
         del self.variables
         del self.c_e_n
         del self.c_e_p
@@ -114,12 +114,12 @@ def test_creation(self):
         ]
 
         # negative electrode Butler-Volmer is Multiplication
-        self.assertIsInstance(j_n, pybamm.Multiplication)
-        self.assertEqual(j_n.domain, ["negative electrode"])
+        assert isinstance(j_n, pybamm.Multiplication)
+        assert j_n.domain == ["negative electrode"]
 
         # positive electrode Butler-Volmer is Multiplication
-        self.assertIsInstance(j_p, pybamm.Multiplication)
-        self.assertEqual(j_p.domain, ["positive electrode"])
+        assert isinstance(j_p, pybamm.Multiplication)
+        assert j_p.domain == ["positive electrode"]
 
     def test_set_parameters(self):
         param = pybamm.LithiumIonParameters()
@@ -159,9 +159,9 @@ def test_set_parameters(self):
         j_p = parameter_values.process_symbol(j_p)
         # Test
         for x in j_n.pre_order():
-            self.assertNotIsInstance(x, pybamm.Parameter)
+            assert not isinstance(x, pybamm.Parameter)
         for x in j_p.pre_order():
-            self.assertNotIsInstance(x, pybamm.Parameter)
+            assert not isinstance(x, pybamm.Parameter)
 
     def test_discretisation(self):
         param = pybamm.LithiumIonParameters()
@@ -219,17 +219,13 @@ def test_discretisation(self):
             [mesh["negative electrode"].nodes, mesh["positive electrode"].nodes]
         )
         y = np.concatenate([submesh**2, submesh**3, submesh**4])
-        self.assertEqual(
-            j_n.evaluate(None, y).shape, (mesh["negative electrode"].npts, 1)
-        )
-        self.assertEqual(
-            j_p.evaluate(None, y).shape, (mesh["positive electrode"].npts, 1)
-        )
+        assert j_n.evaluate(None, y).shape == (mesh["negative electrode"].npts, 1)
+        assert j_p.evaluate(None, y).shape == (mesh["positive electrode"].npts, 1)
 
         # test concatenated butler-volmer
         whole_cell = ["negative electrode", "separator", "positive electrode"]
         whole_cell_mesh = disc.mesh[whole_cell]
-        self.assertEqual(j.evaluate(None, y).shape, (whole_cell_mesh.npts, 1))
+        assert j.evaluate(None, y).shape == (whole_cell_mesh.npts, 1)
 
     def test_diff_c_e_lead_acid(self):
         # With intercalation
@@ -361,27 +357,12 @@ def j_p(delta_phi):
         j_n_FD = parameter_values.process_symbol(
             (j_n(delta_phi + h) - j_n(delta_phi - h)) / (2 * h)
         )
-        self.assertAlmostEqual(
-            j_n_diff.evaluate(inputs={"delta_phi": 0.5})
-            / j_n_FD.evaluate(inputs={"delta_phi": 0.5}),
-            1,
-            places=5,
-        )
+        assert j_n_diff.evaluate(inputs={"delta_phi": 0.5}) / j_n_FD.evaluate(
+            inputs={"delta_phi": 0.5}
+        ) == pytest.approx(1, abs=1e-05)
         j_p_FD = parameter_values.process_symbol(
             (j_p(delta_phi + h) - j_p(delta_phi - h)) / (2 * h)
         )
-        self.assertAlmostEqual(
-            j_p_diff.evaluate(inputs={"delta_phi": 0.5})
-            / j_p_FD.evaluate(inputs={"delta_phi": 0.5}),
-            1,
-            places=5,
-        )
-
-
-if __name__ == "__main__":
-    print("Add -v for more debug output")
-    import sys
-
-    if "-v" in sys.argv:
-        debug = True
-    unittest.main()
+        assert j_p_diff.evaluate(inputs={"delta_phi": 0.5}) / j_p_FD.evaluate(
+            inputs={"delta_phi": 0.5}
+        ) == pytest.approx(1, abs=1e-05)

tests/unit/test_expression_tree/test_concatenations.py

@@ -2,7 +2,6 @@
 # Tests for the Concatenation class and subclasses
 #
 import pytest
-import unittest.mock as mock
 from tests import assert_domain_equal
 
 
@@ -377,7 +376,7 @@ def test_to_equation(self):
         # Test concat_sym
         assert pybamm.Concatenation(a, b).to_equation() == func_symbol
 
-    def test_to_from_json(self):
+    def test_to_from_json(self, mocker):
         # test DomainConcatenation
         mesh = get_mesh_for_testing()
         a = pybamm.Symbol("a", domain=["negative electrode"])
@@ -386,7 +385,7 @@ def test_to_from_json(self):
 
         json_dict = {
             "name": "domain_concatenation",
-            "id": mock.ANY,
+            "id": mocker.ANY,
             "domains": {
                 "primary": ["negative electrode", "separator", "positive electrode"],
                 "secondary": [],
@@ -429,7 +428,7 @@ def test_to_from_json(self):
 
         np_json = {
             "name": "numpy_concatenation",
-            "id": mock.ANY,
+            "id": mocker.ANY,
             "domains": {
                 "primary": [],
                 "secondary": [],

tests/unit/test_expression_tree/test_functions.py

@@ -3,7 +3,6 @@
 #
 
 import pytest
-import unittest.mock as mock
 
 import numpy as np
 from scipy import special
@@ -399,7 +398,7 @@ def test_tanh(self):
             abs=1e-05,
         )
 
-    def test_erf(self):
+    def test_erf(self, mocker):
         a = pybamm.InputParameter("a")
         fun = pybamm.erf(a)
         assert fun.evaluate(inputs={"a": 3}) == special.erf(3)
@@ -416,7 +415,7 @@ def test_erf(self):
         # test creation from json
         input_json = {
             "name": "erf",
-            "id": mock.ANY,
+            "id": mocker.ANY,
             "function": "erf",
             "children": [a],
         }

tests/unit/test_expression_tree/test_input_parameter.py

@@ -4,7 +4,6 @@
 import numpy as np
 import pybamm
 import pytest
-import unittest.mock as mock
 
 
 class TestInputParameter:
@@ -49,12 +48,12 @@ def test_errors(self):
         with pytest.raises(KeyError):
             a.evaluate()
 
-    def test_to_from_json(self):
+    def test_to_from_json(self, mocker):
         a = pybamm.InputParameter("a")
 
         json_dict = {
             "name": "a",
-            "id": mock.ANY,
+            "id": mocker.ANY,
             "domain": [],
             "expected_size": 1,
         }

tests/unit/test_expression_tree/test_operations/test_evaluate_python.py

@@ -6,7 +6,6 @@
 import pybamm
 
 from tests import get_discretisation_for_testing, get_1p1d_discretisation_for_testing
-import unittest
 import numpy as np
 import scipy.sparse
 from collections import OrderedDict
@@ -746,13 +745,3 @@ def test_jax_coo_matrix(self):
 
         with pytest.raises(NotImplementedError):
             A.multiply(v)
-
-
-if __name__ == "__main__":
-    print("Add -v for more debug output")
-    import sys
-
-    if "-v" in sys.argv:
-        debug = True
-    pybamm.settings.debug_mode = True
-    unittest.main()

tests/unit/test_parameters/test_parameter_sets/test_Ecker2015.py

@@ -2,11 +2,11 @@
 # Tests for O'Kane (2022) parameter set
 #
 
+import pytest
 import pybamm
-import unittest
 
 
-class TestEcker2015(unittest.TestCase):
+class TestEcker2015:
     def test_functions(self):
         param = pybamm.ParameterValues("Ecker2015")
         sto = pybamm.Scalar(0.5)
@@ -40,16 +40,6 @@ def test_functions(self):
         }
 
         for name, value in fun_test.items():
-            self.assertAlmostEqual(
-                param.evaluate(param[name](*value[0])), value[1], places=4
+            assert param.evaluate(param[name](*value[0])) == pytest.approx(
+                value[1], abs=0.0001
             )
-
-
-if __name__ == "__main__":
-    print("Add -v for more debug output")
-    import sys
-
-    if "-v" in sys.argv:
-        debug = True
-    pybamm.settings.debug_mode = True
-    unittest.main()