Replace setup() with setup_method() in func tests

bluepyopt/tests/test_l5pc.py

@@ -3,8 +3,11 @@
 import json
 import os
 import sys
-
 from contextlib import contextmanager
+
+import bluepyopt
+from bluepyopt import ephys
+
 if sys.version_info[0] < 3:
     from StringIO import StringIO
 else:
@@ -13,45 +16,43 @@
 
 import pytest
 
-L5PC_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__),
-                                         '../../examples/l5pc'))
+L5PC_PATH = os.path.abspath(
+    os.path.join(os.path.dirname(__file__), "../../examples/l5pc")
+)
 SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
 
 sys.path.insert(0, L5PC_PATH)
 
-import bluepyopt
-from bluepyopt import ephys
 
 neuron_sim = ephys.simulators.NrnSimulator()
 
 neuron_sim.neuron.h.nrn_load_dll(
-    os.path.join(
-        L5PC_PATH,
-        'x86_64/.libs/libnrnmech.so'))
+    os.path.join(L5PC_PATH, "x86_64/.libs/libnrnmech.so")
+)
 
 
 # Parameters in release circuit model
 release_parameters = {
-    'gNaTs2_tbar_NaTs2_t.apical': 0.026145,
-    'gSKv3_1bar_SKv3_1.apical': 0.004226,
-    'gImbar_Im.apical': 0.000143,
-    'gNaTa_tbar_NaTa_t.axonal': 3.137968,
-    'gK_Tstbar_K_Tst.axonal': 0.089259,
-    'gamma_CaDynamics_E2.axonal': 0.002910,
-    'gNap_Et2bar_Nap_Et2.axonal': 0.006827,
-    'gSK_E2bar_SK_E2.axonal': 0.007104,
-    'gCa_HVAbar_Ca_HVA.axonal': 0.000990,
-    'gK_Pstbar_K_Pst.axonal': 0.973538,
-    'gSKv3_1bar_SKv3_1.axonal': 1.021945,
-    'decay_CaDynamics_E2.axonal': 287.198731,
-    'gCa_LVAstbar_Ca_LVAst.axonal': 0.008752,
-    'gamma_CaDynamics_E2.somatic': 0.000609,
-    'gSKv3_1bar_SKv3_1.somatic': 0.303472,
-    'gSK_E2bar_SK_E2.somatic': 0.008407,
-    'gCa_HVAbar_Ca_HVA.somatic': 0.000994,
-    'gNaTs2_tbar_NaTs2_t.somatic': 0.983955,
-    'decay_CaDynamics_E2.somatic': 210.485284,
-    'gCa_LVAstbar_Ca_LVAst.somatic': 0.000333
+    "gNaTs2_tbar_NaTs2_t.apical": 0.026145,
+    "gSKv3_1bar_SKv3_1.apical": 0.004226,
+    "gImbar_Im.apical": 0.000143,
+    "gNaTa_tbar_NaTa_t.axonal": 3.137968,
+    "gK_Tstbar_K_Tst.axonal": 0.089259,
+    "gamma_CaDynamics_E2.axonal": 0.002910,
+    "gNap_Et2bar_Nap_Et2.axonal": 0.006827,
+    "gSK_E2bar_SK_E2.axonal": 0.007104,
+    "gCa_HVAbar_Ca_HVA.axonal": 0.000990,
+    "gK_Pstbar_K_Pst.axonal": 0.973538,
+    "gSKv3_1bar_SKv3_1.axonal": 1.021945,
+    "decay_CaDynamics_E2.axonal": 287.198731,
+    "gCa_LVAstbar_Ca_LVAst.axonal": 0.008752,
+    "gamma_CaDynamics_E2.somatic": 0.000609,
+    "gSKv3_1bar_SKv3_1.somatic": 0.303472,
+    "gSK_E2bar_SK_E2.somatic": 0.008407,
+    "gCa_HVAbar_Ca_HVA.somatic": 0.000994,
+    "gNaTs2_tbar_NaTs2_t.somatic": 0.983955,
+    "decay_CaDynamics_E2.somatic": 210.485284,
+    "gCa_LVAstbar_Ca_LVAst.somatic": 0.000333,
 }
 
 
@@ -65,8 +66,8 @@ def load_from_json(filename):
 def dump_to_json(content, filename):
     """Dump structure to json"""
 
-    with open(filename, 'w') as json_file:
-        return json.dump(content, json_file, indent=4, separators=(',', ': '))
+    with open(filename, "w") as json_file:
+        return json.dump(content, json_file, indent=4, separators=(",", ": "))
 
 
 def test_import():
@@ -78,60 +79,62 @@ def test_import():
 
 
 class TestL5PCModel(object):
-
     """Test L5PC model"""
 
-    def setup(self):
+    def setup_method(self):
         """Set up class"""
         sys.path.insert(0, L5PC_PATH)
 
         import l5pc_model  # NOQA
+
         self.l5pc_cell = l5pc_model.create()
-        assert isinstance(self.l5pc_cell,
-                          bluepyopt.ephys.models.CellModel)
+        assert isinstance(self.l5pc_cell, bluepyopt.ephys.models.CellModel)
         self.nrn = ephys.simulators.NrnSimulator()
 
     def test_instantiate(self):
         """L5PC: test instantiation of l5pc cell model"""
         self.l5pc_cell.freeze(release_parameters)
         self.l5pc_cell.instantiate(sim=self.nrn)
 
-    def teardown(self):
+    def teardown_method(self):
         """Teardown"""
         self.l5pc_cell.destroy(sim=self.nrn)
 
 
 class TestL5PCEvaluator(object):
-
     """Test L5PC evaluator"""
 
-    def setup(self):
+    def setup_method(self):
         """Set up class"""
 
         import l5pc_evaluator  # NOQA
 
         self.l5pc_evaluator = l5pc_evaluator.create()
 
-        assert isinstance(self.l5pc_evaluator,
-                          bluepyopt.ephys.evaluators.CellEvaluator)
+        assert isinstance(
+            self.l5pc_evaluator, bluepyopt.ephys.evaluators.CellEvaluator
+        )
 
     @pytest.mark.slow
     def test_eval(self):
         """L5PC: test evaluation of l5pc evaluator"""
         result = self.l5pc_evaluator.evaluate_with_dicts(
-            param_dict=release_parameters)
+            param_dict=release_parameters
+        )
 
         expected_results = load_from_json(
-            os.path.join(SCRIPT_DIR, 'expected_results.json'))
+            os.path.join(SCRIPT_DIR, "expected_results.json")
+        )
 
         # Use two lines below to update expected result
         # expected_results['TestL5PCEvaluator.test_eval'] = result
         # dump_to_json(expected_results, 'expected_results.json')
 
-        assert set(result.keys(
-        )) == set(expected_results['TestL5PCEvaluator.test_eval'].keys())
+        assert set(result.keys()) == set(
+            expected_results["TestL5PCEvaluator.test_eval"].keys()
+        )
 
-    def teardown(self):
+    def teardown_method(self):
         """Teardown"""
         pass
 
@@ -152,7 +155,8 @@ def stdout_redirector(stream):
 def test_exec():
     """L5PC Notebook: test execution"""
     import numpy
-    numpy.seterr(all='raise')
+
+    numpy.seterr(all="raise")
     old_cwd = os.getcwd()
     output = StringIO()
     try:
@@ -162,14 +166,14 @@ def test_exec():
             # Probably because multiprocessing doesn't work correctly during
             # import
             if sys.version_info[0] < 3:
-                execfile('L5PC.py')  # NOQA
+                execfile("L5PC.py")  # NOQA
             else:
-                with open('L5PC.py') as l5pc_file:
-                    exec(compile(l5pc_file.read(), 'L5PC.py', 'exec'))  # NOQA
+                with open("L5PC.py") as l5pc_file:
+                    exec(compile(l5pc_file.read(), "L5PC.py", "exec"))  # NOQA
         stdout = output.getvalue()
         # first and last values of optimal individual
-        assert '0.001017834439738432' in stdout
-        assert '202.18814057682334' in stdout
+        assert "0.001017834439738432" in stdout
+        assert "202.18814057682334" in stdout
         assert "'gamma_CaDynamics_E2.somatic': 0.03229357096515606" in stdout
     finally:
         os.chdir(old_cwd)
@@ -180,7 +184,8 @@ def test_exec():
 def test_l5pc_validate_neuron_arbor():
     """L5PC Neuron/Arbor validation Notebook: test execution"""
     import numpy
-    numpy.seterr(all='raise')
+
+    numpy.seterr(all="raise")
     old_cwd = os.getcwd()
     output = StringIO()
     try:
@@ -190,19 +195,28 @@ def test_l5pc_validate_neuron_arbor():
             # Probably because multiprocessing doesn't work correctly during
             # import
             if sys.version_info[0] < 3:
-                execfile('l5pc_validate_neuron_arbor_somatic.py')  # NOQA
+                execfile("l5pc_validate_neuron_arbor_somatic.py")  # NOQA
             else:
-                with open('l5pc_validate_neuron_arbor_somatic.py') \
-                        as l5pc_file:
+                with open(
+                    "l5pc_validate_neuron_arbor_somatic.py"
+                ) as l5pc_file:
                     l5pc_globals = {}
-                    exec(compile(l5pc_file.read(),
-                                 'l5pc_validate_neuron_arbor_somatic.py',
-                                 'exec'), l5pc_globals, l5pc_globals)  # NOQA
+                    exec(
+                        compile(
+                            l5pc_file.read(),
+                            "l5pc_validate_neuron_arbor_somatic.py",
+                            "exec",
+                        ),
+                        l5pc_globals,
+                        l5pc_globals,
+                    )  # NOQA
         stdout = output.getvalue()
         # mean relative L1-deviation between Arbor and Neuron below tolerance
-        assert 'Default dt ({:,.3g}): test_l5pc OK!'.format(0.025) + \
-            ' The mean relative Arbor-Neuron L1-deviation and error' \
+        assert (
+            "Default dt ({:,.3g}): test_l5pc OK!".format(0.025)
+            + " The mean relative Arbor-Neuron L1-deviation and error"
             in stdout
+        )
     finally:
         os.chdir(old_cwd)
         output.close()

bluepyopt/tests/test_lfpy.py

@@ -2,13 +2,11 @@
 
 import os
 import sys
+
 import pytest
 
 L5PC_LFPY_PATH = os.path.abspath(
-    os.path.join(
-        os.path.dirname(__file__),
-        '../../examples/l5pc_lfpy'
-    )
+    os.path.join(os.path.dirname(__file__), "../../examples/l5pc_lfpy")
 )
 SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
 
@@ -30,10 +28,10 @@ def test_lfpy_evaluator():
 
     responses = evaluator.run_protocols(
         protocols=evaluator.fitness_protocols.values(),
-        param_values=release_params
+        param_values=release_params,
     )
     values = evaluator.fitness_calculator.calculate_values(responses)
 
     assert len(values) == 21
-    assert abs(values['Step1.soma.AP_height'] - 27.85963902931001) < 1e-5
-    assert len(responses['Step1.MEA.v']["voltage"]) == 40
+    assert abs(values["Step1.soma.AP_height"] - 27.85963902931001) < 1e-5
+    assert len(responses["Step1.MEA.v"]["voltage"]) == 40

bluepyopt/tests/test_simplecell.py

@@ -1,72 +1,67 @@
 """Simple cell example test class"""
 
-import sys
 import os
+import sys
 
-SIMPLECELL_PATH = os.path.abspath(os.path.join(
-    os.path.dirname(__file__),
-    '../../examples/simplecell'))
+SIMPLECELL_PATH = os.path.abspath(
+    os.path.join(os.path.dirname(__file__), "../../examples/simplecell")
+)
 
 # sys.path.insert(0, SIMPLECELL_PATH)
 
 
 class TestSimpleCellClass(object):
-
     """Simple cell example test class for NEURON"""
 
-    def setup(self):
+    def setup_method(self):
         """Setup"""
         self.old_cwd = os.getcwd()
         self.old_stdout = sys.stdout
 
         os.chdir(SIMPLECELL_PATH)
-        sys.stdout = open(os.devnull, 'w')
+        sys.stdout = open(os.devnull, "w")
 
-    @staticmethod
-    def test_exec():
+    def test_exec(self):
         """Simplecell NEURON: test execution"""
         # When using import instead of execfile this doesn't work
         # Probably because multiprocessing doesn't work correctly during
         # import
         if sys.version_info[0] < 3:
-            execfile('simplecell.py')  # NOQA
+            execfile("simplecell.py")  # NOQA
         else:
-            with open('simplecell.py') as sc_file:
-                exec(compile(sc_file.read(), 'simplecell.py', 'exec'))  # NOQA
+            with open("simplecell.py") as sc_file:
+                exec(compile(sc_file.read(), "simplecell.py", "exec"))  # NOQA
 
-    def teardown(self):
+    def teardown_method(self):
         """Tear down"""
 
         sys.stdout = self.old_stdout
         os.chdir(self.old_cwd)
 
 
 class TestSimpleCellArborClass(object):
-
     """Simple cell example test class for Arbor"""
 
-    def setup(self):
+    def setup_method(self):
         """Setup"""
         self.old_cwd = os.getcwd()
         self.old_stdout = sys.stdout
 
         os.chdir(SIMPLECELL_PATH)
-        sys.stdout = open(os.devnull, 'w')
+        sys.stdout = open(os.devnull, "w")
 
-    @staticmethod
-    def test_exec():
+    def test_exec(self):
         """Simplecell Arbor: test execution"""
         # When using import instead of execfile this doesn't work
         # Probably because multiprocessing doesn't work correctly during
         # import
         if sys.version_info[0] < 3:
-            execfile('simplecell_arbor.py')  # NOQA
+            execfile("simplecell_arbor.py")  # NOQA
         else:
-            with open('simplecell_arbor.py') as sc_file:
-                exec(compile(sc_file.read(),
-                    'simplecell_arbor.py', 'exec'))  # NOQA
+            with open("simplecell_arbor.py") as sc_file:
+                exec(compile(sc_file.read(), "simplecell_arbor.py", "exec"))  # NOQA
 
-    def teardown(self):
+    def teardown_method(self):
         """Tear down"""
 
         sys.stdout = self.old_stdout