update tests to use kwargs

Author: stephprince

tests/integration/hdf5/test_image.py

@@ -9,7 +9,7 @@ class TestImageSeriesIO(AcquisitionH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return a test ImageSeries to read/write """
-        self.dev1 = Device('dev1')
+        self.dev1 = Device(name='dev1')
         iS = ImageSeries(
             name='test_iS',
             unit='unit',
@@ -31,7 +31,7 @@ class TestOpticalSeriesIO(NWBH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return a test OpticalSeries to read/write """
-        self.dev1 = Device('dev1')
+        self.dev1 = Device(name='dev1')
         self.optical_series = OpticalSeries(
             name='OpticalSeries',
             distance=8.,

tests/integration/hdf5/test_misc.py

@@ -75,7 +75,7 @@ class TestUnitsFileIO(NWBH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return placeholder Units object. Tested units are added directly to the NWBFile in addContainer """
-        return Units('placeholder')  # this will get ignored
+        return Units(name='placeholder')  # this will get ignored
 
     def addContainer(self, nwbfile):
         """ Add units to the given NWBFile """

tests/integration/hdf5/test_nwbfile.py

@@ -261,7 +261,7 @@ class TestEpochsIO(NWBH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return placeholder epochs object. Tested epochs are added directly to the NWBFile in addContainer """
-        return TimeIntervals('epochs')
+        return TimeIntervals(name='epochs')
 
     def addContainer(self, nwbfile):
         """ Add the test epochs to the given NWBFile """

tests/unit/test_ecephys.py

@@ -25,8 +25,11 @@
 
 def make_electrode_table():
     table = ElectrodeTable()
-    dev1 = Device('dev1')
-    group = ElectrodeGroup('tetrode1', 'tetrode description', 'tetrode location', dev1)
+    dev1 = Device(name='dev1')
+    group = ElectrodeGroup(name='tetrode1', 
+                           description='tetrode description', 
+                           location='tetrode location', 
+                           device=dev1)
     table.add_row(location='CA1', group=group, group_name='tetrode1')
     table.add_row(location='CA1', group=group, group_name='tetrode1')
     table.add_row(location='CA1', group=group, group_name='tetrode1')
@@ -70,9 +73,10 @@ def test_init(self):
 
     def test_link(self):
         table, region = self._create_table_and_region()
-        ts1 = ElectricalSeries('test_ts1', [0, 1, 2, 3, 4, 5], region, timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
-        ts2 = ElectricalSeries('test_ts2', ts1, region, timestamps=ts1)
-        ts3 = ElectricalSeries('test_ts3', ts2, region, timestamps=ts2)
+        ts1 = ElectricalSeries(name='test_ts1', data=[0, 1, 2, 3, 4, 5], electrodes=region, 
+                               timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
+        ts2 = ElectricalSeries(name='test_ts2', data=ts1, electrodes=region, timestamps=ts1)
+        ts3 = ElectricalSeries(name='test_ts3', data=ts2, electrodes=region, timestamps=ts2)
         self.assertEqual(ts2.data, [0, 1, 2, 3, 4, 5])
         self.assertEqual(ts2.timestamps, [0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
         self.assertEqual(ts3.data, [0, 1, 2, 3, 4, 5])
@@ -82,7 +86,8 @@ def test_invalid_data_shape(self):
         table, region = self._create_table_and_region()
         with self.assertRaisesWith(ValueError, ("ElectricalSeries.__init__: incorrect shape for 'data' (got '(2, 2, 2, "
                                                 "2)', expected '((None,), (None, None), (None, None, None))')")):
-            ElectricalSeries('test_ts1', np.ones((2, 2, 2, 2)), region, timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
+            ElectricalSeries(name='test_ts1', data=np.ones((2, 2, 2, 2)), electrodes=region, 
+                             timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
 
     def test_dimensions_warning(self):
         table, region = self._create_table_and_region()
@@ -177,7 +182,7 @@ def test_incorrect_timestamps(self):
 class ElectrodeGroupConstructor(TestCase):
 
     def test_init(self):
-        dev1 = Device('dev1')
+        dev1 = Device(name='dev1')
         group = ElectrodeGroup(name='elec1',
                                description='electrode description',
                                location='electrode location',
@@ -191,17 +196,20 @@ def test_init(self):
 
     def test_init_position_array(self):
         position = np.array((1, 2, 3), dtype=np.dtype([('x', float), ('y', float), ('z', float)]))
-        dev1 = Device('dev1')
-        group = ElectrodeGroup('elec1', 'electrode description', 'electrode location', dev1,
-                               position)
+        dev1 = Device(name='dev1')
+        group = ElectrodeGroup(name='elec1', 
+                               description='electrode description', 
+                               location='electrode location', 
+                               device=dev1,
+                               position=position)
         self.assertEqual(group.name, 'elec1')
         self.assertEqual(group.description, 'electrode description')
         self.assertEqual(group.location, 'electrode location')
         self.assertEqual(group.device, dev1)
         self.assertEqual(group.position, position)
 
     def test_init_position_none(self):
-        dev1 = Device('dev1')
+        dev1 = Device(name='dev1')
         group = ElectrodeGroup(name='elec1',
                                description='electrode description',
                                location='electrode location',
@@ -213,7 +221,7 @@ def test_init_position_none(self):
         self.assertIsNone(group.position)
 
     def test_init_position_bad(self):
-        dev1 = Device('dev1')
+        dev1 = Device(name='dev1')
         with self.assertRaises(ValueError):
             ElectrodeGroup(name='elec1',
                            description='electrode description',
@@ -256,8 +264,11 @@ def test_init(self):
         data = list(range(10))
         ts = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
         table, region = self._create_table_and_region()
-        eS = ElectricalSeries('test_eS', data, region, timestamps=ts)
-        eD = EventDetection('detection_method', eS, (1, 2, 3), (0.1, 0.2, 0.3))
+        eS = ElectricalSeries(name='test_eS', data=data, electrodes=region, timestamps=ts)
+        eD = EventDetection(detection_method='detection_method', 
+                            source_electricalseries=eS, 
+                            source_idx=(1, 2, 3), 
+                            times=(0.1, 0.2, 0.3))
         self.assertEqual(eD.detection_method, 'detection_method')
         self.assertEqual(eD.source_electricalseries, eS)
         self.assertEqual(eD.source_idx, (1, 2, 3))
@@ -279,7 +290,10 @@ def _create_table_and_region(self):
 
     def test_init(self):
         table, region = self._create_table_and_region()
-        sES = SpikeEventSeries('test_sES', list(range(10)), list(range(10)), region)
+        sES = SpikeEventSeries(name='test_sES', 
+                               data=list(range(10)), 
+                               timestamps=list(range(10)), 
+                               electrodes=region)
 
         pm = ProcessingModule(name='test_module', description='a test module')
         ew = EventWaveform()
@@ -344,7 +358,8 @@ def _create_table_and_region(self):
 
     def test_init(self):
         _, region = self._create_table_and_region()
-        eS = ElectricalSeries('test_eS', [0, 1, 2, 3], region, timestamps=[0.1, 0.2, 0.3, 0.4])
+        eS = ElectricalSeries(name='test_eS', data=[0, 1, 2, 3], 
+                              electrodes=region, timestamps=[0.1, 0.2, 0.3, 0.4])
         msg = (
             "The linked table for DynamicTableRegion 'electrodes' does not share "
             "an ancestor with the DynamicTableRegion."
@@ -357,7 +372,10 @@ def test_init(self):
     def test_add_electrical_series(self):
         lfp = LFP()
         table, region = self._create_table_and_region()
-        eS = ElectricalSeries('test_eS', [0, 1, 2, 3], region, timestamps=[0.1, 0.2, 0.3, 0.4])
+        eS = ElectricalSeries(name='test_eS', 
+                              data=[0, 1, 2, 3], 
+                              electrodes=region, 
+                              timestamps=[0.1, 0.2, 0.3, 0.4])
         pm = ProcessingModule(name='test_module', description='a test module')
         pm.add(table)
         pm.add(lfp)
@@ -379,7 +397,10 @@ def _create_table_and_region(self):
 
     def test_init(self):
         _, region = self._create_table_and_region()
-        eS = ElectricalSeries('test_eS', [0, 1, 2, 3], region, timestamps=[0.1, 0.2, 0.3, 0.4])
+        eS = ElectricalSeries(name='test_eS', 
+                              data=[0, 1, 2, 3], 
+                              electrodes=region, 
+                              timestamps=[0.1, 0.2, 0.3, 0.4])
         msg = (
             "The linked table for DynamicTableRegion 'electrodes' does not share "
             "an ancestor with the DynamicTableRegion."
@@ -391,7 +412,10 @@ def test_init(self):
 
     def test_add_electrical_series(self):
         table, region = self._create_table_and_region()
-        eS = ElectricalSeries('test_eS', [0, 1, 2, 3], region, timestamps=[0.1, 0.2, 0.3, 0.4])
+        eS = ElectricalSeries(name='test_eS', 
+                              data=[0, 1, 2, 3], 
+                              electrodes=region, 
+                              timestamps=[0.1, 0.2, 0.3, 0.4])
         pm = ProcessingModule(name='test_module', description='a test module')
         fe = FilteredEphys()
         pm.add(table)
@@ -418,7 +442,10 @@ def test_init(self):
         table, region = self._create_table_and_region()
         description = ['desc1', 'desc2', 'desc3']
         features = [[[0, 1, 2], [3, 4, 5]], [[6, 7, 8], [9, 10, 11]]]
-        fe = FeatureExtraction(region, description, event_times, features)
+        fe = FeatureExtraction(electrodes=region, 
+                               description=description, 
+                               times=event_times, 
+                               features=features)
         self.assertEqual(fe.description, description)
         self.assertEqual(fe.times, event_times)
         self.assertEqual(fe.features, features)
@@ -428,26 +455,42 @@ def test_invalid_init_mismatched_event_times(self):
         table, region = self._create_table_and_region()
         description = ['desc1', 'desc2', 'desc3']
         features = [[[0, 1, 2], [3, 4, 5]]]
-        self.assertRaises(ValueError, FeatureExtraction, region, description, event_times, features)
+        with self.assertRaises(ValueError):
+            FeatureExtraction(electrodes=region, 
+                              description=description, 
+                              times=event_times, 
+                              features=features)
 
     def test_invalid_init_mismatched_electrodes(self):
         event_times = [1]
         table = make_electrode_table()
         region = DynamicTableRegion(name='electrodes', data=[0], description='the first electrode', table=table)
         description = ['desc1', 'desc2', 'desc3']
         features = [[[0, 1, 2], [3, 4, 5]]]
-        self.assertRaises(ValueError, FeatureExtraction, region, description, event_times, features)
+        with self.assertRaises(ValueError):
+            FeatureExtraction(electrodes=region, 
+                              description=description, 
+                              times=event_times, 
+                              features=features)
 
     def test_invalid_init_mismatched_description(self):
         event_times = [1]
         table, region = self._create_table_and_region()
         description = ['desc1', 'desc2', 'desc3', 'desc4']  # Need 3 descriptions but give 4
         features = [[[0, 1, 2], [3, 4, 5]]]
-        self.assertRaises(ValueError, FeatureExtraction, region, description, event_times, features)
+        with self.assertRaises(ValueError):
+            FeatureExtraction(electrodes=region, 
+                              description=description, 
+                              times=event_times, 
+                              features=features)
 
     def test_invalid_init_mismatched_description2(self):
         event_times = [1]
         table, region = self._create_table_and_region()
         description = ['desc1', 'desc2', 'desc3']
         features = [[0, 1, 2], [3, 4, 5]]  # Need 3D feature array but give only 2D array
-        self.assertRaises(ValueError, FeatureExtraction, region, description, event_times, features)
+        with self.assertRaises(ValueError):
+            FeatureExtraction(electrodes=region, 
+                              description=description, 
+                              times=event_times, 
+                              features=features)

tests/unit/test_epoch_legacy.py

@@ -21,7 +21,7 @@ class TestTimeIntervalsIO(NWBH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return placeholder epochs object. Tested epochs are added directly to the NWBFile in addContainer """
-        return TimeIntervals('epochs')
+        return TimeIntervals(name='epochs')
 
     def addContainer(self, nwbfile):
         """ Add the test epochs to the given NWBFile """
@@ -62,7 +62,8 @@ def getContainer(self, nwbfile):
     def test_legacy_format(self):
         description = 'a file to test writing and reading a %s' % self.container_type
         identifier = 'TEST_%s' % self.container_type
-        nwbfile = NWBFile(description, identifier, self.start_time, file_create_date=self.create_date)
+        nwbfile = NWBFile(session_description=description, identifier=identifier, 
+                          session_start_time=self.start_time, file_create_date=self.create_date)
         self.addContainer(nwbfile)
 
         # write the file