keep function behavior for deprecation warnings

src/pynwb/base.py

@@ -51,6 +51,7 @@ def add_container(self, **kwargs):
         Add an NWBContainer to this ProcessingModule
         '''
         warn("add_container is deprecated. Use add instead.", DeprecationWarning)
+        self.add(kwargs['container'])
 
     @docval({'name': 'container_name', 'type': str, 'doc': 'the name of the NWBContainer to retrieve'})
     def get_container(self, **kwargs):

src/pynwb/core.py

@@ -133,18 +133,17 @@ def __init__(self, **kwargs):
                                "Use description instead.")
                     )
             if notes != '' and description is not None:
-                self._error_on_new_warn_on_construct(
-                    error_msg='Cannot provide both notes and description to ScratchData.__init__. The description '
-                                'argument is recommended.'
-                    )
+                raise ValueError('Cannot provide both notes and description to ScratchData.__init__. The description '
+                                 'argument is recommended.')
             description = notes
         if not description:
-            self._error_on_new_warn_on_construct(error_msg='ScratchData.description is required by PyNWB > 3.0.')
+            self._error_on_new_warn_on_construct(error_msg='ScratchData.description is required.')
         self.description = description
 
     @property
     def notes(self):
         warn('Use of ScratchData.notes has been deprecated. Use ScratchData.description instead.', DeprecationWarning)
+        return self.description
 
     @notes.setter
     def notes(self, value):

src/pynwb/file.py

@@ -1053,6 +1053,8 @@ def add_scratch(self, **kwargs):
         if notes is not None or table_description != '':
             warn(('Use of the `notes` or `table_description` argument is deprecated. '
                   'Use the `description` argument instead.'), DeprecationWarning)
+            if description is not None:
+                raise ValueError('Cannot call add_scratch with (notes or table_description) and description')
 
         if isinstance(data, (str, int, float, bytes, np.ndarray, list, tuple, pd.DataFrame)):
             if name is None:

tests/integration/hdf5/test_ecephys.py

@@ -180,7 +180,7 @@ def setUpContainer(self):
         with self.assertRaisesWith(ValueError, error_msg):
             Clustering(**kwargs)
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read
         obj = Clustering.__new__(Clustering, in_construct_mode=True)
         with self.assertWarnsWith(warn_type=UserWarning, exc_msg=error_msg):
             obj.__init__(**kwargs)
@@ -249,7 +249,7 @@ def setUpContainer(self):
         with self.assertRaisesWith(ValueError, msg):
             cw = ClusterWaveforms(self.clustering, 'filtering', means, stdevs)
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read 
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read 
         cw = ClusterWaveforms.__new__(ClusterWaveforms,
                                         container_source=None,
                                         parent=None,

tests/integration/hdf5/test_icephys.py

@@ -153,7 +153,7 @@ def setUpContainer(self):
                                     starting_time=123.6, rate=10e3, electrode=self.elec, gain=0.126,
                                     stimulus_description="gotcha ya!", sweep_number=np.uint(4711))
 
-        # create the sweeptable in construct mode, modelling the behavior of the ObjectMapper on read
+        # create the sweeptable in construct mode, modeling the behavior of the ObjectMapper on read
         sweeptable = SweepTable.__new__(SweepTable)
         sweeptable._in_construct_mode = True
         msg = ("SweepTable is deprecated. Use the IntracellularRecordingsTable instead. "
@@ -228,7 +228,7 @@ def setUpContainer(self):
                                       starting_time=123.6, rate=10e3, electrode=self.elec, gain=0.126,
                                       stimulus_description="gotcha ya!", sweep_number=np.uint(4712))
 
-        # create the sweeptable in construct mode, modelling the behavior of the ObjectMapper on read
+        # create the sweeptable in construct mode, modeling the behavior of the ObjectMapper on read
         sweeptable = SweepTable.__new__(SweepTable)
         sweeptable._in_construct_mode = True
         msg = ("SweepTable is deprecated. Use the IntracellularRecordingsTable instead. "

tests/unit/test_ecephys.py

@@ -287,7 +287,7 @@ def test_init(self):
         with self.assertRaisesWith(ValueError, error_msg):
             cc = Clustering(**kwargs)
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read 
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read 
         cc = Clustering.__new__(Clustering, in_construct_mode=True)
         with self.assertWarnsWith(warn_type=UserWarning, exc_msg=error_msg):
             cc.__init__(**kwargs)
@@ -305,7 +305,7 @@ def test_init(self):
         num = [3, 4]
         peak_over_rms = [5.3, 6.3]
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read 
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read 
         error_msg = "The Clustering neurodata type is deprecated. Use pynwb.misc.Units or NWBFile.units instead"
         cc = Clustering.__new__(Clustering,
                                         container_source=None,
@@ -320,7 +320,7 @@ def test_init(self):
         with self.assertRaisesWith(ValueError, error_msg):
             cw = ClusterWaveforms(cc, 'filtering', means, stdevs)
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read 
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read 
         cw = ClusterWaveforms.__new__(ClusterWaveforms,
                                         container_source=None,
                                         parent=None,

tests/unit/test_file.py

@@ -134,7 +134,7 @@ def test_access_processing(self):
         with self.assertRaisesWith(ValueError, msg):
             self.nwbfile.modules['test_mod']
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read
         self.nwbfile._in_construct_mode = True
         with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
             modules = self.nwbfile.modules['test_mod']

tests/unit/test_icephys.py

@@ -39,14 +39,14 @@ class NWBFileICEphys(TestCase):
     def setUp(self):
         self.icephys_electrode = GetElectrode()
 
-    def test_sweep_table_deprectation_warn(self):
+    def test_sweep_table_deprecation_warn(self):
         msg = ("SweepTable is deprecated. Use the IntracellularRecordingsTable instead. "
                "See also the NWBFile.add_intracellular_recordings function.")
 
         with self.assertRaisesWith(ValueError, msg):
             SweepTable()
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read
         sweepT = SweepTable.__new__(SweepTable, in_construct_mode=True)
         with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
             sweepT.__init__()
@@ -60,7 +60,7 @@ def test_sweep_table_deprectation_warn(self):
         with self.assertRaisesWith(ValueError, msg):
             NWBFile(**kwargs)
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read
         nwbfile = NWBFile.__new__(NWBFile, in_construct_mode=True)
 
         with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
@@ -76,7 +76,7 @@ def test_ic_electrodes_parameter_deprecation(self):
         with self.assertRaisesWith(ValueError, msg):
             NWBFile(**kwargs)
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read
         nwbfile = NWBFile.__new__(NWBFile, in_construct_mode=True)
         with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
             nwbfile.__init__(**kwargs)

tests/unit/test_icephys_metadata_tables.py

@@ -1169,7 +1169,7 @@ def test_deprecate_sweeptable_on_add_stimulus_template(self):
             nwbfile.add_stimulus_template(local_stimulus, use_sweep_table=True)
             # NOTE - the sweep table creation will error but the stimulus template will still be added
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read
         nwbfile._in_construct_mode = True
         with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
             nwbfile.add_stimulus_template(local_stimulus2, use_sweep_table=True)
@@ -1239,7 +1239,7 @@ def test_deprecate_sweepstable_on_init(self):
         with self.assertRaisesWith(ValueError, msg):
             nwbfile = NWBFile(**kwargs)
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read
         nwbfile = NWBFile.__new__(NWBFile, in_construct_mode=True)
         with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
             nwbfile.__init__(**kwargs)
@@ -1250,7 +1250,7 @@ def test_deprecate_sweepstable_on_init(self):
         stimulus = self.__get_stimulus(electrode=electrode)
         nwbfile.add_stimulus(stimulus, use_sweep_table=True)
 
-    def test_deprectation_icephys_filtering_on_init(self):
+    def test_deprecation_icephys_filtering_on_init(self):
         kwargs = dict(session_description='my first synthetic recording',
                 identifier='EXAMPLE_ID',
                 session_start_time=datetime.now(tzlocal()),
@@ -1261,7 +1261,7 @@ def test_deprectation_icephys_filtering_on_init(self):
         with self.assertRaisesWith(ValueError, msg):
             nwbfile = NWBFile(**kwargs)
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read
         nwbfile = NWBFile.__new__(NWBFile, in_construct_mode=True)
         with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
             nwbfile.__init__(**kwargs)
@@ -1281,7 +1281,7 @@ def test_icephys_filtering_roundtrip(self):
         with self.assertRaisesWith(ValueError, msg):
             nwbfile.icephys_filtering = 'test filtering'
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read
         nwbfile._in_construct_mode = True
         with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
             nwbfile.icephys_filtering = 'test filtering'

tests/unit/test_image.py

@@ -154,7 +154,7 @@ def test_external_file_with_incorrect_starting_frame_construct_mode(self):
                     "ImageSeries 'test_iS': The number of frame indices in "
                     "'starting_frame' should have the same length as 'external_file'."
                 )
-                # Create the image series in construct mode, modelling the behavior
+                # Create the image series in construct mode, modeling the behavior
                 # of the ObjectMapper on read while avoiding having to create, write,
                 # and read and entire NWB file
                 obj = ImageSeries.__new__(ImageSeries,
@@ -255,7 +255,7 @@ def test_external_file_default_format(self):
         with self.assertRaisesWith(ValueError, msg):
             ImageSeries(**kwargs)
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read
         iS = ImageSeries.__new__(ImageSeries, in_construct_mode=True)
         with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
             iS.__init__(**kwargs)
@@ -352,7 +352,7 @@ def test_init_bad_unit(self):
         with self.assertRaisesWith(ValueError, msg):
             IndexSeries(**kwargs)
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read
         iS = IndexSeries.__new__(IndexSeries, in_construct_mode=True)
         with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
             iS.__init__(**kwargs)
@@ -377,7 +377,7 @@ def test_init_indexed_ts(self):
         with self.assertRaisesWith(ValueError, msg):
             IndexSeries(**kwargs)
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read
         iS = IndexSeries.__new__(IndexSeries, in_construct_mode=True)
         with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
             iS.__init__(**kwargs)

tests/unit/test_ophys.py

@@ -146,7 +146,7 @@ def test_manifold_deprecated(self):
         with self.assertRaisesWith(ValueError, msg):
             ImagingPlane(**kwargs)
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read
         obj = ImagingPlane.__new__(ImagingPlane, in_construct_mode=True)
         with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
             obj.__init__(**kwargs)
@@ -168,7 +168,7 @@ def test_conversion_deprecated(self):
         with self.assertRaisesWith(ValueError, msg):
             ImagingPlane(**kwargs)
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read
         obj = ImagingPlane.__new__(ImagingPlane, in_construct_mode=True)
         with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
             obj.__init__(**kwargs)
@@ -191,7 +191,7 @@ def test_unit_deprecated(self):
         with self.assertRaisesWith(ValueError, msg):
             ImagingPlane(**kwargs)
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read
         obj = ImagingPlane.__new__(ImagingPlane, in_construct_mode=True)
         with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
             obj.__init__(**kwargs)

tests/unit/test_scratch.py

@@ -33,7 +33,7 @@ def test_scratch_notes_deprecation(self):
         with self.assertRaisesWith(ValueError, msg):
             ScratchData(name='test', data=[1, 2, 3, 4, 5], notes='test notes')
 
-        # create object in construct mode, modelling the behavior of the ObjectMapper on read 
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read 
         data = ScratchData.__new__(ScratchData, in_construct_mode=True)
         with self.assertWarnsWith(UserWarning, msg):
             data.__init__(name='test', data=[1, 2, 3, 4, 5], notes='test notes')