remove warnings on construct for deprecations

src/pynwb/core.py

@@ -155,13 +155,15 @@ def __init__(self, **kwargs):
 
     @property
     def notes(self):
-        warn('Use of ScratchData.notes has been deprecated and will be removed in PyNWB 4.0. Use ScratchData.description instead.', DeprecationWarning)
+        warn(("Use of ScratchData.notes has been deprecated and will be removed in PyNWB 4.0. "
+              "Use ScratchData.description instead."), DeprecationWarning)
         return self.description
 
     @notes.setter
     def notes(self, value):
         self._error_on_new_pass_on_construct(
-                    error_msg='Use of ScratchData.notes has been deprecated and will be removed in PyNWB 4.0. Use ScratchData.description instead.')
+                    error_msg=("Use of ScratchData.notes has been deprecated and will be removed in PyNWB 4.0. "
+                               "Use ScratchData.description instead."))
         self.description = value
 
 

src/pynwb/file.py

@@ -561,6 +561,17 @@ def objects(self):
     def epoch_tags(self):
         return set(self.epochs.tags[:]) if self.epochs is not None else set()
 
+    @property
+    def icephys_filtering(self):
+        return self.fields.get('icephys_filtering')
+
+    @icephys_filtering.setter
+    def icephys_filtering(self, val):
+        if val is not None:
+            self._error_on_new_warn_on_construct("Use of icephys_filtering is deprecated. "
+                                                 "Use the IntracellularElectrode.filtering field instead")
+            self.fields['icephys_filtering'] = val
+
     def __check_epochs(self):
         if self.epochs is None:
             self.epochs = TimeIntervals(name='epochs', description='experimental epochs')
@@ -1017,7 +1028,7 @@ def add_scratch(self, **kwargs):
         data, name, notes, table_description, description = getargs('data', 'name', 'notes', 'table_description',
                                                                     'description', kwargs)
         if notes is not None or table_description != '':
-            warn(('Use of the `notes` or `table_description` argument is deprecate and will be removed in PyNWB 4.0. '
+            warn(('Use of the `notes` or `table_description` argument is deprecated and will be removed in PyNWB 4.0. '
                   'Use the `description` argument instead.'), DeprecationWarning)
             if description is not None:
                 raise ValueError('Cannot call add_scratch with (notes or table_description) and description')

tests/integration/hdf5/test_ecephys.py

@@ -184,22 +184,19 @@ def setUpContainer(self):
             Clustering(**kwargs)
 
         # create object in construct mode, modeling the behavior of the ObjectMapper on read
+        # no warning should be raised
         obj = Clustering.__new__(Clustering, in_construct_mode=True)
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=error_msg):
-            obj.__init__(**kwargs)
+        obj.__init__(**kwargs)
 
         return obj
 
     def roundtripContainer(self, cache_spec=False):
-        # catch the DeprecationWarning raised when reading the Clustering object from file
-        error_msg = "The Clustering neurodata type is deprecated. Use pynwb.misc.Units or NWBFile.units instead"
-        with self.assertWarnsWith(UserWarning, error_msg):
-            return super().roundtripContainer(cache_spec)
+        # no warning or error should be raised when reading the Clustering object from file
+        return super().roundtripContainer(cache_spec)
 
     def roundtripExportContainer(self, cache_spec=False):
-        error_msg = "The Clustering neurodata type is deprecated. Use pynwb.misc.Units or NWBFile.units instead"
-        with self.assertWarnsWith(UserWarning, error_msg):
-            return super().roundtripExportContainer(cache_spec)
+        # no warning or error should be raised when reading the Clustering object from file
+        return super().roundtripExportContainer(cache_spec)
 
 
 class SpikeEventSeriesConstructor(NWBH5IOFlexMixin, TestCase):
@@ -240,11 +237,9 @@ def setUpContainer(self):
         peak_over_rms = [5.3, 6.3]
 
         # raise error on write
-        msg = "The Clustering neurodata type is deprecated. Use pynwb.misc.Units or NWBFile.units instead"
         clust = Clustering.__new__(Clustering, in_construct_mode=True)
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            clust.__init__('description', num, peak_over_rms, times)
-            self.clustering = clust
+        clust.__init__('description', num, peak_over_rms, times)
+        self.clustering = clust
 
         means = [[7.3, 7.3]]
         stdevs = [[8.3, 8.3]]
@@ -253,12 +248,12 @@ def setUpContainer(self):
             cw = ClusterWaveforms(self.clustering, 'filtering', means, stdevs)
 
         # create object in construct mode, modeling the behavior of the ObjectMapper on read 
+        # no warning should be raised
         cw = ClusterWaveforms.__new__(ClusterWaveforms,
                                         container_source=None,
                                         parent=None,
                                         in_construct_mode=True)
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            cw.__init__(self.clustering, 'filtering', means, stdevs)
+        cw.__init__(self.clustering, 'filtering', means, stdevs)
 
         return cw
 
@@ -268,16 +263,12 @@ def addContainer(self, nwbfile):
         nwbfile.add_acquisition(self.container)
 
     def roundtripContainer(self, cache_spec=False):
-        # catch the DeprecationWarning raised when reading the Clustering object from file
-        msg = "The ClusterWaveforms neurodata type is deprecated. Use pynwb.misc.Units or NWBFile.units instead"
-        with self.assertWarnsWith(UserWarning, msg):
-            return super().roundtripContainer(cache_spec)
+        # no warning or error should be raised when reading the Clustering object from file
+        return super().roundtripContainer(cache_spec)
 
     def roundtripExportContainer(self, cache_spec=False):
-        # catch the DeprecationWarning raised when reading the Clustering object from file
-        msg = "The ClusterWaveforms neurodata type is deprecated. Use pynwb.misc.Units or NWBFile.units instead"
-        with self.assertWarnsWith(UserWarning, msg):
-            return super().roundtripExportContainer(cache_spec)
+        # no warning or error should be raised when reading the Clustering object from file
+        return super().roundtripExportContainer(cache_spec)
 
 
 class FeatureExtractionConstructor(NWBH5IOFlexMixin, TestCase):

tests/integration/hdf5/test_icephys.py

@@ -154,12 +154,11 @@ def setUpContainer(self):
                                     stimulus_description="gotcha ya!", sweep_number=np.uint(4711))
 
         # create the sweeptable in construct mode, modeling the behavior of the ObjectMapper on read
+        # no user warning or error should be raised
         sweeptable = SweepTable.__new__(SweepTable)
         sweeptable._in_construct_mode = True
-        msg = ("SweepTable is deprecated. Use the IntracellularRecordingsTable instead. "
-                     "See also the NWBFile.add_intracellular_recordings function.")
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            sweeptable.__init__(name='sweep_table')
+        sweeptable.__init__(name='sweep_table')
+        sweeptable._in_construct_mode = False
 
         return sweeptable
 
@@ -181,17 +180,13 @@ def getContainer(self, nwbfile):
 
     def roundtripContainer(self, cache_spec=False):
         # catch the DeprecationWarning raised when reading the SweepTable object from file
-        msg = ("SweepTable is deprecated. Use the IntracellularRecordingsTable instead. "
-               "See also the NWBFile.add_intracellular_recordings function.")
-        with self.assertWarnsWith(UserWarning, msg):
-            return super().roundtripContainer(cache_spec)
+        # no warning or error message should be raised
+        return super().roundtripContainer(cache_spec)
 
     def roundtripExportContainer(self, cache_spec=False):
         # catch the DeprecationWarning raised when reading the SweepTable object from file
-        msg = ("SweepTable is deprecated. Use the IntracellularRecordingsTable instead. "
-               "See also the NWBFile.add_intracellular_recordings function.")
-        with self.assertWarnsWith(UserWarning, msg):
-            return super().roundtripExportContainer(cache_spec)
+        # no warning or error message should be raised
+        return super().roundtripExportContainer(cache_spec)
 
     def test_container(self):
         """ Test properties of the SweepTable read from file """
@@ -229,12 +224,11 @@ def setUpContainer(self):
                                       stimulus_description="gotcha ya!", sweep_number=np.uint(4712))
 
         # create the sweeptable in construct mode, modeling the behavior of the ObjectMapper on read
+        # no warning or error should be raised
         sweeptable = SweepTable.__new__(SweepTable)
         sweeptable._in_construct_mode = True
-        msg = ("SweepTable is deprecated. Use the IntracellularRecordingsTable instead. "
-               "See also the NWBFile.add_intracellular_recordings function.")
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            sweeptable.__init__(name='sweep_table')
+        sweeptable.__init__(name='sweep_table')
+        sweeptable._in_construct_mode = False
 
         return sweeptable
 
@@ -258,18 +252,12 @@ def getContainer(self, nwbfile):
         return nwbfile.sweep_table
 
     def roundtripContainer(self, cache_spec=False):
-        # catch the DeprecationWarning raised when reading the SweepTable object from file
-        msg = ("SweepTable is deprecated. Use the IntracellularRecordingsTable instead. "
-               "See also the NWBFile.add_intracellular_recordings function.")
-        with self.assertWarnsWith(UserWarning, msg):
-            return super().roundtripContainer(cache_spec)
+        # no warning or error should be raised when reading the SweepTable object from file
+        return super().roundtripContainer(cache_spec)
 
     def roundtripExportContainer(self, cache_spec=False):
-        # catch the DeprecationWarning raised when reading the SweepTable object from file
-        msg = ("SweepTable is deprecated. Use the IntracellularRecordingsTable instead. "
-               "See also the NWBFile.add_intracellular_recordings function.")
-        with self.assertWarnsWith(UserWarning, msg):
-            return super().roundtripExportContainer(cache_spec)
+        # no warning or error should be raised when reading the SweepTable object from file
+        return super().roundtripExportContainer(cache_spec)
 
     def test_container(self):
         """ Test properties of the SweepTable read from file """

tests/unit/test_base.py

@@ -45,15 +45,17 @@ def test_add_data_interface(self):
 
     def test_deprecated_add_data_interface(self):
         ts = self._create_time_series()
+        msg = 'add_data_interface is deprecated and will be removed in PyNWB 4.0. Use add instead.'
         with self.assertWarnsWith(warn_type=DeprecationWarning,
-                                  exc_msg="add_data_interface is deprecated. Use add instead."
+                                  exc_msg=msg
         ):
             self.pm.add_data_interface(ts)
 
     def test_deprecated_add_container(self):
         ts = self._create_time_series()
+        msg = 'add_container is deprecated and will be removed in PyNWB 4.0. Use add instead.'
         with self.assertWarnsWith(warn_type=DeprecationWarning, 
-                                  exc_msg="add_container is deprecated. Use add instead."
+                                  exc_msg=msg
         ):
             self.pm.add_container(ts)
 
@@ -68,17 +70,19 @@ def test_get_data_interface(self):
     def test_deprecated_get_data_interface(self):
         ts = self._create_time_series()
         self.pm.add(ts)
+        msg = 'get_data_interface is deprecated and will be removed in PyNWB 4.0. Use get instead.'
         with self.assertWarnsWith(warn_type=DeprecationWarning, 
-                                  exc_msg="get_data_interface is deprecated. Use get instead."
+                                  exc_msg=msg
         ):
             tmp = self.pm.get_data_interface("test_ts")
             self.assertIs(tmp, ts)
 
     def test_deprecated_get_container(self):
         ts = self._create_time_series()
         self.pm.add(ts)
+        msg = 'get_container is deprecated and will be removed in PyNWB 4.0. Use get instead.'
         with self.assertWarnsWith(warn_type=DeprecationWarning, 
-                                  exc_msg="get_container is deprecated. Use get instead."
+                                  exc_msg=msg
         ):
             tmp = self.pm.get_container("test_ts")
             self.assertIs(tmp, ts)

tests/unit/test_ecephys.py

@@ -288,9 +288,9 @@ def test_init(self):
             cc = Clustering(**kwargs)
 
         # create object in construct mode, modeling the behavior of the ObjectMapper on read 
+        # no error or warning should be raised
         cc = Clustering.__new__(Clustering, in_construct_mode=True)
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=error_msg):
-            cc.__init__(**kwargs)
+        cc.__init__(**kwargs)
 
         self.assertEqual(cc.description, 'description')
         self.assertEqual(cc.num, num)
@@ -306,13 +306,11 @@ def test_init(self):
         peak_over_rms = [5.3, 6.3]
 
         # 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,
                                         parent=None,
                                         in_construct_mode=True)
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=error_msg):
-            cc.__init__('description', num, peak_over_rms, times)
+        cc.__init__('description', num, peak_over_rms, times)
 
         means = [[7.3, 7.3]]
         stdevs = [[8.3, 8.3]]
@@ -321,12 +319,12 @@ def test_init(self):
             cw = ClusterWaveforms(cc, 'filtering', means, stdevs)
 
         # create object in construct mode, modeling the behavior of the ObjectMapper on read 
+        # no error or warning should be raised
         cw = ClusterWaveforms.__new__(ClusterWaveforms,
                                         container_source=None,
                                         parent=None,
                                         in_construct_mode=True)
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=error_msg):
-            cw.__init__(cc, 'filtering', means, stdevs)
+        cw.__init__(cc, 'filtering', means, stdevs)
 
         self.assertEqual(cw.clustering_interface, cc)
         self.assertEqual(cw.waveform_filtering, 'filtering')

tests/unit/test_file.py

@@ -126,23 +126,14 @@ def test_access_group_after_io(self):
 
         remove_test_file("electrodes_mwe.nwb")
 
-    def test_access_processing(self):
+    def test_access_processing_with_modules(self):
         self.nwbfile.create_processing_module('test_mod', 'test_description')
-        msg = 'NWBFile.modules is deprecated. Use NWBFile.processing instead.'
 
         # create object with deprecated argument
-        with self.assertRaisesWith(ValueError, msg):
+        msg = "'NWBFile' object has no attribute 'modules'"
+        with self.assertRaisesWith(AttributeError, msg):
             self.nwbfile.modules['test_mod']
 
-        # 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']
-        self.assertIs(self.nwbfile.processing['test_mod'], modules)
-
-        # reset construct mode for other tests
-        self.nwbfile._in_construct_mode = False
-
     def test_epoch_tags(self):
         tags1 = ['t1', 't2']
         tags2 = ['t3', 't4']
@@ -178,7 +169,7 @@ def test_add_stimulus(self):
 
     def test_add_stimulus_timeseries_arg(self):
         """Test nwbfile.add_stimulus using the deprecated 'timeseries' keyword argument"""
-        msg = ("NWBFile.add_stimulus: unrecognized argument: 'timeseries'")
+        msg = ("NWBFile.add_stimulus: missing argument 'stimulus', unrecognized argument: 'timeseries'")
         with self.assertRaisesWith(TypeError, msg):
             self.nwbfile.add_stimulus(
                 timeseries=TimeSeries(
@@ -191,9 +182,9 @@ def test_add_stimulus_timeseries_arg(self):
 
     def test_add_stimulus_no_stimulus_arg(self):
         """Test nwbfile.add_stimulus using the deprecated 'timeseries' keyword argument"""
-        msg = ("The 'stimulus' keyword argument is required.")
-        with self.assertRaisesWith(ValueError, msg):
-            self.nwbfile.add_stimulus(None)
+        msg = ("NWBFile.add_stimulus: missing argument 'stimulus'")
+        with self.assertRaisesWith(TypeError, msg):
+            self.nwbfile.add_stimulus()
         self.assertEqual(len(self.nwbfile.stimulus), 0)
 
     def test_add_stimulus_dynamic_table(self):
@@ -525,26 +516,14 @@ def test_ec_electrodes_deprecation(self):
         nwbfile.add_electrode(location='loc1', group=elecgrp, id=0)
 
         # test that NWBFile.ec_electrodes property warns or errors
-        msg = "NWBFile.ec_electrodes is deprecated. Use NWBFile.electrodes instead."
-        with self.assertRaisesWith(ValueError, msg):
+        msg = "'NWBFile' object has no attribute 'ec_electrodes'"
+        with self.assertRaisesWith(AttributeError, msg):
             nwbfile.ec_electrodes
 
-        nwbfile._in_construct_mode = True
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            nwbfile.ec_electrodes
-        self.assertEqual(nwbfile.ec_electrodes.location[0], 'loc1')
-        nwbfile._in_construct_mode = False
-
         # test that NWBFile.ec_electrode_groups warns or errors
-        msg = "NWBFile.ec_electrode_groups is deprecated. Use NWBFile.electrode_groups instead."
-        with self.assertRaisesWith(ValueError, msg):
-            nwbfile.ec_electrode_groups
-
-        nwbfile._in_construct_mode = True
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
+        msg = "'NWBFile' object has no attribute 'ec_electrode_groups'"
+        with self.assertRaisesWith(AttributeError, msg):
             nwbfile.ec_electrode_groups
-        self.assertEqual(nwbfile.ec_electrode_groups['name'].description, 'desc')
-        nwbfile._in_construct_mode = False
 
 class SubjectTest(TestCase):
     def setUp(self):